Reassortment and evolutionary dynamics of tilapia lake virus genomic segments

• Published in: Virus research 2022-01, Vol.308, p.198625-198625, Article 198625
• Main Authors: Verma, Dev Kumar, Sood, Neeraj, Paria, Anutosh, Swaminathan, T.R., Mohan, C.V., Rajendran, K.V., Pradhan, P.K.
• Format: Article
• Language: English
• Subjects: Animals; DNA Viruses; Fish Diseases; Genome; Mutation; Nucleotides; RNA Viruses - genetics; Selection; Substitution rate; Tilapia; Tilapia lake virus (TiLV); Viruses; Viruses, Unclassified
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2021.198625

•TiLV is an emerging viral pathogen which has threatened the global aquaculture industry.•Phylogenomic analysis provides evidence of reassortment in TiLV.•Each genomic region has been subjected to intense purifying selection.•Nucleotide substitution rate per site per year is comparable with other RNA viruses.•Reassortment plays crucial role in the evolution of TiLV. The tilapia lake virus (TiLV), a highly infectious negative-sense single-stranded segmented RNA virus, has caused several outbreaks worldwide since its first report from Israel in 2014, and continues to pose a major threat to the global tilapia industry. Despite its economic importance, little is known about the underlying mechanisms in the genomic evolution of this highly infectious viral pathogen. Using phylogenomic approaches to the genome sequences of TiLV isolates from various geographic regions, we report on the pervasive role of reassortment, selection, and mutation in TiLV evolution. Our findings provided the evidence of genome-wide reassortment in this newly discovered RNA virus. The rate of non-synonymous (dN) to synonymous (dS) substitutions was less than one (dN/dS = 0.076 to 0.692), indicating that each genomic segment has been subjected to purifying selection. Concurrently, the rate of nucleotide substitution for each genomic segment was in the order of 1–3 × 10−3 nucleotide substitutions per site per year, which is comparable to the rate of other RNA viruses. Collectively, in line with the results of the previous studies, our results demonstrated that reassortment is the dominant force in the evolution and emergence of this highly infectious segmented RNA virus.