Genome reports detail rapid spread of Delta variant in Delhi this year

The documents give a previously unseen estimate of how the variants of concern (VOCs) took hold in Delhi

The share of samples in Delhi’s labs with the fast-spreading Delta variant of the Sars-Cov-2 grew from 0 to 91% between February and July, according to documents detailing the genome surveillance during the fourth wave of the pandemic which, the assessment shows, was sparked off by the Alpha variant before the Delta took hold and spread like wildfire.

A critical Covid-19 patient being taken to Lok Nayak Hospital in New Delhi. (Amal KS/HT PHOTO)

The documents give a previously unseen estimate of how the variants of concern (VOCs) took hold in Delhi: In March, 47.4% of the samples accounted for the Alpha variant (also known as B.1.1.7, first found in UK) with Delta being only 0.9%. The following month, Alpha samples reduced to 12.1% while Delta rose to 54%. The trend continued and by July, Delta accounted for 91% while Alpha reduced to 2.3%. The rest were other lineages. (see box)

The findings are based on the whole genome sequencing of 6,673 samples processed collectively by the laboratories in the National Centre for Disease Control (NCDC), Institute of Liver and Billiary Sciences (ILBS) and Lok Nayak Hospital.

The information was shared by the health department to the Delhi Disaster Management Authority (DDMA) in a meeting on August 27, the minutes of which were notified on Wednesday.

Both Alpha and Delta variants have been classified as “variants of concern” by the World Health Organisation (WHO). The Delta variant was identified in India in December 2020 and has subsequently been detected in over 95 countries.

A flurry of scientific evidence since India’s devastating April-May peak has established the Delta variant, also known as B.1.617.2, to be harder to contain since it is significantly more transmissible and can also resist immunity triggered by a past infection or elicited by vaccines.

“The huge increase in the number of cases was not anticipated because the older variant was not as infectious and would now have caused it. Now, a huge proportion of the people have been exposed to the infection and many others have been vaccinated, leaving only a small pool of susceptible persons. Now, we need to be on the lookout for a variant that might evade immunity. Without that, the virus will not spread because of limited susceptible population,” said Dr Jugal Kishore, head of the department of community medicine at Safadrjung hospital.

Earlier this week, a research paper published in the journal Nature found that there was a six-fold drop in the ability of antibodies from a past infection to neutralise the Delta variant, and a greater eight-fold reduction in the potency of antibodies elicited by vaccines.

In comparison, the Alpha variant (first found in the UK) triggered only a 2.3-fold drop in potency of antibodies drawn from recovered Covid-19 patients. Another part of the analysis also showed the most evasive variant was Beta (first found in South Africa), followed by Delta and Alpha.

The study, which included researchers from India, UK and Japan, also pointed to the variant’s molecular biology that made it more transmissible: it achieves this by having mutated to make its fusion with the host cell more efficient. Once within a cell, it also replicates more widely as compared to the Alpha variant.