| Autor: |
Bani Jolly, Sajeeth Kumar Keeriyatt Govindan, Kalpana George, Disha Sharma, Gyan Ranjan, Midhun Mohan, Rahul C. Bhoyar, Priyanka Raveendranadhan Nair, Abhinav Jain, Fairoz Cheriyalingal Parambath, Sridhar Sivasubbu, Beena Philomina Jose, Sheela Mathew, Mohamed Imran, Thulaseedharan Nallaveettil Kesavan, Mohit Kumar Divakar, Prasanth Viswanathan, Rajendran V Raman, Mohit Mangla, Shameer Vadekkandiyil, Chandni Radhakrishnan, Mercy Rophina, Afra Shamnath, Jayesh Kumar Poovullathil, Vineeth Gladson, Vinod Scaria |
| Rok vydání: |
2020 |
| Předmět: |
|
| DOI: |
10.1101/2020.09.09.289892 |
| Popis: |
Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
|
