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Scibona P, Burgos Pratx LD, Savoy N, Recart D, Elia Y, Seoane FN, Arrigo D, Portalis MR, Roldan A, Cassoratti BA, Diaz JC, Antonelli CE, Perez L, Posadas-Martinez L, Belloso WH, Simonovich V. Long-term antibody titers variation in unvaccinated patients receiving convalescent plasma or placebo for severe SARS-CoV-2 pulmonary infection. Transfus Apher Sci 2023; 62:103785. [PMID: 37620184 DOI: 10.1016/j.transci.2023.103785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Convalescent plasma (CP) became a prominent treatment in the early stages of the SARS-CoV-2 pandemic. In Argentina, a randomized clinical trial was executed to compare the use of CP in inpatients with severe COVID-19 pneumonia versus placebo. No differences in clinical outcomes or overall mortality between groups were observed. We conducted a cohort study in outpatients enrolled in the trial to describe long-term antibody titer variations between CP and placebo recipients. METHODS Patients' total SARS-CoV-2 IgG antibodies against spike protein were collected 3, 6 and 12 months after hospital discharge from August 2020 to December 2021. In addition, reinfections, deaths and vaccination status were retrieved. Statistical analysis was performed using antibody geometric mean titers (GMT). All estimations were made considering the date of the trial infusion (placebo or CP) as time 0. RESULTS From the 93 patients included in the follow-up, 64 had received CP and 29 placebo. We excluded all 12-month measurements because they were collected after the patients' vaccination date. At 90 days post-infusion, patients had an antibody GMT of 8.1 (IQR 7.4-8.1) in the CP group and 8.8 (IQR 8.1-9.1) in the placebo group. At 180 days, both groups had a GMT of 8.1 (IQR 7.4-8.1). No statistical differences in GMT were found between CP and placebo groups at 90 days (p = 0.12) and 180 days (p = 0.25). No patients registered a new COVID-19 infection; one died in the CP group from an ischemic stroke. CONCLUSIONS No differences were observed in long-term antibody titers in unvaccinated patients that received CP or placebo after severe COVID-19 pneumonia.
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Affiliation(s)
- Paula Scibona
- Clinical Pharmacology Section, Internal Medicine Service, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
| | - Leandro Daniel Burgos Pratx
- Transfusional Medicine Department, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199 Buenos Aires, Argentina
| | - Nadia Savoy
- Clinical Pharmacology Section, Internal Medicine Service, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
| | - Delfina Recart
- Clinical Pharmacology Section, Internal Medicine Service, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina.
| | - Yasmin Elia
- Clinical Pharmacology Section, Internal Medicine Service, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
| | - Facundo Nahuel Seoane
- Virology Section, Central Laboratory, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
| | - Diego Arrigo
- Virology Section, Central Laboratory, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
| | - Maximo Rousseau Portalis
- Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, C1121A6B Buenos Aires, Argentina
| | - Agustina Roldan
- Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, C1121A6B Buenos Aires, Argentina
| | | | - Julio Cesar Diaz
- Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, C1121A6B Buenos Aires, Argentina
| | | | - Lucia Perez
- Department of Research, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199 Buenos Aires, Argentina
| | - Lourdes Posadas-Martinez
- Department of Research, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199 Buenos Aires, Argentina
| | - Waldo H Belloso
- Terra Nova Innovation Unit, Hospital Italiano de Buenos Aires, Argentina
| | - Ventura Simonovich
- Clinical Pharmacology Section, Internal Medicine Service, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190 C1199, Buenos Aires, Argentina
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McCabe R, Whittaker C, Sheppard RJ, Abdelmagid N, Ahmed A, Alabdeen IZ, Brazeau NF, Ahmed Abd Elhameed AE, Bin-Ghouth AS, Hamlet A, AbuKoura R, Barnsley G, Hay JA, Alhaffar M, Koum Besson E, Saje SM, Sisay BG, Gebreyesus SH, Sikamo AP, Worku A, Ahmed YS, Mariam DH, Sisay MM, Checchi F, Dahab M, Endris BS, Ghani AC, Walker PG, Donnelly CA, Watson OJ. Alternative epidemic indicators for COVID-19 in three settings with incomplete death registration systems. SCIENCE ADVANCES 2023; 9:eadg7676. [PMID: 37294754 PMCID: PMC10256151 DOI: 10.1126/sciadv.adg7676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
Not all COVID-19 deaths are officially reported, and particularly in low-income and humanitarian settings, the magnitude of reporting gaps remains sparsely characterized. Alternative data sources, including burial site worker reports, satellite imagery of cemeteries, and social media-conducted surveys of infection may offer solutions. By merging these data with independently conducted, representative serological studies within a mathematical modeling framework, we aim to better understand the range of underreporting using examples from three major cities: Addis Ababa (Ethiopia), Aden (Yemen), and Khartoum (Sudan) during 2020. We estimate that 69 to 100%, 0.8 to 8.0%, and 3.0 to 6.0% of COVID-19 deaths were reported in each setting, respectively. In future epidemics, and in settings where vital registration systems are limited, using multiple alternative data sources could provide critically needed, improved estimates of epidemic impact. However, ultimately, these systems are needed to ensure that, in contrast to COVID-19, the impact of future pandemics or other drivers of mortality is reported and understood worldwide.
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Affiliation(s)
- Ruth McCabe
- Department of Statistics, University of Oxford, Oxford, UK
- NIHR Health Research Protection Unit in Emerging and Zoonotic Infections, Liverpool, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Richard J. Sheppard
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Nada Abdelmagid
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Sudan COVID-19 Research Group, Khartoum, Sudan
| | - Aljaile Ahmed
- Sudan COVID-19 Research Group, Khartoum, Sudan
- Sudan Youth Peer Education Network, Khartoum, Sudan
| | | | - Nicholas F. Brazeau
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | | | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rahaf AbuKoura
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Sudan COVID-19 Research Group, Khartoum, Sudan
| | - Gregory Barnsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - James A. Hay
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mervat Alhaffar
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Syria Research Group (SyRG), co-hosted by the London School of Hygiene and Tropical Medicine, London, UK and Saw Swee Hock School of Public Health, Singapore, Singapore
| | - Emilie Koum Besson
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Semira Mitiku Saje
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Binyam Girma Sisay
- School of Exercise and Nutrition Science, Institute for Physical Activity and Nutrition (IPAN), Deakin University, Melbourne, Victoria, Australia
| | - Seifu Hagos Gebreyesus
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Petros Sikamo
- School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aschalew Worku
- School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Damen Haile Mariam
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mitike Molla Sisay
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Francesco Checchi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Maysoon Dahab
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Sudan COVID-19 Research Group, Khartoum, Sudan
| | - Bilal Shikur Endris
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Azra C. Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Patrick G. T. Walker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A. Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- NIHR Health Research Protection Unit in Emerging and Zoonotic Infections, Liverpool, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J. Watson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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Beahm DR, Deng Y, DeAngelo TM, Sarpeshkar R. Drug Cocktail Formulation via Circuit Design. IEEE TRANSACTIONS ON MOLECULAR, BIOLOGICAL, AND MULTI-SCALE COMMUNICATIONS 2023; 9:28-48. [PMID: 37397625 PMCID: PMC10312325 DOI: 10.1109/tmbmc.2023.3246928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Electronic circuits intuitively visualize and quantitatively simulate biological systems with nonlinear differential equations that exhibit complicated dynamics. Drug cocktail therapies are a powerful tool against diseases that exhibit such dynamics. We show that just six key states, which are represented in a feedback circuit, enable drug-cocktail formulation: 1) healthy cell number; 2) infected cell number; 3) extracellular pathogen number; 4) intracellular pathogenic molecule number; 5) innate immune system strength; and 6) adaptive immune system strength. To enable drug cocktail formulation, the model represents the effects of the drugs in the circuit. For example, a nonlinear feedback circuit model fits measured clinical data, represents cytokine storm and adaptive autoimmune behavior, and accounts for age, sex, and variant effects for SARS-CoV-2 with few free parameters. The latter circuit model provided three quantitative insights on the optimal timing and dosage of drug components in a cocktail: 1) antipathogenic drugs should be given early in the infection, but immunosuppressant timing involves a tradeoff between controlling pathogen load and mitigating inflammation; 2) both within and across-class combinations of drugs have synergistic effects; 3) if they are administered sufficiently early in the infection, anti-pathogenic drugs are more effective at mitigating autoimmune behavior than immunosuppressant drugs.
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Affiliation(s)
| | - Yijie Deng
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Thomas M DeAngelo
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Rahul Sarpeshkar
- Departments of Engineering, Physics, Microbiology & Immunobiology, and Molecular & Systems Biology, Dartmouth College, Hanover, NH 03755 USA
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Shimbashi R, Shiino T, Ainai A, Moriyama S, Arai S, Morino S, Takanashi S, Arashiro T, Suzuki M, Matsuzawa Y, Kato K, Hasegawa M, Koshida R, Kitaoka M, Ueno T, Shimizu H, Yuki H, Takeda T, Nakamura-Uchiyama F, Takasugi K, Iida S, Shimada T, Kato H, Fujimoto T, Iwata-Yoshikawa N, Sano K, Yamada S, Kuroda Y, Okuma K, Nojima K, Nagata N, Fukushi S, Maeda K, Takahashi Y, Suzuki T, Ohnishi M, Tanaka-Taya K. Specific COVID-19 risk behaviors and the preventive effect of personal protective equipment among healthcare workers in Japan. Glob Health Med 2023; 5:5-14. [PMID: 36865900 PMCID: PMC9974228 DOI: 10.35772/ghm.2022.01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
As coronavirus disease 2019 (COVID-19) outbreaks in healthcare facilities are a serious public health concern, we performed a case-control study to investigate the risk of COVID-19 infection in healthcare workers. We collected data on participants' sociodemographic characteristics, contact behaviors, installation status of personal protective equipment, and polymerase chain reaction testing results. We also collected whole blood and assessed seropositivity using the electrochemiluminescence immunoassay and microneutralization assay. In total, 161 (8.5%) of 1,899 participants were seropositive between August 3 and November 13, 2020. Physical contact (adjusted odds ratio 2.4, 95% confidence interval 1.1-5.6) and aerosol-generating procedures (1.9, 1.1-3.2) were associated with seropositivity. Using goggles (0.2, 0.1-0.5) and N95 masks (0.3, 0.1-0.8) had a preventive effect. Seroprevalence was higher in the outbreak ward (18.6%) than in the COVID-19 dedicated ward (1.4%). Results showed certain specific risk behaviors of COVID-19; proper infection prevention practices reduced these risks.
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Affiliation(s)
- Reiko Shimbashi
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Teiichiro Shiino
- Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Satoru Arai
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Saeko Morino
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Sayaka Takanashi
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Takeshi Arashiro
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Yukimasa Matsuzawa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | | | | | - Rie Koshida
- Kanazawa City Health Center, Kanazawa, Ishikawa, Japan
| | | | | | | | | | | | | | | | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Tomoe Shimada
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Hirofumi Kato
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Tsuguto Fujimoto
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Naoko Iwata-Yoshikawa
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Souichi Yamada
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Kazu Okuma
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
- Department of Microbiology, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kiyoko Nojima
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Shuetsu Fukushi
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Makoto Ohnishi
- Deputy Director-General, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Keiko Tanaka-Taya
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
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5
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Bedekar P, Kearsley AJ, Patrone PN. Prevalence estimation and optimal classification methods to account for time dependence in antibody levels. J Theor Biol 2023; 559:111375. [PMID: 36513210 DOI: 10.1016/j.jtbi.2022.111375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/14/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Serology testing can identify past infection by quantifying the immune response of an infected individual providing important public health guidance. Individual immune responses are time-dependent, which is reflected in antibody measurements. Moreover, the probability of obtaining a particular measurement from a random sample changes due to changing prevalence (i.e., seroprevalence, or fraction of individuals exhibiting an immune response) of the disease in the population. Taking into account these personal and population-level effects, we develop a mathematical model that suggests a natural adaptive scheme for estimating prevalence as a function of time. We then combine the estimated prevalence with optimal decision theory to develop a time-dependent probabilistic classification scheme that minimizes the error associated with classifying a value as positive (history of infection) or negative (no such history) on a given day since the start of the pandemic. We validate this analysis by using a combination of real-world and synthetic SARS-CoV-2 data and discuss the type of longitudinal studies needed to execute this scheme in real-world settings.
