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Shi C, Zhang Y, Ye S, Zhou J, Zhu F, Gao Y, Wang Y, Cong B, Deng S, Li Y, Lu B, Wang X. Infection Rates and Symptomatic Proportion of SARS-CoV-2 and Influenza in Pediatric Population, China, 2023. Emerg Infect Dis 2024; 30:1809-1818. [PMID: 39106459 DOI: 10.3201/eid3009.240065] [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] [Indexed: 08/09/2024] Open
Abstract
We conducted a longitudinal cohort study of SARS-CoV-2 and influenza rates in childcare centers and schools in Wuxi, China, collecting 1,760 environmental samples and 9,214 throat swabs from 593 students (regardless of symptoms) in weekly collections during February-June 2023. We estimated a cumulative infection rate of 124.8 (74 episodes)/1,000 persons for SARS-CoV-2 and 128.2 (76 episodes)/1,000 persons for influenza. The highest SARS-CoV-2 infection rate was in persons 18 years of age, and for influenza, in children 4 years of age. The asymptomatic proportion of SARS-CoV-2 was 59.6% and 66.7% for influenza; SARS-CoV-2 symptomatic proportion was lower in 16-18-year-olds than in 4-6-year-olds. Only samples from frequently touched surface tested positive for SARS-CoV-2 (4/1,052) and influenza (1/1,052). We found asynchronous circulation patterns of SARS-CoV-2 and influenza, similar to trends in national sentinel surveillance. The results support vaccination among pediatric populations and other interventions, such as environmental disinfection in educational settings.
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Guan M, Zuo Y, Yuan Y, Zhu H, Zheng H. High-dose Vitamin C intake and COVID-19 related symptoms during the SARS-CoV-2 pandemic. Am J Med Sci 2024; 368:265-268. [PMID: 38788926 DOI: 10.1016/j.amjms.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Affiliation(s)
- Mingcheng Guan
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, Suzhou, PR China
| | - Yibo Zuo
- Department / Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China; International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, PR China; Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, PR China
| | - Yukang Yuan
- Department / Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China; International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, PR China; Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, PR China
| | - Hong Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, Suzhou, PR China
| | - Hui Zheng
- Department / Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China; International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, PR China.
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3
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Cori A, Kucharski A. Inference of epidemic dynamics in the COVID-19 era and beyond. Epidemics 2024; 48:100784. [PMID: 39167954 DOI: 10.1016/j.epidem.2024.100784] [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: 03/22/2024] [Revised: 06/25/2024] [Accepted: 07/11/2024] [Indexed: 08/23/2024] Open
Abstract
The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required - from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.
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Affiliation(s)
- Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom.
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, United Kingdom.
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4
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Sun K, Bhiman JN, Tempia S, Kleynhans J, Madzorera VS, Mkhize Q, Kaldine H, McMorrow ML, Wolter N, Moyes J, Carrim M, Martinson NA, Kahn K, Lebina L, du Toit JD, Mkhencele T, von Gottberg A, Viboud C, Moore PL, Cohen C. SARS-CoV-2 correlates of protection from infection against variants of concern. Nat Med 2024:10.1038/s41591-024-03131-2. [PMID: 39060660 DOI: 10.1038/s41591-024-03131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/11/2024] [Indexed: 07/28/2024]
Abstract
Serum neutralizing antibodies (nAbs) induced by vaccination have been linked to protection against symptomatic and severe coronavirus disease 2019. However, much less is known about the efficacy of nAbs in preventing the acquisition of infection, especially in the context of natural immunity and against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune-escape variants. Here we conducted mediation analysis to assess serum nAbs induced by prior SARS-CoV-2 infections as potential correlates of protection against Delta and Omicron infections, in rural and urban household cohorts in South Africa. We find that, in the Delta wave, D614G nAbs mediate 37% (95% confidence interval: 34-40%) of the total protection against infection conferred by prior exposure to SARS-CoV-2, and that protection decreases with waning immunity. In contrast, Omicron BA.1 nAbs mediate 11% (95% confidence interval: 9-12%) of the total protection against Omicron BA.1 or BA.2 infections, due to Omicron's neutralization escape. These findings underscore that correlates of protection mediated through nAbs are variant specific, and that boosting of nAbs against circulating variants might restore or confer immune protection lost due to nAb waning and/or immune escape. However, the majority of immune protection against SARS-CoV-2 conferred by natural infection cannot be fully explained by serum nAbs alone. Measuring these and other immune markers including T cell responses, both in the serum and in other compartments such as the nasal mucosa, may be required to comprehensively understand and predict immune protection against SARS-CoV-2.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Jinal N Bhiman
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vimbai Sharon Madzorera
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Qiniso Mkhize
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Haajira Kaldine
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, MD, USA
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacques D du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Mashinini DP, Kelly NK, Mataboge P, Hill F, Nair H, Palattiyil G, Kahn K, Pettifor A. COVID-19-related stigma within a rural South African community: A mixed methods analysis. PLoS One 2024; 19:e0306821. [PMID: 39024376 PMCID: PMC11257259 DOI: 10.1371/journal.pone.0306821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 06/24/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Infectious disease-related stigma is a pervasive global issue that impedes disease control efforts by increasing reluctance to seek treatment or engagement in prevention behaviors for fear of ostracism. Despite this, there is limited research on COVID-19 stigma in Africa, specifically rural South Africa, which has faced infectious disease-related stigma throughout the HIV epidemic. METHODS Population-based surveys were conducted among 1,662 adults living in the Agincourt Health and Socio-Demographic Surveillance System (AHDSS) area in Mpumalanga, South Africa, in August-October 2020 and August-October 2021. Surveys measured anticipated COVID-19-related stigma from low to high levels. Changes in stigma between surveys were compared using Wilcoxon ranked sign tests, and log-binomial models estimated the association between socio-demographic factors and anticipated stigma at both intervals. Qualitative interviews were conducted in 2022 among 31 adults who completed the original surveys, and the data were analyzed thematically to describe anticipated, perceived, and enacted stigma. RESULTS Anticipated stigma significantly decreased from the first to the second survey (p-value:<0.0001). Stigma was significantly higher among older age groups. In 2020, those less knowledgeable about COVID-19 were 2.24 times as likely to have higher levels of anticipated stigma compared to those who were more knowledgeable (RR:2.24, 95% CI: 1.90,2.64). Fear of being stigmatized influenced willingness to disclose infection. Participants perceived COVID-19 stigma as similar to HIV/AIDS stigma, but concern and fear reduced over time, with differences observed across generations and sexes. For some, fear of death and mistrust of others endorsed enacting stigma toward others. CONCLUSION While COVID-19 stigma decreased over time in rural South Africa, different forms of stigma persisted and influenced participants' willingness to reveal their COVID-19 infection status. Given South Africa's history with infectious disease-related stigma hindering public health efforts, it is crucial that government bodies prioritize strategies to mitigate stigma in rural communities.
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Affiliation(s)
- Duduzile P. Mashinini
- Carolina Population Center, Biosocial Training Program, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nicole K. Kelly
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Palesa Mataboge
- MRC/Wits Rural Public Health Transitions Research Unit, School of Public Health, Faculty of Health Science University of the Witwatersrand, Johannesburg, South Africa
| | - Frantasia Hill
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Harish Nair
- MRC/Wits Rural Public Health Transitions Research Unit, School of Public Health, Faculty of Health Science University of the Witwatersrand, Johannesburg, South Africa
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - George Palattiyil
- Social Work, School of Social and Political Science, University of Edinburgh, Edinburgh, United Kingdom
- Department of Social Work and Community Development, University of Johannesburg, Johannesburg, South Africa
| | - Kathleen Kahn
- MRC/Wits Rural Public Health Transitions Research Unit, School of Public Health, Faculty of Health Science University of the Witwatersrand, Johannesburg, South Africa
| | - Audrey Pettifor
- Carolina Population Center, Biosocial Training Program, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- MRC/Wits Rural Public Health Transitions Research Unit, School of Public Health, Faculty of Health Science University of the Witwatersrand, Johannesburg, South Africa
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Smith P, Little F, Hermans S, Davies MA, Wood R, Orrell C, Pike C, Peters F, Dube A, Georgeu-Pepper D, Curran R, Fairall L, Bekker LG. A prospective randomised controlled trial investigating household SARS-CoV-2 transmission in a densely populated community in Cape Town, South Africa - the transmission of COVID-19 in crowded environments (TRACE) study. BMC Public Health 2024; 24:1924. [PMID: 39020307 PMCID: PMC11256445 DOI: 10.1186/s12889-024-19462-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND South Africa's first SARS-CoV-2 case was identified 5th March 2020 and national lockdown followed March 26th. Households are an important location for secondary SARS-CoV-2 infection. Physical distancing and sanitation - infection mitigation recommended by the World Health Organization (WHO) at the time - are difficult to implement in limited-resource settings because of overcrowded living conditions. METHODS This study (ClinicalTrials.gov NCT05119348) was conducted from August 2020 to September 2021 in two densely populated, low socioeconomic Cape Town community sub-districts. New COVID-19 index cases (ICs) identified at public clinics were randomised to an infection mitigation intervention (STOPCOV) delivered by lay community health workers (CHWs) or standard of care group. STOPCOV mitigation measures included one initial household assessment conducted by a CHW in which face masks, sanitiser, bleach and written information on managing and preventing spread were provided. This was followed by regular telephonic follow-up from CHWs. SARS-CoV-2 PCR and IgM/IgG serology was performed at baseline, weeks 1, 2, 3 and 4 of follow-up. RESULTS The study randomised 81 ICs with 245 HHCs. At baseline, no HHCs in the control and 7 (5%) in the intervention group had prevalent SARS-CoV-2. The secondary infection rate (SIR) based on SARS-CoV-2 PCR testing was 1.9% (n = 2) in control and 2.9% (n = 4) in intervention HHCs (p = 0.598). At baseline, SARS-CoV-2 antibodies were present in 15% (16/108) of control and 38% (52/137) of intervention participants. At study end incidence was 8.3% (9/108) and 8.03% (11/137) in the intervention and control groups respectively. Antibodies were present in 23% (25/108) of control HHCs over the course of the study vs. 46% (63/137) in the intervention arm. CHWs made twelve clinic and 47 food parcel referrals for individuals in intervention households in need. DISCUSSION Participants had significant exposure to SARS-CoV-2 infections prior to the study. In this setting, household transmission mitigation was ineffective. However, CHWs may have facilitated other important healthcare and social referrals.
