Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Abstract

Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.136: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%, B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences. Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

“…N440K mutation found in B.1.36, was first perceived in Visakhapatnam and other parts of South India [105,106]. This substitution has been linked with higher transmission and infectivity as well as immune escape across the Fig.…”

COVID mortality in India: National survey data and health facility deaths

“…India's significantly higher COVID death rate in 2021 compared to the lower than expected death rate in 2020 requires further research. The spread of infection to rural areas in 2021 is one factor, but there might also be differences in the pathogenicity between the original virus (Wuhan) in 2020 and the mix of alpha and delta variants accounting for most of the 2021 viral wave (26), or other biological predictors of severe infection which changed between these two waves. Similarly, tracking death rates will be essential to understanding the effects of the Omicron wave currently underway in India, or future viral variants.…”

Postoperative Outcomes After Emergency Surgery in COVID-19 Patients: An Ambispective Matched Cohort Study

“…However, whether the socioeconomic disparity contributed to excess mortality in our study cohort or it was because of greater severity of presenting surgical pathologies, possibly caused by delayed presentation to the hospital, weaker immune response, or synergistic action of SARS-CoV-2 and surgery is not clear [ 25 ]. Further with the progression of the pandemic, natural selection and evolution selection of the genomic variants of SARS-CoV-2) associated with higher transmission, severe disease, re-infection, and immune escape may be a reason for higher mortality in our patients [ 26 ]. The findings of the current study have direct implications for assessing the burden of COVID-19 on perioperative outcomes.…”