Genomic analysis of a Chinese isolate of Getah-like virus and its phylogenetic relationship with other Alphaviruses.
An alphavirus, M-1 strain, was isolated from a pool of culicine mosquitoes collected in Hainan island of China during an arbovirus survey in 1964. In the present study, we determined the complete nucleotide sequence of the M-1 strain using RT-PCR and RACE techniques. The M-1 genome is 11,690 nucleotides (nt) in length and contains two open reading frames (ORFs) encoding four nonstructural proteins and five structural proteins, respectively. Searches using Blast and comparison analyses suggested that M-1 is closely linked to Sagiyama virus (SAGV, AB032553) with 98% identity and Getah viruse (GETV, AY702913) with 97.8% identity in the full-length nucleotide sequence. However, compared with SAGV, there is 1 deletion (3 nucleotides in length) in the Capsid region, a deletion in the 3' untranslated region (10 nucleotides in length) and 2 insertions in the 3' untranslated region involving a total of 5 nucleotides. Interestingly, from the 5' UTR to the end of coding region, M-1 share the highest identity with GETV, even though the identity of 3' UTR drops dramatically to 76.2%. Furthermore, phylogenetic analysis based on the complete genomic sequences and sequences for structural or non-structural proteins of M-1 and 15 alphaviruses showed that M-1 grouped with GETV first and then grouped together with SAGV. Based on the comparison analysis and phylogenetic analysis, we conclude that M-1 strain can be considered as a strain that is a Chinese isolate of Getah-like virus.
Wen
Jin-Sheng
JS
Department of Microbiology, Zhongshan Medical College, Sun Yat-sen University, 74 Zhong shan Road II, Guangzhou 510080, PR China.
Zhao
Wen-Zhong
WZ
Liu
Jian-Wei
JW
Zhou
Hong
H
Tao
Jian-Ping
JP
Yan
Hui-Jun
HJ
Liang
Yu
Y
Zhou
Jing-Jiao
JJ
Jiang
Li-Fang
LF
D020413:3' Untranslated Regions / Q000235:genetics; D000524:Alphavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D000818:Animals; D002681:China; D009033:Culicidae / Q000821:virology; D016679:Genome, Viral / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012398:Ross River virus / Q000235:genetics; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D017385:Sequence Homology; D017361:Viral Nonstructural Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
D020413:3' Untranslated Regions; D017361:Viral Nonstructural Proteins; D015678:Viral Structural Proteins