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Affiliation(s)
- Philip Smith
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa.
| | - Francesca Little
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Sabine Hermans
- Amsterdam UMC, Department of Global Health, University of Amsterdam, Amsterdam, The Netherlands
- Centre for Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam UMC, Amsterdam Institute for Immunology and Infectious Diseases, University of Amsterdam, Amsterdam Public Health - Global Health, Amsterdam, The Netherlands
| | - Mary-Ann Davies
- Center for Infectious Diseases Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Robin Wood
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Catherine Orrell
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Carey Pike
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Fatima Peters
- Western Cape Department of Health, Cape Town, South Africa
| | - Audry Dube
- Knowledge Translation Unit, University of Cape Town, Cape Town, South Africa
| | | | - Robyn Curran
- Knowledge Translation Unit, University of Cape Town, Cape Town, South Africa
| | - Lara Fairall
- Knowledge Translation Unit, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa.
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7
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Vasylyev M, Buhiichyk V, Buhiichyck N, Groenendijk A, Ben I, Ostapiuk L, Sluzhynska M, Bierman WFW, van Kampen JJA, Wit FWNM, Reiss P, Rijnders BJA, Sluzhynska O, Rokx C. COVID-19 epidemiology and performance of the WHO clinical algorithm to diagnose COVID-19 in people with HIV from Ukraine. Int J STD AIDS 2024; 35:510-515. [PMID: 38318789 DOI: 10.1177/09564624241231016] [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] [Indexed: 02/07/2024]
Abstract
BACKGROUND The two main objectives were to evaluate the COVID-19 point prevalence and the test performance of the WHO case definition to diagnose COVID-19 clinically in people with HIV in West Ukraine. METHODS Multicenter cross-sectional study in Lviv, Ukraine, from October 2020-November 2021. COVID-19 unvaccinated people with HIV were included regardless of COVID-19 symptoms at routine clinical visits and had standardized medical, quality of life (EQ(5D)) and SARS-CoV-2 serology assessments. Reported symptoms indicating potential COVID-19 events at inclusion or between March 2020 and inclusion were classified by the WHO case definition as suspected, probable or confirmed. A clinical COVID-19 case was defined as being SARS-CoV-2 seropositive with at least a suspected COVID-19 according to the WHO case definition. The primary endpoints were the clinical COVID-19 prevalence and the test characteristics of the WHO case definition with SARS-CoV-2 serology as reference. (Clinicaltrials.gov:NCT04711954). RESULTS The 971 included people with HIV were median 40 years, 38.8% women, 44.8% had prior AIDS, and 55.6% had comorbidities. SARS-CoV-2 seroprevalence was 40.1% (95%CI:37.0-43.1) and 20.5% (95%CI:18.0-23.1) had clinical COVID-19 median 4 months (IQR:2-7) before inclusion. Clinical COVID-19 occurred less frequently in people with HIV with tuberculosis history, injecting drug use, CD4+ T-cells <200/mL and unemployment. The quality of life was not impacted after COVID-19. An at least probable COVID-19 classification by the WHO case definition had 44.1% sensitivity (95%CI:38.7-49.7), 85.2% specificity (95%CI:81.5-88.4), 66.6% positive predictive value (95%CI:59.8-73.0) and 69.5% negative predictive value (95%CI:65.5-73.3) to diagnose COVID-19. CONCLUSIONS COVID-19 unvaccinated people with HIV from Ukraine had a significant COVID-19 rate and using the WHO case definition had insufficient diagnostic accuracy to diagnose these cases. The lower burden in vulnerable people with HIV was unexpected but might reflect a shielding effect.
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Affiliation(s)
- Marta Vasylyev
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Astar Medical Center, Lviv, Ukraine
| | | | | | - Albert Groenendijk
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Iryna Ben
- Department of Infectious Diseases, Danylo Halytsky National Medical University, Lviv, Ukraine
| | | | | | - Wouter F W Bierman
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeroen J A van Kampen
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ferdinand W N M Wit
- Stichting HIV Monitoring, Amsterdam, The Netherlands
- Amsterdam UMC, Location University of Amsterdam, Global Health, Meibergdreef 9, Amsterdam, The Netherlands
| | - Peter Reiss
- Amsterdam UMC, Location University of Amsterdam, Global Health, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Global Health and Development, Paasheuvelweg 25, Amsterdam, The Netherlands
| | - Bart J A Rijnders
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Casper Rokx
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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Biddle J, Bonenfant G, Grijalva C, Zhu Y, Halasa N, Chappell J, Mellis A, Reed C, Talbot H, Zhou B, Rolfes M. Association of Symptoms and Viral Culture Positivity for SARS-CoV-2-Tennessee, April-July 2020. Influenza Other Respir Viruses 2024; 18:e13318. [PMID: 39031815 PMCID: PMC11190945 DOI: 10.1111/irv.13318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 07/22/2024] Open
Abstract
BACKGROUND Understanding how symptoms are associated with SARS-CoV-2 culture positivity is important for isolation and transmission control guidelines. METHODS Individuals acutely infected with SARS-CoV-2 in Tennessee and their household contacts were recruited into a prospective study. All participants self-collected nasal swabs daily for 14 days and completed symptom diaries from the day of illness onset through day 14 postenrollment. Nasal specimens were tested for SARS-CoV-2 using RT-qPCR. Positive specimens with cycle threshold values < 40 were sent to the Centers for Disease Control and Prevention (CDC) for viral culture. First, we modeled the association between symptoms and the risk of culture positivity using an age-adjusted generalized additive model (GAM) accounting for repeated measurements within participants and a symptom-day spline. Next, we investigated how timing of symptom resolution was associated with the timing of culture resolution. RESULTS In a GAM restricted to follow-up days after symptoms began, the odds of a specimen being culture positive was significantly increased on days when wheezing, loss of taste or smell, runny nose, nasal congestion, sore throat, fever, or any symptom were reported. For all symptoms except sore throat, it was more common for participants to have culture resolution before symptom resolution than for culture to resolve after or on the same day as symptom resolution. CONCLUSIONS Overall, symptomatic individuals were more likely to be SARS-CoV-2 viral culture positive. For most symptoms, culture positivity was more likely to end before symptoms resolved. However, a proportion of individuals remained culture positive after symptom resolved, across all symptoms.
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Affiliation(s)
- Jessica E. Biddle
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Gaston Bonenfant
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Carlos G. Grijalva
- Department of Health PolicyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Yuwei Zhu
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Natasha B. Halasa
- Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - James D. Chappell
- Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Alexandra Mellis
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Carrie Reed
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - H. Keipp Talbot
- Department of Health PolicyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Bin Zhou
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Melissa A. Rolfes
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
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9
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Jarju S, Wenlock RD, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA, Gaye H, Gaye B, Tunkara A, Kandeh S, Gomes M, Sylva EL, Toure F, Hornsby H, Lindsey BB, Nicklin MJ, Sayers JR, Sesay AK, Kucharski A, Hodgson D, Kampmann B, de Silva TI. High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia. Nat Commun 2024; 15:3814. [PMID: 38714680 PMCID: PMC11076623 DOI: 10.1038/s41467-024-48098-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study of 349 participants from 52 households in The Gambia between March 2021 and June 2022, with routine weekly SARS-CoV-2 RT-PCR and 6-monthly SARS-CoV-2 serology. Attack rates of 45% and 57% were seen during Delta and Omicron BA.1 waves respectively. Eighty-four percent of RT-PCR-positive infections were asymptomatic. Children under 5-years had a lower incidence of infection than 18-49-year-olds. One prior SARS-CoV-2 infection reduced infection risk during the Delta wave only, with immunity from ≥2 prior infections required to reduce the risk of infection with early Omicron lineage viruses. In an African population with high levels of infection-driven immunity and low vaccine coverage, we find high attack rates during SARS-CoV-2 waves, with a high proportion of asymptomatic infections and young children remaining relatively protected from infection.
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Affiliation(s)
- Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Rhys D Wenlock
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Madikoi Danso
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Dawda Jobe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Michelle Kumado
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Yusupha Jallow
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Mamlie Touray
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ebrima A Ceesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hoja Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Biran Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Abdoulie Tunkara
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Sheriff Kandeh
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Marie Gomes
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ellen Lena Sylva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Fatoumata Toure
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Benjamin B Lindsey
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Martin J Nicklin
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Jon R Sayers
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Abdul K Sesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Institute for International Health, Charité Universitätsmedizin, Berlin, Germany.
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK.
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK.
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Aboagye FT, Annison L, Hackman HK, Acquah ME, Ashong Y, Owusu-Frimpong I, Egyam BC, Annison S, Osei-Adjei G, Antwi-Baffour S. Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown. Adv Virol 2024; 2024:2993144. [PMID: 38584794 PMCID: PMC10997420 DOI: 10.1155/2024/2993144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/31/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown. Methods This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41-50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41-50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection. Conclusion There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.
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Affiliation(s)
- Frank T. Aboagye
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research–Water Research Institute, Accra, Ghana
| | - Lawrence Annison
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Henry Kwadwo Hackman
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Maame E. Acquah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Yvonne Ashong
- Department of Parasitology, Noguchi Memorial Institute of Medical Research, College of Medical Sciences, University of Ghana, Legon, Accra, Ghana
| | - Isaac Owusu-Frimpong
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research–Water Research Institute, Accra, Ghana
| | - Bill C. Egyam
- Department of Molecular Biology, MDS Lancet Laboratories Ghana Limited, East Legon, Accra, Ghana
| | - Sharon Annison
- Department of Epidemiology and Disease Control, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - George Osei-Adjei
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Samuel Antwi-Baffour
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
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11
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Townsley H, Gahir J, Russell TW, Greenwood D, Carr EJ, Dyke M, Adams L, Miah M, Clayton B, Smith C, Miranda M, Mears HV, Bailey C, Black JRM, Fowler AS, Crawford M, Wilkinson K, Hutchinson M, Harvey R, O’Reilly N, Kelly G, Goldstone R, Beale R, Papineni P, Corrah T, Gilson R, Caidan S, Nicod J, Gamblin S, Kassiotis G, Libri V, Williams B, Gandhi S, Kucharski AJ, Swanton C, Bauer DLV, Wall EC. COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history. PLoS One 2024; 19:e0294897. [PMID: 38512960 PMCID: PMC10956747 DOI: 10.1371/journal.pone.0294897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION NCT04750356.