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Affiliation(s)
- Prajakta Bedekar
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
| | - Anthony J Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Paul N Patrone
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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6
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Espinosa-Gómez FC, Bautista E, Palacios-Cruz OE, Téllez-Ramírez A, Vázquez-Briones DB, Flores de Los Ángeles C, Abella-Medrano CA, Escobedo-Straffón JL, Aguirre-Alarcón H, Pérez-Silva NB, Solís-Hernández M, Navarro-López R, Aguirre AA. Host traits, ownership behaviour and risk factors of SARS-CoV-2 infection in domestic pets in Mexico. Zoonoses Public Health 2023; 70:327-340. [PMID: 36757053 DOI: 10.1111/zph.13030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 12/22/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
SARS-CoV-2 can infect pets under natural conditions, which raises questions about the risk factors related to the susceptibility of these animals to infection. The status of pet infection by SARS-CoV-2 in Mexico is not well-understood. We aimed to estimate the frequency of positive household cats and dogs to viral RNA and antibodies for SARS-CoV-2 during the second wave of human infections in Mexico, and to recognize the major risk factors related to host and pet ownership behaviour. We evaluated two study groups, cats and dogs from COVID-19-infected/-suspected households (n = 44) and those admitted for veterinary care for any reason at several veterinary hospitals in Puebla City, Mexico (n = 91). Using RT-PCR, we identified the presence of SARS-CoV-2 RNA in swabs of four dogs (18.18%) and zero cats in COVID-19-infected/-suspected households; within this group, 31.82% of dogs and 27.27% of cats were tested IgG ELISA-positive; and neutralizing antibodies were detected in one dog (4.55%) and two cats (9.09%). In the random group (pets evaluated at private clinics and veterinary teaching hospital), 25.00% of dogs and 43.59% of cats were ELISA-positive and only one cat showed neutralizing antibodies (2.56%). Older than 4-year-old, other pets at home, and daily cleaning of pet dish, were each associated with an increase in SARS-CoV-2 infection (p < 0.05). Allowing face lick, sharing bed/food with pets and owner tested positive or suspected COVID-19 were not significant risk factors, but more than 4 h the owner spent away from home during the lockdown for COVID-19 (OR = 0.37, p = 0.01), and outdoor pet food tray (OR = 0.32, p = 0.01) significantly decreased the risks of SARS-CoV-2 infection in pets, suggesting that time the owner spends with their pet is an important risk factor.
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Affiliation(s)
| | - Elizabeth Bautista
- Laboratorio de Biotecnología Médica y Farmacéutica, Facultad de Biotecnología, Universidad Popular y Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Oscar Emilio Palacios-Cruz
- Especialidad en Medicina y Cirugía de Perros y Gatos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Alejandra Téllez-Ramírez
- Especialidad en Medicina y Cirugía de Perros y Gatos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Daniela Belem Vázquez-Briones
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - César Flores de Los Ángeles
- Laboratorio de Diagnóstico Molecular, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Carlos Antonio Abella-Medrano
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | | | - Héctor Aguirre-Alarcón
- Laboratorio de Biotecnología Médica y Farmacéutica, Facultad de Biotecnología, Universidad Popular y Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Nancy Bibiana Pérez-Silva
- Laboratorio de Diagnóstico Molecular, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Mario Solís-Hernández
- Comisión México Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales del Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Ciudad de México, Mexico
| | - Roberto Navarro-López
- Comisión México Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales del Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Ciudad de México, Mexico
| | - A Alonso Aguirre
- Warner College of Natural Resources, Colorado State University, Fort Collins, Colorado, USA
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7
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Brynjolfsson SF, Sigurgrimsdottir H, Gudlaugsson O, Kristjansson M, Kristinsson KG, Ludviksson BR. Determining SARS-CoV-2 non-infectivity state-A brief overview. Front Public Health 2022; 10:934242. [PMID: 36033758 PMCID: PMC9412020 DOI: 10.3389/fpubh.2022.934242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/18/2022] [Indexed: 01/25/2023] Open
Abstract
From the beginning of the COVID-19 pandemic, it has claimed over 6 million lives, and globally the pandemic rages with detrimental consequences, with the emergence of new more infectious and possibly virulent variants. A clinical obstacle in this battle has been to determine when an infected individual has reached a non-infectious state. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be transmitted under diverse circumstances, and various rules and regulations, along with different testing methods, have been applied in an attempt to confine the transmission. However, that has proven to be a difficult task. In this review, we take together recently published data on infectivity and transmission of SARS-CoV-2 and have combined it with the clinical experience that physicians in Iceland have accumulated from the pandemic. In addition, we suggest guidelines for determining when patients with COVID-19 reach a non-infectious state based on a combination of clinical experience, scientific data, and proficient use of available tests. This review has addressed some of the questions regarding contagiousness and immunity against SARS-CoV-2.
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Affiliation(s)
- Siggeir F. Brynjolfsson
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,*Correspondence: Siggeir F. Brynjolfsson
| | - Hildur Sigurgrimsdottir
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Olafur Gudlaugsson
- Department of Infectious Diseases, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Mar Kristjansson
- Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Infectious Diseases, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Karl G. Kristinsson
- Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Clinical Microbiology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjorn R. Ludviksson
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Bjorn R. Ludviksson
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8
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Zavaglio F, Cassaniti I, Sammartino JC, Tonello S, Sainaghi PP, Novelli V, Meloni F, Lilleri D, Baldanti F. mRNA BNT162b Vaccine Elicited Higher Antibody and CD4 + T-Cell Responses than Patients with Mild COVID-19. Microorganisms 2022; 10:microorganisms10061250. [PMID: 35744768 PMCID: PMC9228401 DOI: 10.3390/microorganisms10061250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
We compared the development and persistence of antibody and T-cell responses elicited by the mRNA BNT162b2 vaccine or SARS-CoV-2 infection. We analysed 37 post-COVID-19 patients (15 with pneumonia and 22 with mild symptoms) and 20 vaccinated subjects. Anti-Spike IgG and neutralising antibodies were higher in vaccinated subjects and in patients with pneumonia than in patients with mild COVID-19, and persisted at higher levels in patients with pneumonia while declining in vaccinated subjects. However, the booster dose restored the initial antibody levels. The proliferative CD4+ T-cell response was similar in vaccinated subjects and patients with pneumonia, but was lower in mild COVID-19 patients and persisted in both vaccinated subjects and post-COVID patients. Instead, the proliferative CD8+ T-cell response was lower in vaccinated subjects than in patients with pneumonia, decreased six months after vaccination, and was not restored after the booster dose. The cytokine profile was mainly TH1 in both vaccinated subjects and post-COVID-19 patients. The mRNA BNT162b2 vaccine elicited higher levels of antibody and CD4+ T-cell responses than those observed in mild COVID-19 patients. While the antibody response declined after six months and required a booster dose to be restored at the initial levels, the proliferative CD4+ T-cell response persisted over time.
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Affiliation(s)
- Federica Zavaglio
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.Z.); (I.C.); (J.C.S.); (F.B.)
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.Z.); (I.C.); (J.C.S.); (F.B.)
| | - Josè Camilla Sammartino
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.Z.); (I.C.); (J.C.S.); (F.B.)
| | - Stelvio Tonello
- Immunoreumatology Laboratory, Center for Translational Research on Autoimmune and Allergic Disease-CAAD, University of Piemonte Orientale, 28100 Novara, Italy; (S.T.); (P.P.S.)
- Internal Medicine Laboratory, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Pier Paolo Sainaghi
- Immunoreumatology Laboratory, Center for Translational Research on Autoimmune and Allergic Disease-CAAD, University of Piemonte Orientale, 28100 Novara, Italy; (S.T.); (P.P.S.)
- Internal Medicine Laboratory, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Immunorheumatology Unit, Division of Internal Medicine, “Maggiore della Carità” Univerisity Hospital, 28100 Novara, Italy
| | - Viola Novelli
- Medical Direction, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Federica Meloni
- Research Laboratory of Lung Diseases, Section of Cell Biology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Daniele Lilleri
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.Z.); (I.C.); (J.C.S.); (F.B.)
- Correspondence: ; Tel.: +39-0382-501501
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.Z.); (I.C.); (J.C.S.); (F.B.)
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
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9
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Hendriks J, Schasfoort R, Koerselman M, Dannenberg M, Cornet AD, Beishuizen A, van der Palen J, Krabbe J, Mulder AHL, Karperien M. High Titers of Low Affinity Antibodies in COVID-19 Patients Are Associated With Disease Severity. Front Immunol 2022; 13:867716. [PMID: 35493512 PMCID: PMC9043688 DOI: 10.3389/fimmu.2022.867716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Background Almost 2 years from the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there is still a lot unknown how the humoral response affects disease progression. In this study, we investigated humoral antibody responses against specific SARS-CoV2 proteins, their strength of binding, and their relationship with COVID severity and clinical information. Furthermore, we studied the interactions of the specific receptor-binding domain (RBD) in more depth by characterizing specific antibody response to a peptide library. Materials and Methods We measured specific antibodies of isotypes IgM, IgG, and IgA, as well as their binding strength against the SARS-CoV2 antigens RBD, NCP, S1, and S1S2 in sera of 76 COVID-19 patients using surface plasmon resonance imaging. In addition, these samples were analyzed using a peptide epitope mapping assay, which consists of a library of peptides originating from the RBD. Results A positive association was observed between disease severity and IgG antibody titers against all SARS-CoV2 proteins and additionally for IgM and IgA antibodies directed against RBD. Interestingly, in contrast to the titer of antibodies, the binding strength went down with increasing disease severity. Within the critically ill patient group, a positive association with pulmonary embolism, d-dimer, and antibody titers was observed. Conclusion In critically ill patients, antibody production is high, but affinity is low, and maturation is impaired. This may play a role in disease exacerbation and could be valuable as a prognostic marker for predicting severity.
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Affiliation(s)
- Jan Hendriks
- Department of Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | - Richard Schasfoort
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | - Michelle Koerselman
- Department of Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | - Maureen Dannenberg
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | | | | | - Job van der Palen
- Medical School, Medisch Spectrum Twente, Enschede, Netherlands.,Section Cognition, Education and Data, Faculty of Behavioural, Management and Social Sciences, University of Twente, Enschede, Netherlands
| | - Johannes Krabbe
- Department of Clinical Chemistry, Medlon BV, Enschede, Netherlands.,Department of Clinical Chemistry and Laboratory Medicine, Medisch Spectrum Twente, Enschede, Netherlands
| | - Alide H L Mulder
- Department of Clinical Chemistry, Medlon BV, Enschede, Netherlands.,Department of Clinical Chemistry, Ziekenhuis Groep Twente, Almelo, Netherlands
| | - Marcel Karperien
- Department of Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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10
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García-Jiménez ÁF, Cáceres-Martell Y, Fernández-Soto D, Martínez Fleta P, Casasnovas JM, Sánchez-Madrid F, Frade JMR, Valés-Gómez M, Reyburn HT. Cross-reactive cellular, but not humoral, immunity is detected between OC43 and SARS-CoV-2 NPs in people not infected with SARS-CoV-2: Possible role of cT FH cells. J Leukoc Biol 2022; 112:339-346. [PMID: 35384035 PMCID: PMC9088540 DOI: 10.1002/jlb.4covcra0721-356rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
Multiple questions about SARS-CoV-2 humoral and cellular immunity remain unanswered. One key question is whether preexisting memory T or B cells, specific for related coronaviruses in SARS-CoV-2-unexposed individuals, can recognize and suppress COVID-19, but this issue remains unclear. Here, we demonstrate that antibody responses to SARS-CoV-2 antigens are restricted to serum samples from COVID-19 convalescent individuals. In contrast, cross-reactive T cell proliferation and IFN-γ production responses were detected in PBMCs of around 30% of donor samples collected prepandemic, although we found that these prepandemic T cell responses only elicited weak cTFH activation upon stimulation with either HCoV-OC43 or SARS-CoV-2 NP protein. Overall, these observations confirm that T cell cross-reactive with SARS-CoV-2 antigens are present in unexposed people, but suggest that the T cell response to HCoV-OC43 could be deficient in some important aspects, like TFH expansion, that might compromise the generation of cross-reactive TFH cells and antibodies. Understanding these differences in cellular responses may be of critical importance to advance in our knowledge of immunity against SARS-CoV-2.
