Even if the new variant — VOC 201212/01 — that is thought to be more transmissible is already present in India, it might not be able to spread wildly as a sizeable percentage of people are already infected. Suspending flights from UK might be able to stop its introduction into India, but the N501Y mutation can arise independently here. Hence more genome sequencing and genomic epidemiology is needed.
On December 29, the Health Ministry said a total of six samples of passengers who had returned from the U.K. had tested positive for the new SARS-CoV-2 virus variant (VOC 201212/01) first detected in the U.K.
About 33,000 passengers from the U.K. had arrived at various airports in India between November 25 and December 23. Of them, 114 tested positive for the virus using RT-PCR. All the 114 positive samples have been sent to 10 INSACOG (Indian SARS-CoV-2 Genomics Consortium) labs for genome sequencing.
While India temporarily suspended flights from the UK from December 23-31, it is possible that many people infected with the new variant have already arrived in India days and weeks before flights from the UK were suspended. While the new variant first identified in the UK in September has been spreading “rapidly” since end-November, preliminary results have shown it does not cause increased reinfection risk or disease severity.
The genomic analysis undertaken by COVID-19 Genomics UK Consortium (COG-UK Consortium) found that this particular lineage was growing around 70% faster in the UK. Is it cause for concern in India?
At the moment, the variant does not seem to pose a huge risk to India. Given the higher transmissible nature of the virus, we should have seen a spike in cases in at least some cities in India, which is not the case, says Dr. Giridhara Babu, Professor of Epidemiology at the Public Health Foundation of India, Bengaluru.
Hurdles in new variant spread
Since the preliminary study indicates that the variant is unlikely to cause increased risk of reinfection, the new variant might not spread wildly here due to difficulty in finding dense pockets of susceptible people, says Dr. Babu. This is because 40%-50% of urban India, particularly in Tier-1 and Tier-2 cities, and about 30% of people across India would have already been infected.
The emergence of the new variant with higher infectivity brings to the fore the importance of undertaking more genome sequencing of the virus. Though the total number of recorded cases stands at over 10.2 million, India has so far sequenced only around 6,300 genomes of the SARS-CoV-2 virus. In contrast, the U.K. has sequenced nearly 1,57,000 genomes of the virus though the total number of cases is only about one-fourth of India’s.
The National Task Force (NTF) on COVID-19 had a few days back belatedly recommended the setting up of a Genomic Surveillance Consortium (INSACOG) to map the various strains circulating in India. It has also wanted whole genome sequencing to be done for 5% of the positive cases from all the States and Union Territories.
The new variant shows how important genome sequencing is and the need to link genome data with epidemiological and clinical information in order to make a difference in controlling the disease, Prof. Sharon Peacock, Director of COG-UK Consortium says in The Guardian.
More virus genomes need to be sequenced
A team of researchers from CSIR-IGIB led by Dr. Vinod Scaria has demonstrated the importance of undertaking more genome sequencing of SARS-CoV-2 virus. In a study (preprint which has not been peer-reviewed) of 120 unique variants reported in literature based on genome sequencing of SARS-CoV-2 virus, the researchers found that 86 were genetic variants associated with immune escapes, particularly antibody escapes, had emerged in global populations. Of the 86 variants, nine had over 1% frequency in the respective countries.
The question of homoplasy
The CSIR-IGIB team identified a variant (N440K) having a frequency of 2.1% in India and a high prevalence in Andhra Pradesh (33.8% of 272 genomes). The same variant has been identified in the UK, Denmark and Australia. Though the epidemiological and clinical significance of the N440K variant is yet to be studied, its emergence in India and three other countries is an example of homoplasy — the ability of a mutation/variant to emerge independently in different genetic lineages.
The N440K variant was found in a healthcare worker who was found to have been reinfected. At this point the presence of N440K in the reinfected person is only an observation. It is too early to draw a causal relationship or even a correlation between N440K and reinfection, says Dr. Scaria.
The N501Y mutation in the new variant first identified in the UK is believed to increase the binding affinity thereby making the variant more transmissible. N501Y has independently arisen in South Africa too. Due to homoplasy, the possibility of N501Y arising independently in India cannot be ruled out.
The possibility of dangerous mutations arising independently in distant locations underscores the need to undertake more genome sequencing of the virus to identify variants on time and undertake genomic epidemiology to study the spread of the variants. Linking the genome data with clinical and epidemiological information can go a long way in controlling the spread of any variants that cause more infections or severe disease.