Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.
Viruses. 2022 Mar 28;14(4):696. doi: 10.3390/v14040696.
Porcine circovirus-like virus P1 can infect many kinds of animals and mainly causes postweaning multisystemic wasting syndrome. In China, the genetic diversity, variation, and evolutionary processes of this virus have not been described yet. To improve our knowledge of its genetic diversity, evolution, and gene flow, we performed a bioinformatics analysis using the available nucleotide sequences of the P1 virus; among them, 12 nucleotide sequences were from ten pig farms in Jiangsu Province in this epidemiological survey, and 84 sequences were downloaded from GenBank. The P1 sequences showed a rich composition of AT nucleotides. Analyses of the complete genomic sequences were polymorphic and revealed high haplotype (gene) diversity and nucleotide diversity. A phylogenetic analysis based on the NJ method showed that all P1 virus sequences formed two distinct groups: A and B. High genetic differentiation was observed between strains from groups A and B. The codon usage pattern of P1 was affected by dinucleotide compositions. Dinucleotide UU/CC was overrepresented, and dinucleotide CG was underrepresented. The mean evolutionary rate of the P1 virus was estimated to be 3.64 × 10 nucleotide substitutions per site per year (subs/site/year). The neutrality tests showed negative values. The purifying selection and recombination events may play a major driving role in generating the genetic diversity of the P1 population. The information from this research may be helpful to obtain new insights into the evolution of P1.
猪圆环病毒样病毒 P1 可感染多种动物，主要引起断奶后多系统消耗综合征。在中国，该病毒的遗传多样性、变异和进化过程尚未得到描述。为了提高我们对其遗传多样性、进化和基因流的认识，我们使用 P1 病毒的可用核苷酸序列进行了生物信息学分析；其中，12 个核苷酸序列来自本次流行病学调查中江苏省的 10 个猪场，84 个序列从 GenBank 下载。P1 序列显示出丰富的 AT 核苷酸组成。对完整基因组序列的分析显示出高度的多态性，并显示出高的单倍型（基因）多样性和核苷酸多样性。基于 NJ 方法的系统发育分析显示，所有 P1 病毒序列形成了两个明显的组：A 和 B。组 A 和 B 之间的菌株表现出高度的遗传分化。P1 的密码子使用模式受二核苷酸组成的影响。UU/CC 二核苷酸过度表达，CG 二核苷酸表达不足。P1 病毒的平均进化率估计为每年每个位点 3.64×10 个核苷酸取代（subs/site/year）。中性检验显示负值。纯化选择和重组事件可能在 P1 群体遗传多样性的产生中起主要驱动作用。本研究的信息可能有助于深入了解 P1 的进化。
