Biology subjects

Porter, A. F.

Publications and source records attributed to Porter, A. F..

2 recordsLinked to original sources

bioRxiv2021

Metagenomic identification of viral sequences in laboratory reagents

2.Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterize the complete infectome (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing ("metatranscriptomics") we documented the presence of contaminant viral sequences in multiple libraries of blank negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank libraries, as well as contaminating sequences from the RNA virus families Totiviridae, Tombusviridae and Lentiviridae. These data suggest that the contamination of common laboratory reagents is likely widespread and can comprise a wide variety of viruses. 3. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. 1.5 RepositoriesThe viral genome sequence data generated in this study has been deposited in the NCBI database under accession numbers MZ824225-MZ824237. Sequence reads are available at the public Sequence Read Archive (SRA) database with accession SRX6803604 and under the BioProject accession PRJNA735051 reference numbers SRR14737466-71 and BioSample numbers SAMN20355437-40.

molecular biology↗

bioRxiv2020

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus - each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

microbiology↗