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Wang P, Hu T, Liu H, Zhu X. Exploring the impact of under-reported cases on the COVID-19 spatiotemporal distributions using healthcare workers infection data. CITIES (LONDON, ENGLAND) 2022; 123:103593. [PMID: 35068649 PMCID: PMC8761553 DOI: 10.1016/j.cities.2022.103593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 05/07/2023]
Abstract
A timely understanding of the spatiotemporal pattern and development trend of COVID-19 is critical for timely prevention and control. However, the under-reporting of casesis widespread in fields associated with public health. It is also possible to draw biased inferences and formulate inappropriate prevention and control policies if the phenomenon of under-reporting is not taken into account. Therefore, in this paper, a novel framework was proposed to explore the impact of under-reporting on COVID-19 spatiotemporal distributions, and empirical analysis was carried out using infection data of healthcare workers in Wuhan and Hubei (excluding Wuhan). The results show that (1) the lognormal distribution was the most suitable to describe the evolution of epidemic with time; (2) the estimated peak infection time of the reported cases lagged the peak infection time of the healthcare worker cases, and the estimated infection time interval of the reported cases was smaller than that of the healthcare worker cases. (3) The impact of under-reporting cases on the early stages of the pandemic was greater than that on its later stages, and the impact on the early onset area was greater than that on the late onset area. (4) Although the number of reported cases was lower than the actual number of cases, a high spatial correlation existed between the cumulatively reported cases and healthcare worker cases. The proposed framework of this study is highly extensible, and relevant researchers can use data sources from other counties to carry out similar research.
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Affiliation(s)
- Peixiao Wang
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan 430079, China
| | - Tao Hu
- Department of Geography, Oklahoma State University, OK 74078, USA
- Center for Geographic Analysis, Harvard University, Cambridge, MA 02138, USA
| | - Hongqiang Liu
- College of Geodesy and Geomatics, Shandong University of Science and Technology, Qingdao 266590, China
| | - Xinyan Zhu
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan 430079, China
- Collaborative Innovation Center of Geospatial Technology, Wuhan 430079, China
- Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, Wuhan University, Wuhan 430079, China
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2
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Dhar MS, Marwal R, VS R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, VR A, 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, Gupta RK, Singh SK, Agrawal A, Rakshit P. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 PMCID: PMC7612010 DOI: 10.1126/science.abj9932] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
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.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A. Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden VR
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - The Indian SARS-CoV-2 Genomics Consortium (INSACOG)‡
- National Centre for Disease Control, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Ravindra K. Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, Vr A, 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, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Arunachal Udupi G, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 DOI: 10.1101/2021.06.02.21258076] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
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.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden Vr
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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Mandal S, Arinaminpathy N, Bhargava B, Panda S. Plausibility of a third wave of COVID-19 in India: A mathematical modelling based analysis. Indian J Med Res 2021; 153:522-532. [PMID: 34643562 PMCID: PMC8555606 DOI: 10.4103/ijmr.ijmr_1627_21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES In the context of India's ongoing resurgence of COVID-19 (second wave since mid-February 2021, following the subsiding of the first wave in September 2020), there has been increasing speculation on the possibility of a future third wave of infection, posing a burden on the healthcare system. Using simple mathematical models of the transmission dynamics of SARS-CoV-2, this study examined the conditions under which a serious third wave could occur. METHODS Using a deterministic, compartmental model of SARS-CoV-2 transmission, four potential mechanisms for a third wave were examined: (i) waning immunity restores previously exposed individuals to a susceptible state, (ii) emergence of a new viral variant that is capable of escaping immunity to previously circulating strains, (iii) emergence of a new viral variant that is more transmissible than the previously circulating strains, and (iv) release of current lockdowns affording fresh opportunities for transmission. RESULTS Immune-mediated mechanisms (waning immunity, or viral evolution for immune escape) are unlikely to drive a severe third wave if acting on their own, unless such mechanisms lead to a complete loss of protection among those previously exposed. Likewise, a new, more transmissible variant would have to exceed a high threshold (R0>4.5) to cause a third wave on its own. However, plausible mechanisms for a third wave include: (i) a new variant that is more transmissible and at the same time capable of escaping prior immunity, and (ii) lockdowns that are highly effective in limiting transmission and subsequently released. In both cases, any third wave seems unlikely to be as severe as the second wave. Rapid scale-up of vaccination efforts could play an important role in mitigating these and future waves of the disease. INTERPRETATION & CONCLUSIONS This study demonstrates plausible mechanisms by which a substantial third wave could occur, while also illustrating that it is unlikely for any such resurgence to be as large as the second wave. Model projections are, however, subject to several uncertainties, and it remains important to scale up vaccination coverage to mitigate against any eventuality. Preparedness planning for any potential future wave will benefit by drawing upon the projected numbers based on the present modelling exercise.
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Affiliation(s)
- Sandip Mandal
- Clinical Studies, Projection & Policy Unit, Indian Council of Medical Research, New Delhi, India
| | - Nimalan Arinaminpathy
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | | | - Samiran Panda
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
- ICMR-National AIDS Research Institute, Pune, India
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