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Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Open accessPreprint — published as 10.1126/science.abj9932
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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“Studies in India have estimated that the delta variant could be up to 50% more transmissible than the alpha variant.8”
From Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study (2022) · cites this paper as [8]
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Metadata
- 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)
- 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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