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

• Published in: Science (American Association for the Advancement of Science) 2021-11, Vol.374 (6570), p.995-999
• Main Authors: Dhar, Mahesh S, Marwal, Robin, Vs, Radhakrishnan, 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, Bhatheja, Nitin, Divakar, Mohit Kumar, Singh, Manoj K, Imran, Mohamed, Senthivel, Vigneshwar, Maurya, Ranjeet, Jha, Neha, Mehta, Priyanka, A, Vivekanand, Sharma, Pooja, Vr, Arvinden, 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, Gupta, Ravindra K, Singh, Sujeet K, Agrawal, Anurag, Rakshit, Partha, Nandicoori, Vinay, Tallapaka, Karthik Bharadwaj, Sowpati, Divya Tej, Thangaraj, K, Bashyam, Murali Dharan, Dalal, Ashwin, Sivasubbu, Sridhar, Scaria, Vinod, Parida, Ajay, Raghav, Sunil K, Prasad, Punit, Sarin, Apurva, Mayor, Satyajit, Ramakrishnan, Uma, Palakodeti, Dasaradhi, Seshasayee, Aswin Sai Narain, Bhat, Manoj, Shouche, Yogesh, Pillai, Ajay, Dikid, Tanzin, Das, Saumitra, Maitra, Arindam, Chinnaswamy, Sreedhar, Biswas, Nidhan Kumar, Desai, Anita Sudhir, Pattabiraman, Chitra, Manjunatha, M V, Mani, Reeta S, Arunachal Udupi, Gautam, Abraham, Priya, Atul, Potdar Varsha, Cherian, Sarah S
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Antibodies; Avidity; Bayesian analysis; Child; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - immunology; COVID-19 - transmission; COVID-19 - virology; Epidemiology; Genome, Viral; Genomics; Humans; Immune Evasion; Immune response; India - epidemiology; Molecular Epidemiology; Mutation; Phylogeny; Polymerase chain reaction; Reinfection; Sensitivity; Seroepidemiologic Studies; Severe acute respiratory syndrome coronavirus 2; Vaccination; Viral diseases; Young Adult
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.abj9932

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >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 reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.