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Affiliation(s)
- Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Joshua Gahir
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | - Matala Dyke
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Murad Miah
- The Francis Crick Institute, London, United Kingdom
| | | | - Callie Smith
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
| | - James R. M. Black
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | | | | | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, United Kingdom
| | - Richard Gilson
- Camden and North West London NHS Community Trust, London, United Kingdom
| | - Simon Caidan
- The Francis Crick Institute, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - George Kassiotis
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St Mary’s Hospital, Imperial College London, London, United Kingdom
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
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12
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Cohen C, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit J, Gómez-Olivé FX, Dawood FS, Mkhencele T, Tempia S. Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST-C community cohort study, South Africa, 2020-2021. BMC Infect Dis 2024; 24:336. [PMID: 38515050 PMCID: PMC10956206 DOI: 10.1186/s12879-024-09209-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. METHODS We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. RESULTS We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value <30 (vs >35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged <5 (aOR 6.7, 95%CI1.4-31.2) and 5-12 years (aOR 6.6 95%CI2.6-16.7)(vs 19-39) and Ct value <30 (aOR 4.5, 95%CI 1.3-15.5) and 30-35 (aOR 6.0, 95%CI 2.3-15.7)(vs >35). CONCLUSIONS Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness.
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Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Africa Health Research Institute, Mtubatuba, KwaZulu-Natal, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacques du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatimah S Dawood
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
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13
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Dall’Amico L, Kleynhans J, Gauvin L, Tizzoni M, Ozella L, Makhasi M, Wolter N, Language B, Wagner RG, Cohen C, Tempia S, Cattuto C. Estimating household contact matrices structure from easily collectable metadata. PLoS One 2024; 19:e0296810. [PMID: 38483886 PMCID: PMC10939291 DOI: 10.1371/journal.pone.0296810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 03/17/2024] Open
Abstract
Contact matrices are a commonly adopted data representation, used to develop compartmental models for epidemic spreading, accounting for the contact heterogeneities across age groups. Their estimation, however, is generally time and effort consuming and model-driven strategies to quantify the contacts are often needed. In this article we focus on household contact matrices, describing the contacts among the members of a family and develop a parametric model to describe them. This model combines demographic and easily quantifiable survey-based data and is tested on high resolution proximity data collected in two sites in South Africa. Given its simplicity and interpretability, we expect our method to be easily applied to other contexts as well and we identify relevant questions that need to be addressed during the data collection procedure.
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Affiliation(s)
| | - Jackie Kleynhans
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laetitia Gauvin
- ISI Foundation, Turin, Italy
- Institute for Research on sustainable Development, UMR215 PRODIG, Aubervilliers, France
| | - Michele Tizzoni
- ISI Foundation, Turin, Italy
- Department of Sociology and Social Research, University of Trento, Trento, Italy
| | | | - Mvuyo Makhasi
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Brigitte Language
- Unit for Environmental Science and Management, Climatology Research Group, North-West University, Potchefstroom, South Africa
| | - Ryan G. Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Agincourt, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ciro Cattuto
- ISI Foundation, Turin, Italy
- Department of Informatics, University of Turin, Turin, Italy
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14
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Höft MA, Burgers WA, Riou C. The immune response to SARS-CoV-2 in people with HIV. Cell Mol Immunol 2024; 21:184-196. [PMID: 37821620 PMCID: PMC10806256 DOI: 10.1038/s41423-023-01087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
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Affiliation(s)
- Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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15
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Harriman NW, Bassil DT, Farrell MT, Du Toit J, Gómez-Olivé Casas FX, Tollman SM, Berkman LF. Associations between cohort derived dementia and COVID-19 serological diagnosis among older Black adults in rural South Africa. Front Public Health 2024; 11:1304572. [PMID: 38249406 PMCID: PMC10796535 DOI: 10.3389/fpubh.2023.1304572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
Objectives This study investigates the association between cohort derived dementia and serologically confirmed SARS-CoV-2 infection, an underexplored phenomena in low-and middle-income countries. Examining this relationship in a rural South African community setting offers insights applicable to broader healthcare contexts. Methods Data were collected from Black South Africans in the Mpumalanga province who participated in the Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa. Cohort derived dementia was developed using a predictive model for consensus-based dementia diagnosis. Multinomial logistic regression models estimated the association between predicted dementia probability in 2018 and SARS-CoV-2 infection risk in 2021, controlling for demographics, socioeconomic status, and comorbidities. Results Fifty-two percent of the tested participants had serologically confirmed SARS-CoV-2 infections. In the fully adjusted model, cohort derived dementia was significantly associated with over twice the risk of serological diagnosis of COVID-19 (RRR = 2.12, p = 0.045). Conclusion Complying with COVID-19 prevention recommendations may be difficult for individuals with impaired cognitive functioning due to their symptoms. Results can inform community-based public health initiatives to reduce COVID-19 transmission among South Africa's rapidly aging population.
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Affiliation(s)
- Nigel Walsh Harriman
- Harvard Center for Population and Development Studies, Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, MA, United States
| | - Darina T. Bassil
- Harvard Center for Population and Development Studies, Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, MA, United States
| | - Meagan T. Farrell
- Harvard Center for Population and Development Studies, Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, MA, United States
| | - Jacques Du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - F. Xavier Gómez-Olivé Casas
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Stephen M. Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Lisa F. Berkman
- Harvard Center for Population and Development Studies, Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, MA, United States
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16
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Cohen C, Kleynhans J, Moyes J, McMorrow ML, Treurnicht FK, Hellferscee O, Wolter N, Martinson NA, Kahn K, Lebina L, Mothlaoleng K, Wafawanaka F, Gómez-Olivé FX, Mkhencele T, Mathunjwa A, Carrim M, Mathee A, Piketh S, Language B, von Gottberg A, Tempia S. Incidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018. Nat Commun 2024; 15:116. [PMID: 38167333 PMCID: PMC10761814 DOI: 10.1038/s41467-023-44275-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Data on respiratory syncytial virus (RSV) incidence and household transmission are limited. To describe RSV incidence and transmission, we conducted a prospective cohort study in rural and urban communities in South Africa over two seasons during 2017-2018. Nasopharyngeal swabs were collected twice-weekly for 10 months annually and tested for RSV using PCR. We tested 81,430 samples from 1,116 participants in 225 households (follow-up 90%). 32% (359/1116) of individuals had ≥1 RSV infection; 10% (37/359) had repeat infection during the same season, 33% (132/396) of infections were symptomatic, and 2% (9/396) sought medical care. Incidence was 47.2 infections/100 person-years and highest in children <5 years (78.3). Symptoms were commonest in individuals aged <12 and ≥65 years. Individuals 1-12 years accounted for 55% (134/242) of index cases. Household cumulative infection risk was 11%. On multivariable analysis, index cases with ≥2 symptoms and shedding duration >10 days were more likely to transmit; household contacts aged 1-4 years vs. ≥65 years were more likely to acquire infection. Within two South African communities, RSV attack rate was high, and most infections asymptomatic. Young children were more likely to introduce RSV into the home, and to be infected. Future studies should examine whether vaccines targeting children aged <12 years could reduce community transmission.
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Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Coronavirus and Other Respiratory Viruses Division (proposed), Centers for Disease Control and Prevention, Atlanta, GA, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, MD, USA
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Katlego Mothlaoleng
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Mathee
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa
| | - Stuart Piketh
- Unit for Environmental Science and Management, Climatology Research Group, North-West University, Potchefstroom, South Africa
| | - Brigitte Language
- Unit for Environmental Science and Management, Climatology Research Group, North-West University, Potchefstroom, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- MassGenics, Duluth, GA, USA
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17
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Chansaenroj J, Suntronwong N, Kanokudom S, Assawakosri S, Vichaiwattana P, Klinfueng S, Wongsrisang L, Thongmee T, Aeemjinda R, Khanarat N, Srimuan D, Thatsanathorn T, Yorsaeng R, Katanyutanon A, Thanasopon W, Bhunyakitikorn W, Sonthichai C, Angsuwatcharakorn P, Withaksabut W, Wanlapakorn N, Sudhinaraset N, Poovorawan Y. Seroprevalence of SARS-CoV-2 anti-nucleocapsid total Ig, anti-RBD IgG antibodies, and infection in Thailand: a cross-sectional survey from October 2022 to January 2023. Sci Rep 2023; 13:15595. [PMID: 37730917 PMCID: PMC10511501 DOI: 10.1038/s41598-023-42754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023] Open
Abstract
Seroprevalence studies on SARS-CoV-2 are essential for estimating actual prevalence rates of infection and vaccination in communities. This study evaluated infection rates based on total anti-nucleocapsid immunoglobulin (N) and/or infection history. We determined the seroprevalence of anti-receptor binding domain (RBD) antibodies across age groups. A cross-sectional study was conducted in Chonburi province, Thailand, between October 2022 and January 2023. Participants included newborns to adults aged up to 80 years. All serum samples were tested for anti-N total Ig and anti-RBD IgG. The interviewer-administered questionnaires queried information on infection history and vaccination records. Of 1459 participants enrolled from the Chonburi population, ~ 72.4% were infected. The number of infections was higher in children aged < 5 years, with evidence of SARS-CoV-2 infection decreasing significantly with increasing age. There were no significant differences based on sex or occupation. Overall, ~ 97.4% of participants had an immune response against SARS-CoV-2. The anti-RBD IgG seroprevalence rate was lower in younger vaccinated individuals and was slightly increased to 100% seropositivity at ages > 60 years. Our findings will help predict the exact number of infections and the seroprevalence of SARS-CoV-2 in the Thai population. Furthermore, this information is essential for public health decision-making and the development of vaccination strategies.
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Affiliation(s)
- Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sitthichai Kanokudom
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Osteroarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Suvichada Assawakosri
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Osteroarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Preeyaporn Vichaiwattana
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Lakana Wongsrisang
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanunrat Thongmee
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ratchadawan Aeemjinda
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nongkanok Khanarat
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Donchida Srimuan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thaksaporn Thatsanathorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ritthideach Yorsaeng
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Apirat Katanyutanon
- Chonburi Provincial Public Health Office, Bansuan, Mueang Chonburi, 20000, Chonburi, Thailand
| | - Wichai Thanasopon
- Chonburi Provincial Public Health Office, Bansuan, Mueang Chonburi, 20000, Chonburi, Thailand
| | - Wichan Bhunyakitikorn
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Chaninan Sonthichai
- Vaccine Protection, Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Piyada Angsuwatcharakorn
- Vaccine Protection, Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Withak Withaksabut
- Chonburi Provincial Public Health Office, Bansuan, Mueang Chonburi, 20000, Chonburi, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Natthinee Sudhinaraset
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, 10300, Thailand.
