SRX3403374 1562-23 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697288 IPNV/O.mykiss/I/UD/715/Dec98 1562-23 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403375 1562-22 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697289 IPNV/S.trutta/I/UD/393/May98 1562-22 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403376 1562-21 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697290 IPNV/Salvelinus_spp/I/UD/664/Dec97 1562-21 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403377 1562-50 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697292 IPNV/O.mykiss/I/TN/430/Oct11 1562-50 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403378 1562-19 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697293 IPNV/O.mykiss/I/PN/159/Mar97 1562-19 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403379 1562-18 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697294 IPNV/O.mykiss/I/PN/410/Jun90 1562-18 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403380 1562-17 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697295 IPNV/S.trutta/I/UD/406/Jun90 1562-17 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403381 1562-16 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697296 IPNV/O.mykiss/I/PN/208/Mar88 1562-16 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403382 1562-69 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697297 IPNV/O.mykiss/I/TN/214/May14 1562-69 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403383 1562-26 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697298 IPNV/S.trutta/I/UD/112a/Mar15 1562-26 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403384 1562-25 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697299 IPNV/O.mykiss/I/UD/710/Dec99 1562-25 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403385 1562-77 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697300 IPNV/O.mykiss/I/UD/155a/Feb13 1562-77 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403386 1562-76 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697301 IPNV/O.mykiss/I/UD/154/Nov12 1562-76 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403387 1562-75 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697302 IPNV/O.mykiss/I/VI/135/Mar15 1562-75 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403388 1562-20 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697303 IPNV/O.mykiss/I/PN/322/May97 1562-20 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403389 1562-72 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697304 IPNV/O.mykiss/I/UD/148a/Nov12 1562-72 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403390 1562-71 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697305 IPNV/S.trutta/I/UD/112b/Mar15 1562-71 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403391 1562-70 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697306 IPNV/O.mykiss/I/TN/57/Feb15 1562-70 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403392 1562-68 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697307 IPNV/O.mykiss/I/TN/76/Mar14 1562-68 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403393 1562-94 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697308 IPNV/O.mykiss/I/TN/345/May16 1562-94 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403394 1562-93 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697309 IPNV/O.mykiss/I/TN/344/May16 1562-93 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403395 1562-96 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697310 IPNV/O.mykiss/I/UD/155b/Feb13 1562-96 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403396 1562-95 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697311 IPNV/O.mykiss/I/UD/148b/Nov12 1562-95 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403397 17RS1075 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697364 IPNV/O.mykiss/I/UD/313/Mar17 17RS1075 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403398 1562-79 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697313 IPNV/O.mykiss/I/TN/165/Mar15 1562-79 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403399 1562-78 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697315 IPNV/O.mykiss/I/PN/158/Mar13 1562-78 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403400 1562-30 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697314 IPNV/O.mykiss/I/TN/5609/Nov78 1562-30 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403401 1562-29 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697365 IPNV/Salvelinus_spp/I/TN/23/Feb11 1562-29 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403402 1562-28 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697316 IPNV/O.mykiss/I/VR/2/Jan11 1562-28 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403403 1562-27 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697317 IPNV/S.trutta/I/TN/5244/Oct78 1562-27 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403404 1562-34 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697318 IPNV/O.mykiss/I/VI/46/Mar11 1562-34 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403405 1562-33 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697319 IPNV/O.mykiss/I/TN/44/Feb11 1562-33 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403406 1562-32 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697320 IPNV/Salvelinus_spp/I/TN/44/Feb11 1562-32 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403407 1562-31 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697321 IPNV/O.mykiss/I/TN/43/Feb11 1562-31 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403408 1562-36 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697322 IPNV/O.mykiss/I/TN/79/Mar11 1562-36 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403409 1562-35 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697323 IPNV/O.mykiss/I/TN/53/Mar11 1562-35 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403410 1562-57 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697324 IPNV/O.mykiss/I/PN/495/Oct12 1562-57 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403411 1562-56 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697326 IPNV/O.mykiss/I/TN/458/Oct12 1562-56 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403412 1562-73 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697325 IPNV/O.mykiss/I/UD/153/Nov12 1562-73 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403413 1562-82 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697328 IPNV/O.mykiss/I/UD/473/Dec12 1562-82 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403414 1562-85 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697329 IPNV/O.mykiss/I/PN/525/Oct15 1562-85 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403415 1562-53 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697330 IPNV/O.mykiss/I/TN/157/Mar12 1562-53 