川、渝、黔地区猪圆环病毒3型PCR检测及全基因组序列分析

PCR detection and whole genome sequence analysis of porcine circovirus type 3 in Sichuan,Chongqing and Guizhou

为了解川、渝、黔地区猪圆环病毒3型(PCV3)的感染现状及流行毒株的分子遗传特征,本试验对2020年1月至2021年1月期间3省市共30个区县639份临床样本进行了检测,对阳性样本进行全基因组测序并与国内外毒株比对分析。结果显示,共检测到7份阳性样本,整体阳性率1.10%。5份阳性样本(重庆3份、四川1份、贵州1份)经过测序拼接,发现病毒全基因组长度均为2000 bp,GenBank登录号分别为OK334614~OK334618,同源性比对显示与国内外毒株的相似性在98.2%~99.2%之间,与PCV2和PCV4的同源性较低,分别为44.9%~45.5%和46.3%~46.9%。通过对Cap蛋白的氨基酸序列分析,发现重庆和四川地区4份样本感染毒株的基因型均属于PCV3a型,而贵州地区样本感染毒株的第24和27位氨基酸分别为亮氨酸(L)和赖氨酸(K),为一种新的变异基因型,不属于目前分类标准下的任何一种。该结果为进一步了解PCV3的遗传变异及其在我国西南部分省份的分子流行特征提供了依据。

In order to understand the infection status of porcine circovirus type 3(PCV3)and the molecular genetic characteristics of epidemic strains in Sichuan,Chongqing and Guizhou,639 clinical samples from 30 districts or counties in the above three provinces(municipality)from January 2020 to January 2021 were tested.The positive samples were sequenced and compared with domestic and foreign strains.The results showed that a total of seven positive samples were detected,and the overall positive rate was 1.10%.Five positive samples(three in Chongqing,one in Sichuan and one in Guizhou)were sequenced and spliced.The whole genome sequences of the five samples were all 2000 bp in length and they were deposited in GenBank with the accession numbers OK334614-OK334618,respectively.The homological analysis indicated that these PCV3 strains shared 98.2%-99.2%similarity with domestic and foreign strains,while lower homology was found when compared with PCV2 and PCV4,which was 44.9%-45.5%and 46.3%-46.9%,respectively.Through the amino acid sequence analysis of Cap,it was found that the genotypes of all the four samples in Chongqing and Sichuan belonged to PCV3a.However,the amino acids at positions 24and 27in virus from Guizhou sample were leucine(L)and lysine(K).According to the current classification criteria,it did not belong to any genotype,indicating that it was a new variant genotype.Our results provided a basis for further understanding of the genetic variation of PCV3and its molecular epidemic characteristics in the southwest of China.