COVID-19 genome sequencing in Odisha reveals 5 clades

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Bhubaneswar: Union Minister of Science and Technology Dr. Harsh Vardhan announced the completion of 1000 COVID-19 viral genomes by the Autonomous Institutes of the Department of Biotechnology, Govt.  of India. ILS, Bhubaneswar; NIBMG, Kalyani; CDFD, Hyderabad; NCCS, Pune and in STEM, Bangalore carried out analysis of the 1062 genomes from 18 states of India. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and South East Asia.

Institute of Life Sciences in collaboration with RMRC analyzed 225 viral genomes of COVID-19 positive patients those migrated from 13 Indian states and the samples for sequencing were collected during March and July 2020. The sequencing, data analysis and interpretation was carried out by the team led by Dr. Sunil Raghav of ILS and Dr. Jyotirmayee Turuk of RMRC using advanced sequencing facility at ILS.

Analysis of Odisha samples showed the presence of all five reported clades 19A, 19B, 20A, 20B and 20C of COVID-19 genome. Clade 19B was found to be much more prevalent in analysed samples (17%) as compared to other genomes reported so far from India. The study showed evolution of 19A and 19B in parallel. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state suggesting it to be one of the major initial points of disease transmission during month of March and April.  The phylogenetic analysis showed that clades 20A and 20B evolved quite rapidly in the Indian population and are major source of disease transmission in the country. Whereas 20C strain is rarely detected and appeared to be less adapted or somehow contracted at early stages of infection. The analysis also revealed higher proportion symptomatic patients with clades 20A, 20B and 20C. The Clade 20C was observed in Odisha and not present any other isolates included in 1000 genome analysis. From these results it is obvious that Europe and Southeast Asia are two major routes of disease transmission in Odisha, said Dr. SanghamitraPati, Director, RMRC.

The study also showed occurrence of as many as 247 single nucleotide mutations from 202 SARS-CoV2 isolates. Out of these 156 variants were observed only in single isolates, 25 variants were classified as common variants with occurrence in more than 5% isolates and 19 variants as rare with 2-5% occurrence in all samples which indicates that these strains have some selective advantage with time for increased transmission.

This is a major development in understanding the disease dynamics through genomics studies, said Dr.Parida. He mentioned that using in house facility we have been able to sequence 225 viral genomes at a relatively short period of time and significant findings from this study will pave way for new avenues of research on COVID-19. He also mentioned that further sequencing of virus genome is being carried out at ILS using recent samples. This study was undertaken as a part of PAN-DBT 1000 COVID genome sequencing initiative and with active support of Govt. of Odisha,

Dr. Harsh Vardhan also launched the network of Biorepositories of COVID clinical samples including the one at ILS, Bhubaneswar.

Salient findings

  • Samples analyzed had migration from 13 Indian States
  • All five reported clades 19A, 19B, 20A, 20B and 20C found.
  • Total of 247 single nucleotide variants were identified.
  • Europe and Southeast Asia as two major routes of disease transmission in India.
  • Recently evolved clades 20A and 20B showed prevalence of four common mutations

Distribution of Clades in Odisha Samples
Phylogenic analysis of 225 isolates
Evolution of Virus genome in different time period in Odisha

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