Evolutionary trajectory of fishPiscine novirhabdovirus(=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification

Abstract

Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G‐gene sequence variation, in comparison with whole‐genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G‐gene haplotypes from 2003 to 2017, stemming from two originals (“a” and “b”). G‐gene haplotypes “a” and “b” differed by just one synonymous single‐nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group “a” descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group “b” descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole‐genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G‐gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV‐IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.

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

“…Other VHSV-IVb-positive isolates were recovered from Lakes Michigan and Erie in 2016, whose viral titers were too low for genome sequencing [ 51 , 57 ], further indicating that infection levels differ spatially and temporally. One of the first 2006 outbreaks intensely affected the Lake St. Clair gizzard shad population [ 16 ], as well as its 2017 outbreak (G. Whelan, Michigan Department of Natural Resources, personal communication 2017).…”

“…We defined a haplotype as “a unique gene sequence differing by one or more nucleotide substitutions” from C03MU. Population genetic relationships, based on this dataset, are evaluated separately [ 51 ].…”

“…Cell culture amplified stocks are labelled “Cell” in our results. Due to low concentrations, the original E16LB sample was only partially sequenced, which matched E16GSa in those sequence regions [ 51 , 57 ]. The cell culture amplified reference control (CellC03) was derived from C03MU.…”

“…Since RNA viruses mutate just below the maximum limit to maintain their functionality, they can readily adapt to the host’s defense modulations [ 50 ]. VHSV-IVb has been mutating over time since its appearance in the Great Lakes [ 11 , 14 , 15 , 51 ], however, little is known about how its more recent isolates behave during infection. The rising importance of the aquaculture industry has raised concerns about fish pathogens, from economic and sustainability perspectives [ 52 – 54 ].…”

“…We further evaluate the differential pathogenicity and immunogenic effects of VHSV-IVb 2016 isolates on susceptible host cells, versus the original 2003 isolate. Additionally, we published a companion study of population genetic changes in VHSV-IVb over time, using these whole genome sequences in concert with a larger data set of partial G -gene sequences to analyze spatial and temporal patterns [ 51 ]. Knowledge of evolutionary changes across VHSV-IVb’s genome and the functional roles of its genes will aid our understanding of how such changes regulate the co-evolutionary “arms race” interactions between this pathogen and its hosts.…”