SARS-CoV-2 had spread widely throughout India in the first wave, with initial results from the Indian Council of Medical Research (ICMR) finding one in five (21 per cent) adults and one in four (25 per cent) in the 10 to 17 year adolescent bracket infected. The figures were much higher in Indian megacities: by February 2021, over half (56 per cent) the individuals in Delhi were thought to have been infected.

Since the first case of Covid-19 was detected in Delhi in March 2020, the national capital experienced multiple outbreaks in June, September and November 2020. After reaching a high of almost 9,000 daily cases in November 2020, new infections steadily declined, with very few new infections between December 2020 and March 2021.

The situation reversed dramatically in April 2021, going from approximately 2,000 to 20,000 between March 31 and April 16. This was accompanied by a rapid rise in hospitalisations and ICU admissions, severely stressing the healthcare system, with daily deaths spiking to levels three-fold higher than previous waves.

In research published on Friday, an international team of scientists used genomic and epidemiological data, together with mathematical modelling, to study the outbreak.

The work was led by the National Centre of Disease Control and the CSIR Institute of Genomics and Integrative Biology, India, with collaborators from the University of Cambridge and Imperial College London, UK, and the University of Copenhagen, Denmark.

Beneficiaries are administered Covid-19 vaccines at a school in New Delhi in August 2021. (Express Photo: Abhinav Saha)

To determine whether SARS-CoV-2 variants were responsible for the April 2021 outbreak in Delhi, the team sequenced and analysed viral samples from Delhi from the previous outbreak in November 2020 until June 2021, Dr Anurag Agarwal, Director CSIR IGIB said.

They found that the 2020 outbreaks in Delhi were unrelated to any variant of concern. The Alpha variant (B.1.1.7) was identified only occasionally, primarily in foreign travellers, until January 2021. The Alpha variant increased in Delhi to about 40 per cent of the cases in March 2021, before it was displaced by a rapid increase in the Delta variant (B.1.617.2) in April.

Applying mathematical modelling to the epidemiological and genomic data, the researchers found the Delta variant was between 30-70 per cent more transmissible than previous SARS-CoV-2 lineages in Delhi, including the Alpha variant.

Importantly, the model also suggested that the Delta variant was able to infect people who had previously been infected by SARS-CoV-2 – prior infection provided only 50-90 per cent of the protection against infection.

To look for actual evidence of reinfection to support their modelling work, the researchers examined a cohort of individuals recruited by the Council of Scientific and Industrial Research (CSIR), India. In February, 42.1 per cent of unvaccinated subjects participating in the study had tested positive for antibodies against SARS-CoV-2. In June, the corresponding number was 88.5 per cent, suggesting very high infection rates during the second wave. Among 91 subjects with prior infection before Delta, about one-quarter (27.5 per cent) showed serologic evidence of reinfection.

When the team sequenced all the samples of vaccination-breakthrough cases at a single centre over the period of the study, they found that among 24 reported cases, Delta was seven-fold more likely to lead to vaccination breakthroughs than non-Delta lineages.

Dr Agrawal, a senior author and co-lead investigator, said: “This work helps understand the global outbreaks of Delta, including in highly vaccinated populations, because the Delta variant can transmit through vaccinated or previously infected people to reach those who are susceptible. Thus, herd immunity is harder to reach. Importantly, none of the vaccination breakthroughs or reinfections in our study led to severe disease. Thus, with India poised to cross one billion vaccine doses next week, we are well prepared for future variants.”

At a hospital in New Delhi. (Express Photo: Amit Mehra)

Professor Ravindra Gupta from the Cambridge Institute of Therapeutic Immunology and Infectious Disease at the University of Cambridge, UK, said: “The concept of herd immunity is critical in ending outbreaks, but the situation in Delhi shows that infection with previous coronavirus variants will be insufficient for reaching herd immunity against Delta. The only way of ending or preventing outbreaks of Delta is either by infection with this variant or by using vaccine boosters that raise antibody levels high enough to overcome Delta’s ability to evade neutralisation.”

Dr Shekhar C Mande, Director-General of Council of Scientific and Industrial Research said, “These are very valuable insights, and this understanding gained will help plan for the future. This was possible in a short timeframe due to multi-institutional collaborations, which highlight the importance of partnerships with complementary and diverse groups, especially in such emergencies such as the Covid-19 pandemic, and these must be sustained.”

Previous research led by Professor Gupta and the team of researchers from CSIR and NCDC showed the Delta variant has most likely spread through its ability to evade neutralising antibodies and its increased infectivity.

The research was supported by the Indian Ministry of Health and Family Welfare, Council of Scientific and Industrial Research, and Department of Biotechnology.