Archives of Virology

, Volume 163, Issue 11, pp 3135–3140 | Cite as

Genetic characterization of chikungunya viruses isolated during the 2015-2017 outbreaks in different states of India, based on their E1 and E2 genes

  • Jayashri Patil
  • Ashwini More
  • Poonam Patil
  • Santosh Jadhav
  • Priyanka Newase
  • Megha Agarwal
  • Sarika Amdekar
  • C. G. Raut
  • Deepti ParasharEmail author
  • Sarah S. CherianEmail author
Brief Report


During 2015-2017, chikungunya virus (CHIKV) showed a resurgence in several parts of India with Karnataka, Maharashtra and New Delhi accounting for a majority of the cases. E2-E1 gene based characterization revealed Indian subcontinent sublineage strains possessing Aedes aegypti mosquito-adaptive mutations E1: K211E and E2:V264A, with the 211 site positively selected. Novel mutational sites E1: K16E/Q, E1: K132Q/T, E1: S355T, E2: C19R and E2:S185Y could be associated with epitopes or virulence determining domains. The study examines the role of host, vector and viral factors and fills gaps in our molecular epidemiology data for these regions which are known to possess a dynamic population.



Authors are thankful to Dr. S.N. Kalashetty, Pune; National Institute of Malaria Research, New Delhi, Nasik Municipal Corporation for referring human clinical samples for the investigation of chikungunya virus etiology. Authors are grateful to Mr. Atul Walimbe for useful input in the Molecular clock studies.


This study received institutional funding from National Institute of Virology, Pune.

Compliance with ethical standards

Conflict of interest

The authors declare that there are no conflicts of interest.

Ethical approval

The research described in the paper does not use any human or animal subjects.

Supplementary material

705_2018_3974_MOESM1_ESM.tif (3.7 mb)
Supplementary material 1 (TIFF 3756 kb) Suppl. Fig. 1. Phylogenetic tree (Indian Ocean Lineage) based on E2-E1 gene region sequences (n=233) constructed by the Bayesian Markov Chain Monte Carlo (MCMC) method. Posterior supports for all nodes are indicated. The mean root age of IOL and the tMRCAs of the Indian ocean and Indian subcontinent sublineage are also shown. Branch color codes are: Red (Indian isolates of this study); Blue (other Indian isolates); Black (global isolates). Groups highlighted in pink possess E1:A226V mutation while the group in blue possesses E2:V264A and E1:K211E
705_2018_3974_MOESM2_ESM.doc (53 kb)
Supplementary material 2 (DOC 53 kb) Supplementary Table 1: Details of the Chikungunya virus isolates used in this study along with their GenBank accession numbers
705_2018_3974_MOESM3_ESM.doc (62 kb)
Supplementary material 3 (DOC 62 kb) Supplementary Table 2: Novel mutations in the CHIKV E2-E1 genes reported in this study
705_2018_3974_MOESM4_ESM.doc (42 kb)
Supplementary material 4 (DOC 41 kb) Supplementary Table 3: Experimentally known epitopes in the CHIKV structural polyprotein available in Immune Epitope Database (IEDB) and Analysis resource
705_2018_3974_MOESM5_ESM.doc (78 kb)
Supplementary material 5 (DOC 78 kb) Supplementary Table 4: List of publicly available Indian sequences used in sequence analysis


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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Jayashri Patil
    • 1
  • Ashwini More
    • 1
  • Poonam Patil
    • 1
  • Santosh Jadhav
    • 2
  • Priyanka Newase
    • 1
  • Megha Agarwal
    • 2
  • Sarika Amdekar
    • 1
  • C. G. Raut
    • 1
  • Deepti Parashar
    • 1
    Email author
  • Sarah S. Cherian
    • 2
    Email author
  1. 1.Dengue-Chikungunya GroupNational Institute of VirologyPuneIndia
  2. 2.Bioinformatics GroupNational Institute of VirologyPuneIndia

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