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403416 1562-52 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697331 IPNV/O.mykiss/I/TN/132/Mar12 1562-52 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403417 1562-92 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697333 IPNV/O.mykiss/I/TN/407/May16 1562-92 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403418 1562-55 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697332 IPNV/Salvelinus_spp/I/TN/435/Oct10 1562-55 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403419 1562-83 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697334 IPNV/O.mykiss/I/PN/474/Dec12 1562-83 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403420 1562-58 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697335 IPNV/Salvelinus_spp/I/TN/567/Nov12 1562-58 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403421 1562-59 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697336 IPNV/O.mykiss/I/VR/595/Dec12 1562-59 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403422 1562-61 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697337 IPNV/O.mykiss/I/VI/78/Apr13 1562-61 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403423 1562-54 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697338 IPNV/O.mykiss/I/TN/262/May12 1562-54 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403424 1562-63 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697339 IPNV/O.mykiss/I/TV/206/May13 1562-63 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403425 1562-64 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697340 IPNV/O.mykiss/I/VR/217/Jun13 1562-64 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403426 1562-65 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697341 IPNV/O.mykiss/I/UD/264/Jul13 1562-65 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403427 1562-66 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697342 IPNV/O.mykiss/I/BZ/268/Jun13 1562-66 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403428 1562-67 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697343 IPNV/O.mykiss/I/TN/550/Nov13 1562-67 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403429 1562-48 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697345 IPNV/O.mykiss/I/TN/380/Oct11 1562-48 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403430 1562-80 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697344 IPNV/O.mykiss/I/TN/189/Apr15 1562-80 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403431 1562-81 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697346 IPNV/Salvelinus_spp/I/TN/424/Aug15 1562-81 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403432 1562-87 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697348 IPNV/O.mykiss/I/TN/560/Nov15 1562-87 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403433 1562-88 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697347 IPNV/O.mykiss/I/TN/603/Nov15 1562-88 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403434 1562-84 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697349 IPNV/O.mykiss/I/UD/475/Dec12 1562-84 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403435 1562-47 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697350 IPNV/O.mykiss/I/TN/361/Sep11 1562-47 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403436 1562-43 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697352 IPNV/O.mykiss/I/PN/134/Apr11 1562-43 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403437 1562-44 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697351 IPNV/O.mykiss/I/PN/168/May11 1562-44 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403438 1562-41 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697353 IPNV/Salvelinus_spp/I/TN/140a/Apr11 1562-41 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403439 1562-42 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697354 IPNV/Salvelinus_spp/I/TN/140b/Apr11 1562-42 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403440 1562-39 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697355 IPNV/O.mykiss/I/VI/113/Apr11 1562-39 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403441 1562-40 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697356 IPNV/O.mykiss/I/TN/122/Apr11 1562-40 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403442 1562-37 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697357 IPNV/O.mykiss/I/TN/83/Mar11 1562-37 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403443 1562-38 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697358 IPNV/O.mykiss/I/VI/95/Apr11 1562-38 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403444 1562-49 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697359 IPNV/O.mykiss/I/TN/394/Oct11 1562-49 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403445 1562-91 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697360 IPNV/O.mykiss/I/VI/169/Mar16 1562-91 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403446 1562-45 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697361 IPNV/O.mykiss/I/TN/196/May11 1562-45 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403447 1562-46 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697362 IPNV/S.alpinus/I/TN/305/Aug11 1562-46 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq SRX3403448 1562-62 SRP125178 PRJNA418407 Total RNA was purified from 140 _l of cell culture supernatant using the QIAamp Viral RNA Mini kit (Qiagen), and subsequently quantified spectrophotometrically with Nanodrop OneC (ThermoFisher Scientific). The nucleotide regions corresponding to the viral polymerase (VP1) and the mature outer capsid protein (VP2) were amplified using the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity (ThermoFisher Scientific) and specific primer sets (Table 1). In detail, the 25 _l RT-PCR mix contained 1X reaction mix, 5 mM MgSO4, 0.4 _M of each primer, 0.5 _l enzyme mix, 5 _l template RNA, 10 U RNasin Plus Ribonuclease Inhibitor (Promega) and distilled water to volume. The following thermal profile was applied: 30 min retrotranscription at 55¡C, 2 min pre-denaturation at 94¡C, 40 cycles of 15 sec denaturation at 94¡C, 30 sec annealing at 56¡C, 3 min elongation at 68¡C, and a final elongation step at 68¡C for 5 min. PCR products were purified with Agencourt AMPure XP (Beckman Coulter) and quantified with Qubit dsDNA HS assay kit (Thermofisher). Libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina) and Agencourt AMPure XP (Beckman Coulter) was used for fragments selection. Fragments quality and size were checked with High Sensitivity DNA Analysis kit (Agilent). Libraries were pooled at an equimolar concentration and finally sequenced with the Miseq v3 Reagent Kit (600-cycle) using the Illumina MiSeq platform. SRS2697363 IPNV/O.mykiss/I/TN/152/May13 1562-62 RNA-Seq VIRAL RNA RANDOM Illumina MiSeq