BHUBANESWAR: Genomics researchers found 20C clade of SARS-CoV-2 was specific to Odisha and not present in any other isolates included in the 1062 genomes sequenced across the country.
A recent study carried out jointly by Institute of Life Sciences (ILS), Bhubaneswar and Regional Medical Research Centre (RMRC) found 20C clade in four samples. All five clades - 19A, 19B, 20A, 20B and 20C were observed in 225 genomes sequenced in the State.
The study showed evolution of 19A and 19B in parallel. Majority of the 19A and 19B clades were present in people that migrated from Gujarat suggesting it to be one of the major initial points of disease transmission during March and April.
Odisha was among 18 States that were part of the nationwide study on coronavirus conducted by five research institutes. As part of the study, 1062 genomes were sequenced, of which 225 samples of Covid-19 positive patients those migrated from 13 States were collected in the State during March and June.
ILS Director Dr Ajay Parida said 19B clade was found to be more prevalent (17 per cent) in analysed samples as compared to other clades reported so far in the country. “The phylogenetic analysis showed that clades 20A and 20B evolved quite rapidly and are major source of disease transmission. Whereas 20C strain is rarely detected and appeared to be less adapted or somehow contracted at early stages of infection,” he said.
While 20A clade was found in highest 73 samples and 20B in 60 samples, 19B and 19A were present in 36 and 29 samples respectively. The clade 19A is the Wuhan clade from China.
The analysis also revealed higher proportion symptomatic patients with 20A, 20B and 20C clades. “Europe and Southeast Asia were found to be two major routes of disease transmission in Odisha,” Parida said.
It has been observed that 20A clade, which is prevalent in Europe, became abundant in Odisha from April representing the top cluster, while the bottom cluster represents samples belonging to clade 19A, 19B having a common origin in South-east Asia.
The study also revealed occurrence of as many as 247 single nucleotide mutations from 202 SARS-CoV2 isolates. Of these, 156 variants were observed only in single isolates, 25 variants were classified as common variants with occurrence in more than five pc isolates and 19 variants as rare with two to five pc occurrence in all samples which indicates that these strains have some selective advantage with time for increased transmission.
“The genomics study will help understand the disease dynamics. It will pave way for new avenues of research on Covid-19 vaccines. We will soon carry out sequencing of samples collected in July,” Parida added.
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 by using amplicon sequencing-based methodology at ILS facility.