SRP006837 Viral contigs only Viral and retroviral-related contiguous sequences and assembled reads from Eidolon helvum Emerging infectious diseases are an increasingly significant burden on global public health and arise primarily from zoonotic transmission. The majority of zoonotic emergence events arise from wildlife reservoirs and bats have received considerable attention in this arena as they have been found to harbour a variety of viral zoonoses, including lyssaviruses, henipaviruses, filoviruses and SARS-like coronaviruses. Metagenomics and Next Generation Sequencing (NGS) technology have facilitated the discovery and characterisation of numerous mammalian viruses. Here, we describe the application of NGS to an abundant African fruit bat species suspected of harbouring viral zoonoses. Samples targeting excretion routes (throat swabs, urine and lung tissue) were collected from a population roosting in West Africa, a geographical ‘hot-spot’ for zoonotic emergence. We found a predominance of viral sequences related to mammalian-infecting viruses, including Herpesviridae, Papillomaviridae, Poxviridae, Circoviridae and Picornaviridae. Our results have extended the scope and diversity of known chiropteran viruses and identified potential candidates of zoonotic infections.