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.1.36: 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, 37 of these were in the B.1.36 lineage (37/65, 56.92%) 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.

Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala

“…We also found other variants such as Alpha and Beta with very low numbers of representation during the period. Our findings and its comparison with waves in other Indian States, mainly seen in cities such as Chennai, Mumbai, Delhi and other countries, showed a similar pattern ( 25 – 27 ). Region specific and time bound information is very important in utilizing the data on genomic sequences for tracking the infection and for timely interventions in required points ( 26 , 28 ).…”

SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study

“…A sudden surge in cases of SARS-CoV-2 in a population rests upon several factors among which emergence of novel mutations in the viral genome leading to the appearance of possibly more virulent and fatal variants is a huge cause for concern in this ongoing pandemic ( 6 ). In India, as has been observed by many studies, the spread of COVID-19 infection is attributable to rising novel variants and their spread ( 7 , 8 ). Studying SARS-CoV-2 genomic variants and their tracking with time might help us in understanding viral evolution, behavior, and infection trajectory.…”

Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru

“…It serves as a major hub for national and international travel due to the presence of many educational institutes and universities and job opportunities, especially the globalized IT sector. The first cases of COVID-19 in the Bengaluru city were associated with international and or interstate travel 7,12 .…”

“…To combat this, various public health policy-3 makers have advocated monitoring the importation of such variants from international travelers and containing their spread in the community by enforcing social distancing norms, lockdowns and contact tracing along with active genomic surveillance of COVID-19 cases in the community. However, once VoCs are seen in the community, a surge in COVID-19 cases is most likely 7,8 .…”