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Affiliation(s)
| | - Yaiza Cáceres-Martell
- Department of Immunology and Oncology, National Centre for Biotechnology, CNB-CSIC, Madrid, Spain
| | - Daniel Fernández-Soto
- Department of Immunology and Oncology, National Centre for Biotechnology, CNB-CSIC, Madrid, Spain
| | | | - José M Casasnovas
- Department of Macromolecular Structures, National Centre for Biotechnology, CNB-CSIC, CNB, Madrid, Spain
| | | | | | - Mar Valés-Gómez
- Department of Immunology and Oncology, National Centre for Biotechnology, CNB-CSIC, Madrid, Spain
| | - Hugh T Reyburn
- Department of Immunology and Oncology, National Centre for Biotechnology, CNB-CSIC, Madrid, Spain
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11
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Herzog SA, De Bie J, Abrams S, Wouters I, Ekinci E, Patteet L, Coppens A, De Spiegeleer S, Beutels P, Van Damme P, Hens N, Theeten H. Seroprevalence of IgG antibodies against SARS-CoV-2 - a serial prospective cross-sectional nationwide study of residual samples, Belgium, March to October 2020. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35241216 PMCID: PMC8895468 DOI: 10.2807/1560-7917.es.2022.27.9.2100419] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BackgroundTo control epidemic waves, it is important to know the susceptibility to SARS-CoV-2 and its evolution over time in relation to the control measures taken.AimTo assess the evolving SARS-CoV-2 seroprevalence and seroincidence related to the first national lockdown in Belgium, we performed a nationwide seroprevalence study, stratified by age, sex and region using 3,000-4,000 residual samples during seven periods between 30 March and 17 October 2020.MethodsWe analysed residual sera from ambulatory patients for IgG antibodies against the SARS-CoV-2 S1 protein with a semiquantitative commercial ELISA. Weighted seroprevalence (overall and by age category and sex) and seroincidence during seven consecutive periods were estimated for the Belgian population while accommodating test-specific sensitivity and specificity.ResultsThe weighted overall seroprevalence initially increased from 1.8% (95% credible interval (CrI): 1.0-2.6) to 5.3% (95% CrI: 4.2-6.4), implying a seroincidence of 3.4% (95% CrI: 2.4-4.6) between the first and second collection period over a period of 3 weeks during lockdown (start lockdown mid-March 2020). Thereafter, seroprevalence stabilised, however, significant decreases were observed when comparing the third with the fifth, sixth and seventh period, resulting in negative seroincidence estimates after lockdown was lifted. We estimated for the last collection period mid-October 2020 a weighted overall seroprevalence of 4.2% (95% CrI: 3.1-5.2).ConclusionDuring lockdown, an initially small but increasing fraction of the Belgian population showed serologically detectable signs of exposure to SARS-CoV-2, which did not further increase when confinement measures eased and full lockdown was lifted.
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Affiliation(s)
- Sereina Annik Herzog
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria.,Centre for Health Economics Research and Modelling of Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Jessie De Bie
- Global Health Institute (GHI), Family Medicine and Population Health (FAMPOP), University of Antwerp, Wilrijk, Belgium.,Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Steven Abrams
- Data Science Institute (DSI), Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt, Hasselt, Belgium.,Global Health Institute (GHI), Family Medicine and Population Health (FAMPOP), University of Antwerp, Wilrijk, Belgium
| | - Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Esra Ekinci
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Lisbeth Patteet
- Algemeen Medisch Laboratorium (AML), Sonic Healthcare, Antwerp, Belgium
| | - Astrid Coppens
- Algemeen Medisch Laboratorium (AML), Sonic Healthcare, Antwerp, Belgium
| | | | - Philippe Beutels
- Centre for Health Economics Research and Modelling of Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Niel Hens
- Data Science Institute (DSI), Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt, Hasselt, Belgium.,Centre for Health Economics Research and Modelling of Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
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12
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Gaikwad S, Pandve H, Bawa M, Desale A, Patil T, Dadewar A. Community-Based Cross-Sectional Study of the Relationship between Sars-Cov-2 Antibody Titres and Clinico-Epidemiological Profile of Population above 6 Years of Age in the Pimpri Chinchwad, Pune, Maharashtra. MEDICAL JOURNAL OF DR. D.Y. PATIL VIDYAPEETH 2022. [DOI: 10.4103/mjdrdypu.mjdrdypu_80_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Letizia AG, Arnold CE, Adhikari BN, Voegtly LJ, Glang L, Rice GK, Goforth CW, Schilling MA, Weir DL, Malagon F, Ramos I, Vangeti S, Gonzalez-Reiche AS, Cer RZ, Sealfon SC, van Bakel H, Bishop-Lilly KA. Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit. Pathogens 2021; 10:pathogens10121589. [PMID: 34959544 PMCID: PMC8709254 DOI: 10.3390/pathogens10121589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
We used epidemiologic and viral genetic information to identify a case of likely reinfection in an otherwise healthy, young Marine recruit enrolled in the prospective, longitudinal COVID-19 Health Action Response for Marines (CHARM) study, and we paired these findings with serological studies. This participant had a positive RT-PCR to SARS-CoV-2 upon routine sampling on study day 7, although he was asymptomatic at that time. He cleared the infection within seven days. On study day 46, he had developed symptoms consistent with COVID-19 and tested positive by RT-PCR for SARS-CoV-2 again. Viral whole genome sequencing was conducted from nares swabs at multiple time points. The day 7 sample was determined to be lineage B.1.340, whereas both the day 46 and day 49 samples were B.1.1. The first positive result for anti-SARS-CoV-2 IgM serology was collected on day 49 and for IgG on day 91. This case appears most consistent with a reinfection event. Our investigation into this case is unique in that we compared sequence data from more than just paired specimens, and we also assayed for immune response after both the initial infection and the later reinfection. These data demonstrate that individuals who have experienced an infection with SARS-CoV-2 may fail to generate effective or long-lasting immunity, similar to endemic human beta coronaviruses.
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Affiliation(s)
- Andrew G. Letizia
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Catherine E. Arnold
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Bishwo N. Adhikari
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Carl W. Goforth
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Megan A. Schilling
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Dawn L. Weir
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Correspondence:
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14
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Gilboa T, Cohen L, Cheng C, Lazarovits R, Uwamanzu‐Nna A, Han I, Griswold K, Barry N, Thompson DB, Kohman RE, Woolley AE, Karlson EW, Walt DR. A SARS‐CoV‐2 Neutralization Assay Using Single Molecule Arrays. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tal Gilboa
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Limor Cohen
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Chi‐An Cheng
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Roey Lazarovits
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Augusta Uwamanzu‐Nna
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
| | - Isaac Han
- Harvard Medical School Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Kettner Griswold
- Harvard Medical School Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Nick Barry
- Harvard Medical School Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - David B. Thompson
- Harvard Medical School Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Richie E. Kohman
- Harvard Medical School Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
| | - Ann E. Woolley
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Medicine Boston MA 02115 USA
| | - Elizabeth W. Karlson
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Medicine Boston MA 02115 USA
| | - David R. Walt
- Harvard Medical School Boston MA 02115 USA
- Brigham and Women's Hospital Department of Pathology Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
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15
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Gilboa T, Cohen L, Cheng C, Lazarovits R, Uwamanzu‐Nna A, Han I, Griswold K, Barry N, Thompson DB, Kohman RE, Woolley AE, Karlson EW, Walt DR. A SARS-CoV-2 Neutralization Assay Using Single Molecule Arrays. Angew Chem Int Ed Engl 2021; 60:25966-25972. [PMID: 34534408 PMCID: PMC8653099 DOI: 10.1002/anie.202110702] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Indexed: 11/09/2022]
Abstract
Coronavirus disease 2019 (COVID-19) manifests with high clinical variability and warrants sensitive and specific assays to analyze immune responses in infected and vaccinated individuals. Using Single Molecule Arrays (Simoa), we developed an assay to assess antibody neutralization with high sensitivity and multiplexing capabilities based on antibody-mediated blockage of the ACE2-spike interaction. The assay does not require live viruses or cells and can be performed in a biosafety level 2 laboratory within two hours. We used this assay to assess neutralization and antibody levels in patients who died of COVID-19 and patients hospitalized for a short period of time and show that neutralization and antibody levels increase over time. We also adapted the assay for SARS-CoV-2 variants and measured neutralization capacity in pre-pandemic healthy, COVID-19 infected, and vaccinated individuals. This assay is highly adaptable for clinical applications, such as vaccine development and epidemiological studies.
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Affiliation(s)
- Tal Gilboa
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Limor Cohen
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Chi‐An Cheng
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Roey Lazarovits
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Augusta Uwamanzu‐Nna
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
| | - Isaac Han
- Harvard Medical SchoolBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Kettner Griswold
- Harvard Medical SchoolBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Nick Barry
- Harvard Medical SchoolBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - David B. Thompson
- Harvard Medical SchoolBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Richie E. Kohman
- Harvard Medical SchoolBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Ann E. Woolley
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of MedicineBostonMA02115USA
| | - Elizabeth W. Karlson
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of MedicineBostonMA02115USA
| | - David R. Walt
- Harvard Medical SchoolBostonMA02115USA
- Brigham and Women's HospitalDepartment of PathologyBostonMA02115USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
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16
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Andriamandimby SF, Brook CE, Razanajatovo N, Randriambolamanantsoa TH, Rakotondramanga JM, Rasambainarivo F, Raharimanga V, Razanajatovo IM, Mangahasimbola R, Razafindratsimandresy R, Randrianarisoa S, Bernardson B, Rabarison JH, Randrianarisoa M, Nasolo FS, Rabetombosoa RM, Ratsimbazafy AM, Raharinosy V, Rabemananjara AH, Ranaivoson CH, Razafimanjato H, Randremanana R, Héraud JM, Dussart P. Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar. Epidemics 2021; 38:100533. [PMID: 34896895 PMCID: PMC8628610 DOI: 10.1016/j.epidem.2021.100533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/23/2021] [Accepted: 11/27/2021] [Indexed: 01/12/2023] Open
Abstract
As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.
