A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa

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dc.contributor.author Geldenhuys, M.
dc.contributor.author Mortlock, M.
dc.contributor.author Weyer, J.
dc.contributor.author Bezuidt, O.
dc.contributor.author Seamark, E.C.J
dc.contributor.author Kearney, T.
dc.date.accessioned 2020-01-15T14:14:28Z
dc.date.available 2020-01-15T14:14:28Z
dc.date.issued 2018-03
dc.identifier.citation Geldenhuys, M.et al. 2018. A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa. Plos ONE 13(3), Article number e0194527 en_ZA
dc.identifier.issn 1932-6203(ELECTRONIC)
dc.identifier.uri https://hdl.handle.net/10539/28747
dc.description.abstract Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard. en_ZA
dc.language.iso en en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights © 2018 Public Library of Science. All Rights Reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmi tted, modifie d, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. en_ZA
dc.subject Adenoviridae en_ZA
dc.subject animal en_ZA
dc.subject bat en_ZA
dc.subject biology en_ZA
dc.subject Coronavirinae en_ZA
dc.subject Coronavirus infection en_ZA
dc.subject Computational Biology en_ZA
dc.subject Chiroptera en_ZA
dc.subject Genetic Variation en_ZA
dc.subject Mammals en_ZA
dc.subject South Africa en_ZA
dc.subject humans en_ZA
dc.subject Gastrointestinal Tract en_ZA
dc.subject Genome, Viral en_ZA
dc.title A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa en_ZA
dc.type Article en_ZA
dc.journal.volume 13 en_ZA
dc.journal.title PLoS ONE en_ZA
dc.description.librarian NLB2020 en_ZA
dc.citation.doi 10.1371/journal.pone.0194527 en_ZA
dc.funder National Research Foundation (NRF) of South Africa; Poliomyelitis Research Foundation en_ZA
dc.journal.issue 3 en_ZA
dc.faculty Faculty of Science en_ZA

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