Indian researchers have identified 7,684 variants in SARS-CoV-2 (novel coronavirus) genomes from samples collected within the country. A recently published research paper analysing the viral variants has also listed out the top 61 non-synonymous Indian variants with details of the genomic mutation and the corresponding amino acid change in the associated viral protein.
The research paper "SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants" by the scientists of Cellular and Molecular Biology (CCMB), Hyderabad emphasises the need to keep a lookout for new and emergent strains and localized disease outbreaks. "The evolution of SARS-CoV-2 can render it more infectious via adaptive mutations that increase affinity or enhance binding to host cells, while escape mutations that can help it evade the immune response have serious implications for vaccines and therapeutics and can adversely impact the severity and mortality of the disease," the study says.
The findings of the study become significant as in many parts of the world, mutant variants of the virus are causing a new surge in COVID-19 cases. The current increase in the number of infections in some Indian states may also be due to the presence of virus variants, it is feared.
The research paper also highlights the key spike mutations of global concern which are a priority for surveillance in the Indian landscape. This includes the UK, South African, Brazilian and Nigerian variants and variants that carry the lineage of such variants. A mutation named N440K with high frequency in Andhra Pradesh is also in the list.
The ongoing collaborative effort has the participation of 35 laboratories covering 22 states of India. Genome Evolution Analysis Resource for COVID-19 (GEAR-19) initiative is coordinated by CCMB.
The paper points out that the mutation landscape of SARS-CoV-2 has been under constant global scrutiny to understand the effect of these changes on the infectivity and antigenicity of the virus. While most mutations are of little to no consequence, sometimes the virus acquires a mutation that gives it an advantage over other strains, it points out. "The spike protein is used by the virus to enter human cells via the ACE2 receptor. Thus, spike mutations can potentially facilitate better affinity or binding and enable easier entry into the host cell. Mutations can putatively also render the virus resistant to neutralisation by host antibodies and thus need to be identified and monitored for the efficacy of antibody therapeutics," the paper says.
Stating that some of the spike mutations recently identified that are of concern include the N439K, N440K, Q493K and E484K, as they are prone to immune escape the paper says the N440K variant has been found in 42 percent of the samples from Andhra Pradesh and E484K in 3 samples from Maharashtra . Most of the other mutations are absent in currently sequenced samples from Indian isolates and need to be actively monitored, it suggests.
Even among the top 61 non-synonymous Indian variants of SARS-CoV-2 not all are equally prevalent in Indian samples. The researchers say that some of these variants are relatively new and hence have a low prevalence among the samples sequenced in India so far, but warn that they are strong candidates for increased viral transmission and/or immune escape.
The study concludes that as the COVID-19 pandemic enters its second year, it is crucial to keep a lookout for new and emergent strains and localised disease outbreaks. "The evolution of SARS-CoV-2 can render it more infectious via adaptive mutations that increase affinity or enhance binding to host cells, while escape mutations that can help it evade the immune response have serious implications for vaccines and therapeutics and can adversely impact the severity and mortality of the disease. As multiple vaccines are rolled out in the year ahead, the virus will be subjected to new selection pressures and evolution modes," it says.
The study also points out that India has so far not been sequencing SARSCoV-2 isolates to full capacity, having deposited only about 6,400 genomes of the over 10.4 million recorded cases (0.06%). "Exploiting advances in genomic epidemiology by monitoring and increasing sequencing efforts following local spikes will go a long way in staying on top of mutations of concern while their biology and effects are studied in greater detail. Studying the virus under a genomic lens has played a pivotal role in tackling key challenges in pandemic management so far," it suggests.
A new country-wide consortium named INSACOG was established in December 2020 to identify new and circulating variants by genome sequencing across multiple states. One of the main goals of this consortium is to sequence 5 per cent of all COVID-19 positive cases in the country.