Detection of SARS-CoV-2 variants in India from UK returnees

Abstract

The epidemiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been marked by the emergence of new variants globally. The diversification is normal as a part of the evolutionary and adaptation processes. Most emerging mutations and variants are not known to have any major impact on the spread of the virus. Some mutations may however give a selective advantage to the virus-like change in virulence, transmissibility etc. Among the variants noted in the recent past, a new SARS-CoV-2 variant, VOC 202012/01, was reported from United Kingdom (UK) that was noted to have emerged in late September 2020 [1]. This variant resulted in an increasing proportion of cases in Kent, a county in south-eastern England, London and other parts of the UK and was reported in early December as a variant of concern. Preliminary analyses have indicated that the new variant has increased transmissibility compared to previously circulating variants, with no increase in infection severity. Since late December 2020, a few VOC 202012/01 cases have also been reported in other European countries such as Belgium, Denmark, Finland, France, Germany, Switzerland, Iceland, Ireland, Italy, the Netherlands, Norway, Portugal, Spain and Sweden and globally in countries including Australia, Canada, Hong Kong SAR, Israel, Japan, Jordan, Lebanon, South Korea, and Singapore. Genomic analysis revealed that this new variant of SARS CoV-2 in a lineage named as B.1.1.7 branched-out from the rest of the phylogenetic tree [2]. The U.K. lineage of SARSCoV-2 has picked 17 mutations that lead to 14 amino acid changes in multiple proteins and 3 deletions [2]. Crucial mutations were in the gene that encodes the spike, a protein on the viral surface that the pathogen uses to enter human cells. The Government of India (GoI) had suspended air travel from the UK since December 23, 2020, in order to check the influx of the new variant of SARS-CoV-2 into the country. Further, to monitor the spread of the UK variant in the country, GoI released a guideline wherein the respective State governments need to ensure that all passengers travelling from or transiting through airports in the UK and disembarking in India need be subjected to the RT-PCR test for SARS-CoV-2 on arrival. Further on, the samples of passengers testing positive should be sent to the Indian Council of Medical Research-National Institute of Virology (ICMRNIV), Pune or any other appropriate laboratory for genomic sequencing. December 23, 2020 onwards, ICMR-NIV, Pune started receiving samples of the COVID-19 positive UK