Genomic sequence results in Karnataka show SARS-CoV-2 picking up new mutations

The genomic sequencing report submitted to the Karnataka government has suggested that SARS-CoV-2 virus is changing and currently the Delta and sub-lineages of Delta are spreading across Bengaluru Urban and picking up new mutations.

The report said, of these mutations, N439 mutant has already exihibited potential to increase the fitness of the virus.

The report cautioned: "We need to monitor any increase in the frequency of these mutations. As that might be a signal for a new variant, which may not be covered by the protection from vaccines," the report quoted in bold letters.

This report comes ahead of a similar report of results of 300 samples sent for genomic sequencing is expected to be released soon and discussed by the Committee for Covid-19 Whole Genome Sequencing (WGS) which is to meet on Thursday for discussing the findings.

Strand Precision Medicine Sciences, a genomics-based research and diagnostics company mandated to conduct genomic sequencing by the Karnataka government to help detect trends in mutations has submitted its report to the health ministry on September 1.

The report has also been sent to the Karnataka Covid Task Force, Chairman of Genomic Surveillance Committee, Karnataka; Bruhat Bengaluru Mahanagara Palike (BBMP) Commissioner and health commissioner, BBMP.

Samples processed include 34 sequences from children, 28 sequences from vaccinated individuals, partial as well as fully vaccinated and 6 fully vaccinated individuals. The investigations were conducted on 298 complete sequences.

The outputs suggested the identification of four lineages and all are delta or sub-lineages of delta. The report also said, three lineages, Delta and two sub-lineages of Delta AY.4 and AY.12 were found across Bengaluru Urban and in all groups.

The report also spoke about new mutations. "This sequencing showed 133 mutations in spike protein alone. Many of these are known mutations," the report said.

"We found several new mutations at low frequency (>0.3percent<4.5percent) in the spike protein in the 439-446 positions, in Delta, AY.4 and AY.12. Some of these are novel and not yet reported in global databases," the report mentioned.

N439K mutant found in 7 sequences, N440Y/T/F mutant in 8 sequences, L441Y/S/G/A/C/D/V found in 7 sequences, D4421/V/Y/F in 9 sequences, S443E/V/Y/W/F in 7 sequences, K444F/N/V/T/S/V mutants found in 7 sequences.

However, experts opine that Genomic sequencing results are not a cause for worry as most samples collected from persons who were being treated at home.

Strand Precision Medicine Solutions was tasked with the responsibility of study of mutations through genome sequencing by the Covid Task Force in Karnataka. The sequencing indicated 30 percent mutation in the Delta AY.4 variant and 3 percent in AY.12 mutant.

Total 298 swabs were collected from Covid-19 patients in Bengaluru for genomic sequencing also showed that Delta and its sub-lineages AY4 & A12 were found to be dominant across the age groups in Bengaluru.

The test also showed that, Covid virus was changing and Delta's sub-lineages are spread across Bengaluru urban areas and new mutations are being reported.