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

Dominique L Chaput,John P Bignell,Md Mehedi Alam,Ronny Van Aerle,Mohammad Mahfujul Haque,David Bass,Grant D Stentiford,Karen Moore,Neaz Al Hasan,Charles R Tyler

doi:10.3390/v12030258

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.

Highlights

Tilapia are the second most important farmed finfish worldwide due to their affordability, protein and micronutrient content, resistance to disease and tolerance of high-density aquaculture conditions [1].In Bangladesh, tilapia farming has grown markedly over the last 20 years, with Bangladeshranking fourth worldwide for tilapia production [1]
In the absence of local and international regulatory frameworks of aquaculture, tilapia farmers do not follow any Better Management Practices (BMPs) and with the increasing growth of tilapia aquaculture in uncontrolled systems, disease is an emerging issue threatening the sector in Bangladesh
As early as 2009, huge losses of cultured tilapia were reported in Israel, and the causative agent, tilapia lake virus (TiLV), was formally identified in 2014 [6]

Summary

Introduction

Tilapia are the second most important farmed finfish worldwide due to their affordability, protein and micronutrient content, resistance to disease and tolerance of high-density aquaculture conditions [1].In Bangladesh, tilapia farming has grown markedly over the last 20 years, with Bangladesh (in 2015)ranking fourth worldwide for tilapia production [1]. Providing a major food supply, income and employment generation for millions of poor people in rural and urban areas Farming of this species is generally characterised by earthen pond husbandry systems, with high stocking densities, intensive feeding, and drug and chemical use for water and disease treatment [3,4,5]. TiLV is an enveloped virus with a 10 segment, negative-sense RNA genome [7] encoding 14 predicted proteins [8], initially proposed to belong to the family Orthomyxoviridae due to similarities in the structure of its segment termini [7], but subsequently placed in a new family, Amnoonviridae, in the same order as the Orthomyxoviridae (Articulavirales) [9] It appears to infect tilapia at all growth stages, including fertilised eggs, egg yolk larvae, fry and fingerlings [10]. Reported mortality rates in aquaculture ponds range from as low as 5%

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