The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh
dc.contributor.author | Chaput, DL | |
dc.contributor.author | Bass, D | |
dc.contributor.author | Alam, MM | |
dc.contributor.author | Hasan, NA | |
dc.contributor.author | Stentiford, GD | |
dc.contributor.author | Aerle, RV | |
dc.contributor.author | Moore, K | |
dc.contributor.author | Bignell, JP | |
dc.contributor.author | Haque, MM | |
dc.contributor.author | Tyler, CR | |
dc.date.accessioned | 2020-03-03T16:05:39Z | |
dc.date.issued | 2020-02-27 | |
dc.description.abstract | Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible. | en_GB |
dc.description.sponsorship | Newton Fund | en_GB |
dc.description.sponsorship | Department for International Development | en_GB |
dc.description.sponsorship | Indian Department of Biotechnology | en_GB |
dc.description.sponsorship | Biotechnology and Biological Sciences Research Council (BBSRC) | en_GB |
dc.description.sponsorship | Economic and Social Research Council (ESRC) | en_GB |
dc.identifier.citation | Vol. 12 (3), article 258 | en_GB |
dc.identifier.doi | 10.3390/v12030258 | |
dc.identifier.grantnumber | BB/N00504X/1 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/120149 | |
dc.language.iso | en | en_GB |
dc.publisher | MDPI | en_GB |
dc.rights | © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). | en_GB |
dc.subject | Tilapia lake virus | en_GB |
dc.subject | reassortment | en_GB |
dc.subject | segmented genome | en_GB |
dc.subject | phylogenetic analysis | en_GB |
dc.subject | RNA virus | en_GB |
dc.title | The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2020-03-03T16:05:39Z | |
dc.description | This is the final version. Available on open access from MDPI via the DOI in this record | en_GB |
dc.description | Data Availability: The raw RNA-seq data are available in the NCBI Sequence Read Archive under BioProject number PRJNA604966. The assembled genome sequence of Bangladesh TiLV isolate BD-2017 is available in NCBI GenBank, accession numbers MN939372-MN939381 (segments 1–10). QualiMap output from genome assembly is Supplementary data 1 and on Figshare, Viruses 2020, 12, 258 5 of 17 10.6084/m9.figshare.11812143. Multiple sequence alignments of partial segments 1, 2, 3, 4 and 9 are available as Supplementary data 2 and on Figshare, doi:10.6084/m9.figshare.11617563. Multiple sequence alignments of full coding regions of all ten segments are available as Supplementary data 3 and on Figshare, doi:10.6084/m9.figshare.11617545. Results from each quartet analysis are available as Supplementary data 4 and on Figshare, doi:10.6084/m9.figshare.11625774. | en_GB |
dc.identifier.eissn | 1999-4915 | |
dc.identifier.journal | Viruses | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2020-02-26 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2020-02-27 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2020-03-03T16:02:45Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2020-03-03T16:05:46Z | |
refterms.panel | A | en_GB |
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