Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

Abstract Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the maj...

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Published in:bioRxiv 2021-01
Main Authors: Pallavali Roja Rani, Mohamed, Imran, J Vijaya Lakshmi, Jolly, Bani, Afsar, S, Jain, Abhinav, Divakar, Mohit Kumar, Panyam Suresh, Sharma, Disha, Nambi Rajesh, Bhoyar, Rahul C, Dasari Ankaiah, Sanaga, Shanthi Kumari, Ranjan, Gyan, Valluri, Anitha Lavanya, Rophina, Mercy, Umadevi, S, Sehgal, Paras, Avula, Renuka Devi, Surekha, A, Pulala Chandra Sekhar, Hymavathy, Rajamadugu, Vanaja, Pr, Scaria, Vinod, Sivasubbu, Sridhar
Format: Article
Language:English
Subjects:
Coronaviruses
COVID-19
Epidemiology
Genetic analysis
Genomes
Genomics
Infectivity
Pandemics
Phylogeny
Polymerase chain reaction
Severe acute respiratory syndrome coronavirus 2
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Summary:Abstract Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh. Competing Interest Statement The authors have declared no competing interest.
ISSN:2692-8205
DOI:10.1101/2021.01.22.427775