Chikungunya virus molecular evolution in India since its re-emergence in 2005

Abstract

Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005-20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.

Keywords: chikungunya virus (CHIKV); phylogeny; variants; whole-genome sequencing.

Figure 1.

The ML phylogenetic (midpoint rooted) tree of Indian CHIKV strains using complete genome sequences (n = 99). Numbers adjacent to branches show bootstrap values >70 per cent. Red colour nodes represent sequences from the present study. Sequences downloaded from the public database are coloured in violet.

Figure 2.

The DensiTree showing the uncertainty between isolates. In this tree set, there are seven clearly distinguishable clades with different colours, showing large uncertainty of the topologies. Further details such as node ages and tree scale are provided in Supplementary Fig. S3.

Figure 3.

Hierarchical clustering of non-synonymous mutations in CHIK samples. A total of thirty-nine non-synonymous mutations was observed in the structural (E1, E2, E3, C, and 6K/TF) and non-structural (nsP1, nsP2, nsP3, and nsP4) protein genes in a total of forty-one samples collected between 2010 and 2016. The blue colour represents the absence of mutation in the respective sample, while the red colour shows the mutation’s presence.

Figure 4.

Principal component analysis of 2010, 2011, 2012, 2013, and 2016 CHIKV strains.

Figure 5.

Median joining network analysis to represent region-wise mutations in CHIKV strains. The numbers between strains show the frequencies of mutations. Circles in pink colour represent strains from Delhi, mustard from Maharashtra, blue from Kerala, yellow from Karnataka, light green from Gujarat, forest green from West Bengal, and sky blue from remaining parts of India.