SRX1760545 Bahia01_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436390 Zika-Bahia01 Bahia01_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760546 Bahia01_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436390 Zika-Bahia01 Bahia01_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760547 Bahia07_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436391 Zika-Bahia07 Bahia07_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760548 Bahia08_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436392 Zika-Bahia08 Bahia08_mNGS OTHER METAGENOMIC RANDOM 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760549 Bahia08_mNGS_2ndcDNAprep SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436392 Zika-Bahia08 Bahia08_mNGS_2ndcDNAprep OTHER METAGENOMIC RANDOM 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760550 Bahia08_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436392 Zika-Bahia08 Bahia08_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760551 Bahia09_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436393 Zika-Bahia09 Bahia09_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760552 Bahia11_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436394 Zika-Bahia11 Bahia11_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760553 Bahia11_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436394 Zika-Bahia11 Bahia11_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760554 Bahia12_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436395 Zika-Bahia12 Bahia12_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760555 Bahia12_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436395 Zika-Bahia12 Bahia12_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760556 Bahia15_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436396 Zika-Bahia15 Bahia15_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760557 Bahia02_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436397 Zika-Bahia02 Bahia02_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760559 Bahia15_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436396 Zika-Bahia15 Bahia15_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760560 Bahia02_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436397 Zika-Bahia02 Bahia02_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760561 Bahia03_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436399 Zika-Bahia03 Bahia03_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760562 Bahia03_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean and Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436399 Bahia03_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760563 Bahia04_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436400 Zika-Bahia04 Bahia04_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760564 Bahia04_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436400 Zika-Bahia04 Bahia04_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1760565 Bahia05_mNGS SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436401 Zika-Bahia05 Bahia05_mNGS OTHER METAGENOMIC RANDOM Illumina MiSeq SRX1760566 Bahia05_XGen SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436401 Zika-Bahia05 Bahia05_XGen OTHER METAGENOMIC other 502 0 Application Read Forward 1 1 Application Read Reverse 252 Illumina MiSeq SRX1761173 Bahia05_XGen-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436401 Zika-Bahia05 Bahia05_XGen OTHER METAGENOMIC other 161 0 Application Read Forward 1 Illumina MiSeq SRX1761174 Bahia15_XGen-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436396 Zika-Bahia15 Bahia15_XGen OTHER METAGENOMIC other 161 0 Application Read Forward 1 Illumina MiSeq SRX1761175 Bahia12_XGen-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436395 Zika-Bahia12 Bahia12_XGen OTHER METAGENOMIC other 161 0 Application Read Forward 1 Illumina MiSeq SRX1761176 Bahia11_XGen-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436394 Zika-Bahia11 Bahia11_XGen OTHER METAGENOMIC other 161 0 Application Read Forward 1 Illumina MiSeq SRX1761177 Bahia08_XGen-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436392 Zika-Bahia08 Bahia08_XGen OTHER METAGENOMIC other 161 0 Application Read Forward 1 Illumina MiSeq SRX1761178 Bahia08_mNGS-single SRP078817 PRJNA329513 RNA metagenomic libraries were constructed from the patient's serum sample as previously described (Greninger, et al., 2015, Genome Medicine). Total nucleic acid was extracted using the QIAamp Viral RNA mini kit (Qiagen, Valencia CA). 20ul of extract was treated with Turbo DNase (Ambion, Waltham MA) and Baseline Zero DNase (Epicentre Bioscience) followed by cleanup using the RNA Clean & Concentrator kit (Zymo Research). Eluted RNA was reverse transcribed to cDNA using SuperScript III Reverse Transcriptase (Invitrogen) mediated by random hexamers, and second strand synthesis was conducted using SequenaseS Version 2.0 DNA Polymerase (Affymetrix) for 10 minutes at 37C following denaturation. Double stranded cDNA was cleaned up using the DNA Clean & Concentrator kit (Zymo Research) and NGS libraries were generated form the entirety of the eluate utilizing the Nextera XT DNA Library Prep Kit (Illumina, San Diego CA). The Nextera XT library was cleaned using Ampure XP beads (Beckman-Coulter). Dual-indexed, barcoded NGS libraries were quantitated on the Qubit 3.0 fluoremeter, mixed equally by concentration and quantified for size and concentration on the BioAnalyzer (Agilent, Santa Clara CA) using the high sensitivity dsDNA kit. Libraries were run on the Illumina HiSeq (1 x 160 bp runs and 250 PE runs). Metagenomic NGS data was analyzed for pathogens using automated SURPI ("sequence-based ultra-rapid pathogen identification") computational pipeline and the updated National Center for Biotechnology Information (NCBI) nt database as of March 2015 (Naccache, et al., 2014, Genome Research). SRS1436392 Zika-Bahia08 Bahia08_mNGS OTHER METAGENOMIC RANDOM 161 0 Application Read Forward 1 Illumina MiSeq