PreprintCited by 298SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studiesCOVID-19 Clinical Research Studies

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

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Dhar, Mahesh S, Marwal, Robin, Radhakrishnan, VS, Ponnusamy, Kalaiarasan, Jolly, Bani, Bhoyar, Rahul C., Sardana, Viren, Naushin, Salwa, Rophina, Mercy, Mellan, Thomas A, Mishra, Swapnil, Whittaker, Charles, Fatihi, Saman, Datta, Meena, Singh, Priyanka, Sharma, Uma, Ujjainiya, Rajat, Batheja, Nitin, Divakar, Mohit Kumar, Singh, Manoj K, Imran, Mohamed, Senthivel, Vigneshwar, Maurya, Ranjeet, Jha, Neha, Mehta, Priyanka, Vivekanand, A, Sharma, Pooja, Arvinden, VR, Chaudhary, Urmila, Soni, Namita, Thukral, Lipi, Flaxman, Seth, Bhatt, Samir, Pandey, Rajesh, Dash, Debasis, Faruq, Mohammed, Lall, Hemlata, Gogia, Hema, Madan, Preeti, Kulkarni, Sanket, Chauhan, Himanshu, Sengupta, Shantanu, Kabra, Sandhya, The Indian SARS-CoV-2 Genomics Consortium (INSACOG), Gupta, Ravindra K., Singh, Sujeet K, Agrawal, Anurag, Rakshit, Partha·2021·Science

DOI 10.1101/2021.06.02.21258076PMC PMC7612010

Preprint — published as 10.1126/science.abj9932

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Abstract

Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached a population seropositivity of over 50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and partial reduction of immunity elicited by prior infection (median estimates; ×1.5-fold, 20% reduction). Seropositivity of an employee and family cohort increased from 42% to 86% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi. One-Sentence Summary: Delhi experienced an overwhelming surge of COVID-19 cases and fatalities peaking in May 2021 as the highly transmissible and immune evasive Delta variant replaced the Alpha variant.

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Authors: Dhar, M. S., Marwal, R., Radhakrishnan, V., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., Mishra, S., Whittaker, C., Fatihi, S., Datta, M., Singh, P., Sharma, U., Ujjainiya, R., Batheja, N., Divakar, M. K., Singh, M. K., Imran, M., Senthivel, V., Maurya, R., Jha, N., Mehta, P., Vivekanand, A., Sharma, P., Arvinden, V., Chaudhary, U., Soni, N., Thukral, L., Flaxman, S., Bhatt, S., Pandey, R., Dash, D., Faruq, M., Lall, H., Gogia, H., Madan, P., Kulkarni, S., Chauhan, H., Sengupta, S., Kabra, S., The Indian SARS-CoV-2 Genomics Consortium (INSACOG), Gupta, R. K., Singh, S. K., Agrawal, A., & Rakshit, P.
Affiliations: National Center for Disease Control (IN)
Institute of Genomics and Integrative Biology (IN)
Imperial College London (GB)
University of Copenhagen (DK)
University of Cambridge (GB)
Corresponding author: Dhar, Mahesh S
Marwal, Robin
Radhakrishnan, VS
Ponnusamy, Kalaiarasan
Jolly, Bani
Bhoyar, Rahul C.
Agrawal, Anurag
Rakshit, Partha
ORCID: Dhar, Mahesh S
Marwal, Robin
Radhakrishnan, VS
Ponnusamy, Kalaiarasan
Jolly, Bani
Bhoyar, Rahul C.
Sardana, Viren
Naushin, Salwa
Rophina, Mercy
Mellan, Thomas A
Mishra, Swapnil
Whittaker, Charles
Fatihi, Saman
Singh, Priyanka
Sharma, Uma
Ujjainiya, Rajat
Divakar, Mohit Kumar
Singh, Manoj K
Imran, Mohamed
Senthivel, Vigneshwar
Maurya, Ranjeet
Jha, Neha
Mehta, Priyanka
Vivekanand, A
Sharma, Pooja
Arvinden, VR
Chaudhary, Urmila
Thukral, Lipi
Flaxman, Seth
Bhatt, Samir
Pandey, Rajesh
Dash, Debasis
Faruq, Mohammed
Lall, Hemlata
Madan, Preeti
Kulkarni, Sanket
Chauhan, Himanshu
Sengupta, Shantanu
Gupta, Ravindra K.
Singh, Sujeet K
Agrawal, Anurag
Rakshit, Partha
Venue: Science
Publisher: openRxiv
Published: 2021-06-03
Volume: 374
Issue: 6570
Pages: 995-999
ISSN: 0036-8075 (ISSN-L)
DOI: 10.1101/2021.06.02.21258076
PMC: PMC7612010
OpenAlex: W3205588626
Cited by: 296
References: 43
Citations by year: 2026: 7 · 2025: 19 · 2024: 38 · 2023: 65 · 2022: 115 · 2021: 51
FWCI: 21.30
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
Locations: Science (publishedVersion, cc-by)
medRxiv (acceptedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
Greater South Information System
Funders: Wellcome Trust (108082/A/15/Z, 108082)
Novo Nordisk Fonden (NNF20OC0059309)
Medical Research Council (MR/R015600/1, MC_PC_19012)
Engineering and Physical Sciences Research Council (EP/V002910/1, EP/V002910/2)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
Keywords: SARS-CoV-2, Delta variant, B.1.1.7 Alpha variant, COVID-19 outbreak, Delhi, genomic profiling, epidemiology, transmissibility, immune evasion, reinfection, seroprevalence, antibody response, Bayesian model
MeSH terms: Reinfection, COVID-19, Adolescent, Adult, Child, Humans, India, Phylogeny, Seroepidemiologic Studies, Genome, Viral, Molecular Epidemiology, Young Adult, Immune Evasion

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

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