Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes

Abstract

A unique and highly virulent subgenogroup (-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary changes from 48 isolates in relation to immunogenicity in cell culture. Our investigation compares genomic and genetic variation, selection, and rates of sequence changes in VHSV-IVb, in relation to other VHSV genogroups (VHSV-I, VHSV-II, VHSV-III, and VHSV-IVa) and with other Novirhabdoviruses. Results show that the VHSV-IVb isolates we sequenced contain 253 SNPs (2.3% of the total 11,158 nucleotides) across their entire genomes, with 85 (33.6%) of them being non-synonymous. The most substitutions occurred in the non-coding region (NCDS; 4.3%), followed by the Nv- (3.8%), and M- (2.8%) genes. Proportionally more M-gene substitutions encoded amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHSV genogroups and subgenogroups, VHSV-IVa from the northeastern Pacific Ocean has shown the fastest substitution rate (2.01x10-3), followed by VHSV-IVb (6.64x10-5) and by the VHSV-I, -II and-III genogroups from Europe (4.09x10-5). A 2016 gizzard shad (Dorosoma cepedianum) from Lake Erie possessed the most divergent VHSV-IVb sequence. The in vitro immunogenicity analysis of that sample displayed reduced virulence (as did the other samples from 2016), in comparison to the original VHSV-IVb isolate (which had been traced back to 2003, as an origin date). The 2016 isolates that we tested induced milder impacts on fish host cell innate antiviral responses, suggesting altered phenotypic effects. In conclusion, our overall findings indicate that VHSV-IVb has undergone continued sequence change and a trend to lower virulence over its evolutionary history (2003 through present-day), which may facilitate its long-term persistence in fish host populations.

Tissue Distribution of the Piscine Novirhabdovirus Genotype IVb in Muskellunge (Esox masquinongy)

“…Except for the rainbow trout (Oncorhynchus mykiss) and turbot, the distribution of each VHSV genotype and sublineage within its susceptible host(s) has not been thoroughly investigated because it was assumed that VHSV pathogenesis in other species resembles that of VHSV genotype Ia in the rainbow trout. This is particularly true for VHSV genotype IVb, the most recent VHSV sublineage to emerge [4] with its genome continues to undergo relatively fast substitutions [7]. Muskellunge is highly susceptible to VHSV-IVb [28] and is widely present in the Great Lakes basin, Upper Mississippi drainage, as well as inland lakes, rivers, and embayments in the Midwest [29] and therefore is an ideal candidate for surveillance and monitoring purposes in the waterbodies where VHSV-IVb is expected to spread.…”

“…The virus has four genotype (I-IV) and in 2003, a unique sublineage of the North American genotype (IV) emerged in the Great Lakes basin, designated VHSV-IVb [4]. The virus has been isolated and detected in >30 fish species in a geographical range that extends to all five Great Lakes and its presence is often associated with mass mortality episodes [5][6][7]. The virus has also been recovered from apparently healthy fish [5], amphipods [8], and piscicolid leeches [9].…”

“…The emerging VHSV-IVb sublineage exhibits a number of unique features that range from its fast substitutions in its nucleic acid [7], wide range of fish species, its exclusive presence in a freshwater system unlike most other VHSV strains, the plethora of lesions it causes, to the temperature range associated with wildfish mortality episodes, to variations in pathogenicity (reviewed in [11,17]). Variability in morbidity, mortality, and pathology is particularly apparent in VHSV-IVb, whose pathogenicity varied widely even among closely related fish species.…”