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

Wellcome Open Research

article

Chitra Pattabiraman¹  Pramada Prasad¹  Anson K. George¹  Darshan Sreenivas¹  Risha Rasheed¹  Nakka Vijay Kiran Reddy¹  Anita Desai¹  Ravi Vasanthapuram² 

[1] Neurovirology, National Institute of Mental Health and Neurosciences;Nodal Officer Genetic Confirmation of SARS-CoV-2

关键词: SARS-CoV-2;    variants;    Variants of Concern;    VOC;    COVID-19;    COVID-19 India;    Karnataka;    India;    genomic epidemiology;    outbreak investigation;    SARS-CoV-2 spread;    SARS-CoV-2 variants of concern;   

DOI  :  10.12688/wellcomeopenres.16768.2

学科分类：内科医学

来源: Wellcome

【 摘 要 】

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.

【 授权许可】

CC BY