As anxiety over a possible third wave of COVID-19 escalates, Kerala is banking on real time genomic surveillance data to watch out for the emergence of possible new SARS-CoV-2 variants or any changes in disease patterns amongst various groups in the community that might signal a potential change in disease transmission.
The first wave of COVID never really ended and transmission continued at low levels — 2,500 daily cases — till March this year when relaxations in COVID protocols, election campaigning, and primarily the arrival of new virus variants in the State led to a sudden and massive surge in the epidemic curve.
While preparing the health system ahead for managing a third wave could be an opportunity to improve the State’s health infrastructure, the third wave is neither inevitable nor is it expected to be more vicious than the second wave.
“The second wave peaked mid-May and we expect that the curve will remain on a higher plateau than before, at perhaps 5,000-6,000 new cases per day. Some surge in transmission is inevitable when the unlock happens but unless a more transmissible virus variant emerges, the circulating dominant strain, Delta (B.1.617.2) will continue to maintain the equilibrium it has found,” feels Rakhal Gaitonde, public health expert and Professor, Achutha Menon Centre for Health Science Studies.
The “unlocking” will have to be a more scheduled and controlled affair because, given the high transmissibility of the Delta variant, even small mistakes can be costly, he warns.
Since mid-April 2021, after the extremely transmissible Delta variant emerged as the dominant circulating virus in the State, the Rajiv Gandhi Centre for Biotechnology (RGCB) and the multidisciplinary research lab at the Medical College Hospital, Kozhikode, have been doing targeted genetic sequencing studies.
As part of this initiative, viral RNA samples are being collected from across districts under five categories. Representative samples are being collected from places which recorded a high test positivity rate; from locations where case clusters were reported; samples from persons who had re-infections; samples from persons who contracted COVID after receiving one/two doses of the vaccine; and samples from persons who had no comorbidities but had serious COVID and required ICU care.
“We are regularly checking out existing mutations (L452R, Delta, Kappa) as well as random mutations in the virus. Our effort is to detect any patterns in mutations and if it correlates with any particular category of samples. If so, we can identify the sample location, study the clinical profile of cases and plan further interventions,” says E. Sreekumar, senior scientist at the RGCB.
While this is expected to be a continuous activity, public health experts point out that unless the State takes a conscious effort to go beyond laboratory findings and integrate the genomic surveillance data obtained from time to time into suitable policy decisions on the ground, these are likely to remain mere academic exercises.
“We now have people who derived natural immunity through infection with the virus before it mutated, those who have vaccine-derived immunity as well as those achieved natural immunity through infection by the mutant strain. Right now, we have no idea how long this protection lasts or how strong it is because we have seen re-infections in those who got infected by the original strain, as well as breakthrough infections in those who got vaccinated. It is highly unlikely, but we need to watch if a new new variant will emerge, leading to re-infections in those who were infected by the Delta variant,” says Dr. Sreekumar.
“We thought that vaccines will bring us herd immunity but we now know that while vaccines can reduce the severity of disease and prevent deaths, it cannot stop disease transmission. COVID will eventually become endemic, occasionally creating outbreaks in communities. The only strategy going forward will be to prime the health system, while investing in good genomic and disease surveillance measures,” he says.
