Frontiers in Genetics (Mar 2021)
Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions
- Chandni Radhakrishnan,
- Mohit Kumar Divakar,
- Mohit Kumar Divakar,
- Abhinav Jain,
- Abhinav Jain,
- Prasanth Viswanathan,
- Rahul C. Bhoyar,
- Bani Jolly,
- Bani Jolly,
- Mohamed Imran,
- Mohamed Imran,
- Disha Sharma,
- Mercy Rophina,
- Mercy Rophina,
- Gyan Ranjan,
- Gyan Ranjan,
- Paras Sehgal,
- Paras Sehgal,
- Beena Philomina Jose,
- Rajendran Vadukkoot Raman,
- Thulaseedharan Nallaveettil Kesavan,
- Kalpana George,
- Sheela Mathew,
- Jayesh Kumar Poovullathil,
- Sajeeth Kumar Keeriyatt Govindan,
- Priyanka Raveendranadhan Nair,
- Shameer Vadekkandiyil,
- Vineeth Gladson,
- Midhun Mohan,
- Fairoz Cheriyalingal Parambath,
- Mohit Mangla,
- Mohit Mangla,
- Afra Shamnath,
- Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium,
- Sridhar Sivasubbu,
- Sridhar Sivasubbu,
- Vinod Scaria,
- Vinod Scaria
Affiliations
- Chandni Radhakrishnan
- Government Medical College, Kozhikode, India
- Mohit Kumar Divakar
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Mohit Kumar Divakar
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Abhinav Jain
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Abhinav Jain
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Prasanth Viswanathan
- Government Medical College, Kozhikode, India
- Rahul C. Bhoyar
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Bani Jolly
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Bani Jolly
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Mohamed Imran
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Mohamed Imran
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Disha Sharma
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Mercy Rophina
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Mercy Rophina
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Gyan Ranjan
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Gyan Ranjan
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Paras Sehgal
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Paras Sehgal
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Beena Philomina Jose
- Government Medical College, Kozhikode, India
- Rajendran Vadukkoot Raman
- Government Medical College, Kozhikode, India
- Thulaseedharan Nallaveettil Kesavan
- Government Medical College, Kozhikode, India
- Kalpana George
- Government Medical College, Kozhikode, India
- Sheela Mathew
- Government Medical College, Kozhikode, India
- Jayesh Kumar Poovullathil
- Government Medical College, Kozhikode, India
- Sajeeth Kumar Keeriyatt Govindan
- Government Medical College, Kozhikode, India
- Priyanka Raveendranadhan Nair
- Government Medical College, Kozhikode, India
- Shameer Vadekkandiyil
- Government Medical College, Kozhikode, India
- Vineeth Gladson
- Government Medical College, Kozhikode, India
- Midhun Mohan
- Government Medical College, Kozhikode, India
- Fairoz Cheriyalingal Parambath
- Government Medical College, Kozhikode, India
- Mohit Mangla
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Mohit Mangla
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Afra Shamnath
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium
- Sridhar Sivasubbu
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Sridhar Sivasubbu
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Vinod Scaria
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Vinod Scaria
- Academy of Scientific and Innovative Research, Ghaziabad, India
- DOI
- https://doi.org/10.3389/fgene.2021.630542
- Journal volume & issue
-
Vol. 12
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.
Keywords
