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

Frontiers in Genetics

Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium¹  Gyan Ranjan²  Mohit Mangla²  Paras Sehgal²  Vinod Scaria²  Bani Jolly²  Mohamed Imran²  Sridhar Sivasubbu²  Mercy Rophina²  Mohit Kumar Divakar²  Abhinav Jain²  Disha Sharma³  Afra Shamnath³  Rahul C. Bhoyar³  Rajendran Vadukkoot Raman⁴  Kalpana George⁴  Priyanka Raveendranadhan Nair⁴  Jayesh Kumar Poovullathil⁴  Vineeth Gladson⁴  Sheela Mathew⁴  Shameer Vadekkandiyil⁴  Prasanth Viswanathan⁴  Thulaseedharan Nallaveettil Kesavan⁴  Sajeeth Kumar Keeriyatt Govindan⁴  Beena Philomina Jose⁴  Chandni Radhakrishnan⁴  Fairoz Cheriyalingal Parambath⁴  Midhun Mohan⁴ 

[1] ;Academy of Scientific and Innovative Research, Ghaziabad, India;Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India;Government Medical College, Kozhikode, India;

关键词: COVID-19;    COVIDSeq;    Kerala;    genetic epidemiology;    variants;   

DOI  :  10.3389/fgene.2021.630542

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown