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

被引：211

作者：

Dhar, Mahesh S. ^{[1
]}

Marwal, Robin ^{[1
]}

Radhakrishnan, V. S. ^{[1
]}

Ponnusamy, Kalaiarasan ^{[1
]}

Jolly, Bani ^{[2
,3
]}

Bhoyar, Rahul C. ^{[2
]}

Sardana, Viren ^{[2
,3
]}

Naushin, Salwa ^{[2
,3
]}

Rophina, Mercy ^{[2
,3
]}

Mellan, Thomas A. ^{[4
]}

Mishra, Swapnil ^{[4
]}

Whittaker, Charles ^{[4
]}

Fatihi, Saman ^{[2
,3
]}

Datta, Meena ^{[1
]}

Singh, Priyanka ^{[1
]}

Sharma, Uma ^{[1
]}

Ujjainiya, Rajat ^{[2
,3
]}

Bhatheja, Nitin ^{[2
]}

Divakar, Mohit Kumar ^{[2
,3
]}

Singh, Manoj K. ^{[1
]}

Imran, Mohamed ^{[2
,3
]}

Senthivel, Vigneshwar ^{[2
,3
]}

Maurya, Ranjeet ^{[2
,3
]}

Jha, Neha ^{[2
]}

Mehta, Priyanka ^{[2
]}

Vivekanand, A. ^{[2
,3
]}

Sharma, Pooja ^{[2
,3
]}

Arvinden, V. R. ^{[2
,3
]}

Chaudhary, Urmila ^{[1
]}

Soni, Namita ^{[1
]}

Thukral, Lipi ^{[2
,3
]}

Flaxman, Seth ^{[5
]}

Bhatt, Samir ^{[4
,6
]}

Pandey, Rajesh ^{[2
,3
]}

Dash, Debasis ^{[2
,3
]}

Faruq, Mohammed ^{[2
,3
]}

Lall, Hemlata ^{[1
]}

Gogia, Hema ^{[1
]}

Madan, Preeti ^{[1
]}

Kulkarni, Sanket ^{[1
]}

Chauhan, Himanshu ^{[1
]}

Sengupta, Shantanu ^{[2
,3
]}

Kabra, Sandhya ^{[1
]}

Gupta, Ravindra K. ^{[7
,8
]}

Singh, Sujeet K. ^{[1
]}

Agrawal, Anurag ^{[2
,3
]}

Rakshit, Partha ^{[1
]}

机构：

[1] Natl Ctr Dis Control, Delhi, India

[2] CSIR Inst Genom & Integrat Biol, New Delhi, India

[3] Acad Sci & Innovat Res, Ghaziabad, India

[4] Imperial Coll London, Med Res Council MRC Ctr Global Infect Dis Anal, Sch Publ Hlth, Jameel Inst, London, England

[5] Imperial Coll London, Dept Math, London, England

[6] Univ Copenhagen, Dept Publ Hlth, Sect Epidemiol, Copenhagen, Denmark

[7] Univ Cambridge, Cambridge Inst Therapeut Immunol & Infect Dis CIT, Dept Med, Cambridge, England

[8] Africa Hlth Res Inst, Kwa Zulu, South Africa

来源：

SCIENCE | 2021年 / 374卷 / 6570期

基金：

英国工程与自然科学研究理事会; 英国医学研究理事会;

关键词：

HEALTH-CARE WORKERS; POPULATION;

D O I：

10.1126/science.abj9932

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：995 / +

页数：29

共 33 条

[21]

Mlcochova P., 2021, Nature, V599, P114

[22] SARS-CoV-2 seroprevalence among the general population and healthcare workers in India, December 2020-January 2021 [J].

Murhekar, Manoj, V ;

Bhatnagar, Tarun ;

Thangaraj, Jeromie Wesley Vivian ;

Saravanakumar, V ;

Kumar, Muthusamy Santhosh ;

Selvaraju, Sriram ;

Rade, Kiran ;

Kumar, C. P. Girish ;

Sabarinathan, R. ;

Turuk, Alka ;

Asthana, Smita ;

Balachandar, Rakesh ;

Bangar, Sampada Dipak ;

Bansal, Avi Kumar ;

Chopra, Vishal ;

Das, Dasarathi ;

Deb, Alok Kumar ;

Devi, Kangjam Rekha ;

Dhikav, Vikas ;

Dwivedi, Gaurav Raj ;

Khan, S. Muhammad Salim ;

Kumar, M. Sunil ;

Laxmaiah, Avula ;

Madhukar, Major ;

Mahapatra, Amarendra ;

Rangaraju, Chethana ;

Turuk, Jyotirmayee ;

Yadav, Rajiv ;

Andhalkar, Rushikesh ;

Arunraj, K. ;

Bharadwaj, Dinesh Kumar ;

Bharti, Pravin ;

Bhattacharya, Debdutta ;

Bhat, Jyothi ;

Chahal, Ashrafjit S. ;

Chakraborty, Debjit ;

Chaudhury, Anshuman ;

Deval, Hirawati ;

Dhatrak, Sarang ;

Dayal, Rakesh ;

Elantamilan, D. ;

Giridharan, Prathiksha ;

Haq, Inaamul ;

Hudda, Ramesh Kumar ;

Jagjeevan, Babu ;

Kalliath, Arshad ;

Kanungo, Srikanta ;

Krishnan, Nivethitha N. ;

Kshatri, Jaya Singh ;

Kumar, Alok .

