Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang Universitygrid.13402.34, Hangzhou, China.
Microbiol Spectr. 2022 Jun 29;10(3):e0024222. doi: 10.1128/spectrum.00242-22. Epub 2022 Jun 1.
is a rapidly growing family of viruses, whose potential for cross-species transmission makes it difficult to predict the harm of newly emerging viruses to humans and animals. To better understand their diversity, evolutionary history, and co-evolution with their hosts, we analyzed a collection of porcine parainfluenza virus (PPIV) genomes to reconstruct the species classification basis and evolutionary history of the genus. We sequenced 17 complete genomes of porcine respirovirus 1 (also known as porcine parainfluenza virus 1; PPIV-1), thereby nearly tripling the number of currently available PPIV-1 genomes. We found that PPIV-1 was widely prevalent in China with two divergent lineages, PPIV-1a and PPIV-1b. We further provided evidence that a new species, porcine parainfluenza virus 2 (PPIV-2), had recently emerged in China. Our results pointed to a need for revising the current species demarcation criteria of the genus. In addition, we used PPIV-1 as an example to explore recombination and diversity of the genus. Interestingly, we only detected heterosubtypic recombination events between PPIV-1a and PPIV-1b with no intrasubtypic recombination events. The recombination hotspots highlighted a diverse geography-dependent genome structure of paramyxovirus infecting swine in China. Furthermore, we found no evidence of co-evolution between respirovirus and its host, indicating frequent cross-species transmission. In summary, our analyses showed that swine can be infected with a broad range of respiroviruses and recombination may serve as an important evolutionary mechanism for the genus' greater diversity in genome structure than previously anticipated. Livestock have emerged as critically underrecognized sources of paramyxovirus diversity, including pigs serving as the source of Nipah virus (NiV) and swine parainfluenza virus type 3, and goats and bovines harboring highly divergent viral lineages. Here, we identified a new species of genus named PPIV-2 in swine and proposed to revise the species demarcation criteria of the genus. We found heterosubtypic recombination events and high genetic diversity in PPIV-1. Further, we showed that genetic recombination may have occurred in the genus which may be associated with host range expansion. The continued expansion of genus diversity in livestock with relatively high human contact rates requires enhanced surveillance and ongoing evaluation of emerging cross-species transmission threats.
副黏病毒科是一个快速增长的病毒家族，其跨物种传播的潜力使得难以预测新出现的病毒对人类和动物的危害。为了更好地了解它们的多样性、进化历史以及与宿主的共同进化，我们分析了一组猪副黏病毒（PPIV）基因组，以重建该属的物种分类基础和进化历史。我们对 17 株完整的猪呼吸道病毒 1（也称为猪副流感病毒 1；PPIV-1）进行了测序，从而使目前可用的 PPIV-1 基因组数量几乎增加了两倍。我们发现 PPIV-1 在我国广泛流行，存在两个分化的谱系，PPIV-1a 和 PPIV-1b。我们进一步提供了证据表明，一种新的病毒，猪副流感病毒 2（PPIV-2）最近在中国出现。我们的研究结果表明需要修订该属的当前物种划分标准。此外，我们还以 PPIV-1 为例探讨了该属的重组和多样性。有趣的是，我们只检测到 PPIV-1a 和 PPIV-1b 之间的异源亚型重组事件，而没有检测到同型亚型重组事件。重组热点突出了中国感染猪的副黏病毒具有多样化的地理相关基因组结构。此外，我们没有发现呼吸道病毒与其宿主之间存在共同进化的证据，表明其频繁的跨种传播。总之，我们的分析表明，猪可能会感染广泛的呼吸道病毒，重组可能是该属在基因组结构上比以前预期的更大多样性的一个重要进化机制。 家畜已成为被严重低估的副黏病毒多样性来源，包括作为尼帕病毒（NiV）和猪 3 型副流感病毒来源的猪，以及携带高度分化病毒谱系的山羊和牛。在这里，我们在猪中鉴定出了一个新的属名 PPIV-2，并提出修订该属的物种划分标准。我们发现 PPIV-1 存在异源亚型重组事件和高遗传多样性。此外，我们表明，遗传重组可能已经发生在该属中，这可能与宿主范围的扩大有关。具有相对较高人类接触率的家畜中副黏病毒属多样性的持续扩大需要加强监测，并不断评估新出现的跨种传播威胁。
