Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense?
Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense?
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DOI：
10.3390/v12030265
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发表时间：
2020-03-01
期刊：
影响因子：
4.7
通讯作者：
Segales, Joaquim
中科院分区：
文献类型：
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作者：
Franzo, Giovanni;Delwart, Eric;Segales, Joaquim
全球分布的猪圆环病毒（猪圆环病毒 3；PCV-3）的发现引发了激烈的研究活动和大量分子数据的产生。不同的研究小组对该病毒提出了几种但并不总是一致的基因型。虽然这些类别可以帮助更容易地解释 PCV-3 分子流行病学，但任何在实际环境中有用的分类都必须是明确的，并且有助于理解潜在的生物学特征和流行病学。基于这些前提，在 PCV-3 完整基因组 (n = 357) 和开放阅读框 2 (ORF2，n = 653) 序列的最广泛可用数据集上评估了定义 PCV-3 基因型的可能性。选择遗传距离和系统发育聚类作为主要客观标准。还考虑了其他因素，包括簇内序列的数量、宿主和地理聚类、不同基因组区域之间的一致性以及分析方法，以生成可有效应用于研究和诊断环境的分类。完整基因组的最大基因型内遗传距离为 3%，ORF2 水平的最大基因型内遗传距离为 6%，引导支持高于 90%，分析方法之间的一致性使我们能够清楚地定义两个可能被定义为基因型的进化枝。由于 PCV-3 与其生物学/流行病学特征之间缺乏有意义的关联，因此不建议进一步细分。尽管如此，由于其中一个进化枝仅包含两种毒株，因此迄今为止我们正式提出了仅一种PCV-3基因型（PCV-3a）的定义。当更多菌株序列被表征时，既定的标准将使我们能够自动识别其他基因型。
The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easier interpretation of PCV-3 molecular epidemiology, any classification, to be useful in practical settings, must be univocal and of help in the understanding of underlying biological features and epidemiology. Based on these premises, the possibility of defining PCV-3 genotypes was evaluated on the broadest available dataset of PCV-3 complete genome (n = 357) and open reading frame 2 (ORF2, n = 653) sequences. Genetic distance and phylogenetic clustering were selected as the main objective criteria. Additional factors, including the number of within-cluster sequences, host and geographic clustering, concordance between different genomic regions, and analysis method were also taken in account to generate a classification that could be effectively applied in research and diagnostic settings. A maximum within-genotype genetic distance of 3% at the complete genome and 6% at the ORF2 levels, bootstrap support higher than 90%, and concordance between analysis methods allowed us to clearly define two clades which could be potentially defined as genotypes. Further subdivision was not suggested due to the absence of a meaningful association between PCV-3 and its biological/epidemiological features. Nevertheless, since one of the clades included two strains only, thus far we formally propose the definition of only one PCV-3 genotype (PCV-3a). The established criteria will allow us to automatically recognize other genotypes when more strain sequences are characterized.