Canuti Marta, Pénzes Judit J, Lang Andrew S
Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John's NL A1C 5S7, Canada.
Institute for Quantitative Biomedicine, Rutgers the State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA.
Virus Evol. 2022 Jun 17;8(1):veac056. doi: 10.1093/ve/veac056. eCollection 2022.
Amdoparvoviruses (genus , family ) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species ) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.
微小病毒科细小病毒属病毒主要感染食肉动物，但最近的研究表明，其宿主范围可能还扩展到啮齿动物和翼手目动物。虽然它们的分类基于主要非结构蛋白（NS1）的完整序列，但一些关于微小病毒多样性的研究集中在部分序列上，这导致难以准确确定物种界限，使得几种病毒未被分类。在本研究中，我们报告了从一只美国水貂中鉴定出的一种新型微小病毒（不列颠哥伦比亚微小病毒，BCAV）的完整基因组序列，同时研究了所有与微小病毒相关序列的系统发育关系，并对其多样性和进化进行了全面的重新评估。在排除重组序列后，系统发育分析和成对序列同一性分析使我们能够确定14种不同的病毒，包括目前分类的5个物种、BCAV以及另外4种符合国际病毒分类委员会物种分类标准的病毒。我们发现，历史上被称为阿留申水貂病病毒（物种）的病毒群应被视为至少4个独立病毒物种的簇，它们在水貂养殖场中共同传播，促进了种间重组的发生。该属病毒的基因组结构、剪接供体和受体位点以及蛋白质序列基序惊人地保守。与NS1相比，主要衣壳蛋白病毒蛋白2（VP2）的序列在种间和种内的保守性明显更高，这种现象可能与抗体依赖增强（ADE）有关。同源模型表明，位于衣壳二十面体三重轴附近的刺突具有高度的保守性，该区域与ADE相关。在衣壳的腔内三重轴和二重轴上发现了数量惊人的不同氨基酸位置，这些区域的功能迄今未知。我们强调了完整基因组分析的重要性，鉴于全基因组存在明显的系统发育不一致性，建议获取不同菌株的完整编码序列。需要对微小病毒的生物学、结构以及流行病学和病毒发现进行进一步研究，以更好地描述这一重要病毒群的生态学和进化。
