A new study has uncovered genetic changes in a group of similar SARS-CoV-2 variants in India. The researchers performed genomic surveillance of 54 SARS-CoV-2 positive samples. The samples were collected from August 2020 to October 2020 (Term3) and comprise all SARS-CoV-2 genome sequences in West Bengal except for one.
The team notes the Term3 genetic sequences are different from India’s because they show a higher amount of ‘O’ clade and 20A clade. The Term3 sequences also differed from SARS-CoV-2 genetic sequences collected from April 2020 to July 2020 (Term 2). In Term2, the West Bengal region had an 82% higher amount of ‘G’ and 83% higher amount of 20A clade distribution than the other states of India. They indicate the viral clades in West Bengal are evolving slowly. The researchers tracked the evolutionary changes of SARS-CoV-2 in other areas in Indian patients. When looking at the variation of co-mutations across Indian states and union territories, the researchers observed the emergence of non-clade defining mutations during Term2 and Term3. Specifically, in Term 2, India’s states such as Telangana, Maharashtra, and Karnataka showed five or more co-mutations.
At the same time, the West Bengal area and Gujarat had SARS-CoV-2 strains with less than five co-mutations. By Term 3, there were more sequences of Telangana and Maharashtra with higher co-mutating residues than those of West Bengal. The rise of distinct mutations may be associated with a significant increase of coronavirus cases in Maharashtra and Karnataka compared to West Bengal and Gujarat during ‘Term2’ and ‘Term3’. The researchers also correlated mutations to disease severity.
All sequences showed the D614G and NSP12 mutations. However, people who had symptomatic COVID-19 infection or who died from COVID-19 were more likely to show more NS9b(P10S), N(P13L), NSP12(A97V), and NSP3(T1198K) mutations than asymptomatic patients. There was also a co-mutation triad in [NSP6(L37F)-NSP12(P323L)-Spike(D614G)] in patients who are deceased or who have mild or symptomatic COVID-19 infection. Among 5 mutations in deceased and symptomatic patients, 3 mutations were observed in mild infection, with only the NSP6(L37F) mutation appearing in asymptomatic patients.
The co-mutation network was shown in 51% of patients with asymptomatic disease and 20.41% of mild infections. However, the co-mutation network was not seen in symptomatic cases and the deceased. New co-mutation networks were noted across time in different clades and states of India.