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Affiliation(s)
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, United States
| | | | | | | | | | | | | | | | | | | | - Barivola Bernardson
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar
| | | | | | | | | | | | | | | | | | | | - Rindra Randremanana
- Virology Unit, Institut Pasteur de Madagascar, Madagascar; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar
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17
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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: 165] [Impact Index Per Article: 55.0] [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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18
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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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19
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Robust and Persistent B- and T-Cell Responses after COVID-19 in Immunocompetent and Solid Organ Transplant Recipient Patients. Viruses 2021; 13:v13112261. [PMID: 34835067 PMCID: PMC8621286 DOI: 10.3390/v13112261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 12/18/2022] Open
Abstract
The development and persistence of SARS-CoV-2-specific immune response in immunocompetent (IC) and immunocompromised patients is crucial for long-term protection. Immune response to SARS-CoV-2 infection was analysed in 57 IC and 15 solid organ transplanted (TX) patients. Antibody responses were determined by ELISA and neutralization assay. T-cell response was determined by stimulation with peptide pools of the Spike, Envelope, Membrane, and Nucleocapsid proteins with a 20-h Activation Induced Marker (AIM) and 7-day lymphoproliferative assays. Antibody response was detected at similar levels in IC and TX patients. Anti-Spike IgG, IgA and neutralizing antibodies persisted for at least one year, while anti-Nucleocapsid IgG declined earlier. Patients with pneumonia developed higher antibody levels than patients with mild symptoms. Similarly, both rapid and proliferative T-cell responses were detected within the first two months after infection at comparable levels in IC and TX patients, and were higher in patients with pneumonia. T-cell response persisted for at least one year in both IC and TX patients. Spike, Membrane, and Nucleocapsid proteins elicited the major CD4+ and CD8+ T-cell responses, whereas the T-cell response to Envelope protein was negligible. After SARS-CoV-2 infection, antibody and T-cell responses develop rapidly and persist over time in both immunocompetent and transplanted patients.
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20
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Czuppon P, Schertzer E, Blanquart F, Débarre F. The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection. J R Soc Interface 2021; 18:20210575. [PMID: 34784776 PMCID: PMC8596012 DOI: 10.1098/rsif.2021.0575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging epidemics and local infection clusters are initially prone to stochastic effects that can substantially impact the early epidemic trajectory. While numerous studies are devoted to the deterministic regime of an established epidemic, mathematical descriptions of the initial phase of epidemic growth are comparatively rarer. Here, we review existing mathematical results on the size of the epidemic over time, and derive new results to elucidate the early dynamics of an infection cluster started by a single infected individual. We show that the initial growth of epidemics that eventually take off is accelerated by stochasticity. As an application, we compute the distribution of the first detection time of an infected individual in an infection cluster depending on testing effort, and estimate that the SARS-CoV-2 variant of concern Alpha detected in September 2020 first appeared in the UK early August 2020. We also compute a minimal testing frequency to detect clusters before they exceed a given threshold size. These results improve our theoretical understanding of early epidemics and will be useful for the study and control of local infectious disease clusters.
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Affiliation(s)
- Peter Czuppon
- Institute of Ecology and Environmental Sciences of Paris (iEES-Paris, UMR 7618), Sorbonne Université, CNRS, UPEC, IRD, INRAE, Paris 75252, France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris 75005, France
- Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | | | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris 75005, France
- Infection Antimicrobials Modelling Evolution, UMR 1137, INSERM, Université de Paris, Paris 75018, France
| | - Florence Débarre
- Institute of Ecology and Environmental Sciences of Paris (iEES-Paris, UMR 7618), Sorbonne Université, CNRS, UPEC, IRD, INRAE, Paris 75252, France
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21
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Nakagama Y, Komase Y, Candray K, Nakagama S, Sano F, Tsuchida T, Kunishima H, Imai T, Shintani A, Nitahara Y, Kaku N, Kido Y. Serological Testing Reveals the Hidden COVID-19 Burden among Health Care Workers Experiencing a SARS-CoV-2 Nosocomial Outbreak. Microbiol Spectr 2021; 9:e0108221. [PMID: 34550021 PMCID: PMC8557877 DOI: 10.1128/spectrum.01082-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 11/20/2022] Open
Abstract
We describe the results of testing health care workers, from a tertiary care hospital in Japan that had experienced a coronavirus disease 2019 (COVID-19) outbreak during the first peak of the pandemic, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody seroconversion. Using two chemiluminescent immunoassays and a confirmatory surrogate virus neutralization test, serological testing revealed that a surprising 42% of overlooked COVID-19 diagnoses (27/64 cases) occurred when case detection relied solely on SARS-CoV-2 nucleic acid amplification testing (NAAT). Our results suggest that the NAAT-positive population is only the tip of the iceberg and the portion left undetected might potentially have led to silent transmissions and triggered the spread. A questionnaire-based risk assessment was further indicative of exposures to specific aerosol-generating procedures (i.e., noninvasive ventilation and airway suctioning) having mediated transmission and served as the origins of the outbreak. Our observations are supportive of a multitiered testing approach, including the use of serological diagnostics, in order to accomplish exhaustive case detection along the whole COVID-19 spectrum. IMPORTANCE We describe the results of testing frontline health care workers, from a hospital in Japan that had experienced a COVID-19 outbreak, for SARS-CoV-2-specific antibodies. Antibody testing revealed that a surprising 42% of overlooked COVID-19 diagnoses occurred when case detection relied solely on PCR-based viral detection. COVID-19 clusters have been continuously striking the health care system around the globe. Our findings illustrate that such clusters are lined with hidden infections eluding detection with diagnostic PCR and that the cluster burden in total is more immense than actually recognized. The mainstays of diagnosing infectious diseases, including COVID-19, generally consist of two approaches, one aiming to detect molecular fragments of the invading pathogen and the other to measure immune responses of the host. Considering antibody testing as one trustworthy option to test our way through the pandemic can aid in the exhaustive case detection of COVID-19 patients with variable presentations.
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Affiliation(s)
- Yu Nakagama
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yuko Komase
- Department of Respiratory Internal Medicine, St. Marianna University School of Medicine, Yokohama City Seibu Hospital, Yokohama, Japan
| | - Katherine Candray
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Sachie Nakagama
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Fumiaki Sano
- Department of Hematology and Oncology, St. Marianna University School of Medicine, Yokohama City Seibu Hospital, Yokohama, Japan
| | - Tomoya Tsuchida
- Division of General Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroyuki Kunishima
- Department of Infectious Diseases, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Takumi Imai
- Department of Medical Statistics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Ayumi Shintani
- Department of Medical Statistics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yuko Nitahara
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Natsuko Kaku
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yasutoshi Kido
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
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22
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Rouka E, Kotsiou OS, Perlepe G, Pagonis A, Pantazopoulos I, Gourgoulianis KI. Temporal Associations of the SARS-CoV-2 NP Antigen and Anti-Spike Total Ig Levels with Laboratory Parameters in a Greek Cohort of Hospitalized COVID-19 Patients. Can Respir J 2021; 2021:6590528. [PMID: 34621457 PMCID: PMC8490794 DOI: 10.1155/2021/6590528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Background The direct effect of SARS-CoV-2 on the lungs results in increased hospitalization rates of patients with pneumonia. Severe COVID-19 patients often develop ARDS which is associated with poor prognosis. Assessing risk factors for COVID-19 severity is indispensable for implementing and evaluating therapeutic interventions. We investigated the temporal associations between the SARS-CoV-2 antigen (Ag), total Immunoglobulin (Ig) levels, and several laboratory parameters in hospitalized patients with varying degrees of COVID-19 severity. Methods The SARS-CoV-2 nucleocapsid protein (NP) and total Ig Spike (S) protein-specific antibodies were determined for each patient with lateral flow assays through repeated sampling every two days. Hematological and biochemical parameters were evaluated at the same time points. Results 40 Greek COVID-19 patients (31 males, 9 females) with a median age of 59.50 ± 16.21 years were enrolled in the study. The median time from symptom onset to hospitalization was 8.0 ± 4.19 days. A significant negative correlation was observed between the SARS-CoV-2 Ag and total Ig levels. The temporal correlation patterns of the SARS-CoV-2 NP Ag and anti-S total Ig levels with laboratory markers varied among patients with differing degrees of COVID-19 severity. Severe-critical cases had lower SARS-CoV-2 Ag and increased total Ig levels as compared to mild-moderate cases. Conclusions Distinct temporal profiles of the SARS-CoV-2 NP Ag and anti-S total Ig levels may distinguish different groups of COVID-19 severity.
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Affiliation(s)
- Erasmia Rouka
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
| | - Ourania S Kotsiou
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
- Nursing Department, School of Health Sciences, University of Thessaly, GAIOPOLIS,41110, Larissa, Greece
| | - Garyfallia Perlepe
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
| | - Athanasios Pagonis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
| | - Ioannis Pantazopoulos
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS,41110, Larissa, Greece
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23
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O'Brien MP, Forleo-Neto E, Sarkar N, Isa F, Hou P, Chan KC, Musser BJ, Bar KJ, Barnabas RV, Barouch DH, Cohen MS, Hurt CB, Burwen DR, Marovich MA, Brown ER, Heirman I, Davis JD, Turner KC, Ramesh D, Mahmood A, Hooper AT, Hamilton JD, Kim Y, Purcell LA, Baum A, Kyratsous CA, Krainson J, Perez-Perez R, Mohseni R, Kowal B, DiCioccio AT, Stahl N, Lipsich L, Braunstein N, Herman G, Yancopoulos GD, Weinreich DM. Subcutaneous REGEN-COV Antibody Combination in Early Asymptomatic SARS-CoV-2 Infection: A Randomized Clinical Trial. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.14.21258569. [PMID: 34159343 PMCID: PMC8219113 DOI: 10.1101/2021.06.14.21258569] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
IMPORTANCE Easy-to-administer antiviral treatments may be used to prevent progression from asymptomatic infection to COVID-19 and to reduce viral carriage. OBJECTIVE Evaluate the efficacy and safety of subcutaneous casirivimab and imdevimab antibody combination (REGEN-COV) to prevent progression from early asymptomatic SARS-CoV-2 infection to COVID-19. DESIGN Randomized, double-blind, placebo-controlled, phase 3 study that enrolled asymptomatic close contacts living with a SARS-CoV-2-infected household member (index case). Participants who were SARS-CoV-2 RT-qPCR-positive at baseline were included in the analysis reported here. SETTING Multicenter trial conducted at 112 sites in the United States, Romania, and Moldova. PARTICIPANTS Asymptomatic individuals ≥12 years of age were eligible if identified within 96 hours of collection of the index case's positive SARS-CoV-2 test sample. INTERVENTIONS A total of 314 asymptomatic, SARS-CoV-2 RT-qPCR-positive individuals living with an infected household contact were randomized 1:1 to receive a single dose of subcutaneous REGEN-COV 1200mg (n=158) or placebo (n=156). MAIN OUTCOMES AND MEASURES The primary endpoint was the proportion of participants who developed symptomatic COVID-19 during the 28-day efficacy assessment period. The key secondary efficacy endpoints were the number of weeks of symptomatic SARS-CoV-2 infection and the number of weeks of high viral load (>4 log10 copies/mL). Safety was assessed in all treated participants. RESULTS Subcutaneous REGEN-COV 1200mg significantly prevented progression from asymptomatic to symptomatic disease compared with placebo (31.5% relative risk reduction; 29/100 [29.0%] vs 44/104 [42.3%], respectively; P=.0380). REGEN-COV reduced the overall population burden of high-viral load weeks (39.7% reduction vs placebo; 48 vs 82 total weeks; P=.0010) and of symptomatic weeks (45.3% reduction vs placebo; 89.6 vs 170.3 total weeks; P=.0273), the latter corresponding to an approximately 5.6-day reduction in symptom duration per symptomatic participant. Six placebo-treated participants had a COVID-19-related hospitalization or ER visit versus none for those receiving REGEN-COV. The proportion of participants receiving placebo who had ≥1 treatment-emergent adverse events was 48.1% compared with 33.5% for those receiving REGEN-COV, including events related (39.7% vs 25.8%, respectively) or not related (16.0% vs 11.0%, respectively) to COVID-19. CONCLUSIONS AND RELEVANCE Subcutaneous REGEN-COV 1200mg prevented progression from asymptomatic SARS-CoV-2 infection to COVID-19, reduced the duration of high viral load and symptoms, and was well tolerated. TRIAL REGISTRATION ClinicalTrials.gov Identifier, NCT04452318.