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18
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Bullen M, Heriot GS, Jamrozik E. Herd immunity, vaccination and moral obligation. JOURNAL OF MEDICAL ETHICS 2023; 49:636-641. [PMID: 37277175 PMCID: PMC10511978 DOI: 10.1136/jme-2022-108485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/25/2022] [Indexed: 06/07/2023]
Abstract
The public health benefits of herd immunity are often used as the justification for coercive vaccine policies. Yet, 'herd immunity' as a term has multiple referents, which can result in ambiguity, including regarding its role in ethical arguments. The term 'herd immunity' can refer to (1) the herd immunity threshold, at which models predict the decline of an epidemic; (2) the percentage of a population with immunity, whether it exceeds a given threshold or not; and/or (3) the indirect benefit afforded by collective immunity to those who are less immune. Moreover, the accumulation of immune individuals in a population can lead to two different outcomes: elimination (for measles, smallpox, etc) or endemic equilibrium (for COVID-19, influenza, etc). We argue that the strength of a moral obligation for individuals to contribute to herd immunity through vaccination, and by extension the acceptability of coercion, will depend on how 'herd immunity' is interpreted as well as facts about a given disease or vaccine. Among other things, not all uses of 'herd immunity' are equally valid for all pathogens. The optimal conditions for herd immunity threshold effects, as illustrated by measles, notably do not apply to the many pathogens for which reinfections are ubiquitous (due to waning immunity and/or antigenic variation). For such pathogens, including SARS-CoV-2, mass vaccination can only be expected to delay rather than prevent new infections, in which case the obligation to contribute to herd immunity is much weaker, and coercive policies less justifiable.
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Affiliation(s)
- Matthew Bullen
- Box Hill Hospital, Eastern Health, Melbourne, Victoria, Australia
| | - George S Heriot
- Department of Infectious Diseases, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
| | - Euzebiusz Jamrozik
- Ethox Centre and Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Royal Melbourne Hospital Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
- Monash Bioethics Centre, Monash University, Melbourne, Victoria, Australia
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19
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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294416. [PMID: 37662226 PMCID: PMC10473782 DOI: 10.1101/2023.08.22.23294416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. Results We enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive ≥21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR-positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation. Conclusions In this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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Dias Assis BR, Gomes IP, de Castro JT, Rivelli GG, de Castro NS, Gomez-Mendoza DP, Bagno FF, Hojo-Souza NS, Chaves Maia AL, Lages EB, da Fonseca FG, Ribeiro Teixeira SM, Fernandes AP, Gazzinelli RT, Castro Goulart GA. Quality attributes of CTVad1, a nanoemulsified adjuvant for phase I clinical trial of SpiN COVID-19 vaccine. Nanomedicine (Lond) 2023; 18:1175-1194. [PMID: 37712604 DOI: 10.2217/nnm-2023-0122] [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] [Indexed: 09/16/2023] Open
Abstract
Aim: To develop, characterize and evaluate an oil/water nanoemulsion with squalene (CTVad1) to be approved as an adjuvant for the SpiN COVID-19 vaccine clinical trials. Materials & methods: Critical process parameters (CPPs) of CTVad1 were standardized to meet the critical quality attributes (CQAs) of an adjuvant for human use. CTVad1 and the SpiN-CTVad1 vaccine were submitted to physicochemical, stability, in vitro and in vivo studies. Results & conclusion: All CQAs were met in the CTVad1 production process. SpiN- CTVad1 met CQAs and induced high levels of antibodies and specific cellular responses in in vivo studies. These results represented a critical step in the process developed to meet regulatory requirements for the SpiN COVID-19 vaccine clinical trial.
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Affiliation(s)
- Bruna Rodrigues Dias Assis
- Department of Pharmaceuticals, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Isabela Pereira Gomes
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Júlia Teixeira de Castro
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Graziella Gomes Rivelli
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Natália Salazar de Castro
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Diana Paola Gomez-Mendoza
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Flávia Fonseca Bagno
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Natália Satchiko Hojo-Souza
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz-Minas, Belo Horizonte, MG, 30190-002, Brazil
| | - Ana Luiza Chaves Maia
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Eduardo Burgarelli Lages
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
| | - Flávio Guimaraes da Fonseca
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Santuza Maria Ribeiro Teixeira
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
- Department of Biochemistry & Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Ana Paula Fernandes
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
- Department of Clinical & Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Ricardo Tostes Gazzinelli
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz-Minas, Belo Horizonte, MG, 30190-002, Brazil
- Department of Biochemistry & Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Gisele Assis Castro Goulart
- Department of Pharmaceuticals, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Centro de Tecnologia de Vacinas da Universidade Federal de Minas Gerais, Belo Horizonte, Belo Horizonte, MG, 31310-260, Brazil
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21
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Sun K, Loria V, Aparicio A, Porras C, Vanegas JC, Zúñiga M, Morera M, Avila C, Abdelnour A, Gail MH, Pfeiffer R, Cohen JI, Burbelo PD, Abed MA, Viboud C, Hildesheim A, Herrero R, Prevots DR. Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica. COMMUNICATIONS MEDICINE 2023; 3:102. [PMID: 37481623 PMCID: PMC10363136 DOI: 10.1038/s43856-023-00325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/21/2023] [Indexed: 07/24/2023] Open
Abstract
INTRODUCTION Variability in household secondary attack rates and transmission risks factors of SARS-CoV-2 remain poorly understood. METHODS We conducted a household transmission study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. We fitted a chain binomial model to the serologic data, to account for exogenous community infection risk and potential multi-generational transmissions within the household. RESULTS Overall seroprevalence was 53% (95% confidence interval (CI) 48-58%) among household contacts. The estimated household secondary attack rate is 34% (95% CI 5-75%). Mask wearing by the index case is associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and not sharing bedroom with the index case is associated with the risk reduction of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates is highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. CONCLUSIONS Modeling analysis suggests that behavioral factors are important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Viviana Loria
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Amada Aparicio
- Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Juan Carlos Vanegas
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Michael Zúñiga
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Melvin Morera
- Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Carlos Avila
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | | | - Mitchell H Gail
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ruth Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Mehdi A Abed
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA.
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Kleynhans J, Dall'Amico L, Gauvin L, Tizzoni M, Maloma L, Walaza S, Martinson NA, von Gottberg A, Wolter N, Makhasi M, Cohen C, Cattuto C, Tempia S. Association of close-range contact patterns with SARS-CoV-2: a household transmission study. eLife 2023; 12:e84753. [PMID: 37461328 DOI: 10.7554/elife.84753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Background Households are an important location for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, especially during periods when travel and work was restricted to essential services. We aimed to assess the association of close-range contact patterns with SARS-CoV-2 transmission. Methods We deployed proximity sensors for two weeks to measure face-to-face interactions between household members after SARS-CoV-2 was identified in the household, in South Africa, 2020-2021. We calculated the duration, frequency, and average duration of close-range proximity events with SARS-CoV-2 index cases. We assessed the association of contact parameters with SARS-CoV-2 transmission using mixed effects logistic regression accounting for index and household member characteristics. Results We included 340 individuals (88 SARS-CoV-2 index cases and 252 household members). On multivariable analysis, factors associated with SARS-CoV-2 acquisition were index cases with minimum Ct value <30 (aOR 16.8 95% CI 3.1-93.1) vs >35, and female contacts (aOR 2.5 95% CI 1.3-5.0). No contact parameters were associated with acquisition (aOR 1.0-1.1) for any of the duration, frequency, cumulative time in contact, or average duration parameters. Conclusions We did not find an association between close-range proximity events and SARS-CoV-2 household transmission. Our findings may be due to study limitations, that droplet-mediated transmission during close-proximity contacts plays a smaller role than airborne transmission of SARS-CoV-2 in the household, or due to high contact rates in households. Funding Wellcome Trust (Grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth, and Development Office, United Kingdom.
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Affiliation(s)
- Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Laetitia Gauvin
- ISI Foundation, Turin, Italy
- Institute for Research on Sustainable Development, Aubervilliers, France
| | - Michele Tizzoni
- ISI Foundation, Turin, Italy
- Department of Sociology and Social Research, University of Trento, Trento, Italy
| | - Lucia Maloma
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, United States
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mvuyo Makhasi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ciro Cattuto
- ISI Foundation, Turin, Italy
- Department of Informatics, University of Turin, Turin, Italy
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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23
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Kaboré NF, Ouédraogo S, Mamguem AK, Traoré IT, Kania D, Badolo H, Sanou G, Koné A, Yara M, Kagoné T, Ouédraogo E, Konaté B, Médah R, de Rekeneire N, Poda A, Diendéré AE, Ouédraogo B, Billa O, Paradis G, Dabakuyo-Yonli TS, Tinto H. Incidence rate and predictors of COVID-19 in the two largest cities of Burkina Faso - prospective cohort study in 2021 (ANRS-COV13). BMC Infect Dis 2023; 23:394. [PMID: 37308819 DOI: 10.1186/s12879-023-08361-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Early data on COVID-19 (based primarily on PCR testing) indicated a low burden in Sub-Saharan Africa. To better understand this, this study aimed to estimate the incidence rate and identify predictors of SARS-CoV-2 seroconversion in the two largest cities of Burkina Faso. This study is part of the EmulCOVID-19 project (ANRS-COV13). METHODS Our study utilized the WHO Unity protocol for cohort sero-epidemiological studies of COVID-19 in general population. We conducted random sampling stratified by age group and sex. Individuals aged 10 years and older in the cities of Ouagadougou and Bobo-Dioulasso, Burkina Faso were included and surveyed at 4 time points, each 21 days apart, from March 3 to May 15, 2021. WANTAI SARS-CoV-2 Ab ELISA serological tests were used to detect total antibodies (IgM, IgG) in serum. Predictors were investigated using Cox proportional hazards regression. RESULTS We analyzed the data from 1399 participants (1051 in Ouagadougou, 348 in Bobo-Dioulasso) who were SARS-CoV-2 seronegative at baseline and had at least one follow-up visit. The incidence rate of SARS-CoV-2 seroconversion was 14.3 cases [95%CI 13.3-15.4] per 100 person-weeks. The incidence rate was almost three times higher in Ouagadougou than in Bobo-Dioulasso (Incidence rate ratio: IRR = 2.7 [2.2-3.2], p < 0.001). The highest incidence rate was reported among women aged 19-59 years in Ouagadougou (22.8 cases [19.6-26.4] per 100 person-weeks) and the lowest among participants aged 60 years and over in Bobo-Dioulasso, 6.3 cases [4.6-8.6] per 100 person-weeks. Multivariable analysis showed that participants aged 19 years and older were almost twice as likely to seroconvert during the study period compared with those aged 10 to 18 years (Hazard ratio: HR = 1.7 [1.3-2.3], p < 0.001). Those aged 10-18 years exhibited more asymptomatic forms than those aged 19 years and older, among those who achieved seroconversion (72.9% vs. 40.4%, p < 0.001). CONCLUSION The spread of COVID-19 is more rapid in adults and in large cities. Strategies to control this pandemic in Burkina Faso, must take this into account. Adults living in large cities should be the priority targets for vaccination efforts against COVID-19.
