India needs a national surveillance plan
The announcement of a new rapidly spreading mutated variant of the Sars-CoV2 virus in the United Kingdom (UK) has been followed by a variety of reactions. It was always likely that a mutated Sars-CoV2 variant may emerge that is worse. While it is in UK today, with similar reports from South Africa and Brazil, it could easily be in India tomorrow. While this variant is currently in the spotlight, others may lurk in the shadows. Sars-CoV2 is a virus that like any other virus, makes billions of copies of itself inside infected patients. The longer it takes to eliminate the virus, the more such mutations may accumulate. If such mutations become beneficial for virus survival and propagation from human to human, they can rapidly spread in the community.
In the case of the variant first reported in UK, named lineage B.1.1.7, there is an unusually large divergence from its nearest ancestor, suggesting that it may have come from a person with a prolonged infection. These new mutations seem to have enabled it to spread more effectively. While measures such as hand-washing, distancing and masks will remain effective, increased transmission rate could be devastating in countries where the infection is exponentially increasing and the health systems are under pressure. So far, this variant has not been associated with more severe disease or higher risk of death.
We also do not expect this variant to be able to evade immunity induced by either previous infection or vaccines since this is typically due to recognition of multiple sites by antibodies as well as by immune cells. Therefore, based on available data, I do not see the B.1.1.7 variant as a major worry for India right now. But any increase in severity or reduction in immunity still needs to be carefully monitored, and rapid spreading in itself can increase avoidable deaths if health care systems get overwhelmed by numbers.
Mass-scale production of generic drugs and vaccines was always our strength. The year 2020 has additionally seen India become more “atmanirbhar” in areas ranging from diagnostics to devices. The recent procurement by the Delhi government of over a thousand Swasth-Vayu non-invasive BiPAP ventilators, indigenously developed at the CSIR National Aeronautical Laboratory, would have been difficult to imagine in 2019. Innovative diagnostics are also gaining traction. For example, we expect to be able to rapidly modify the CRISPR-based Sars-CoV2 test (Feluda) to discriminate the UK variant, if it is clinically required going forward. Thus, I expect any B.1.1.7 or related outbreak in India to be containable and in the worst case scenario, manageable.
Despite my conviction that we are well- placed to weather the current storm, complacence must be avoided. We should continue doing what we have already done well, and also prepare ourselves for new twists and turns in this pandemic, as well as for future ones.
A good start is to appreciate the molecular and epidemiological surveillance efforts by UK that have led us to know about this variant in a timely manner; hopefully early enough to limit its global spread. In India, Kerala and CSIR-IGIB have already conducted similar studies and some other states had also expressed interest. Rapidly scaling up such capacity across India is achievable through national coordination; scientifically we are ready. This would help to not only to discover and limit spread of this variant, but also any future ones. After all, the virus mutates inside people. With our massive population, over 10 million known cases, and undiagnosed cases probably numbering over twenty times that, India may well be the place for the next important variant to emerge. Going forward, we need as much caution within India, as for incoming international travellers.
So how do we maintain surveillance of Sars-CoV2 and future pandemics? Regarding the emergence of worrisome strains or new pathogens, it is really not a question of whether, but when. Scientists had previously warned of a future pandemic based on identification of coronaviruses similar to Sars-CoV2, in China. Hopefully, we will do better in future.
Large scale sequencing is now easier than ever before. We have successfully used sequencers (devices that can determine the sequence of DNA/RNA) that are as small as a pencil box and cost less than a high-end television, to sequence over a 1,000 Sars-CoV2 genomes at costs comparable to what an RT-PCR used to be in March 2020. These can become micro-labs that can take sequencing to point of care diagnostics, such that you sequence the sample to determine not only positive or negative, but also the strain, within the same day. We have also used larger machines to affordably sequence more than a 1,000 samples in a single run, which can be part of mega-lab national hubs serving lakhs. Using these technologies, we can ask questions limited not only to Sars-CoV2, but for any known organism e.g. for tuberculosis, as well as interrogate unknown ones such as a potential future pathogen. What is now required is a national surveillance plan of current and future pandemics, building capacity and preparedness. In the spirit of never wasting a good crisis, let us use the current public attention as a catalyst for change.
Anurag Agrawal is director of CSIR Institute of Genomics and Integrative Biology.
The views expressed are personal.