Department of Environmental Sciences, University of Toledo, Toledo, Ohio, United States of America.
School of Oceanography, University of Washington, Seattle, WA, United States of America.
PLoS One. 2021 May 28;16(5):e0232923. doi: 10.1371/journal.pone.0232923. eCollection 2021.
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.
一种独特且具有高度传染性的鲤鱼疱疹病毒亚群（-IVb），也被称为病毒性出血性败血症病毒（VHSV），于 2005 年和 2006 年突然出现在 Laurentian 大湖区，导致大量鱼类死亡，并影响了超过 32 种淡水鱼类。2007 年、2008 年和 2017 年，较小规模且地理范围更有限的疫情出现了明显的休眠期。在这项研究中，我们对迄今为止最大的 VHSV-IVb 全基因组测序分析进行了评估，根据细胞培养中的免疫原性，研究了其进化变化。我们的调查比较了 VHSV-IVb 的基因组和遗传变异、选择以及序列变化率，以及与其他 VHSV 基因群（VHSV-I、VHSV-II、VHSV-III 和 VHSV-IVa）和其他虹彩病毒的关系。结果表明，我们测序的 VHSV-IVb 分离株在整个基因组中含有 253 个单核苷酸多态性（SNP）（占总核苷酸 11158 的 2.3%），其中 85 个（33.6%）是非同义 SNP。非编码区（NCDS；4.3%）发生的替换最多，其次是 Nv-（3.8%）和 M-（2.8%）基因。比例上，更多的 M 基因替换编码了氨基酸变化（52.9%），其次是 Nv-（50.0%）、G-（48.6%）、N-（35.7%）和 L-（23.1%）基因。在 VHSV 基因群和亚群中，来自东北太平洋的 VHSV-IVa 显示出最快的替换率（2.01x10-3），其次是 VHSV-IVb（6.64x10-5）和来自欧洲的 VHSV-I、-II 和-III 基因群（4.09x10-5）。2016 年，来自伊利湖的一条湖鲱（Dorosoma cepedianum）携带了最具差异的 VHSV-IVb 序列。与最初的 VHSV-IVb 分离株（可追溯到 2003 年）相比，该样本的体外免疫原性分析显示出较低的毒力（2016 年的其他样本也是如此）。我们测试的 2016 年分离株对鱼类宿主细胞固有抗病毒反应的影响更温和，表明表型效应发生了改变。总之，我们的研究结果表明，VHSV-IVb 在其进化历史（2003 年至今）中经历了持续的序列变化和降低毒力的趋势，这可能有助于其在鱼类宿主种群中的长期存在。
