Some of these amino acid replacements either singly or in combination have been shown to influence transmission of the virus, interfere with neutralization of the virus, and are associated with an increase in the number of hospitalizationsĨ. Viruses of the lineage B.1 have acquired several other amino acid replacements in the Receptor Binding Domain of the Spike protein – specifically in the lineages which have been designated as VOCs, namely -B.1.1.7 (N501Y), B.1.351 (N501Y, E484K, K417T) and P.1 from the lineage B.1.1.28 (N501Y, E484K, K417T). Several studies have now shown that viruses in this lineage transmit better, with increased infectivity in cell culture This lineage is now the dominant lineage across the world. The viruses responsible for the catastrophic outbreak in Italy, in early 2020, with an amino acid change in the spike protein D614G and were classified into lineage B.1Ģ8. While viruses of both lineages are circulating across the world, viruses of lineage B are more widespread and prominent in number. There are two ancestral lineages of SARS-CoV-2 in the PANGO classification system, A and BĢ8. Multiple lineages of SARS-CoV-2 have been reported from across the world and in IndiaĢ7. Studies of sequences from India juxtaposed with sequences from all over the world, suggest that mutations associated with immune escape and re-infection are already circulating in the population In the genomic epidemiology study, no particular lineages were associated with disease severityĢ2.

These data have contributed to our understanding of how the virus enters, spreads, and evolves in a population. Detailed analysis of the contact network of COVID-19 cases to look at transmission within the state emphasized the role of symptomatic individuals in spreading the virusĢ3. We found multiple introductions of SARS-CoV-2 into the state and at least seven distinct lineages were already circulating in the state by May 2020. We have previously performed detailed genomic epidemiology of SARS-CoV-2 in the South Indian state of Karnataka, with a population of 64.1 million (Census 2014)Ģ2. Genomic studies in India have shown that several lineages of SARS-CoV-2 have been introduced, have spread, and fallen below the limit of detection since January 2020Ģ2. The primary concern is that they may herald the second wave of SARS-CoV-2 in the county and/or undermine the vaccination drive. As with other countries in the world, India too started vaccination campaigns in January 2021, at about the same time that reports of VOCs were communicated from the United Kingdom (UK), Brazil, and South Africaġ1. It is only after 11 million cases and over 150,000 deaths that the numbers declined, signalling the end of the first wave of SARS-CoV-2 in the countryġ1. In India, the COVID-19 pandemic began with the importation of the virus in January 2020ġ0⁠. Such variants may influence the trend of the pandemic and are therefore broadly known as Variants of Concern (VOCs) However, the emergence of variants with distinct biological properties which include one or more mutations that confer higher infectivity, increased transmission, severe disease, re-infection, and immune escape are a cause for concernĩ. The evolution of the virus did not initially alarm public health specialists or those involved in vaccine developmentĢ. The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives and has affected people living in all parts of the globeġ.

Geneious prime 2020 citation