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Affiliation(s)
| | | | - Neena Sarkar
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Flonza Isa
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Peijie Hou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | - Katharine J Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruanne V Barnabas
- Department of Global Health, University of Washington, Seattle, WA, USA; Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Myron S Cohen
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher B Hurt
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Dale R Burwen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mary A Marovich
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elizabeth R Brown
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - John D Davis
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Divya Ramesh
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | - Yunji Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Alina Baum
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | - Bari Kowal
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Neil Stahl
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Leah Lipsich
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Gary Herman
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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24
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Kinetics of Nucleocapsid, Spike and Neutralizing Antibodies, and Viral Load in Patients with Severe COVID-19 Treated with Convalescent Plasma. Viruses 2021; 13:v13091844. [PMID: 34578426 PMCID: PMC8473255 DOI: 10.3390/v13091844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
COVID-19 is an ongoing pandemic with high morbidity and mortality. Despite meticulous research, only dexamethasone has shown consistent mortality reduction. Convalescent plasma (CP) infusion might also develop into a safe and effective treatment modality on the basis of recent studies and meta-analyses; however, little is known regarding the kinetics of antibodies in CP recipients. To evaluate the kinetics, we followed 31 CP recipients longitudinally enrolled at a median of 3 days post symptom onset for changes in binding and neutralizing antibody titers and viral loads. Antibodies against the complete trimeric Spike protein and the receptor-binding domain (Spike-RBD), as well as against the complete Nucleocapsid protein and the RNA binding domain (N-RBD) were determined at baseline and weekly following CP infusion. Neutralizing antibody (pseudotype NAb) titers were determined at the same time points. Viral loads were determined semi-quantitatively by SARS-CoV-2 PCR. Patients with low humoral responses at entry showed a robust increase of antibodies to all SARS-CoV-2 proteins and Nab, reaching peak levels within 2 weeks. The rapid increase in binding and neutralizing antibodies was paralleled by a concomitant clearance of the virus within the same timeframe. Patients with high humoral responses at entry demonstrated low or no further increases; however, virus clearance followed the same trajectory as in patients with low antibody response at baseline. Together, the sequential immunological and virological analysis of this well-defined cohort of patients early in infection shows the presence of high levels of binding and neutralizing antibodies and potent clearance of the virus.
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25
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Silveira MF, Mesenburg MA, Dellagostin OA, de Oliveira NR, Maia MA, Santos FD, Vale A, Menezes AMB, Victora GD, Victora CG, Barros AJ, Vidaletti LP, Hartwig FP, Barros FC, Hallal PC, Horta BL. Time-dependent decay of detectable antibodies against SARS-CoV-2: A comparison of ELISA with two batches of a lateral-flow test. Braz J Infect Dis 2021; 25:101601. [PMID: 34391693 PMCID: PMC8339571 DOI: 10.1016/j.bjid.2021.101601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/28/2021] [Accepted: 07/10/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Large-scale epidemiological studies of seroprevalence of antibodies against SARS-CoV-2 often rely on point-of-care tests that provide immediate results to participants. Yet, little is known on how long rapid tests remain positive after the COVID-19 episode, or how much variability exists across different brands and even among batches of the same test. METHODS In November 2020, we assessed the sensitivity of three tests applied to 133 individuals with a previous positive PCR result between April and October. All subjects provided finger prick blood samples for two batches (A and B) of the Wondfo lateral-flow IgG/IgM test, and dried blood spot samples for the S-UFRJ ELISA test. RESULTS Overall sensitivity levels were 92.5% (95% CI 86.6-96.3), 63.2% (95% CI 54.4-71.4) and 33.8% (95% CI 25.9-42.5) for the S-UFRJ test, Wondfo A and Wondfo B tests, respectively. There was no evidence of a decline in the positivity of S-UFRJ with time since the diagnosis, but the two Wondfo batches showed sharp reductions to as low as 41.9% and 19.4%, respectively, for subjects with a positive PCR in June or earlier. Positive results for batch B of the rapid test were 35% to 54% lower than for batch A at any given month of diagnosis. INTERPRETATION Whereas the ELISA test showed high sensitivity and stability of results over the five months of the study, both batches of the rapid test showed substantial declines, with one of the batches consistently showing lower sensitivity levels than the other. ELISA tests based on dried-blood spots are an inexpensive alternative to rapid lateral-flow tests in large-scale epidemiological studies. FUNDING The study was funded by the "Todos Pela Saúde" initiative, Instituto Serrapilheira, Brazilian Ministry of Health, Brazilian Collective Health Association (ABRASCO) and the JBS S.A. initiative 'Fazer o Bem Faz Bem'.
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Affiliation(s)
| | - Marilia A Mesenburg
- Universidade Federal de Pelotas, Pelotas, RS, Brazil; Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil.
| | | | | | - Mara Ac Maia
- Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| | | | - André Vale
- Universidade Federal do Rio de Janeiro, Rio de Janeiro,RJ, Brazil.
| | | | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, Rockefeller University, New York, United States.
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26
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Hay JA, Kennedy-Shaffer L, Kanjilal S, Lennon NJ, Gabriel SB, Lipsitch M, Mina MJ. Estimating epidemiologic dynamics from cross-sectional viral load distributions. Science 2021; 373:eabh0635. [PMID: 34083451 PMCID: PMC8527857 DOI: 10.1126/science.abh0635] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022]
Abstract
Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance-in the form of cycle threshold (Ct) values obtained from reverse transcription quantitative polymerase chain reaction testing-changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining data from multiple such samples improves the precision and robustness of this estimation. We apply our methods to Ct values from surveillance conducted during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.
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Affiliation(s)
- James A Hay
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lee Kennedy-Shaffer
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Mathematics and Statistics, Vassar College, Poughkeepsie, NY, USA
| | - Sanjat Kanjilal
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michael J Mina
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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27
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Lipsitch M, Kahn R. Interpreting vaccine efficacy trial results for infection and transmission. Vaccine 2021; 39:4082-4088. [PMID: 34130883 PMCID: PMC8197448 DOI: 10.1016/j.vaccine.2021.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/20/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
Randomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines' effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary RCT outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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28
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Nilles EJ, Karlson EW, Norman M, Gilboa T, Fischinger S, Atyeo C, Zhou G, Bennett CL, Tolan NV, Oganezova K, Walt DR, Alter G, Simmons DP, Schur P, Jarolim P, Woolley AE, Baden LR. Evaluation of Three Commercial and Two Non-Commercial Immunoassays for the Detection of Prior Infection to SARS-CoV-2. J Appl Lab Med 2021; 6:1561-1570. [PMID: 34196711 PMCID: PMC8420636 DOI: 10.1093/jalm/jfab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/15/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Serological testing provides a record of prior infection with SARS-CoV-2, but assay performance requires independent assessment. METHODS We evaluated 3 commercial (Roche Diagnostics pan-IG, and Epitope Diagnostics IgM and IgG) and 2 non-commercial (Simoa and Ragon/MGH IgG) immunoassays against 1083 unique samples that included 251 PCR-positive and 832 prepandemic samples. RESULTS The Roche assay registered the highest specificity 99.6% (3/832 false positives), the Ragon/MGH assay 99.5% (4/832), the primary Simoa assay model 99.0% (8/832), and the Epitope IgG and IgM 99.0% (8/830) and 99.5% (4/830), respectively. Overall sensitivities for the Simoa, Roche pan-IG, Epitope IgG, Ragon/MGH IgG, and Epitope IgM were 92.0%, 82.9%, 82.5%, 64.5% and 47.0%, respectively. The Simoa immunoassay demonstrated the highest sensitivity among samples stratified by days postsymptom onset (PSO), <8 days PSO (57.69%) 8-14 days PSO (93.51%), 15-21 days PSO (100%), and > 21 days PSO (95.18%). CONCLUSIONS All assays demonstrated high to very high specificities while sensitivities were variable across assays.
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Affiliation(s)
- Eric J Nilles
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Elizabeth W Karlson
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA,Address correspondence to this author at: Brigham and Women’s Hospital, 75 Francis St., Boston, MA 02115, USA. Fax 508-785-0351; e-mail
| | - Maia Norman
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA,Tufts University School of Medicine, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Tal Gilboa
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | | | - Guohai Zhou
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Christopher L Bennett
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA,Massachusetts General Hospital, Boston, MA
| | - Nicole V Tolan
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | | | - David R Walt
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Galit Alter
- Harvard Medical School, Boston, MA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Daimon P Simmons
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Peter Schur
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Petr Jarolim
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Ann E Woolley
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
| | - Lindsey R Baden
- Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA
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29
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van der Toorn W, Oh DY, Bourquain D, Michel J, Krause E, Nitsche A, von Kleist M. An intra-host SARS-CoV-2 dynamics model to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation. PATTERNS (NEW YORK, N.Y.) 2021; 2:100262. [PMID: 33899034 PMCID: PMC8057735 DOI: 10.1016/j.patter.2021.100262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/20/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Non-pharmaceutical interventions (NPIs) remain decisive tools to contain SARS-CoV-2. Strategies that combine NPIs with testing may improve efficacy and shorten quarantine durations. We developed a stochastic within-host model of SARS-CoV-2 that captures temporal changes in test sensitivities, incubation periods, and infectious periods. We used the model to simulate relative transmission risk for (1) isolation of symptomatic individuals, (2) contact person management, and (3) quarantine of incoming travelers. We estimated that testing travelers at entry reduces transmission risks to 21.3% ([20.7, 23.9], by PCR) and 27.9% ([27.1, 31.1], by rapid diagnostic test [RDT]), compared with unrestricted entry. We calculated that 4 (PCR) or 5 (RDT) days of pre-test quarantine are non-inferior to 10 days of quarantine for incoming travelers and that 8 (PCR) or 10 (RDT) days of pre-test quarantine are non-inferior to 14 days of post-exposure quarantine. De-isolation of infected individuals 13 days after symptom onset may reduce the transmission risk to <0.2% (<0.01, 6.0).
