Retracted: Tilapia lake virus disease: Phylogenetic analysis reveals that two distinct clades are circulating in Israel simultaneously

Abstract

Tilapia lake virus (TiLV) is an emerging viral disease that affects several tilapia species in different countries since 2014. In 2017–2018, 129 samples were collected from 14 tilapia farms in Israel. Ninety samples represented TiLV‐suspected cases (TSC), and 39 were used as control samples (CS). RT‐qPCR was performed on 89 and 39 duplicate brain and liver tissue samples from TSC samples and CS, respectively. TiLV was diagnosed in 37 (40.1%) of TSC, and two of the CS samples (5%) were also positive for TiLV. Additional validation RT‐PCR was performed on positive samples, and amplified products were sequenced. Maximum‐likelihood phylogenetic analysis of segment‐3 of 25 selected sequences revealed two distinct clades: one virtually identical to sequences from India and the second closely related to isolates from Ecuador, Thailand, Egypt and Peru, apparently imported to Israel from Thailand. Thus, our results indicate that at least two distinct clades of TiLV are circulating in Israel simultaneously. As of today, the number of TiLV sequences available in free publicly accessible databases is limited. Nevertheless, our study provides new molecular epidemiology baseline for further epidemiological studies of TiLV.

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

“…With segment 2, two African strains (from Tanzania and Uganda) clustered with Israel AD-2016, while the other Israel strain formed a cluster with the two South American and the Bangladesh strain. Segment 3 formed some regional clusters (South America, India, Egypt), but it split the Thai sequences, and formed three separate Israel clusters (though did not distinguish the two clades identified by Skornik et al 2019 [22]). Furthermore, the relationships between the regions could not generally be resolved.…”

“…We confirmed the presence of TiLV causing disease in tilapia in Bangladesh and obtained the near-complete genome sequence of this isolate, BD-2017, including the full coding regions of all ten segments and most of the segment termini. While phylogenetic analysis based on a short fragment of one or a few segments is often used to infer how TiLV has moved between geographical areas [18,22], we have shown that TiLV segments have different degrees of nucleotide and amino acid variation, and that TiLV has a history of genome reassortment, notably involving segments 5 and 6 (but perhaps also segments 1 and 2). Consequently, such conclusions depend largely on which TiLV segment is sequenced.…”

“…The Peru F3-4 isolate, which was asymptomatic, did have differences in several amino acids from the type strain in most segments, but other isolates from severe outbreaks had similar numbers of substitutions, with similarly high predicted impact on protein structure and function, notably EC-2012 and TV1. The only suggested link between specific amino acid changes and severity came from the set of segment 3 sequences from Israel [22], which all had severity information. A change from lysine (K) to arginine (R) at position 127 appears only in moderate strains and not in any severe strain.…”

“…However, any method used to determine how a virus arrived in a new location must be robust, as such conclusions can have significant political and economic consequences relating to trade. Phylogenetic analysis can reconstruct how pathogens have dispersed across the globe, and inferences about the movement of TiLV have been made based on phylogenetic analysis of short sequences from a single segment [18,22]. Whether this is appropriate for TiLV, with its segmented, negative-sense RNA genome that may be prone to reassortment, does not appear to have been tested, though previous studies with limited sequence data noted an absence of reassortment in this virus [14,18].…”

Tilapia lake virus: The story so far

“…In a separate study, comparison of nucleotide sequences of segment 2 from Tanzania and Uganda, isolated from Lake Victoria, showed more than 99.8% and were clustered with strains from Israel and Thailand by phylogenetic analysis, suggesting that the virus from Lake Victoria could share a common origin with the virus from Thailand and Israel (Mugimba et al., 2018). A recent phylogenetic study of TiLV isolated from farmed tilapia in Israel showed two different clades: an Israeli clade and an Ecuadorian clade which is circulating in Israel (Skornik et al., 2020). However, whole‐genome sequencing and phylogenetic analyses are essential to properly track TiLV movement since a recent study showed a possible reassortment event involving an Ecuador isolate EC‐2012 and Israel isolate Til‐4‐2011 in segments 5 and 6 of TiLV isolates from Bangladesh (BD‐2017) while concatenated 10 segment coding regions placed BD‐2017 in a clade from Thailand (Chaput et al., 2020).…”