Genome sequencing finds Delta plus COVID variants less contagious than Delta

New Delhi: AY.1, the sub-lineages of Delta variant commonly known as the Delta Plus and AY.2 are found to have less contagious than its parent in genome sequencing of coronavirus done by INSACOG, a consortium of a government panel.

In its recent bulletin, INSACOG said that the presence of these two sub-lineages is below 1 per cent in the genome samples sequenced in the country in June.

INSACOG also said AY.3 has been identified as a new Delta sub-lineage and it is defined by ORF1a: I3731V common AY.1 mutations except for S: K417.

This is primarily seen in the US with single reclassified cases in the UK and India. However, there is "no known significant property" of this mutation. But since it is a Delta variant of concern (VOC) sub-lineage, INSACOG will continue to monitor it, the bulletin stated.

"Delta sub-lineages AY.1 and AY.2 are declining globally with near-zero cases in the last week of June in either the UK or US, where they were most frequently seen. They also continue to be below 1 per cent in available sequences from June in India.

"It is likely that neither AY.1 nor AY.2 is more transmissible than Delta," the INSACOG said, adding there is no indication of a rising trend in the four clusters of Ratnagiri and Jalgaon in Maharashtra, Bhopal in Madhya Pradesh and Chennai in Tamil Nadu.

INSACOG said the Delta variant (B.1.617.2) is the dominant lineage for new cases across all parts of India in recent samples and remains the most rapidly rising lineage globally.

Delta variant and its sub-lineages are the only VOC in India at this time, it added.

It was a prime variant driving the second wave of the coronavirus that swept India between March to May this year, killing thousands and infecting lakhs. It is also a primary variant that has been currently leading to a spike in infections in other parts of the world.

This also led to apprehension among many that its sub-lineages AY.1 (Delta Plus) and AY.2 will be more virulent than the Delta variant

The INSACOG said in the vaccine efficacy report from Public Health England, two doses of the AstraZeneca (Covishield) vaccine are estimated to provide 94 per cent protection against death from COVID-19 in people aged 65 and over.

Recently released vaccine efficacy report for Covaxin also shows high efficacy against severe disease, but reduced efficacy against infection. There are recent reports from Israel about the reduced efficacy of the Pfizer vaccine in preventing infection, it added

On Alpha variant (B.1.1.7, first documented in the UK), the INSACOG said its prevalence has declined in India and globally. Beta (B.1.351, first documented in South Africa) is also at very low levels in India at this time.

"Gamma (P.1, first documented in Brazil) and Lambda (C.37, first documented in Peru) are not seen in over 10,000 community samples sequenced by INSACOG since May. However, in view of possibly high immune escape properties, they will continue to be specifically monitored," it said.

Continuing outbreaks across India are attributable to the Delta variant, susceptible population, and opportunities for transmission. Public health measures to reduce transmission and vaccination remain critical.

The Indian SARS-CoV-2 Genomics Consortium (INSACOG), jointly initiated by the Union Health Ministry of Health, and the Department of Biotechnology (DBT) with the Council for Scientific and Industrial Research (CSIR) and Indian Council of Medical Research (ICMR), is a consortium of 28 national laboratories to monitor the genomic variations in the SARS-CoV-2.