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

Abstract

After escaping relatively unscathed during the first wave of the COVID-19 pandemic, India witnessed a ferocious second COVID-19 wave, starting in March 2021 and accounting for about half of global cases by the first week of May. SARS-CoV-2 had spread widely throughout India in the first wave, with the third national serosurvey in January 2021 finding that 21.4% of adults and 25.3% of 10-to 17-year-old adolescents were seropositive (1). Delhi, the national capital, was not included in the national serosurvey but had undergone multiple periods of high transmission in 2020 (Fig. 1A). In a district-wise stratified serosurvey conducted by the Delhi Government in January 2021, overall seropositivity was reported to be 56.1% (95% CI, 55.5-56.8%), ranging from 49.1% to 62.2% across 11 districts (2). This was expected to confer some protection from future outbreaks.Despite high seropositivity, Delhi was amongst the most affected cities during the second wave. The rise in new cases was exceptionally rapid in April, going from approximately 2000 to 20,000 between 31 March and 16 April. This was accompanied by a rapid rise in hospitalizations and ICU admissions (Fig. 1B). In this emergency situation with saturated bed occupancy by 12 April, major private hospitals were declared by the state as full COVID care-only and senior medical students, including from alternative medicine branches, were pressed into service (3). Deaths rose proportionately (Fig. 1C) and the case-fatality ratio (CFR), estimated as the scaling factor between time-advanced cases and deaths (Fig. 1D), was stable (mean, SD; 1.9, 0.3%). Population spread of SARS-CoV-2 is underestimated by test positive cases alone (1, 2). To better understand the degree of spread and the factors leading to the unexpectedly severe outbreak, we used all available data including testing, sequencing, serosurveys, and serially followed cohorts.In the absence of finely resolved or serial data from national and state surveys, we focused on data for Delhi participants of a national serosurvey of Council of Scientific and

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

“…Here we have combined in vitro experimentation and molecular epidemiology to propose that increased replication fitness and reduced sensitivity of SARS-CoV-2 B.1.617.2 to neutralizing antibodies have contributed to the recent rapid increase of B.1.617.2, compared with B.1.1.7 and other lineages such as B.1.617.1, despite high vaccination rates in adults and/or high prevalence of prior infection 16 . These data are consistent with modelling analyses that support combination of immune evasion and higher transmissibility as likely drivers of the increase in Delta in Delhi 17 .…”

COVID-19 Delta Variant: Perceptions, Worries, and Vaccine-Booster Acceptability among Healthcare Workers

“…The Delta variant of SARS-CoV-2 initially detected in India in September 2020 and had spread subsequently to 115 countries globally [4]. The emergence of the Delta variant in India was followed by a significant increase in the cases and in the positivity rate to reach 30% at the end of April 2021 [5]. In Delhi, the Delta variant accounted for 60% of all sequenced samples [5,6].…”

“…The emergence of the Delta variant in India was followed by a significant increase in the cases and in the positivity rate to reach 30% at the end of April 2021 [5]. In Delhi, the Delta variant accounted for 60% of all sequenced samples [5,6]. In Saudi Arabia, a recent pre-publication study of 320 SARS-CoV-2 sequenced samples showed that 40.9% to be Delta variant, 15.9% Beta, and 11.6% alpha variant [7].…”

Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

“…In order to characterize SARS-CoV-2 in various parts of India and to understand lineage diversity and distribution, genome sequencing has been carried out since the onset of the pandemic [8][9][10][11][12]. Several genome sequencing studies were performed to characterize SARS-CoV-2 isolates sampled in various States and Union Territories (UTs) of India.…”

“…The national capital and UT of Delhi reported several outbreaks in 2020 and 2021 [3]. The Delta variant displaced Alpha and all other variants due to its high transmissibility and immune evasion, thus causing reinfections [12,18].…”