Delta COVID-19 variant caused second wave in India over April and May, says consortium of national labs

New Delhi: The surge of COVID-19 cases in the country in the last two months shows a correlation with the rise in B.1.617 variant of the SARS-CoV-2, according to INSACOG, a grouping of 10 national laboratories. April and May witnessed a deadly second wave of coronavirus cases that swept through the country, stretching the healthcare infrastructure to its limits. According to INSACOG, the B.1.1.7 lineage of the virus, which was first identified in the United Kingdom is declining in proportion across India in the last one and half month. The B.1.1.7 variant of the coronavirus has been named ‘Alpha’. The B.1.617 lineage of SARS CoV-2 was first reported from Maharashtra but it is now seen in other states such as West Bengal, Andhra Pradesh, Delhi, Gujarat, Telangana. “The current surge in cases seen over the last two months in some states shows a correlation with the rise in the B.1.617 lineage of SARS CoV-2,” the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) said. The B.1.617 lineage has further evolved into three sub lineages — B.1.617.1, B.1.617.2 and B.1.617.3. Early data shows B.1.617.2, dubbed Delta by the WHO, has higher transmission advantages over the other two sub-lineages. B.1.617, initially termed a double mutant, has three new spike protein mutations. Two mutations — E484Q and L452R — are in the area important for antibody-based neutralisation. The third mutation — P681R in B.1.617 — along with the reversion of E484Q allows its sub-lineage to be more infectious. It was found in high levels in genomes sequenced in Maharashtra (2,077), West Bengal (630), Delhi (1,458), Karnataka (225) as of May 28, and accumulates new mutations in spike and other genes, the INSACOG found in the genomes sequenced as of May 28. The World Health Organisation (WHO) has termed it a ‘Variant of Concern’. B.1.617.1 and B.1.617.3 sub-lineages have two receptor binding domain mutations — L452R and E484Q. The former has seven spike mutations, while the latter has seven to eight. In the case of B.1.617.2, it has nine to 10 spike mutations and two receptor binding domain mutations — L452R and T478K. B.1.6171.1 and B.1.617.2 have higher transmission rate and reduced susceptibility to neutralisation antibodies. In the case of all the three sub-lineages, it has the potential to reduced antibody efficacy and potential reduced neutralisation by vaccine sera, which, however, remains to be established. B.1.1.7, also known as the Alpha variant, has 50 percent increased transmission. It also has increased severity. The INSACOG is a grouping of 10 national laboratories that was established by the Ministry of Health and Family Welfare on December 25 last year. It has been carrying out genomic sequencing and analysis of COVID-19 viruses and correlating epidemiological trends with genomic variants. Genomic variants of various viruses are a natural phenomenon and are found in almost all countries.