First isolation and identification of Getah virus SC1210 in Sichuan

Abstract

Objective To study the genome molecular characteristics of Getah virus (SC1210) which isolated in Sichuan province in 2012. Methods Reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify the isolate and the genome was sequenced by the second Ion Torrent PGM. Computer softwares, including Mega Align and Mega 6, were used to analyze the nucleotide and deduced amino acid sequence, and draw phylogenetic trees. Results SC1210 was identified as Getah virus. The full genome sequence was 11 690nt, the nucleotide and amino acid homology of the full sequence with other strains were 99.2%-99.7% and 96.5%-99.4%.The capsid protein of SC1210 consisting of 804 nucleotides, encoding 268 amino acids and the full-length of E2 protein, had 1 266 nucleotides, encoding 422 amino acids. The nucleotide homology of the capsid protein and the E2 protein with other strains were 94.9%-99.2% and 94.6%-99.6%, and the amino acid were 97%-99.6% and 97.1%-99.5%. The 3′ UTR of the virus included 402 nucleotides and there were three repeat sequence elements and 19 nucleotides conservation sequence. Conclusions The first GETV isolate SC1210 in Sichuan province has a closer relationship with Yunnan strain YN040 and a far genetic relationship with MM2021. Key words: Getah virus; Capsid gene; E2 protein gene; 3′ untranslated region; Nucleotide sequence