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

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

doi: https://doi.org/10.1101/2021.06.02.21258076

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.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

Support from Ministry of Health and Family Welfare, Council of Scientific and Industrial Research, and Department of Biotechnology, India, is acknowledged.

Author Declarations

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The SARSCoV2 genomic study was approved by the NCDC Ethics Review Committee vide approval 2020/NERC/14. The serology study was approved by the Institutional Human Ethics Committee of CSIRIGIB vide approval CSIR IGIB/IHEC/2019_20

All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.

Yes

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Yes

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Yes

Footnotes

Manuscript revised with better representation of data and one more co-author.