Genetic divergence of Chikungunya viruses in India (1963-2006) with special reference to the 2005-2006 explosive epidemic

National Institute of Virology, 130/1 Sus Road, Pashan, Pune 411021, India Correspondence Vidya A. Arankalle v_arankalle{at}yahoo.co.in Re-emergence of Chikungunya (CHIK), caused by CHIK virus, was recorded in India during 2005–2006 after a gap of 32 years, causing 1.3 million cases in 13 states. Se...

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Bibliographic Details
Published in:Journal of general virology 2007-07, Vol.88 (7), p.1967-1976
Main Authors: Arankalle, Vidya A, Shrivastava, Shubham, Cherian, Sarah, Gunjikar, Rashmi S, Walimbe, Atul M, Jadhav, Santosh M, Sudeep, A. B, Mishra, Akhilesh C
Format: Article
Language:English
Subjects:
Alphavirus Infections - epidemiology
Alphavirus Infections - virology
Amino Acid Substitution
Animals
Base Sequence
Biological and medical sciences
Chikungunya virus - classification
Chikungunya virus - genetics
Chikungunya virus - isolation & purification
Culicidae - virology
Disease Outbreaks
DNA, Viral - genetics
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
Genes, Viral
Genetic Variation
Genetics
Genotype
Humans
India - epidemiology
Microbiology
Miscellaneous
Molecular Sequence Data
Phylogeny
Recombination, Genetic
Selection, Genetic
Sequence Homology, Nucleic Acid
Time Factors
Virology
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Summary:National Institute of Virology, 130/1 Sus Road, Pashan, Pune 411021, India Correspondence Vidya A. Arankalle v_arankalle{at}yahoo.co.in Re-emergence of Chikungunya (CHIK), caused by CHIK virus, was recorded in India during 2005–2006 after a gap of 32 years, causing 1.3 million cases in 13 states. Several islands of the Indian Ocean reported similar outbreaks in the same period. These outbreaks were attributed to the African genotype of CHIK virus. To examine relatedness of the Indian isolates (IND-06) with Reunion Island isolates (RU), full-genome sequences of five CHIK virus isolates representative of different Indian states were determined. In addition, an isolate obtained from mosquitoes in the year 2000 (Yawat-2000), identified as being of the African genotype, and two older strains isolated in 1963 and 1973 (of the Asian genotype), were sequenced. The IND-06 isolates shared 99.9 % nucleotide identity with RU isolates, confirming involvement of the same strain in these outbreaks. The IND-06 isolates shared 98.2 % identity with the Yawat-2000 isolate. Of two crucial substitutions reported for RU isolates in the E1 region, M269V was noted in the Yawat-2000 and IND-06 isolates, whereas D284E was seen only in the IND-06 isolates. The A226V shift observed with the progression of the epidemic in Reunion Island, probably associated with adaptation to the mosquito vector, was absent in all of the Indian isolates. Three unique substitutions were noted in the IND-06 isolates: two (T128K and T376M) in the Nsp1 region and one (P23S) in the capsid protein. The two Asian strains showed 99.4 % nucleotide identity to each other, indicating relative stability of the virus. No evidence of recombination of the Asian and African genotypes, or of positive selection was observed. The results may help in understanding the association, if any, of the unique mutations with the explosive nature of the CHIK outbreak. The GenBank/EMBL/DDBJ accession numbers for the full genome sequences of eight CHIK virus isolates determined in this study are EF027134–EF027141. Supplementary tables are available with the online version of this paper.
ISSN:0022-1317
1465-2099
DOI:10.1099/vir.0.82714-0