A virus that changes stripes

The emergence of the new variant shows that more genome sequencing of SARS-CoV-2 is needed

December 31, 2020 12:15 am | Updated 01:09 am IST

Passengers arriving from the U.K. wait to register themselves for COVID-19 testing at the Chennai International Airport on December 22, 2020.

Passengers arriving from the U.K. wait to register themselves for COVID-19 testing at the Chennai International Airport on December 22, 2020.

On December 29, six samples of passengers who had returned from the U.K. to India had been found to contain the new variant of the SARS-CoV-2 virus (VOC 201212/01) . 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.

India temporarily suspended flights from the U.K. from December 23 to 31 to prevent the new strain from entering the country. However, it is possible that many people infected with the new variant had already arrived here days or even weeks before the suspension of flights. Only through detailed epidemiological studies combined with genome sequencing data can we confirm the presence and spread of the variant in India. While the new variant, first identified in the U.K. in September, has been spreading “rapidly” there since end-November, preliminary results have shown it does not cause increased reinfection risk or disease severity .

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The genomic analysis undertaken by the COVID-19 Genomics U.K. Consortium (COG-UK Consortium) found that this particular lineage was growing around 70% faster in the U.K. Is that a cause for concern in India? At the moment, the variant does not seem to pose a huge risk to India — given its propensity to spread faster, the variant should have already caused a spike in cases in some cities, which is not the case. 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. 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.

More sequencing needed

The emergence of the new variant 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.

A few days ago, the National Task Force on COVID-19 belatedly recommended the setting up of a Genomic Surveillance Consortium (INSACOG) to map the various strains circulating in India. It has also said whole genome sequencing would be done for 5% of the positive cases from all the States and Union Territories. The new variant shows the importance of genome sequencing and the need to link genome data with epidemiological and clinical information in order to make a difference in controlling the disease, says Professor Sharon Peacock, Director of the COG-UK Consortium, in The Guardian .

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Independent emergence of variants

A team of researchers from CSIR-IGIB led by Dr. Vinod Scaria has demonstrated the importance of undertaking more genome sequencing of the SARS-CoV-2 virus. In a study of 120 unique variants reported in literature based on genome sequencing of the SARS-CoV-2 virus, the team found that 86 were genetic variants associated with immune escapes. Of the 86 variants, nine had over 1% frequency in the respective countries.

One of the variants (N440K) identified has 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 U.K., 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. The presence of N440K in the reinfected person is only an observation. More studies are needed to draw a causal relationship or even a correlation between N440K and reinfection.

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The N501Y mutation in the new variant first identified in the U.K. is believed to make the variant more transmissible. The N501Y mutation has independently arisen in South Africa too. Due to homoplasy, the possibility of N501Y arising independently in India cannot be ruled out. So, only through increased genomic sequencing can we stay prepared.

The possibility of dangerous mutations arising independently in distant locations underscores the need for more genome sequencing of the virus to identify variants on time and for 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.


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