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The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

1
Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
2
Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK
3
International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK
4
Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
5
Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Received: 10 February 2020 / Revised: 25 February 2020 / Accepted: 26 February 2020 / Published: 27 February 2020
(This article belongs to the Section Animal Viruses)
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. View Full-Text
Keywords: tilapia lake virus; reassortment; segmented genome; phylogenetic analysis; RNA virus tilapia lake virus; reassortment; segmented genome; phylogenetic analysis; RNA virus
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MDPI and ACS Style

Chaput, D.L.; Bass, D.; Alam, M.M.; Al Hasan, N.; Stentiford, G.D.; van Aerle, R.; Moore, K.; Bignell, J.P.; Haque, M.M.; Tyler, C.R. The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh. Viruses 2020, 12, 258. https://0-doi-org.brum.beds.ac.uk/10.3390/v12030258

AMA Style

Chaput DL, Bass D, Alam MM, Al Hasan N, Stentiford GD, van Aerle R, Moore K, Bignell JP, Haque MM, Tyler CR. The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh. Viruses. 2020; 12(3):258. https://0-doi-org.brum.beds.ac.uk/10.3390/v12030258

Chicago/Turabian Style

Chaput, Dominique L., David Bass, Md. M. Alam, Neaz Al Hasan, Grant D. Stentiford, Ronny van Aerle, Karen Moore, John P. Bignell, Mohammad M. Haque, and Charles R. Tyler 2020. "The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh" Viruses 12, no. 3: 258. https://0-doi-org.brum.beds.ac.uk/10.3390/v12030258

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