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Affiliation(s)
- Wiep van der Toorn
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Djin-Ye Oh
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Daniel Bourquain
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Eva Krause
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
| | - the Working Group on SARS-CoV-2 Diagnostics at RKI
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
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30
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Lipsitch M, Kahn R. Interpreting vaccine efficacy trial results for infection and transmission. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.25.21252415. [PMID: 33655276 PMCID: PMC7924301 DOI: 10.1101/2021.02.25.21252415] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Randomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines' effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FCS, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MUG, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Proença-Modena JL, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 2021; 372:815-821. [PMID: 33853970 PMCID: PMC8139423 DOI: 10.1126/science.abh2644] [Citation(s) in RCA: 892] [Impact Index Per Article: 297.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022]
Abstract
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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Affiliation(s)
- Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Ingra M Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C S Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J G Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucas A M Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S Andrade
- Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil
| | - Thais M Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A M Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L Proença-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A Hay
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | | | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Raphael Sonabend
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, London, UK
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Vitor H Nascimento
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Marc A Suchard
- Department of Biomathematics, Department of Biostatistics, and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | - Nick J Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P S S Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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32
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Chen X, Chen Z, Azman AS, Deng X, Sun R, Zhao Z, Zheng N, Chen X, Lu W, Zhuang T, Yang J, Viboud C, Ajelli M, Leung DT, Yu H. Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis. Lancet Glob Health 2021; 9:e598-e609. [PMID: 33705690 PMCID: PMC8049592 DOI: 10.1016/s2214-109x(21)00026-7] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND A rapidly increasing number of serological surveys for antibodies to SARS-CoV-2 have been reported worldwide. We aimed to synthesise, combine, and assess this large corpus of data. METHODS In this systematic review and meta-analysis, we searched PubMed, Embase, Web of Science, and five preprint servers for articles published in English between Dec 1, 2019, and Dec 22, 2020. Studies evaluating SARS-CoV-2 seroprevalence in humans after the first identified case in the area were included. Studies that only reported serological responses among patients with COVID-19, those using known infection status samples, or any animal experiments were all excluded. All data used for analysis were extracted from included papers. Study quality was assessed using a standardised scale. We estimated age-specific, sex-specific, and race-specific seroprevalence by WHO regions and subpopulations with different levels of exposures, and the ratio of serology-identified infections to virologically confirmed cases. This study is registered with PROSPERO, CRD42020198253. FINDINGS 16 506 studies were identified in the initial search, 2523 were assessed for eligibility after removal of duplicates and inappropriate titles and abstracts, and 404 serological studies (representing tests in 5 168 360 individuals) were included in the meta-analysis. In the 82 studies of higher quality, close contacts (18·0%, 95% CI 15·7-20·3) and high-risk health-care workers (17·1%, 9·9-24·4) had higher seroprevalence than did low-risk health-care workers (4·2%, 1·5-6·9) and the general population (8·0%, 6·8-9·2). The heterogeneity between included studies was high, with an overall I2 of 99·9% (p<0·0001). Seroprevalence varied greatly across WHO regions, with the lowest seroprevalence of general populations in the Western Pacific region (1·7%, 95% CI 0·0-5·0). The pooled infection-to-case ratio was similar between the region of the Americas (6·9, 95% CI 2·7-17·3) and the European region (8·4, 6·5-10·7), but higher in India (56·5, 28·5-112·0), the only country in the South-East Asia region with data. INTERPRETATION Antibody-mediated herd immunity is far from being reached in most settings. Estimates of the ratio of serologically detected infections per virologically confirmed cases across WHO regions can help provide insights into the true proportion of the population infected from routine confirmation data. FUNDING National Science Fund for Distinguished Young Scholars, Key Emergency Project of Shanghai Science and Technology Committee, Program of Shanghai Academic/Technology Research Leader, National Science and Technology Major project of China, the US National Institutes of Health. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland; Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Ruijia Sun
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zeyao Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Nan Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinghui Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wanying Lu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Tingyu Zhuang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Daniel T Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
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33
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Hellewell J, Russell TW, Beale R, Kelly G, Houlihan C, Nastouli E, Kucharski AJ. Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections. BMC Med 2021; 19:106. [PMID: 33902581 PMCID: PMC8075718 DOI: 10.1186/s12916-021-01982-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time. METHODS We fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection; we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection. RESULTS We estimated that the probability that the PCR test detected infection peaked at 77% (54-88%) 4 days after infection, decreasing to 50% (38-65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1-3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day. CONCLUSIONS Our results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.
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Affiliation(s)
- Joel Hellewell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute; Division of Medicine, UCL, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Catherine Houlihan
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Infection and Immunity, University College London, London, UK
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Eleni Nastouli
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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34
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Ejima K, Kim KS, Iwanami S, Fujita Y, Li M, Zoh RS, Aihara K, Miyazaki T, Wakita T, Iwami S. Time variation in the probability of failing to detect a case of polymerase chain reaction testing for SARS-CoV-2 as estimated from a viral dynamics model. J R Soc Interface 2021; 18:20200947. [PMID: 33878277 PMCID: PMC8086922 DOI: 10.1098/rsif.2020.0947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Viral tests including polymerase chain reaction (PCR) tests are recommended to diagnose COVID-19 infection during the acute phase of infection. A test should have high sensitivity; however, the sensitivity of the PCR test is highly influenced by viral load, which changes over time. Because it is difficult to collect data before the onset of symptoms, the current literature on the sensitivity of the PCR test before symptom onset is limited. In this study, we used a viral dynamics model to track the probability of failing to detect a case of PCR testing over time, including the presymptomatic period. The model was parametrized by using longitudinal viral load data collected from 30 hospitalized patients. The probability of failing to detect a case decreased toward symptom onset, and the lowest probability was observed 2 days after symptom onset and increased afterwards. The probability on the day of symptom onset was 1.0% (95% CI: 0.5 to 1.9) and that 2 days before symptom onset was 60.2% (95% CI: 57.1 to 63.2). Our study suggests that the diagnosis of COVID-19 by PCR testing should be done carefully, especially when the test is performed before or way after symptom onset. Further study is needed of patient groups with potentially different viral dynamics, such as asymptomatic cases.
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Affiliation(s)
- Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yasuhisa Fujita
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Roger S Zoh
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Taiga Miyazaki
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.,MIRAI, JST, Saitama, Japan.,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Science Groove Inc., Fukuoka, Japan
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35
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Chvatal-Medina M, Mendez-Cortina Y, Patiño PJ, Velilla PA, Rugeles MT. Antibody Responses in COVID-19: A Review. Front Immunol 2021; 12:633184. [PMID: 33936045 PMCID: PMC8081880 DOI: 10.3389/fimmu.2021.633184] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/25/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide as a severe pandemic. Although its seroprevalence is highly variable among territories, it has been reported at around 10%, but higher in health workers. Evidence regarding cross-neutralizing response between SARS-CoV and SARS-CoV-2 is still controversial. However, other previous coronaviruses may interfere with SARS-CoV-2 infection, since they are phylogenetically related and share the same target receptor. Further, the seroconversion of IgM and IgG occurs at around 12 days post onset of symptoms and most patients have neutralizing titers on days 14-20, with great titer variability. Neutralizing antibodies correlate positively with age, male sex, and severity of the disease. Moreover, the use of convalescent plasma has shown controversial results in terms of safety and efficacy, and due to the variable immune response among individuals, measuring antibody titers before transfusion is mostly required. Similarly, cellular immunity seems to be crucial in the resolution of the infection, as SARS-CoV-2-specific CD4+ and CD8+ T cells circulate to some extent in recovered patients. Of note, the duration of the antibody response has not been well established yet.
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Affiliation(s)
- Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | | | - Pablo J. Patiño
- Grupo Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Paula A. Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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36
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Ziemssen F, Feng YS, Schnichels S, Bayyoud T, Ueffing M, Bartz-Schmidt KU, Martus P, Peter A. Testing for SARS-CoV-2 seroprevalence: experiences of a tertiary eye centre. BMJ Open Ophthalmol 2021; 6:e000688. [PMID: 34192154 PMCID: PMC8050881 DOI: 10.1136/bmjophth-2020-000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 03/13/2021] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The actual prevalence of a SARS-CoV-2 infection and the individual assessment of being or having been infected may differ. Facing the great uncertainty-especially at the beginning of the pandemic-and the possibility of asymptomatic or mildly symptomatic, subclinical infections, we evaluate the experience of SARS-CoV-2 antibody screening at a tertiary clinical setting. METHODS AND ANALYSIS All employees of a tertiary eye centre and a research institute of ophthalmology were offered antibody testing in May 2020, using a sequential combination of different validated assays/antigens and point-of-care (POC) testing for a subset (NCT04446338). Before taking blood, a systematic inquiry into past symptoms, known contacts and a subjective self-assessment was documented. The correlations between serostatus, patient contacts and demographic characteristics were analysed. Different tests were compared by Kappa statistics. RESULTS Among 318 participants, SARS-CoV-2 antibodies were detected in 9 employees. Chemiluminescence assays (chemiluminescence immunoassay and electrochemiluminescence) showed superior specificity and high reproducibility, compared with ELISA and POC results.In contrast to the low seropositivity (2.8%) of healthcare workers, higher than that of the other departments of the hospital, a large proportion mistakenly assumed that they might have already been infected. Antiviral antibody titres increased and remained on a plateau for at least 3 months. CONCLUSIONS The great demand and acceptance confirmed the benefit of highly sensitive testing methods in the early phase of the pandemic. The coincidence of low seroprevalence and anxious employees may have contributed to internalising the need of hygiene measures.
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Affiliation(s)
- Focke Ziemssen
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - You-Shan Feng
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Sven Schnichels
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Tarek Bayyoud
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | | | - Peter Martus
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Andreas Peter
- Institute of Clinical Chemistry and Pathobichemistry, Department of Internal Medicine, Eberhard Karls Universitat Tubingen, Tubingen, Germany
- Institute for Diabetes Research and Metabolic Diseases, German Center for Diabetes Research (DZD) Helmholtz Zentrum München at the University of Tübingen, Eberhard Karls Universitat Tubingen, Tubingen, Germany
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S. Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.26.21252554. [PMID: 33688664 PMCID: PMC7941639 DOI: 10.1101/2021.02.26.21252554] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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Affiliation(s)
- Nuno R. Faria
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Thomas A. Mellan
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Charles Whittaker
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S. Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Swapnil Mishra
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C. Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucas A. M. Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S. Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M. Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A. M. Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S. Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M. Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M. de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C. de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J. T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J. Laydon
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | | | | | | | | | | | | | - Renato S. Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L. P. Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A. Hay
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Melodie Monod
- Department of Mathematics, Imperial College London, UK
| | | | - Helen Coupland
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Raphael Sonabend
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Michaela Vollmer
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, UK
| | - Marc A. Suchard
- Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergei L. K. Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | | | - Neil M. Ferguson
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | - Nick J. Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A. Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P. S. S. Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Samir Bhatt
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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González-Stegmaier R, Cereceda K, Briones JL, Beltran-Pávez C, Oyarzún-Arrau A, Riquelme-Barrios S, Selman C, Yarad F, Mahave M, Caglevic C, Morales R, Aguirre A, Valiente-Echeverría F, Soto-Rifo R, Marsiglia H, Gazitua R, Villarroel-Espindola F. Seroconversion and Abundance of IgG Antibodies against S1-RBD of SARS-CoV-2 and Neutralizing Activity in the Chilean Population. J Immunol Res 2021; 2021:6680337. [PMID: 33644235 PMCID: PMC7901042 DOI: 10.1155/2021/6680337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/03/2021] [Accepted: 01/24/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is a pandemic caused by SARS-CoV-2. In Chile, half a million people have been infected and more than 16,000 have died from COVID-19. As part of the clinical trial NCT04384588, we quantified IgG against S1-RBD of SARS-CoV-2 (anti-RBD) in recovered people in Santiago and evaluated their suitability as COVID-19 convalescent plasma donors. ELISA and a luminescent SARS-CoV-2 pseudotype were used for IgG and neutralizing antibody quantification. 72.9% of the convalescent population (468 of 639) showed seroconversion (5-55 μg/mL anti-RBD IgG) and were suitable candidates for plasma donation. Analysis by gender, age, and days after symptom offset did not show significant differences. Neutralizing activity correlated with an increased concentration of anti-RBD IgG (p < 0.0001) and showed a high variability between donors. We confirmed that the majority of the Chilean patients have developed anti-SARS-CoV-2 antibodies. The quantification of anti-RBD IgG in convalescent plasma donors is necessary to increase the detection of neutralizing antibodies.
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Affiliation(s)
- R. González-Stegmaier
- Translational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - K. Cereceda
- Translational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - J. L. Briones
- Haematology Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - C. Beltran-Pávez
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Chile
- HIV/AIDS Work Group, Faculty of Medicine, Universidad de Chile, Chile
| | - A. Oyarzún-Arrau
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Chile
- HIV/AIDS Work Group, Faculty of Medicine, Universidad de Chile, Chile
| | - S. Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Chile
- HIV/AIDS Work Group, Faculty of Medicine, Universidad de Chile, Chile
| | - C. Selman
- Diagnostic Units, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
- Biobank, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - F. Yarad
- Diagnostic Units, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - M. Mahave
- Medical Oncology Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - C. Caglevic
- Cancer Research Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - R. Morales
- Internal Medicine Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - A. Aguirre
- Translational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - F. Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Chile
- HIV/AIDS Work Group, Faculty of Medicine, Universidad de Chile, Chile
| | - R. Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Chile
- HIV/AIDS Work Group, Faculty of Medicine, Universidad de Chile, Chile
| | - H. Marsiglia
- Radiotherapy Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - R. Gazitua
- Haematology Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
| | - F. Villarroel-Espindola
- Translational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
- Cancer Research Department, Instituto Oncológico Fundación Arturo López Pérez, Santiago, Chile
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Hay JA, Kennedy-Shaffer L, Kanjilal S, Lennon NJ, Gabriel SB, Lipsitch M, Mina MJ. Estimating epidemiologic dynamics from cross-sectional viral load distributions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.10.08.20204222. [PMID: 33594381 PMCID: PMC7885940 DOI: 10.1101/2020.10.08.20204222] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but incidence data used for such estimation are confounded by variable testing practices. We show instead that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values, changes during an epidemic and that Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining multiple such samples and the fraction positive improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and demonstrate new approaches for real-time estimates of epidemic trajectories for outbreak management and response.