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Affiliation(s)
- Nongodo Firmin Kaboré
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso.
| | - Samiratou Ouédraogo
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
- Institut National de Santé Publique du Québec (INSPQ), Montréal, Québec, Canada
- The Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Ariane Kamga Mamguem
- Epidemiology and Quality of Life Research Unit, INSERM U1231, Georges Francois Leclerc Centre - UNICANCER, Dijon, France
| | - Isidore Tiandiogo Traoré
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Institut Supérieur des Sciences de la Santé (INSSA), Université Nazi Boni (UNB), Bobo Dioulasso, Burkina Faso
| | - Dramane Kania
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Hermann Badolo
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Guillaume Sanou
- Centre National de Recherche et de Formation sur le Paludisme, Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Amariane Koné
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Mimbouré Yara
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Thérèse Kagoné
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Esperance Ouédraogo
- Département de médicine, pharmacopée traditionnelle et pharmacie, Institut de Recherche en Sciences de la Santé (IRSS) - Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
| | - Blahima Konaté
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Département de Socio-Économie et d'Anthropologie du Développement (DSEAD), Institut des Sciences des Sociétés (INSS) - Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
| | - Rachel Médah
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | | | - Armel Poda
- Institut Supérieur des Sciences de la Santé (INSSA), Université Nazi Boni (UNB), Bobo Dioulasso, Burkina Faso
- Service des maladies infectieuses, Centre Hospitalier Universitaire Sourô Sanou, Bobo Dioulasso, Burkina Faso
| | | | - Boukary Ouédraogo
- Direction des systèmes d'information en santé (DSIS), ministère de la Santé et de l'Hygiène Publique, Ouagadougou, Burkina Faso
| | - Oumar Billa
- Epidemiology and Quality of Life Research Unit, INSERM U1231, Georges Francois Leclerc Centre - UNICANCER, Dijon, France
| | - Gilles Paradis
- Institut National de Santé Publique du Québec (INSPQ), Montréal, Québec, Canada
- The Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | | | - Halidou Tinto
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Institut de Recherche en Sciences de la Santé (IRSS) - Unité de Recherche Clinique de Nanoro, Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
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24
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Bannick MS, Gao F, Brown ER, Janes HE. Retrospective, Observational Studies for Estimating Vaccine Effects on the Secondary Attack Rate of SARS-CoV-2. Am J Epidemiol 2023; 192:1016-1028. [PMID: 36883907 PMCID: PMC10505422 DOI: 10.1093/aje/kwad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/21/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on retrospective, observational studies. Specifically, an increasing number of studies are evaluating vaccine effectiveness against the secondary attack rate of SARS-CoV-2 using data available in existing health-care databases or contact-tracing databases. Since these types of databases were designed for clinical diagnosis or management of COVID-19, they are limited in their ability to provide accurate information on infection, infection timing, and transmission events. We highlight challenges with using existing databases to identify transmission units and confirm potential SARS-CoV-2 transmission events. We discuss the impact of common diagnostic testing strategies, including event-prompted and infrequent testing, and illustrate their potential biases in estimating vaccine effectiveness against the secondary attack rate of SARS-CoV-2. We articulate the need for prospective observational studies of vaccine effectiveness against the SARS-CoV-2 secondary attack rate, and we provide design and reporting considerations for studies using retrospective databases.
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Affiliation(s)
- Marlena S Bannick
- Correspondence to Marlena Bannick, Department of Biostatistics, Hans Rosling Center for Population Health, Box 357232, University of Washington, Seattle, WA 98195 (e-mail: )
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Sabbatucci M, Vitiello A, Clemente S, Zovi A, Boccellino M, Ferrara F, Cimmino C, Langella R, Ponzo A, Stefanelli P, Rezza G. Omicron variant evolution on vaccines and monoclonal antibodies. Inflammopharmacology 2023:10.1007/s10787-023-01253-6. [PMID: 37204696 DOI: 10.1007/s10787-023-01253-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 responsible for the global COVID-19 pandemic has caused almost 760 million confirmed cases and 7 million deaths worldwide, as of end-February 2023. Since the beginning of the first COVID-19 case, several virus variants have emerged: Alpha (B1.1.7), Beta (B135.1), Gamma (P.1), Delta (B.1.617.2) and then Omicron (B.1.1.529) and its sublineages. All variants have diversified in transmissibility, virulence, and pathogenicity. All the newly emerging SARS-CoV-2 variants appear to contain some similar mutations associated with greater "evasiveness" of the virus to immune defences. From early 2022 onward, several Omicron subvariants named BA.1, BA.2, BA.3, BA.4, and BA.5, with comparable mutation forms, have followed. After the wave of contagions caused by Omicron BA.5, a new Indian variant named Centaurus BA.2.75 and its new subvariant BA.2.75.2, a second-generation evolution of the Omicron variant BA.2, have recently been identified. From early evidence, it appears that this new variant has higher affinity for the cell entry receptor ACE-2, making it potentially able to spread very fast. According to the latest studies, the BA.2.75.2 variant may be able to evade more antibodies in the bloodstream generated by vaccination or previous infection, and it may be more resistant to antiviral and monoclonal antibody drug treatments. In this manuscript, the authors highlight and describe the latest evidences and critical issues have emerged on the new SARS-CoV-2 variants.
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Affiliation(s)
- Michela Sabbatucci
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Antonio Vitiello
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Salvatore Clemente
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Andrea Zovi
- Ministry of Health, Directorate General of Hygiene, Food Safety and Nutrition, Viale Giorgio Ribotta 5, 00144, Rome, Italy.
| | | | - Francesco Ferrara
- Pharmaceutical Department, Local Health Unit Napoli 3 Sud, Dell'amicizia Street 22, 80035, Nola, Italy
| | - Carla Cimmino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Roberto Langella
- Department of Pharmaceutics, Agency for Health Protection of the Metropolitan Area of Milan, Milan, Italy
| | | | - Paola Stefanelli
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giovanni Rezza
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
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Zhu Y, Xia Y, Pickering J, Bowen AC, Short KR. The role of children in transmission of SARS-CoV-2 variants of concern within households: an updated systematic review and meta-analysis, as at 30 June 2022. Euro Surveill 2023; 28:2200624. [PMID: 37140450 PMCID: PMC10161681 DOI: 10.2807/1560-7917.es.2023.28.18.2200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/17/2023] [Indexed: 05/05/2023] Open
Abstract
BackgroundMeta-analyses and single-site studies have established that children are less infectious than adults within a household when positive for ancestral SARS-CoV-2. In addition, children appear less susceptible to infection when exposed to ancestral SARS-CoV-2 within a household. The emergence of SARS-CoV-2 variants of concern (VOC) has been associated with an increased number of paediatric infections worldwide. However, the role of children in the household transmission of VOC, relative to the ancestral virus, remains unclear.AimWe aimed to evaluate children's role in household transmission of SARS-CoV-2 VOC.MethodsWe perform a meta-analysis of the role of children in household transmission of both ancestral SARS-CoV-2 and SARS-CoV-2 VOC.ResultsUnlike with the ancestral virus, children infected with VOC spread SARS-CoV-2 to an equivalent number of household contacts as infected adults and were equally as likely to acquire SARS-CoV-2 VOC from an infected family member. Interestingly, the same was observed when unvaccinated children exposed to VOC were compared with unvaccinated adults exposed to VOC.ConclusionsThese data suggest that the emergence of VOC was associated with a fundamental shift in the epidemiology of SARS-CoV-2. It is unlikely that this is solely the result of age-dependent differences in vaccination during the VOC period and may instead reflect virus evolution over the course of the pandemic.
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Affiliation(s)
- Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Wesfarmer's Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Perth, Australia
- These authors contributed equally to this manuscript
| | - Yao Xia
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- These authors contributed equally to this manuscript
| | - Janessa Pickering
- Wesfarmer's Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Perth, Australia
| | - Asha C Bowen
- Wesfarmer's Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Perth, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Perth, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
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Ukwishaka J, Ndayishimiye Y, Destine E, Danwang C, Kirakoya-Samadoulougou F. Global prevalence of coronavirus disease 2019 reinfection: a systematic review and meta-analysis. BMC Public Health 2023; 23:778. [PMID: 37118717 PMCID: PMC10140730 DOI: 10.1186/s12889-023-15626-7] [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: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged with a high transmissibility rate and resulted in numerous negative impacts on global life. Preventive measures such as face masks, social distancing, and vaccination helped control the pandemic. Nonetheless, the emergence of SARS-CoV-2 variants, such as Omega and Delta, as well as coronavirus disease 2019 (COVID-19) reinfection, raise additional concerns. Therefore, this study aimed to determine the overall prevalence of reinfection on global and regional scales. METHODS A systematic search was conducted across three databases, PubMed, Scopus, and ProQuest Central, including all articles pertaining to COVID-19 reinfection without language restriction. After critical appraisal and qualitative synthesis of the identified relevant articles, a meta-analysis considering random effects was used to pool the studies. RESULTS We included 52 studies conducted between 2019 and 2022, with a total sample size of 3,623,655 patients. The overall prevalence of COVID-19 reinfection was 4.2% (95% confidence interval [CI]: 3.7-4.8%; n = 52), with high heterogeneity between studies. Africa had the highest prevalence of 4.7% (95% CI: 1.9-7.5%; n = 3), whereas Oceania and America had lower estimates of 0.3% (95% CI: 0.2-0.4%; n = 1) and 1% (95% CI: 0.8-1.3%; n = 7), respectively. The prevalence of reinfection in Europe and Asia was 1.2% (95% CI: 0.8-1.5%; n = 8) and 3.8% (95% CI: 3.4-4.3%; n = 43), respectively. Studies that used a combined type of specimen had the highest prevalence of 7.6% (95% CI: 5.8-9.5%; n = 15) compared with those that used oropharyngeal or nasopharyngeal swabs only that had lower estimates of 6.7% (95% CI: 4.8-8.5%; n = 8), and 3.4% (95% CI: 2.8-4.0%; n = 12) respectively. CONCLUSION COVID-19 reinfection occurs with varying prevalence worldwide, with the highest occurring in Africa. Therefore, preventive measures, including vaccination, should be emphasized to ensure control of the pandemic.
