AFTER KERALA reported India’s first Covid infection on January 30, in a medical student who had returned from China, the state focused on expatriates and international travellers but the subsequent outbreak originated mainly from three other states, a new genome sequencing study has suggested.
Most of the later cases could be traced to Maharashtra, Odisha and Karnataka, according to the study conducted jointly by the Government Medical College in Kozhikode and two of India’s premier science institutes — CSIR-Institute of Genomics and Integrative Biology, and Academy of Scientific and Innovative Research.
A large number of non-resident Keralites had returned from Maharashtra and Karnataka after the pandemic broke out. So far, Kerala has recorded 1,22,214 Covid cases, with 490 deaths.
The study, published on September 10, covered 200 SARS-nCoV2 samples from a major tertiary care centre in north Kerala, where a significant number of non-resident Keralites had returned from the Middle East, too.
“The major cluster (identified as K1) encompassed 40 genomes from Kerala (35.4%). The analysis suggests that the cluster K1 was potentially generated from an ancestor from the state of Maharashtra before initial dissemination in Kerala. The timing of the introduction of the cluster was estimated as between May 11 and July 22,” the study says.
“The second cluster (K2) encompasses 42 genomes (37.1%) from Kerala and shares 27 genomes from the state of Odisha suggesting ancestry from the state. Timing of the introduction of this cluster is estimated between Feb 12-May 16. The third major cluster (K3) encompasses 25 genomes (22.1%) from Kerala and shares 46 genomes from the state of Karnataka with introduction around March 3-May 27,” it says.
According to the study, a haplotype analysis of the samples suggests that the virus circulating in Kerala is with the D614G variant, which is considered to confer high infectivity.
The study’s findings indicate that the state’s strategy, of focusing mainly on testing, contact-tracing and quarantining expatriates and international travellers, should have also covered those returning from other states.
“Genome analysis suggests limited inter-state introductions followed by extensive local spread contribute to the majority of the isolates in Kerala in contrast to spread from international travellers, suggesting the testing, tracing and quarantine of international travellers was an effective strategy,” it said.
The study also pointed out that the cluster architecture has identified recent but not apparently connected outbreaks spanning multiple districts in the state.
The study did not identify the centre from where the samples were taken. “However, the centre caters to a large population and region and has close proximity to an international airport. Secondly, the sampling was limited to a short period of time, thus enabling only a cross-sectional view of the epidemic and precluding an accurate and temporal view of the dynamics of the epidemic in the state. Nevertheless, this provides a unique opportunity to create a snapshot of the epidemic in time and space,” the report said.
There are two international airports in north Kerala, one in Kozhikode and the other in Kannur.
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