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Affiliation(s)
- James A. Hay
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA
| | - Lee Kennedy-Shaffer
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
- Department of Mathematics and Statistics, Vassar College, Poughkeepsie, NY
| | - Sanjat Kanjilal
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
- Department of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA
| | | | | | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA
| | - Michael J. Mina
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
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Rosado J, Pelleau S, Cockram C, Merkling SH, Nekkab N, Demeret C, Meola A, Kerneis S, Terrier B, Fafi-Kremer S, de Seze J, Bruel T, Dejardin F, Petres S, Longley R, Fontanet A, Backovic M, Mueller I, White MT. Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study. THE LANCET. MICROBE 2021; 2:e60-e69. [PMID: 33521709 PMCID: PMC7837364 DOI: 10.1016/s2666-5247(20)30197-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces an antibody response targeting multiple antigens that changes over time. This study aims to take advantage of this complexity to develop more accurate serological diagnostics. METHODS A multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples collected up to 39 days after symptom onset from 215 adults in four French hospitals (53 patients and 162 health-care workers) with quantitative RT-PCR-confirmed SARS-CoV-2 infection, and negative control serum samples collected from healthy adult blood donors before the start of the SARS-CoV-2 epidemic (335 samples from France, Thailand, and Peru). Machine learning classifiers were trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection, with the best classification performance displayed by a random forests algorithm. A Bayesian mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low-transmission settings. FINDINGS IgG antibody responses to trimeric spike protein (Stri) identified individuals with previous SARS-CoV-2 infection with 91·6% (95% CI 87·5-94·5) sensitivity and 99·1% (97·4-99·7) specificity. Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98·8% (96·5-99·6) sensitivity and 99·3% (97·6-99·8) specificity. Informed by existing data from other coronaviruses, we estimate that 1 year after infection, a monoplex assay with optimal anti-Stri IgG cutoff has 88·7% (95% credible interval 63·4-97·4) sensitivity and that a four-antigen multiplex assay can increase sensitivity to 96·4% (80·9-100·0). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 2%, below the false-positivity rate of many other assays. INTERPRETATION Serological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected more than 6 months ago and measuring seroprevalence in serological surveys in very low-transmission settings. FUNDING European Research Council. Fondation pour la Recherche Médicale. Institut Pasteur Task Force COVID-19.
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Affiliation(s)
- Jason Rosado
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- ED 393, Sorbonne Université, Paris, France
| | - Stéphane Pelleau
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Charlotte Cockram
- Spatial Regulation of Genomes Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Narimane Nekkab
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Caroline Demeret
- Molecular Genetics of RNA Viruses Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Annalisa Meola
- Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Solen Kerneis
- Epidemiology and Modelling of Bacterial Escape to Antimicrobials Unit, Department of Global Health, Institut Pasteur, Paris, France
- Equipe Mobile d'Infectiologie, APHP Centre-Université de Paris, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France
- Paris-Cardiovascular Research Center, INSERM U970, Paris, France
| | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France
- Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Jerome de Seze
- Centre d'Investigation Clinique - INSERM CIC-1434, Strasbourg, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- Vaccine Research Institute, Creteil, France
| | - François Dejardin
- Production and Purification of Recombinant Proteins Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Stéphane Petres
- Production and Purification of Recombinant Proteins Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Rhea Longley
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Arnaud Fontanet
- Epidemiology of Emerging Diseases Unit, Department of Global Health, Institut Pasteur, Paris, France
| | - Marija Backovic
- Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ivo Mueller
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Michael T White
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
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Mariën J, Ceulemans A, Michiels J, Heyndrickx L, Kerkhof K, Foque N, Widdowson MA, Mortgat L, Duysburgh E, Desombere I, Jansens H, Van Esbroeck M, Ariën KK. Evaluating SARS-CoV-2 spike and nucleocapsid proteins as targets for antibody detection in severe and mild COVID-19 cases using a Luminex bead-based assay. J Virol Methods 2021; 288:114025. [PMID: 33227340 PMCID: PMC7678438 DOI: 10.1016/j.jviromet.2020.114025] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023]
Abstract
Large-scale serosurveillance of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) will only be possible if serological tests are sufficiently reliable, rapid and affordable. Many assays are either labour-intensive and require specialised facilities (e.g. virus neutralization assays), or are expensive with suboptimal specificity (e.g. commercial ELISAs and RDTs). Bead-based assays offer a cost-effective alternative and allow for multiplexing to test for antibodies against multiple antigens and against other pathogens. Here, we compare the performance of spike (S) and nucleocapsid (NP) antigens for the detection of SARS-CoV-2 specific IgG, IgM and IgA antibodies in a panel of sera that includes recent (up to six weeks after symptom onset, severe n = 44; and mild cases n = 52) and old infections (five months after symptom onset, mild n = 104), using a Luminex-bead based assay and comparison to a virus neutralization test. While we show that neutralizing antibody levels are significantly lower in mild than in severe cases, we demonstrate that a combination of the recombinant nucleocapsid protein (NP) and receptor-binding domain (RBD) results in highly specific (99 %) IgG antibody detection five months after infection in 96 % of cases. Although most severe Covid-19 cases developed a clear IgM and IgA response, titers fell below the detection threshold in more than 20 % of mild cases in our bead-based assay. In conclusion, our data supports the use of RBD and NP for the development of SARS-CoV-2 serological IgG bead-based assays.
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Affiliation(s)
- Joachim Mariën
- Outbreak Research Team, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Ann Ceulemans
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Johan Michiels
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leo Heyndrickx
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Karen Kerkhof
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nikki Foque
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Laure Mortgat
- Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Els Duysburgh
- Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | | | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium.
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42
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Murrell I, Forde D, Zelek W, Tyson L, Chichester L, Palmer N, Jones R, Morgan BP, Moore C. Temporal development and neutralising potential of antibodies against SARS-CoV-2 in hospitalised COVID-19 patients: An observational cohort study. PLoS One 2021; 16:e0245382. [PMID: 33497420 PMCID: PMC7837461 DOI: 10.1371/journal.pone.0245382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Antibody responses are important in the control of viral respiratory infection in the human host. What is not clear for SARS-CoV-2 is how rapidly this response occurs, or when antibodies with protective capability evolve. Hence, defining the events of SARS-CoV-2 seroconversion and the time frame for the development of antibodies with protective potential may help to explain the different clinical presentations of COVID-19. Furthermore, accurate descriptions of seroconversion are needed to inform the best use of serological assays for diagnostic testing and serosurveillance studies. Here, we describe the humoral responses in a cohort of hospitalised COVID-19 patients (n = 19) shortly following the onset of symptoms. Commercial and 'in-house' serological assays were used to measure IgG antibodies against different SARS-CoV-2 structural antigens-Spike (S) S1 sub-unit and Nucleocapsid protein (NP)-and to assess the potential for virus neutralisation mediated specifically by inhibition of binding between the viral attachment protein (S protein) and cognate receptor (ACE-2). Antibody response kinetics varied amongst the cohort, with patients seroconverting within 1 week, between 1-2 weeks, or after 2 weeks, following symptom onset. Anti-NP IgG responses were generally detected earlier, but reached maximum levels slower, than anti-S1 IgG responses. The earliest IgG antibodies produced by all patients included those that recognised the S protein receptor-binding domain (RBD) and were capable of inhibiting binding to ACE-2. These data revealed events and patterns of SARS-CoV-2 seroconversion that may be important predictors of the outcome of infection and guide the delivery of clinical services in the COVID-19 response.
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Affiliation(s)
- Isa Murrell
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Donall Forde
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Wioleta Zelek
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Linda Tyson
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Lisa Chichester
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Nicki Palmer
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Rachel Jones
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - B. Paul Morgan
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
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43
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Kubo S, Ohtake N, Miyakawa K, Jeremiah SS, Yamaoka Y, Murohashi K, Hagiwara E, Mihara T, Goto A, Yamazaki E, Ogura T, Kaneko T, Yamanaka T, Ryo A. Development of an Automated Chemiluminescence Assay System for Quantitative Measurement of Multiple Anti-SARS-CoV-2 Antibodies. Front Microbiol 2021; 11:628281. [PMID: 33519790 PMCID: PMC7843449 DOI: 10.3389/fmicb.2020.628281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/17/2020] [Indexed: 01/19/2023] Open
Abstract
Objectives Serological tests for COVID-19 have been instrumental in studying the epidemiology of the disease. However, the performance of the currently available tests is plagued by the problem of variability. We have developed a high-throughput serological test capable of simultaneously detecting total immunoglobulins (Ig) and immunoglobulin G (IgG) against nucleocapsid protein (NP) and spike protein (SP) and report its performance in detecting COVID-19 in clinical samples. Methods We designed and prepared reagents for measuring NP-IgG, NP-Total Ig, SP-IgG, and SP-Total Ig (using N-terminally truncated NP (ΔN-NP) or receptor-binding domain (RBD) antigen) dedicated automated chemiluminescent enzyme immunoassay analyzer AIA-CL1200. After determining the basal thresholds based on 17 sera obtained from confirmed COVID-19 patients and 600 negative sera, the clinical validity of the assay was evaluated using independent 202 positive samples and 1,000 negative samples from healthy donors. Results All of the four test parameters showed 100% specificity individually (1,000/1,000; 95%CI, 99.63–100). The sensitivity of the assay increased proportionally to the elapsed time from symptoms onset, and all the tests achieved 100% sensitivity (153/153; 95%CI, 97.63–100) after 13 days from symptoms onset. NP-Total Ig was the earliest to attain maximal sensitivity among the other antibodies tested. Conclusion Our newly developed serological testing exhibited 100% sensitivity and specificity after 13 days from symptoms onset. Hence, it could be used as a reliable method for accurate detection of COVID-19 patients and to evaluate seroprevalence and possibly for surrogate assessment of herd immunity.
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Affiliation(s)
- Sousuke Kubo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Norihisa Ohtake
- Bioscience Division, Reagent Development Department, Tosoh Corporation, Kanagawa, Japan.,Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Yutaro Yamaoka
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Kanagawa, Japan
| | - Kota Murohashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Yokohama, Japan
| | - Eri Hagiwara
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Yokohama, Japan
| | - Takahiro Mihara
- Department of Health Data Science, Yokohama City University Graduate School of Data Science, Yokohama, Japan
| | - Atsushi Goto
- Department of Health Data Science, Yokohama City University Graduate School of Data Science, Yokohama, Japan
| | - Etsuko Yamazaki
- Clinical Laboratory Department, Yokohama City University Hospital, Yokohama, Japan
| | - Takashi Ogura
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeharu Yamanaka
- Department of Health Data Science, Yokohama City University Graduate School of Data Science, Yokohama, Japan.,Department of Biostatistics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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44
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Larremore DB, Wilder B, Lester E, Shehata S, Burke JM, Hay JA, Tambe M, Mina MJ, Parker R. Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening. SCIENCE ADVANCES 2021; 7:eabd5393. [PMID: 33219112 PMCID: PMC7775777 DOI: 10.1126/sciadv.abd5393] [Citation(s) in RCA: 634] [Impact Index Per Article: 211.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/28/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic has created a public health crisis. Because SARS-CoV-2 can spread from individuals with presymptomatic, symptomatic, and asymptomatic infections, the reopening of societies and the control of virus spread will be facilitated by robust population screening, for which virus testing will often be central. After infection, individuals undergo a period of incubation during which viral titers are too low to detect, followed by exponential viral growth, leading to peak viral load and infectiousness and ending with declining titers and clearance. Given the pattern of viral load kinetics, we model the effectiveness of repeated population screening considering test sensitivities, frequency, and sample-to-answer reporting time. These results demonstrate that effective screening depends largely on frequency of testing and speed of reporting and is only marginally improved by high test sensitivity. We therefore conclude that screening should prioritize accessibility, frequency, and sample-to-answer time; analytical limits of detection should be secondary.
