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Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

ABSTRACT: Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.

SUBMITTER: Radhakrishnan C

PROVIDER: S-EPMC8010186 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

Radhakrishnan Chandni C Divakar Mohit Kumar MK Jain Abhinav A Viswanathan Prasanth P Bhoyar Rahul C RC Jolly Bani B Imran Mohamed M Sharma Disha D Rophina Mercy M Ranjan Gyan G Sehgal Paras P Jose Beena Philomina BP Raman Rajendran Vadukkoot RV Kesavan Thulaseedharan Nallaveettil TN George Kalpana K Mathew Sheela S Poovullathil Jayesh Kumar JK Keeriyatt Govindan Sajeeth Kumar SK Nair Priyanka Raveendranadhan PR Vadekkandiyil Shameer S Gladson Vineeth V Mohan Midhun M Parambath Fairoz Cheriyalingal FC Mangla Mohit M Shamnath Afra A Sivasubbu Sridhar S Scaria Vinod V

Frontiers in genetics 20210317

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new ...[more]

PMID: 33815467

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Dataset Information

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

Publications

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

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