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Affiliation(s)
- Joyeuse Ukwishaka
- Maternal Child and Community Health Division, Rwanda Bio-Medical Center, Kigali, Rwanda.
- IntraHealth International, Kigali, Rwanda.
- Centre de Recherche en Epidémiologie, Biostatistique et Recherche Clinique, Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.
| | - Yves Ndayishimiye
- Centre de Recherche en Epidémiologie, Biostatistique et Recherche Clinique, Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | - Esmeralda Destine
- Centre de Recherche en Epidémiologie, Biostatistique et Recherche Clinique, Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Fati Kirakoya-Samadoulougou
- Centre de Recherche en Epidémiologie, Biostatistique et Recherche Clinique, Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
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Zheng Q, Bao C, Ji Y, Li P, Ma Z, Wang X, Meng Q, Pan Q. Treating SARS-CoV-2 Omicron variant infection by molnupiravir for pandemic mitigation and living with the virus: a mathematical modeling study. Sci Rep 2023; 13:5474. [PMID: 37016035 PMCID: PMC10071263 DOI: 10.1038/s41598-023-32619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/30/2023] [Indexed: 04/06/2023] Open
Abstract
Treating severe COVID-19 patients and controlling the spread of SARS-CoV-2 are concurrently important in mitigating the pandemic. Classically, antiviral drugs are primarily developed for treating hospitalized COVID-19 patients with severe diseases to reduce morbidity and/or mortality, which have limited effects on limiting pandemic spread. In this study, we simulated the expanded applications of oral antiviral drugs such as molnupiravir to mitigate the pandemic by treating nonhospitalized COVID-19 cases. We developed a compartmental mathematical model to simulate the effects of molnupiravir treatment assuming various scenarios in the Omicron variant dominated settings in Denmark, the United Kingdom and Germany. We found that treating nonhospitalized cases can limit Omicron spread. This indirectly reduces the burden of hospitalization and patient death. The effectiveness of this approach depends on the intrinsic nature of the antiviral drug and the strategies of implementation. Hypothetically, if resuming pre-pandemic social contact pattern, extensive application of molnupiravir treatment would dramatically (but not completely) mitigate the COVID-19 burden, and thus there remains lifetime cost of living with the virus.
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Affiliation(s)
- Qinyue Zheng
- School of International Affairs and Public Administration, Ocean University of China, Qingdao, China
- School of Management, Shandong Key Laboratory of Social Supernetwork Computation and Decision Simulation, Shandong University, Jinan, China
| | - Chunbing Bao
- School of Management, Shandong Key Laboratory of Social Supernetwork Computation and Decision Simulation, Shandong University, Jinan, China
| | - Yunpeng Ji
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
- Department of Genetics, Inner Mongolian Maternal and Child Care Hospital, Hohhot, Inner Mongolian, China
| | - Pengfei Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Zhongren Ma
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xinwei Wang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial, Equipment, Dalian University of Technology, Dalian, China
| | - Qingchun Meng
- School of Management, Shandong Key Laboratory of Social Supernetwork Computation and Decision Simulation, Shandong University, Jinan, China
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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29
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van Tonder AJ, McCullagh F, McKeand H, Thaw S, Bellis K, Raisen C, Lay L, Aggarwal D, Holmes M, Parkhill J, Harrison EM, Kucharski A, Conlan A. Colonization and transmission of Staphylococcus aureus in schools: a citizen science project. Microb Genom 2023; 9:mgen000993. [PMID: 37074324 PMCID: PMC10210949 DOI: 10.1099/mgen.0.000993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/22/2023] [Indexed: 04/20/2023] Open
Abstract
Aggregation of children in schools has been established to be a key driver of transmission of infectious diseases. Mathematical models of transmission used to predict the impact of control measures, such as vaccination and testing, commonly depend on self-reported contact data. However, the link between self-reported social contacts and pathogen transmission has not been well described. To address this, we used Staphylococcus aureus as a model organism to track transmission within two secondary schools in England and test for associations between self-reported social contacts, test positivity and the bacterial strain collected from the same students. Students filled out a social contact survey and their S. aureus colonization status was ascertained through self-administered swabs from which isolates were sequenced. Isolates from the local community were also sequenced to assess the representativeness of school isolates. A low frequency of genome-linked transmission precluded a formal analysis of links between genomic and social networks, suggesting that S. aureus transmission within schools is too rare to make it a viable tool for this purpose. Whilst we found no evidence that schools are an important route of transmission, increased colonization rates found within schools imply that school-age children may be an important source of community transmission.
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Affiliation(s)
| | | | | | - Sue Thaw
- St Bede's Inter-Church School, Cambridge, UK
| | - Katie Bellis
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Liz Lay
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Dinesh Aggarwal
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M. Harrison
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Andrew Conlan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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30
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Cohen C, Pulliam J. COVID-19 infection, reinfection, and the transition to endemicity. Lancet 2023; 401:798-800. [PMID: 36930672 PMCID: PMC9934854 DOI: 10.1016/s0140-6736(22)02634-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/20/2022] [Indexed: 02/18/2023]
Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg 2193, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Juliet Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
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31
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Turbett SE, Tomkins-Tinch CH, Anahtar MN, Dugdale CM, Hyle EP, Shenoy ES, Shaw B, Egbuonu K, Bowman KA, Zachary KC, Adams GC, Hooper DC, Ryan ET, LaRocque RC, Bassett IV, Triant VA, Siddle KJ, Rosenberg E, Sabeti PC, Schaffner SF, MacInnis BL, Lemieux JE, Charles RC. Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study. Clin Infect Dis 2023; 76:850-860. [PMID: 36268576 PMCID: PMC9619827 DOI: 10.1093/cid/ciac830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/06/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection related to initial infection. We aimed to evaluate the characteristics of SARS-CoV-2 reinfection and persistent RNA detection using independent genomic, clinical, and laboratory assessments. METHODS All individuals at a large academic medical center who underwent a SARS-CoV-2 nucleic acid amplification test (NAAT) ≥45 days after an initial positive test, with both tests between 14 March and 30 December 2020, were analyzed for potential reinfection. Inclusion criteria required having ≥2 positive NAATs collected ≥45 days apart with a cycle threshold (Ct) value <35 at repeat testing. For each included subject, likelihood of reinfection was assessed by viral genomic analysis of all available specimens with a Ct value <35, structured Ct trajectory criteria, and case-by-case review by infectious diseases physicians. RESULTS Among 1569 individuals with repeat SARS-CoV-2 testing ≥45 days after an initial positive NAAT, 65 (4%) met cohort inclusion criteria. Viral genomic analysis characterized mutations present and was successful for 14/65 (22%) subjects. Six subjects had genomically supported reinfection, and 8 subjects had genomically supported persistent RNA detection. Compared to viral genomic analysis, clinical and laboratory assessments correctly distinguished reinfection from persistent RNA detection in 12/14 (86%) subjects but missed 2/6 (33%) genomically supported reinfections. CONCLUSIONS Despite good overall concordance with viral genomic analysis, clinical and Ct value-based assessments failed to identify 33% of genomically supported reinfections. Scaling-up genomic analysis for clinical use would improve detection of SARS-CoV-2 reinfections.
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Affiliation(s)
- Sarah E Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Caitlin M Dugdale
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily P Hyle
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Erica S Shenoy
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bennett Shaw
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, USA
| | | | - Kathryn A Bowman
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Kimon C Zachary
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gordon C Adams
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - David C Hooper
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ingrid V Bassett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Virginia A Triant
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Katherine J Siddle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Harvard University, Boston, Massachusetts, USA
| | - Stephen F Schaffner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jacob E Lemieux
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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32
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Moolla MS, Maponga TG, Moolla H, Kollenberg E, Anie S, Moolla A, Moodley D, Lalla U, Allwood BW, Schrueder N, Preiser W, Koegelenberg CFN, Parker A. A tale of two waves: characteristics and outcomes of COVID-19 admissions during the Omicron-driven fourth wave in Cape Town, South Africa, and implications for the future. IJID REGIONS 2023; 6:42-47. [PMID: 36448029 PMCID: PMC9684091 DOI: 10.1016/j.ijregi.2022.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Objectives The aim of this study was to describe the pattern of admissions during the fourth wave of COVID-19 in order to inform future public health policies. Methods This was a retrospective descriptive study of an early cohort of all adult patients with SARS-CoV-2 infection admitted to a tertiary hospital in Cape Town, South Africa, at the start of the country's fourth wave. This was compared with an early cohort from the first wave at the same institution. Results In total, 121 SARS-CoV-2-positive admissions from the fourth wave were included. Thirty-one (25.6%) patients had COVID-19 pneumonia, while 90 (74.4%) had incidental SARS-CoV-2 infection. (In the first wave all 116 patients had COVID-19 pneumonia.) Thirty-two (26.4%) patients self-reported complete or partial COVID-19 vaccination, of whom 12 (37.5%) were admitted with COVID-19 pneumonia. Compared with the first wave, there were fewer intensive- or high-care admissions (18/121 [14.9%] vs 42/116 [36.2%]; p < 0.001) and mortality was lower (12/121 [9.9%] vs 31/116 [26.7%]; p = 0.001). Conclusion Admissions to the COVID-19 wards during the fourth wave primarily included patients with incidental SARS-CoV-2 infection. There was a reduction in the need for critical care and in-hospital mortality. This changing epidemiology of COVID-19 admissions may be attributed to a combination of natural and/or vaccination-acquired immunity.