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Affiliation(s)
- Daniel B Larremore
- Department of Computer Science, University of Colorado Boulder.
- BioFrontiers Institute, University of Colorado Boulder
| | - Bryan Wilder
- Center for Research on Computation and Society, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University
| | - Evan Lester
- Department of Biochemistry, University of Colorado Boulder
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus
| | - Soraya Shehata
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder
| | - James M Burke
- Department of Biochemistry, University of Colorado Boulder
| | - James A Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health
| | - Milind Tambe
- Center for Research on Computation and Society, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University
| | - Michael J Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder.
- Department of Biochemistry, University of Colorado Boulder
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder
- Howard Hughes Medical Institute
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45
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Galipeau Y, Greig M, Liu G, Driedger M, Langlois MA. Humoral Responses and Serological Assays in SARS-CoV-2 Infections. Front Immunol 2020; 11:610688. [PMID: 33391281 PMCID: PMC7775512 DOI: 10.3389/fimmu.2020.610688] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
In December 2019, the novel betacoronavirus Severe Acute Respiratory Disease Coronavirus 2 (SARS-CoV-2) was first detected in Wuhan, China. SARS-CoV-2 has since become a pandemic virus resulting in hundreds of thousands of deaths and deep socioeconomic implications worldwide. In recent months, efforts have been directed towards detecting, tracking, and better understanding human humoral responses to SARS-CoV-2 infection. It has become critical to develop robust and reliable serological assays to characterize the abundance, neutralization efficiency, and duration of antibodies in virus-exposed individuals. Here we review the latest knowledge on humoral immune responses to SARS-CoV-2 infection, along with the benefits and limitations of currently available commercial and laboratory-based serological assays. We also highlight important serological considerations, such as antibody expression levels, stability and neutralization dynamics, as well as cross-reactivity and possible immunological back-boosting by seasonal coronaviruses. The ability to accurately detect, measure and characterize the various antibodies specific to SARS-CoV-2 is necessary for vaccine development, manage risk and exposure for healthcare and at-risk workers, and for monitoring reinfections with genetic variants and new strains of the virus. Having a thorough understanding of the benefits and cautions of standardized serological testing at a community level remains critically important in the design and implementation of future vaccination campaigns, epidemiological models of immunity, and public health measures that rely heavily on up-to-date knowledge of transmission dynamics.
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Affiliation(s)
- Yannick Galipeau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Matthew Greig
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - George Liu
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- uOttawa Center for Infection, Immunity and Inflammation (CI3), Ottawa, ON, Canada
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46
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Validation of dried blood spot sample modifications to two commercially available COVID-19 IgG antibody immunoassays. Bioanalysis 2020; 13:13-28. [PMID: 33319585 PMCID: PMC7739400 DOI: 10.4155/bio-2020-0289] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: Coronavirus disease 2019 antibody testing often relies on venous blood collection, which is labor-intensive, inconvenient and expensive compared with finger-stick capillary dried blood spot (DBS) collection. The purpose of our work was to determine if two commercially available anti-severe acute respiratory syndrome coronavirus 2 enzyme-linked immunosorbent assays for IgG antibodies against spike S1 subunit and nucleocapsid proteins could be validated for use with DBS. Materials & methods: Kit supplied reagents were used to extract DBS, and in-house DBS calibrators were included on every run. Results: Positive/negative concordance between DBS and serum was 100/99.3% for the spike S1 subunit assay and 100/98% for the nucleocapsid assay. Conclusion: Validation of the DBS Coronavirus disease 2019 IgG antibody assays demonstrated that serum and DBS can produce equivalent results with minimal kit modifications.
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47
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Molenberghs G, Buyse M, Abrams S, Hens N, Beutels P, Faes C, Verbeke G, Van Damme P, Goossens H, Neyens T, Herzog S, Theeten H, Pepermans K, Abad AA, Van Keilegom I, Speybroeck N, Legrand C, De Buyser S, Hulstaert F. Infectious diseases epidemiology, quantitative methodology, and clinical research in the midst of the COVID-19 pandemic: Perspective from a European country. Contemp Clin Trials 2020; 99:106189. [PMID: 33132155 PMCID: PMC7581408 DOI: 10.1016/j.cct.2020.106189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023]
Abstract
Starting from historic reflections, the current SARS-CoV-2 induced COVID-19 pandemic is examined from various perspectives, in terms of what it implies for the implementation of non-pharmaceutical interventions, the modeling and monitoring of the epidemic, the development of early-warning systems, the study of mortality, prevalence estimation, diagnostic and serological testing, vaccine development, and ultimately clinical trials. Emphasis is placed on how the pandemic had led to unprecedented speed in methodological and clinical development, the pitfalls thereof, but also the opportunities that it engenders for national and international collaboration, and how it has simplified and sped up procedures. We also study the impact of the pandemic on clinical trials in other indications. We note that it has placed biostatistics, epidemiology, virology, infectiology, and vaccinology, and related fields in the spotlight in an unprecedented way, implying great opportunities, but also the need to communicate effectively, often amidst controversy.
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Affiliation(s)
- Geert Molenberghs
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; Interuniversity Institute for Biostatistics and statistical Bioinformatics, KU Leuven, Belgium
| | - Marc Buyse
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; International Drug Development Institute, Belgium; CluePoints, Belgium.
| | - Steven Abrams
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; Global Health Institute, Department of Epidemiology and Social Medicine, University of Antwerp, Belgium
| | - Niel Hens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium
| | - Geert Verbeke
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; Interuniversity Institute for Biostatistics and statistical Bioinformatics, KU Leuven, Belgium
| | - Pierre Van Damme
- Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | | | - Thomas Neyens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium; Interuniversity Institute for Biostatistics and statistical Bioinformatics, KU Leuven, Belgium
| | - Sereina Herzog
- Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Heidi Theeten
- Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Koen Pepermans
- Centre for Health Economics Research and Modelling of Infectious Diseases, University of Antwerp, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Ariel Alonso Abad
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, KU Leuven, Belgium
| | | | | | - Catherine Legrand
- Institute of Statistics, Biostatistics and Actuarial Sciences, UC Louvain, Belgium
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48
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Grassly NC, Pons-Salort M, Parker EPK, White PJ, Ferguson NM. Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study. THE LANCET. INFECTIOUS DISEASES 2020; 20:1381-1389. [PMID: 32822577 PMCID: PMC7434438 DOI: 10.1016/s1473-3099(20)30630-7] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND WHO has called for increased testing in response to the COVID-19 pandemic, but countries have taken different approaches and the effectiveness of alternative strategies is unknown. We aimed to investigate the potential impact of different testing and isolation strategies on transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS We developed a mathematical model of SARS-CoV-2 transmission based on infectiousness and PCR test sensitivity over time since infection. We estimated the reduction in the effective reproduction number (R) achieved by testing and isolating symptomatic individuals, regular screening of high-risk groups irrespective of symptoms, and quarantine of contacts of laboratory-confirmed cases identified through test-and-trace protocols. The expected effectiveness of different testing strategies was defined as the percentage reduction in R. We reviewed data on the performance of antibody tests reported by the Foundation for Innovative New Diagnostics and examined their implications for the use of so-called immunity passports. FINDINGS If all individuals with symptoms compatible with COVID-19 self-isolated and self-isolation was 100% effective in reducing onwards transmission, self-isolation of symptomatic individuals would result in a reduction in R of 47% (95% uncertainty interval [UI] 32-55). PCR testing to identify SARS-CoV-2 infection soon after symptom onset could reduce the number of individuals needing to self-isolate, but would also reduce the effectiveness of self-isolation (around 10% would be false negatives). Weekly screening of health-care workers and other high-risk groups irrespective of symptoms by use of PCR testing is estimated to reduce their contribution to SARS-CoV-2 transmission by 23% (95% UI 16-40), on top of reductions achieved by self-isolation following symptoms, assuming results are available at 24 h. The effectiveness of test and trace depends strongly on coverage and the timeliness of contact tracing, potentially reducing R by 26% (95% UI 14-35) on top of reductions achieved by self-isolation following symptoms, if 80% of cases and contacts are identified and there is immediate testing following symptom onset and quarantine of contacts within 24 h. Among currently available antibody tests, performance has been highly variable, with specificity around 90% or lower for rapid diagnostic tests and 95-99% for laboratory-based ELISA and chemiluminescent assays. INTERPRETATION Molecular testing can play an important role in prevention of SARS-CoV-2 transmission, especially among health-care workers and other high-risk groups, but no single strategy will reduce R below 1 at current levels of population immunity. Immunity passports based on antibody tests or tests for infection face substantial technical, legal, and ethical challenges. FUNDING UK Medical Research Council.
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Affiliation(s)
- Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Edward P K Parker
- The Vaccine Centre, Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter J White
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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49
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Baumgarth N, Nikolich-Žugich J, Lee FEH, Bhattacharya D. Antibody Responses to SARS-CoV-2: Let's Stick to Known Knowns. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:2342-2350. [PMID: 32887754 PMCID: PMC7578055 DOI: 10.4049/jimmunol.2000839] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
The scale of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has thrust immunology into the public spotlight in unprecedented ways. In this article, which is part opinion piece and part review, we argue that the normal cadence by which we discuss science with our colleagues failed to properly convey likelihoods of the immune response to SARS-CoV-2 to the public and the media. As a result, biologically implausible outcomes were given equal weight as the principles set by decades of viral immunology. Unsurprisingly, questionable results and alarmist news media articles have filled the void. We suggest an emphasis on setting expectations based on prior findings while avoiding the overused approach of assuming nothing. After reviewing Ab-mediated immunity after coronavirus and other acute viral infections, we posit that, with few exceptions, the development of protective humoral immunity of more than a year is the norm. Immunity to SARS-CoV-2 is likely to follow the same pattern.
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Affiliation(s)
- Nicole Baumgarth
- Center for Immunology and Infectious Diseases, Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA 95616
| | - Janko Nikolich-Žugich
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724
- University of Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA 30322; and
- Lowance Center for Human Immunology, Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724;
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50
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Russell TW, Golding N, Hellewell J, Abbott S, Wright L, Pearson CAB, van Zandvoort K, Jarvis CI, Gibbs H, Liu Y, Eggo RM, Edmunds WJ, Kucharski AJ. Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections. BMC Med 2020; 18:332. [PMID: 33087179 PMCID: PMC7577796 DOI: 10.1186/s12916-020-01790-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures. METHODS Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever ≥ 37.5 °C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment. RESULTS Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6 July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of 7 June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI 5.6-24%) (Belgium). CONCLUSIONS We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's population infected with SARS-CoV-2 worldwide is generally low.
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Affiliation(s)
- Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Nick Golding
- Telethon Kids Institute and Curtin University, Perth, Western Australia, Australia
| | - Joel Hellewell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Lawrence Wright
- Defence Science and Technology Laboratory/Sopra Steria, Fareham, UK
| | - Carl A B Pearson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kevin van Zandvoort
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Christopher I Jarvis
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hamish Gibbs
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Yang Liu
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Rosalind M Eggo
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - W John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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