Whole Genome Sequencing of a Candidate Strain for FMDV Vaccine: Genomic Structure and Genetic Variation
Whole Genome Sequencing of a Candidate Strain for FMDV Vaccine: Genomic Structure and Genetic Variation
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DOI：
10.5376/jvr.2011.01.0001
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发表时间：
2011-06
期刊：
影响因子：
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通讯作者：
Li Huachun
中科院分区：
文献类型：
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作者：
Li Huachun
对口蹄疫病毒（FMDV）疫苗候选株O/YM/YN/2000的全基因组进行了测序分析。利用RT-PCR技术扩增出覆盖O/YM/YN/2000全基因组的7个重叠cDNA片段，并进行了序列测定。结果表明，O/YM/YN/2000株全基因组全长8133 nt，包括1 053 nt的5′非翻译区（UTR）（含18 nt poly C）、6 969 nt的开放阅读框（ORF）、93 nt的3′非翻译区和至少18 nt的poly A尾。对O/YM/YN/2000株与GenBank中已登录的其他FMDV毒株的核苷酸和氨基酸序列进行同源性比较和系统发育分析。基于全基因组和VP 1序列的系统发育分析表明，O/YM/YN/2000株与O型口蹄疫病毒的Cathay拓扑型聚在一起。O/YM/YN/2000中存在片段缺失突变，其中5′-UTR的S片段缺失4个核苷酸，5′-UTR的假结结构域II缺失43个核苷酸，3A蛋白缺失10个氨基酸残基。本研究结果可为口蹄疫疫苗株的筛选提供参考
The complete genome of foot-and-mouth disease virus (FMDV) vaccine candidate strain O/YM/YN/2000 was sequenced and analyzed. Seven overlapping cDNA fragment which covered the O/YM/YN/2000 genome were amplified by RT-PCR and sequenced. The results showed that the complete genome of the strain O/YM/YN/2000 has 8 133 nucleotides (nt) in length including a 1 053 nt 5′- untranslated region (UTR) (including 18 nt poly C), a 6 969 nt open reading frame (ORF), a 93 nt 3′-UTR and at least 18 nt poly A tail. The homologous comparison and phylogenetic analysis of the nucleotide and deduced amino acid (aa) sequences among O/YM/YN/2000 and other FMDV strains available deposited in GenBank were performed. Phylogenetic analysis based on the complete genome and VP1 revealed that that the strain O/YM/YN/2000 is clustered in the FMDV serotype O cathay topotype. Fragment deletions mutation in O/YM/YN/2000 were revealed, deletions involving 4 nt in the S fragment of 5′-UTR, 43 nt which possibly contributed to the loss of pseudo-knot domain II of 5′-UTR and 10 aa residues in 3A protein. The results in this research might provide some information for screening FMDV vaccine strain