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

Simple item page
dc.citation.doi10.1371/journal.pone.0194527en_ZA
dc.contributor.authorGeldenhuys, M.
dc.contributor.authorMortlock, M.
dc.contributor.authorWeyer, J.
dc.contributor.authorBezuidt, O.
dc.contributor.authorSeamark, E.C.J.
dc.contributor.authorKearney, T.
dc.date.accessioned2020-01-15T14:14:28Z
dc.date.available2020-01-15T14:14:28Z
dc.date.issued2018-03
dc.description.abstractSpecies 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.description.librarianNLB2020en_ZA
dc.facultyFaculty of Scienceen_ZA
dc.funderNational Research Foundation (NRF) of South Africa; Poliomyelitis Research Foundationen_ZA
dc.identifier.citationGeldenhuys, 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 e0194527en_ZA
dc.identifier.issn1932-6203 (online)
dc.identifier.urihttps://hdl.handle.net/10539/28747
dc.journal.issue3en_ZA
dc.journal.titlePLoS ONEen_ZA
dc.journal.volume13en_ZA
dc.language.isoenen_ZA
dc.publisherPublic Library of Scienceen_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.subjectAdenoviridaeen_ZA
dc.subjectBaten_ZA
dc.subjectCoronavirinaeen_ZA
dc.subjectCoronavirus infectionen_ZA
dc.subjectComputational Biologyen_ZA
dc.subjectChiropteraen_ZA
dc.subjectGenetic Variationen_ZA
dc.subjectMammalsen_ZA
dc.subjectSouth Africaen_ZA
dc.subjectHumansen_ZA
dc.subjectGastrointestinal tracten_ZA
dc.subjectGenomeen_ZA
dc.titleA metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africaen_ZA
dc.typeArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Geldenhuys_Metagenomic_2018
Size:
21.66 MB
Format:
Adobe Portable Document Format
Description:
Article
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
School of Animal, Plant and Environmental Sciences (Journal Articles)
Academic Wits Research Outputs (All submissions)