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Affiliation(s)
- Muhammad Saadiq Moolla
- Division of Pulmonology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa,Correspondence: Muhammad Saadiq Moolla, Room 3118, 3rd Floor Clinical Building, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Francie van Zijl Drive, Tygerberg 7505, Cape Town, South Africa
| | - Tongai Gibson Maponga
- Division of Medical Virology, University of Stellenbosch and National Health Laboratory Service, Cape Town, South Africa
| | - Haroon Moolla
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Eve Kollenberg
- Division of General Medicine, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Samantha Anie
- Division of General Medicine, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Aisha Moolla
- SAMRC/Wits Centre for Health Economics and Decision Science — PRICELESS SA, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Desiree Moodley
- Division of General Medicine, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Usha Lalla
- Division of Pulmonology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Brian W Allwood
- Division of Pulmonology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Neshaad Schrueder
- Division of General Medicine, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, University of Stellenbosch and National Health Laboratory Service, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Coenraad FN Koegelenberg
- Division of Pulmonology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Arifa Parker
- Division of General Medicine, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
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33
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Msemo OA, Pérez-Alós L, Minja DT, Hansen CB, Gesase S, Mtove G, Mbwana J, Larsen VML, Bøgestad ECS, Grunnet LG, Christensen DL, Bygbjerg IC, Burgner D, Schmiegelow C, Garred P, Hjort L. High anti-SARS-CoV-2 seroprevalence among unvaccinated mother-child pairs from a rural setting in north-eastern Tanzania during the second wave of COVID-19. IJID REGIONS 2023; 6:48-57. [PMID: 36466214 PMCID: PMC9709504 DOI: 10.1016/j.ijregi.2022.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
Background The reported infection rates and burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in low- and middle-income countries, including those in sub-Saharan Africa, are relatively low compared to the rates and burden in Europe and America, partly due to limited testing capability. Unlike many countries, Tanzania has implemented neither mass screening nor restrictive measures such as lockdowns to date. The prevalence of SARS-CoV-2 infection in rural mainland Tanzania is largely unknown. Methods A cross-sectional study was conducted between April and October 2021 to assess the anti-SARS-CoV-2 seroprevalence among mother-child pairs (n = 634 children, n = 518 mothers) in a rural setting in north-eastern Tanzania. Results A very high prevalence of anti-SARS-CoV-2 antibody titres was found, with seroprevalence rates ranging from 29% among mothers and 40% among children, with a dynamic peak in seropositivity incidence at the end of July/early August being revealed. Significant differences in age, socioeconomic status, and body composition were associated with seropositivity in mothers and children. No significant associations were observed between seropositivity and comorbidities, including anaemia, diabetes, malaria, and HIV. Conclusions The transmission of SARS-CoV-2 in a rural region of Tanzania during 2021 was high, indicating a much higher infection rate in rural Tanzania compared to that reported in the UK and USA during the same period. Ongoing immune surveillance may be vital to monitoring the burden of viral infection in rural settings without access to molecular genotyping, where the load of communicable diseases may mask COVID-19. Surveillance could be implemented in tandem with the intensification of vaccination strategies.
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Affiliation(s)
- Omari Abdul Msemo
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Daniel T.R. Minja
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Samwel Gesase
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - George Mtove
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Joyce Mbwana
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Victoria Marie Linderod Larsen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark,Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | - Emilie Caroline Skuladottir Bøgestad
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark,Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | | | - Dirk Lund Christensen
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Ib Christian Bygbjerg
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - David Burgner
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia,Department of Paediatrics, Melbourne University, Melbourne, Victoria, Australia
| | - Christentze Schmiegelow
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark,Department of Obstetrics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Line Hjort
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,Corresponding author: Line Hjort, he Novo Nordisk Foundation Centre for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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34
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Lanier WA, Palmer DK, Willmore DK, Oakeson KF, Young EL, Nolen LD. Investigation of SARS-CoV-2 Transmission in The Tabernacle Choir at Temple Square in the Context of Prevention Protocols, Utah, September-November 2021. Public Health Rep 2023:333549231152198. [PMID: 36734220 PMCID: PMC9899664 DOI: 10.1177/00333549231152198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Group singing and playing of wind instruments increase COVID-19 transmission risk. After a pause during the initial period of the COVID-19 pandemic, The Tabernacle Choir at Temple Square organization (hereinafter, Choir) resumed musical events in September 2021 with prevention protocols, including required vaccination and pre-event rapid antigen testing. We investigated potential SARS-CoV-2 transmission at Choir events during September 21-November 7, 2021. We interviewed COVID-19-positive members (hereinafter, case-members) and identified members exposed when a case-member attended a Choir event during his or her infectious period. We compared whole genome sequencing results to assess the genetic relatedness of available SARS-CoV-2 specimens obtained from case-members. We identified 30 case-members through pre-event testing (n = 10), self-reported positive test results (n = 18), and a review of Utah's disease surveillance system (n = 2). All 30 case-members reported symptoms; 21 (70%) were women and 23 (77%) received a positive test result by nucleic acid amplification test. No hospitalizations or deaths were reported. We identified 176 test-eligible exposed members from 14 instances of case-members attending events during their infectious periods. All were tested at least once 2 to 14 days after exposure: 74 (42%) by rapid antigen test only (all negative) and 102 (58%) by nucleic acid amplification test (4 positive, 97 negative, and 1 equivocal). Among viral sequences available from 15 case-members, the smallest single-nucleotide polymorphism distance between 2 sequences was 2, and the next-smallest distance was 10. The lack of disease detected in most exposed members suggests that minimal, if any, transmission occurred at Choir events. When community COVID-19 incidence is high, prevention protocols might help limit SARS-CoV-2 transmission during group musical activities.
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Affiliation(s)
- William A. Lanier
- Utah Department of Health and Human
Services, Salt Lake City, UT, USA,Career Epidemiology Field Officer
Program, Division of State and Local Readiness, Center for Preparedness and
Response, Centers for Disease Control and Prevention, Atlanta, GA, USA,US Public Health Service, Rockville,
MD, USA,The Tabernacle Choir at Temple Square,
Salt Lake City, UT, USA,William A. Lanier, DVM, MPH, Utah
Department of Health and Human Services, 288 N 1460 W, Salt Lake City, UT 84116,
USA.
| | - David K. Palmer
- The Tabernacle Choir at Temple Square,
Salt Lake City, UT, USA
| | - D. Keith Willmore
- The Tabernacle Choir at Temple Square,
Salt Lake City, UT, USA,Brigham Young University Health Center,
Provo, UT, USA
| | - Kelly F. Oakeson
- Utah Department of Health and Human
Services, Salt Lake City, UT, USA
| | - Erin L. Young
- Utah Department of Health and Human
Services, Salt Lake City, UT, USA
| | - Leisha D. Nolen
- Utah Department of Health and Human
Services, Salt Lake City, UT, USA
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35
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Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa. Nat Commun 2023; 14:246. [PMID: 36646700 PMCID: PMC9842214 DOI: 10.1038/s41467-022-35652-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023] Open
Abstract
South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (< 6%) remained naïve to SARS-CoV-2 and the population immunologic landscape is fragmented with diverse infection/immunization histories. Prior infection with the ancestral strain, Beta, and Delta variants provided 13%, 34%, and 51% protection against Omicron BA.1/2 infection, respectively. Hybrid immunity and repeated prior infections reduced the risks of Omicron BA.1/2 infection by 60% and 85% respectively. Our study sheds light on a rapidly shifting landscape of population immunity in the Omicron era and provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.
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36
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Chen B, Zhao Y, Jin Z, He D, Li H. Twice evasions of Omicron variants explain the temporal patterns in six Asian and Oceanic countries. BMC Infect Dis 2023; 23:25. [PMID: 36639649 PMCID: PMC9839219 DOI: 10.1186/s12879-023-07984-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The ongoing coronavirus 2019 (COVID-19) pandemic has emerged and caused multiple pandemic waves in the following six countries: India, Indonesia, Nepal, Malaysia, Bangladesh and Myanmar. Some of the countries have been much less studied in this devastating pandemic. This study aims to assess the impact of the Omicron variant in these six countries and estimate the infection fatality rate (IFR) and the reproduction number [Formula: see text] in these six South Asia, Southeast Asia and Oceania countries. METHODS We propose a Susceptible-Vaccinated-Exposed-Infectious-Hospitalized-Death-Recovered model with a time-varying transmission rate [Formula: see text] to fit the multiple waves of the COVID-19 pandemic and to estimate the IFR and [Formula: see text] in the aforementioned six countries. The level of immune evasion and the intrinsic transmissibility advantage of the Omicron variant are also considered in this model. RESULTS We fit our model to the reported deaths well. We estimate the IFR (in the range of 0.016 to 0.136%) and the reproduction number [Formula: see text] (in the range of 0 to 9) in the six countries. Multiple pandemic waves in each country were observed in our simulation results. CONCLUSIONS The invasion of the Omicron variant caused the new pandemic waves in the six countries. The higher [Formula: see text] suggests the intrinsic transmissibility advantage of the Omicron variant. Our model simulation forecast implies that the Omicron pandemic wave may be mitigated due to the increasing immunized population and vaccine coverage.
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Affiliation(s)
- Boqiang Chen
- grid.16890.360000 0004 1764 6123Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Yanji Zhao
- grid.16890.360000 0004 1764 6123Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Zhen Jin
- grid.163032.50000 0004 1760 2008Complex Systems Research Center, Shanxi University, Taiyuan, China
| | - Daihai He
- grid.16890.360000 0004 1764 6123Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Huaichen Li
- grid.460018.b0000 0004 1769 9639Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Reinfection rate in a cohort of healthcare workers over 2 years of the COVID-19 pandemic. Sci Rep 2023; 13:712. [PMID: 36639411 PMCID: PMC9837751 DOI: 10.1038/s41598-022-25908-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
In this large cohort of healthcare workers, we aimed to estimate the rate of reinfections by SARS-CoV-2 over 2 years of the COVID-19 pandemic. We investigated the proportion of reinfections among all the cases of SARS-CoV-2 infection from March 10, 2020 until March 10, 2022. Reinfection was defined as the appearance of new symptoms that on medical evaluation were suggestive of COVID-19 and confirmed by a positive RT-PCR. Symptoms had to occur more than 90 days after the previous infection. These 2 years were divided into time periods based on the different variants of concern (VOC) in the city of São Paulo. There were 37,729 medical consultations due to COVID-19 at the hospital's Health Workers Services; and 25,750 RT-PCR assays were performed, of which 23% (n = 5865) were positive. Reinfection by SARS-CoV-2 was identified in 5% (n = 284) of symptomatic cases. Most cases of reinfection occurred during the Omicron period (n = 251; 88%), representing a significant increase on the SARS-CoV-2 reinfection rate before and during the Omicron variant period (0.8% vs. 4.3%; p < 0.001). The mean interval between SARS-CoV-2 infections was 429 days (ranged from 122 to 674). The Omicron variant spread faster than Gamma and Delta variant. All SARS-CoV-2 reinfections were mild cases.
