两株猪细环病毒的全基因组序列分析

Complete genome sequence analysis of two newly emerged Torque teno sus virus isolates

为了研究猪细环病毒(Torque teno sus virus,TTSuV)的流行及遗传变异情况,试验采用PCR方法对从河南省南阳市某规模化养猪场采集的疑似TTSuV阳性猪的淋巴结、肺脏、血清等样品进行检测,并对TTSuV1阳性样品进行全基因组序列测定、同源性分析、遗传进化分析和基因重组分析。结果表明:试验成功从样品中鉴定出2株TTSuV1毒株,其全基因组序列长度分别为2906,2920 bp,分别命名为HeN1-A9株和HeN1-A11株。两毒株与GenBank中TTSuV1型参考毒株的同源性为68.8%~96.0%,与GenBank中TTSuVk2型参考毒株同源性为46.8%~47.6%,两毒株之间的同源性为86.4%。基于TTSuV1全基因组序列构建的遗传进化树分析,两毒株均属于TTSuV1c亚型;而基于TTSuV1第3段基因组序列构建的遗传进化树分析,两毒株均属于TTSuV1b亚型。两毒株均是重组毒株,以西班牙的G21株(GU570201)为亲本毒株,我国的LNJZ株(KT968712)提供重组片段,重组位点分别位于基因组2195~2530 bp和2147~2650 bp处,重组区域为ORF1与ORF3的重叠部分。说明我国已出现新型重组的TTSuV毒株。

In order to study the prevalence and genetic variation of Torque teno sus virus(TTSuV),lymph nodes,lung and serum of suspected TTSuV positive swine collected from a large-scale pig farm in Nanyang City,Henan Province were detected by PCR method.The complete genome sequence determination,homology,genetic evolution and gene recombination of TTSuV1 positive samples were analyzed.The results showed that two TTSuV1 strains were successfully identified from the samples,and their genome sequences were 2906 bp and 2920 bp in length,respectively.They were named HeN1-A9 and HeN1-A11,respectively.The homology between the two strains was 68.8%-96.0%with the reference strain of TTSuV1 in GenBank,46.8%-47.6%with the reference strain of TTSuVK2 in GenBank,and the homology between the two strains was 86.4%.Genetic evolution tree analysis based on the whole genome sequence of TTSuV1 showed that both strains belonged to TTSuV1c subtype.While the genetic evolutionary tree analysis based on the third sequence of TTSuV1 showed that the two virus strains belonged to the TTSuV1b subtype.Both strains were recombinant strains,with the Spanish G21 strain(GU570201)as the parental strain,and LNJZ strain(KT968712)from China provided recombination fragments.The recombination sites were located at 2195-2530 bp and 2147-2650 bp in the genome,respectively.The recombination region was the overlapping part of ORF1 and ORF3.It indicated that a new recombinant TTSuV strain had appeared in China.