Experts from BJMC & SGH begin whole genome sequencing of CHIKV

In February this year, experts from B J Medical College (BJMC) and Sassoon General Hospital (SGH) started whole genome sequencing of the Chikungunya virus (CHIKV) in an effort to rule out significant mutation in the virus and virus strain in circulation, said officials.

Chikungunya is a viral infection transmitted by mosquitoes. The symptoms include fever, muscle pain, headache, fatigue and possible occurrence of rash. Last year, health officials came across a significant number of CHIKV-infected patients, including cases of rare manifestations. According to doctors, there were cases of Chikungunya with Encephalitis, Meningoencephalitis, Myocarditis, Gastroenteritis, kidney injury, sepsis and Guillain-Barré Syndrome (GBS).

According to the BJMC doctors, as many as 24 samples of CHIKV-infected patients will be tested for whole genome sequencing. The CHIKV genomic study is an initiative of the Pune Knowledge Cluster (PKC), a science and technology cluster established by the principal science advisor to the Government of India.

Furthermore, the Centre under its health vertical has established collaborations to aid in understanding the prevalence of infectious diseases using vector dynamics and viral epidemics. The CHIKV genome sequencing is part of the vertical programme of the PKC. The study will help identify any significant mutation in the virus that is likely to cause severe complication/s in patients, officials said.

Dr Rajesh Karyakarte, head of Microbiology, BJMC, who was part of the response team (RRT) formed to investigate the reason behind the surge in Chikungunya cases with rare manifestations in the city, informed that the samples of one patient with cross infection of Dengue and Chikungunya were tested. “The findings of the CHIKV genome sequencing have been sent to the government,” he said. Dr Karyakarte further said that the results indicate that adaptive mutations in the CHIKV are facilitating effective circulation of the virus in areas where the Aedes Aegypti mosquito is prevalent, leading to major CHIKV outbreaks. “The test results showed a double mutant virus containing the E1:K211E and E2:V264A mutations in the background of E1:226A. This double mutant exhibited remarkably higher fitness of virus for Aedes Aegypti, evidenced by a significant increase in virus infectivity (13-fold), dissemination (15-fold), and transmission (62-fold), compared to the parental E1:226A virus. However, the E1-A226V mutation was not observed,” he said.

Last year, doctors in city hospitals witnessed several Chikungunya cases with rare manifestations wherein the positive patients showed severe Dengue-like symptoms and complications. Treating doctors and health officials speculate that the CHIKV has mutated or there is a possibility that a new variant of CHIKV is in circulation that needs to be ruled out. In 2024, CHIKV was found transmitting and dominating the Dengue virus in the state, including Pune.

As per BJMC officials, the CHIKV mutation was shown to mediate improved fitness in Aedes Albopictus regarding midgut infectivity, transference to salivary glands and subsequent transmission to the vertebrate host. The majority of the 2015-17 study strains possessed E1: K211E and E2:V264A, implying that these mutations have been established in the CHIKV population in states such as Maharashtra, Tamil Nadu, and Andhra Pradesh. Partial sequencing of earlier strains from Pune in 2010, had also revealed the existence of these mutations at an earlier point in time.