Complete genome sequencing and evolutionary analysis of dengue virus serotype 1 isolates from an outbreak in Kerala, South India.
In this study, dengue virus (DENV) isolates from a localized, small-scale, non-seasonal dengue outbreak were genetically characterized. The outbreak occurred during the pre-monsoon months (April-May) in a medical college campus in Kerala, South India in 2009 affecting 76 people. Analysis of 39 viral RNA positive serum samples by a serotype specific reverse-transcription polymerase chain reaction identified dengue virus serotype 1 (DENV1) as the causative strain. Formation of a distinct genetic clade was revealed in the initial phylogenetic analysis using nucleotide sequences of a partial (303 bp) Capsid-Pre-membrane protein (C-PrM) coding region of 37 outbreak strains. The sequences of these strains clustered with that of the Genotype III DENV-1 strains from India, and 32 among them formed a single major sub-clade. Whole-genome sequencing (10,693 bp) of two strains (RGCB585/2009 and RGCB592/2009) selected from this major sub-clade, and subsequent phylogenetic analysis using the full-length coding region sequence showed that the sequences grouped with that of the isolates from Thailand (1980), Comoros (1993), Singapore (1993), and Brunei (2005) among the Indo-Pacific isolates. The sequences of the two strains had a nucleotide identity of 97-98 % and an amino acid identity of 98-99 % with these closely related strains. Maximum amino acid similarity was shown with the Singapore 8114/93 isolate (99.6 %). Four mutations-L46M in the capsid, D278N in the NS1, L123I, and L879S in the NS5 protein coding regions-were seen as signature substitutions uniformly in RGCB585/2009 and RGCB592/2009; in another isolate from Kerala (RGCB419/2008) and in the Brunei isolate (DS06-210505). These four isolates also had in common a 21-nucleotide deletion in the hyper-variable region of the 3'-non-translated region. This first report on the complete genome characterization of DENV-1 isolates from India reveals a dengue outbreak caused by a genetically different viral strain. The results point to the possibility of exotic introduction of these circulating viral strains in the region.
Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, 695014 Kerala, India.
M
M
Anoop
Ashish J
AJ
Mathew
B
B
Jayakumar
Aneesh
A
Issac
Sajith
S
Nair
Rachy
R
Abraham
M G
MG
Anupriya
E
E
Sreekumar
D000328:Adult; D000595:Amino Acid Sequence; D003715:Dengue / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology; D003716:Dengue Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D005260:Female; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D007194:India / Q000453:epidemiology; D016013:Likelihood Functions; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012703:Serotyping
D012367:RNA, Viral