Isolation and complete genomic sequence analysis of a new Sindbis-like virus

Abstract

The Sindbis-like virus was first discovered in China in 1986. Its complete genomic sequence consists of more than 11 000 bp encoding more than 3 700 amino acids. It contains a 5′ non-transcriptional region (5′-NTR) in a non-structural region, four non-structural proteins (nsP1, nsP2, nsP3, nsP4) regions, capsids in conserved and non-conserved regions and structural E1, E2, E3, 6K regions and a 3′ non-transcriptional region (3′-NTR). The Sindbis-IMB was isolated from the blood of a patient suspected to have encephalitis, and was followed by identification and passage. The virus RNA was extracted from virus supernatant in infected cells and the whole genome was divided into 12 fragments; RT-PCR was then performed to amplify the 12 fragments for complete sequencing. The results showed that the whole genomic sequence of Sindbis-IMB consists of 11 717 bp encoding 3 773 amino acids. Homology comparison with other Sindbis-like isolates demonstrated the highest similarity was the YN87448 with a variation of 1% strain isolated in Yunnan Province and the second highest to the SAAR86 strain with a variation of ∼1.2%. The nucleotide sequence variations were present in non-structural regions, resulting in amino acids K, E, N, R, H, and L in protein sequences in positions 230, 231, 443,781, 1 582, and 1746 in the new isolation respectively. Furthermore, three additional amino acids—glutamic acid, serine and alanine—were noted in nsp4 terminus as compared to the YN87448 isolate.