The first and the most comprehensive report on the evolution of SARS-CoV-2 isolates from Kerala has reported that the virus strains currently circulating in the State and causing local outbreaks were introduced through inter-State travel early days of the epidemic, followed by local circulation.
Despite being a State with a sizeable expatriate population, none of the virus strains circulating in the State could be traced to international travellers and hence were not brought in by expatriates to Kerala.
The pre-print of “Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions” appears in bioRxiv, an open access preprint repository for the biological sciences.
Scientists after calculating tMCRA (time to most recent common ancestor) to assess the point in time when these strains were introduced into the State, puts it between early March -June, after which local spread occurred.
The study, a collaborative effort of CSIR-Institute of Genomics and Integrative Biology, New Delhi, and Government Medical College, Kozhikode, thus suggests that while focussed measures for testing, tracing contacts and quarantine measures for international travellers very effectively prevented local spread, the same diligence was not applied when inter-State travel resumed post-lockdown.
“What we are essentially seeing today is an extension of the local spread which must have begun in the State early in the epidemic. All the virus samples we sequenced from Kerala belonged to the A2a clade which is predominant in India, within which we identified three clusters, the largest shares genomes from Odisha; the second cluster’s ancestry potentially trace to Maharashtra and the third cluster shares genomes from Karnataka,” Vinod Scaria, senior scientist, CSIR-IGIB, told The Hindu.
Though the study samples are not representative of the entire State, the pattern cannot be very different across the State, said R. Chandni, Head of Emergency Medicine, Kozhikode medical college and the principal investigator of the study.
Mutant variant
It has already been reported that the predominant virus clade A2a, which is predominant in India and currently circulating in Kerala, is marked by the mutant variant D614G.
This study also uncovered a total of four novel genetic variants and 89 variants which were identified only in Kerala and not in the rest of India.
Genome sequencing of SARS-CoV-2 in various countries has led to insights into the temporal and geographical spread of the virus, introductions, and spread of the virus through travellers, local transmission, and disease dynamics.
“Despite reporting the first COVID-19 case in India, Kerala has been rather late in initiating genomic surveillance studies, which could have identified the outbreaks early on. Nevertheless continuous genomic surveillance can still help the State in a major way to uncover potential outbreaks and possibly connect outbreaks which are apparently not related,” a senior scientist said.