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 2021, 108 :145-155

[23] Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2 [J].

Naushin, Salwa ;

Sardana, Viren ;

Ujjainiya, Rajat ;

Bhatheja, Nitin ;

Kutum, Rintu ;

Bhaskar, Akash Kumar ;

Pradhan, Shalini ;

Prakash, Satyartha ;

Khan, Raju ;

Rawat, Birendra Singh ;

Tallapaka, Karthik Bharadwaj ;

Anumalla, Mahesh ;

Chandak, Giriraj Ratan ;

Lahiri, Amit ;

Kar, Susanta ;

Mulay, Shrikant Ramesh ;

Mugale, Madhav Nilakanth ;

Srivastava, Mrigank ;

Khan, Shaziya ;

Srivastava, Anjali ;

Tomar, Bhawana ;

Veerapandian, Murugan ;

Venkatachalam, Ganesh ;

Vijayakumar, Selvamani Raja ;

Agarwal, Ajay ;

Gupta, Dinesh ;

Halami, Prakash M. ;

Peddha, Muthukumar Serva ;

Sundaram, Gopinath M. ;

Veeranna, Ravindra P. ;

Pal, Anirban ;

Agarwal, Vinay Kumar ;

Maurya, Anil Ku ;

Singh, Ranvijay Kumar ;

Raman, Ashok Kumar ;

Anandasadagopan, Suresh Kumar ;

Karuppanan, Parimala ;

Venkatesan, Subramanian ;

Sardana, Harish Kumar ;

Kothari, Anamika ;

Jain, Rishabh ;

Thakur, Anupama ;

Parihar, Devendra Singh ;

Saifi, Anas ;

Kaur, Jasleen ;

Kumar, Virendra ;

Mishra, Avinash ;

Gogeri, Iranna ;

Rayasam, Geethavani ;

Singh, Praveen .

ELIFE, 2021, 10

[24]

O Toole A., 2021, VIRUS EVOL, V7

[25] Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization [J].

Planas, Delphine ;

Veyer, David ;

Baidaliuk, Artem ;

Staropoli, Isabelle ;

Guivel-Benhassine, Florence ;

Rajah, Maaran Michael ;

Planchais, Cyril ;

Porrot, Francoise ;

Robillard, Nicolas ;

Puech, Julien ;

Prot, Matthieu ;

Gallais, Floriane ;

Gantner, Pierre ;

Velay, Aurelie ;

Le Guen, Julien ;

Kassis-Chikhani, Najiby ;

Edriss, Dhiaeddine ;

Belec, Laurent ;

Seve, Aymeric ;

Courtellemont, Laura ;

Pere, Helene ;

Hocqueloux, Laurent ;

Fafi-Kremer, Samira ;

Prazuck, Thierry ;

Mouquet, Hugo ;

Bruel, Timothee ;

Simon-Loriere, Etienne ;

Rey, Felix A. ;

Schwartz, Olivier .

NATURE, 2021, 596 (7871) :276-+

[26] A comparison of five epidemiological models for transmission of SARS-CoV-2 in India [J].

Purkayastha, Soumik ;

Bhattacharyya, Rupam ;

Bhaduri, Ritwik ;

Kundu, Ritoban ;

Gu, Xuelin ;

Salvatore, Maxwell ;

Ray, Debashree ;

Mishra, Swapnil ;

Mukherjee, Bhramar .

BMC INFECTIOUS DISEASES, 2021, 21 (01)

[27] A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology [J].

Rambaut, Andrew ;

Holmes, Edward C. ;

O'Toole, Aine ;

Hill, Verity ;

McCrone, John T. ;

Ruis, Christopher ;

du Plessis, Louis ;

Pybus, Oliver G. .

NATURE MICROBIOLOGY, 2020, 5 (11) :1403-1407

[28] TreeTime: Maximum-likelihood phylodynamic analysis [J].

Sagulenko, Pavel ;

Puller, Vadim ;

Neher, Richard A. .

VIRUS EVOLUTION, 2018, 4 (01)

[29]

Scott J. A., 2020, epidemia: Modeling of Epidemics using Hierarchical Bayesian Models

[30] GISAID: Global initiative on sharing all influenza data - from vision to reality [J].

Shu, Yuelong ;

McCauley, John .

EUROSURVEILLANCE, 2017, 22 (13) :2-4

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