1株塞内卡病毒A型的基因组序列与演化分析

Genome Sequencing and Phylogenetic Analysis of Senecavirus A,CH-HNCY-2019

旨在分析塞内卡病毒A型(Senecavirus A,SVA)CH-HNCY-2019株的基因组特性和演化,参考SVA毒株SVV-001(GenBank No.NC011349)全基因组序列设计8对引物,通过RT-PCR扩增和测序获得SVA CH-HNCY-2019株全基因序列并进行序列分析。结果显示,SVA分离株CH-HNCY-2019基因组全长为7294个核苷酸,与中国分离株核苷酸相似性为95.9%~99%,与美国经典株SVV-001核苷酸相似性最低。CH-HNCY-2019与大多数中国2017—2018年分离毒株亲缘关系较近,处于同一分支,而与中国2015—2016年分离株亲缘关系较远。与包括2019年中国广东4个SVA分离株在内的其他国内外分离株相比,CH-HNCY-2019的VP1蛋白的722位氨基酸由L突变为Q;VP3蛋白的499位氨基酸由A突变为V,528位氨基酸由P突变为S,582位氨基酸由E突变为K。本研究成功获得1株SVA CH-HNCY-2019全基因组序列,研究结果提示,SVA中国流行株具有多样性,而且在不断地演变,应加强SVA的分子流行病学调查、生物安全措施和疫苗研发以防止SVA在我国猪群中的广泛传播。

This study aimed to analyze genomic properties and evolution of a Senecavirus A(SVA)strain CH-HNCY-2019.Eight pairs of primers were designed based on the genome sequence of SVV-001(GenBank No.NC011349)and fragments covering the whole genome of strain CH-HNCY-2019 were amplified by RT-PCR.The whole-genome sequence of CH-HNCY-2019 was determined and analyzed.Results showed that the complete genome of CH-HNCY-2019 is composed of 7294 nucleotides.The phylogenetic evolutionary analysis of the entire genome demonstrated that CH-HNCY-2019 shares 95.9%to 99%nucleotide similarities with Chinese SVA isolates,and has the lowest nucleotide identity with the representative American strain SVV-001.The CH-HNCY-2019 strain has a close phylogenetic relationship with most of Chinese SVA isolates in 2017 and 2018 and a distant genetic relationship with SVA strains isolated in 2015 and 2016 in China.Comparing to the domestic and foreign isolates including four SVA strains isolated in Guangzhou,China in 2019,amino acid substitutions were observed in the CH-HNCY-2019 strain at VP1 position 722(L to Q)and VP3 position 499(A to V),528(P to S),and 582(E to K).The whole-genome sequence of SVA CH-HNCY-2019 was successfully obtained in this study.Sequence analysis results implied the diversity and continuous evolution of current Chinese SVA isolates.SVA molecular epidemiological investigation is critical in comprehensive understanding of the prevalence of SVA in China and provides a solid background for formulating strict biosecurity management and vaccine development to prevent the widespread of SVA in Chinese pig herds.