Why India must tackle a mutating virus head-on

With unprecedented SARS-CoV-2 infections, the country is likely to become a hotspot of future mutations unless the contagion is rapidly controlled, say Anurag Agrawal* and Disha Agrawal**.

doi:10.1038/nindia.2021.61 Published online 28 April 2021

Mutations occur inside infected humans — countries with the most infections produce the most mutations.

© Owais Rashid Hakiem

As India struggles through a massive second wave of COVID-19 infections, the country is simultaneously faced with another recurring but avoidable pattern – that of apportioning blame to ‘mutant’ variants of the SARS-CoV-2 virus for a rampaging pandemic.

While it is correct to inculpate these ‘variants of concern’ or ‘variants of interest’ (VoC / VoI) in some measure, the overall picture is more complex. Importantly, this bit of the pandemic puzzle was not totally unpredictable. A terrifying second wave in the Brazilian city of Manaus, after half its population was tested positive for the novel coronavirus1, is a stark example, often cited in scientific and public discussions to emphasize the need for continued precautions and vaccination. The biggest and most preventable mistake was, of course, laxity in COVID-appropriate behaviour at every level. The sections of society most able to observe the necessary precautions, seemed least inclined to do so. However, just as the P.1 variant drove the resurgence in Brazil, variants with increased transmissibility and potential to escape the human immune system have likely played an important role in India.

In December 2020, India saw an increase in potential immune escape mutations and a few VoCs in viral sample sequences mostly isolated from contacts of travelers. In a highly seropositive population, the emergence of immune escape mutations is inevitable. Some initial outbreaks, such as the January outbreak in Kerala, were investigated and no variant was implicated. Fresh and larger outbreaks in April 2021, however saw the rise of the B.1.1.7 and B.1.617 variants. The indigenous variant now called B.1.617, was independently found in Maharashtra by groups in Pune and Delhi, with the first documented alert in February 2021 by Rajesh Karyekarte’s group at BJ Medical College, Pune, in a small number of samples from Amravati. Sequencing at the National Center for Disease Control, Delhi, also found these variants with L452R and E484Q identified as two potentially important mutations.

Using larger datasets spanning various districts and time-periods, the Indian Council of Medical Research’s lab National Institute of Virology in Pune and the Indian SARS-CoV-2 Genomic Consortia (INSACOG) confirmed this as a potential VoC in March 20212. The lineage B.1.617 was subsequently assigned and evoked global interest. The earliest sequences of this lineage can be traced back to December 2020 and sub-lineages or new variants with L452R are being identified.

© Nature India

Variants need close monitoring

The difference between a potential and a confirmed VoC is a tricky one, but critically determines subsequent action. One needs to be proactive yet cautious, finding the balance between over and under-reacting. Hindsight suggests it is better to be proactive. Learning from the situation at hand and focusing to develop strategies and protocols is the best way forward, continuing well after the second wave wanes, to delay or mitigate a potential third wave. Before delving into the specifics and devising plans, India must clearly recognize certain features of the SARS-CoV-2 virus that have shaped the pandemic.

SARS-CoV-2 is not a fast-mutating virus, though it is an RNA virus, known to mutate faster than DNA viruses. Mutations arise naturally in any RNA virus as a result of faulty replication. RNA is prone to mutate naturally due to its labile nature and unlike higher organisms, RNA viruses do not have a proof-reading system that can weed out errors. Thus, the more the number of infections, the more the replications, and the more the mutations.

A majority of mutations have no effect on the pathogenicity of the virus but a small fraction do, and these mutations either get selected or eliminated as the virus evolves. Evolution tends to select those mutations that enable the virus to propagate better, i.e. infect, replicate and transmit more efficiently, while not killing the host. Unfit mutations are eliminated. As a result, the virus typically tends to evolve towards more infectious and less virulent variants.

Mutations occur inside infected humans and thus, countries with the most infections produce the most mutations. Ineffective therapies, widely prevalent in India during the pandemic, could further increase the likelihood of escape mutations. Wrong use of plasma therapy and antivirals could be especially harmful. The Indian second wave is a threat not only to India, but to the world, and global consequences of local actions must be clearly recognized in this context.

Sequencing more essential now

The only way to identify VoC and VoI in a timely manner is sequencing, sequencing and more sequencing. Any of the three commonly used sequencing platforms – Illumina, Oxford Nanopore, and IonTorrent – are suitable for the purpose. In India, the INSACOG laboratories primarily use Illumina platforms which have the highest accuracy and throughput. However, the cost, portability and speed advantages of Nanopore sequencing have led to their widespread use, especially as sequencing is being scaled up across the country.

Typically, the viral genome is compared against a reference to determine the mutations. Sets of mutations are matched to known VoC or VoI, and isolated mutations are filtered through a list of mutations known to either increase transmissibility or immune escape. Before the lineage B.1.617 was known, the variant was identified using this approach. L452R matched the transmissibility and immune escape lists, and E484Q matched the immune escape list. The incorrect term ‘double mutant’ came from this double match on the list of ‘villainous’ mutations. It may not always be possible to ascertain immediately what the individual mutations achieve, but they can be flagged for further studies, especially if they are in critical hotspot regions such as the receptor binding domain of the spike protein.

While it is essential to sequence a sufficiently large number of samples, the quality of the design is more important than quantity. A well-designed genomic survey covering 0.5 per cent of the population is likely to be more informative than a poorly designed one covering 5 per cent. However, India must strive for both. In Kerala, for instance, a sentinel surveillance with a fixed number of 25 samples per week per district, with additional sampling as required, seems adequate to understand local transmission patterns. This comes with the caveat that it may not be possible to identify a new VoI or VoC at a point in time when they contribute to only a small fraction of the infections.

Epidemiologically correlating new genomic variants with an outbreak is standard practice before calling something a VoI. In-depth studies are necessary before calling it a VoC. However, the actual impact of these on public health actionability is smaller than it first seems, unless fully integrated with other components such as clinical outcome data, registries and vaccine efficacy studies. The population of many Indian states is more than those of several European nations combined and infections have been rising at a furious pace. India is, therefore, likely to become a hotspot for rise of future variants of concern, unless things are rapidly brought under control. Even then, careful surveillance for an extended period must continue. Simple things like masking, COVID appropriate behaviour, and rapid vaccination roll out still remain key in the public health fight.

(*Director, CSIR Institute of Genomics and Integrative Biology, Delhi. **Student, Maulana Azad Medical College, Delhi.)


1. Sabino, E. C. et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet (2021) doi: 10.1016/S0140-6736(21)00183-5

2. Cherian, S. et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Preprint. Biorxiv. doi: 10.1101/2021.04.22.440932