Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India

Abstract

In April 2021, after successfully enduring three waves of the SARS-CoV2 pandemic in 2020, and having reached population seropositivity of about 50%, Delhi, the national capital of India was overwhelmed by the fourth wave. Here, we trace viral, host, and social factors contributing to the scale and exponent of the fourth wave, when compared to preceding waves, in an epidemiological context. Genomic surveillance data from Delhi and surrounding states shows an early phase of the upsurge driven by the entry of the more transmissible B.1.1.7 variant of concern (VOC) into the region in January, with at least one B.1.1.7 super spreader event in February 2021, relatable to known mass gatherings over this period. This was followed by seeding of the B.1.617 VOC, which too is highly transmissible, with rapid expansion of B.1.617.2 sub-lineage outpacing all other lineages. This unprecedented growth of cases occurred in the background of high seropositivity, but with low median neutralizing antibody levels, in a serially sampled cohort. Vaccination breakthrough cases over this period were noted, disproportionately related to VOC in sequenced cases, but usually mild. We find that this surge of SARS-CoV2 infections in Delhi is best explained by the introduction of a new highly transmissible VOC, B.1.617.2, with likely immune-evasion properties; insufficient neutralizing immunity, despite high seropositivity; and social behavior that promoted transmission.

Molecular epidemiology of SARS-CoV-2 in Cyprus

“…[26,[33][34][35][36]. These studies provide valuable information on the routes of importation of new strains and the emergence of critical mutations that change key parameters such as transmissibility or virulence, as was recently highlighted by the discovery of the B.1.617 variant and its B.1.617.2 sub-lineage in India [37], which led to a surge of SARS-CoV-2 infections in Delhi. It could be shown that B.1.617.2 exhibits a very high transmissibility, as much as 50% greater than B.1.1.7, while no increase in the case-fatality ratio (CFR) was observed.…”

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

“…[14,30], epidemiological [10,13], and vaccine studies [15,16,31,32] suggests that variants with E484K, T478K, or E484Q mutations may partially evade prior immunity. Indeed, rapid resurgences followed variant emergence, for example in Manaus, Brazil (P.1) and Delhi, India (B.1.617.2), despite evidence of high levels of prior immunity in the population [11,33,34].…”

Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future

“…S2), where a previously dominant variant (B.1 lineage) was still prevalent by December, and very few genomic sequences have been uploaded from these places in the period of study. (1). The group also showed that this variant is as much as 50 % more transmissible than B.1.1.7 and dominated in the samples (76%) analyzed from vaccine breakthrough infections in Delhi (1).…”

“…Accumulating evidence suggests that B.1.617 lineage variants are more transmissible (5-10) and perhaps more lethal (8) than B.1.1.7 (a.k.a. alpha variant), which had been a dominant strain in Indian population before the arrival of second wave (1). The studies have shown a significant reduction in the neutralization against B.1.617 lineage variants by antibodies received from natural infections and manycurrently used COVID-19 vaccines and multiple monoclonal antibodies (5)(6)(7)(8).…”

“…Until December 2020, B.1.1.7 was a dominant strain in the Indian population, although the first cases of B.1.617 lineage had started appearing by then. By April 2021 India entered a full blown second COVID-19 wave (1,2).…”