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. 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.

Focus on international and domestic travellers are equally important for successful SARS-COV-2 mitigation: ecological comparison of emigrant and migrant travel patterns and COVID-19 trends in Kerala State, India

“…This ecological review of COVID-19 transmission in Kerala State of India suggests that, consistent with genetic epidemiologystudies, 5 seeding of COVID-19 in Kerala leading to the ongoing transmission may not be attributable to Kerala’s international emigrant returnees, rather to domestic travellers arriving from other states of India. Kerala state achieved COVID-19 mitigation through 6 May 2020 and sporadic community seeding of SARS-CoV-2 by international emigrant returnees were interrupted successfully due to combination mitigation measures (as indicated by zero cases on 3 May 2020) including mandatory testing, tracing and quarantine of all international arrivals, the lockdown, social and public event cancellations, risk communication and enforced face coverings and physical distancing.…”

“…We categorized our analysis to three time periods: January to 6 May (mitigated phase); 7 May to 30 June (period commencing with repatriation of emigrants and relaxation of interstate travel); 1 July to 30 September (phase of extensive transmission). 5 …”

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian State of Karnataka

“…Multiple lineages of SARS-CoV-2 have been reported from across the world and in India 12,13,15–17,19–22,27 . There are two ancestral lineages of SARS-CoV-2 in the PANGO classification system, A and B 28 .…”

Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

“…These include states with significantly large populations and air travellers like Andhra Pradesh which has a population of 49 million people, with an estimated 1.5 to 2 million people who are part of the diaspora spread across the world. While a number of genomes have been sequenced from different states in India [3], there is a paucity of genomic data and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh which motivated us to study the genomes from this state in detail. In the present study, we report a total of 293 SARS-CoV-2 genomes from the state of Andhra Pradesh.…”