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Migueres M, Chapuy‐Regaud S, Miédougé M, Jamme T, Lougarre C, Da Silva I, Pucelle M, Staes L, Porcheron M, Diméglio C, Izopet J. Current immunoassays and detection of antibodies elicited by Omicron SARS-CoV-2 infection. J Med Virol 2023; 95:e28200. [PMID: 36207814 PMCID: PMC9874650 DOI: 10.1002/jmv.28200] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/12/2022] [Accepted: 10/03/2022] [Indexed: 01/27/2023]
Abstract
The present study aimed to determine whether current commercial immunoassays are adequate for detecting anti-Omicron antibodies. We analyzed the anti-SARS-CoV-2 antibody response of 23 unvaccinated individuals 1-2 months after an Omicron infection. All blood samples were tested with a live virus neutralization assay using a clinical Omicron BA.1 strain and four commercial SARS-CoV-2 immunoassays. We assessed three anti-Spike immunoassays (SARS-CoV-2 IgG II Quant [Abbott S], Wantaï anti-SARS-CoV-2 antibody ELISA [Wantaï], Elecsys Anti-SARS-CoV-2 S assay [Roche]) and one anti-Nucleocapsid immunoassay (Abbott SARS-CoV-2 IgG assay [Abbott N]). Omicron neutralizing antibodies were detected in all samples with the live virus neutralization assay. The detection rate of the Abbott S, Wantai, Roche, and Abbott N immunoassays were 65.2%, 69.6%, 86.9%, and 91.3%, respectively. The sensitivities of Abbott S and Wantai immunoassays were significantly lower than that of the live virus neutralization assay (p = 0.004, p = 0.009; Fisher's exact test). Antibody concentrations obtained with anti-S immunoassays were correlated with Omicron neutralizing antibody concentrations. These data provide clinical evidence of the loss of performance of some commercial immunoassays to detect antibodies elicited by Omicron infections. It highlights the need to optimize these assays by adapting antigens to the circulating SARS-CoV-2 strains.
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Affiliation(s)
- Marion Migueres
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Sabine Chapuy‐Regaud
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Marcel Miédougé
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Thibaut Jamme
- Laboratoire de Biochimie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | | | - Isabelle Da Silva
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Mélanie Pucelle
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Laetitia Staes
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Marion Porcheron
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Chloé Diméglio
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Jacques Izopet
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
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Wang C, Huang X, Lau EHY, Cowling BJ, Tsang TK. Association Between Population-Level Factors and Household Secondary Attack Rate of SARS-CoV-2: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2022; 10:ofac676. [PMID: 36655186 PMCID: PMC9835764 DOI: 10.1093/ofid/ofac676] [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: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Background Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of population-level factors, such as transmission intensity in the community, on SAR estimates is rarely explored. Methods In this study, we included articles with original data to compute the household SAR. To determine the impact of transmission intensity in the community on household SAR estimates, we explored the association between SAR estimates and the incidence rate of cases by country during the study period. Results We identified 163 studies to extract data on SARs from 326 031 cases and 2 009 859 household contacts. The correlation between the incidence rate of cases during the study period and SAR estimates was 0.37 (95% CI, 0.24-0.49). We found that doubling the incidence rate of cases during the study period was associated with a 1.2% (95% CI, 0.5%-1.8%) higher household SAR. Conclusions Our findings suggest that the incidence rate of cases during the study period is associated with higher SAR. Ignoring this factor may overestimate SARs, especially for regions with high incidences, which further impacts control policies and epidemiological characterization of emerging variants.
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Affiliation(s)
- Can Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaotong Huang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- Correspondence: Tim K. Tsang, PhD, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China ()
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Chen Z, Deng X, Fang L, Sun K, Wu Y, Che T, Zou J, Cai J, Liu H, Wang Y, Wang T, Tian Y, Zheng N, Yan X, Sun R, Xu X, Zhou X, Ge S, Liang Y, Yi L, Yang J, Zhang J, Ajelli M, Yu H. Epidemiological characteristics and transmission dynamics of the outbreak caused by the SARS-CoV-2 Omicron variant in Shanghai, China: A descriptive study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 29:100592. [PMID: 36090701 PMCID: PMC9448412 DOI: 10.1016/j.lanwpc.2022.100592] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND In early March 2022, a major outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant spread rapidly throughout Shanghai, China. Here we aimed to provide a description of the epidemiological characteristics and spatiotemporal transmission dynamics of the Omicron outbreak under the population-based screening and lockdown policies implemented in Shanghai. METHODS We extracted individual information on SARS-CoV-2 infections reported between January 1 and May 31, 2022, and on the timeline of the adopted non-pharmaceutical interventions. The epidemic was divided into three phases: i) sporadic infections (January 1-February 28), ii) local transmission (March 1-March 31), and iii) city-wide lockdown (April 1 to May 31). We described the epidemic spread during these three phases and the subdistrict-level spatiotemporal distribution of the infections. To evaluate the impact on the transmission of SARS-CoV-2 of the adopted targeted interventions in Phase 2 and city-wide lockdown in Phase 3, we estimated the dynamics of the net reproduction number (Rt ). FINDINGS A surge in imported infections in Phase 1 triggered cryptic local transmission of the Omicron variant in early March, resulting in the largest outbreak in mainland China since the original wave. A total of 626,000 SARS-CoV-2 infections were reported in 99.5% (215/216) of the subdistricts of Shanghai until the end of May. The spatial distribution of the infections was highly heterogeneous, with 37% of the subdistricts accounting for 80% of all infections. A clear trend from the city center towards adjacent suburban and rural areas was observed, with a progressive slowdown of the epidemic spread (from 463 to 244 meters/day) prior to the citywide lockdown. During Phase 2, Rt remained well above 1 despite the implementation of multiple targeted interventions. The citywide lockdown imposed on April 1 led to a marked decrease in transmission, bringing Rt below the epidemic threshold in the entire city on April 14 and ultimately leading to containment of the outbreak. INTERPRETATION Our results highlight the risk of widespread outbreaks in mainland China, particularly under the heightened pressure of imported infections. The targeted interventions adopted in March 2022 were not capable of halting transmission, and the implementation of a strict, prolonged city-wide lockdown was needed to successfully contain the outbreak, highlighting the challenges for containing Omicron outbreaks. FUNDING Key Program of the National Natural Science Foundation of China (82130093); Shanghai Rising-Star Program (22QA1402300).
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Affiliation(s)
- Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Liqun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Yanpeng Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Tianle Che
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junyi Zou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jun Cai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuyang Tian
- 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
| | - Xuemei Yan
- 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
| | - Xiangyanyu Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaoyu Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Shijia Ge
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxia Liang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lan Yi
- 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
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Co-corresponding authors at: School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China.
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, 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
- Co-corresponding authors at: School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China.
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Ngarka L, Siewe Fodjo JN, Njamnshi WY, Ditekemena JD, Ahmed MAM, Wanyenze RK, Dula J, Sessou P, Happi CT, Nkengasong JN, Colebunders R, Njamnshi AK. Adherence to COVID-19 preventive measures in Sub-Saharan Africa during the 1st year of the pandemic: Pooled analysis of the International Citizen Project on COVID-19 (ICPCovid) surveys. Front Public Health 2022; 10:1020801. [PMID: 36424955 PMCID: PMC9679527 DOI: 10.3389/fpubh.2022.1020801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Introduction While most governments instituted several interventions to stall the spread of COVID-19, little is known regarding the continued observance of the non-pharmaceutical COVID-19 preventive measures particularly in Sub-Saharan Africa (SSA). We investigated adherence to these preventive measures during the initial 6 months of the COVID-19 outbreak in some SSA countries. Methods Between March and August 2020, the International Citizen Project on COVID-19 consortium (www.icpcovid.com) conducted online surveys in six SSA countries: Benin, Cameroon, Democratic Republic of Congo, Mozambique, Somalia, and Uganda. A five-point individual adherence score was constituted by scoring respondents' observance of the following measures: mask use, physical distancing, hand hygiene, coughing hygiene, and avoiding to touch one's face. Community behaviors (going to public places, traveling during the pandemic) were also assessed. Data were analyzed in two time periods: Period 1 (March-May) and Period 2 (June-August). Results Responses from 26,678 respondents were analyzed (mean age: 31.0 ± 11.1 years; 54.1% males). Mean individual adherence score decreased from 3.80 ± 1.37 during Period 1, to 3.57 ± 1.43 during Period 2; p < 0.001. At the community level, public events/places were significantly more attended with increased travels during Period 2 compared to Period 1 (p < 0.001). Using linear mixed models, predictors of increased individual adherence included: higher age (Coef = 0.005; 95% CI: 0.003-0.007), female gender (Coef = 0.071; 95% CI: 0.039-0.104), higher educational level (Coef = 0.999; 95% CI: 0.885-1.113), and working in the healthcare sector (Coef = 0.418; 95% CI: 0.380-0.456). Conclusion Decreasing adherence to non-pharmaceutical measures over time constitutes a risk for the persistence of COVID-19 in SSA. Younger persons and those with lower education levels constitute target groups for improving adherence to such measures.
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Affiliation(s)
- Leonard Ngarka
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon,Department of Neurology, Yaoundé Central Hospital/Neuroscience Laboratory, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Joseph Nelson Siewe Fodjo
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon,Global Health Institute, University of Antwerp, Antwerp, Belgium
| | | | - John D. Ditekemena
- Ecole de Santé Publique, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Mohammed A. M. Ahmed
- Department of Paediatrics, Faculty of Medicine and Surgery, Mogadishu University, Mogadishu, Somalia,Department of Paediatric Cardiology, Uganda Heart Institute, Kampala, Uganda
| | - Rhoda K. Wanyenze
- School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Janet Dula
- Programa de Politicas e Sistemas de Saúde, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Philippe Sessou
- Research Unit of Communicable Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Cotonou, Benin
| | - Christian T. Happi
- African Center of Excellence for Genomics of Infectious Disease, Redeemer's University, Ede, Nigeria
| | - John N. Nkengasong
- Center for Disease Control and Prevention (CDC) Africa, African Union, Addis Ababa, Ethiopia
| | | | - Alfred K. Njamnshi
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon,Department of Neurology, Yaoundé Central Hospital/Neuroscience Laboratory, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon,*Correspondence: Alfred K. Njamnshi
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Zar HJ, MacGinty R, Workman L, Botha M, Johnson M, Hunt A, Burd T, Nicol MP, Flasche S, Quilty BJ, Goldblatt D. Natural and hybrid immunity following four COVID-19 waves: A prospective cohort study of mothers in South Africa. EClinicalMedicine 2022; 53:101655. [PMID: 36128333 PMCID: PMC9481335 DOI: 10.1016/j.eclinm.2022.101655] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND More than half the global population has been exposed to SARS-CoV-2. Naturally induced immunity influences the outcome of subsequent exposure to variants and vaccine responses. We measured anti-spike IgG responses to explore the basis for this enhanced immunity. METHODS A prospective cohort study of mothers in a South African community through ancestral/beta/delta/omicron SARS-CoV-2 waves (March 2020-February 2022). Health seeking behaviour/illness were recorded and post-wave serum samples probed for IgG to Spike (CoV2-S-IgG) by ECLISA. To estimate protective CoV2-S-IgG threshold levels, logistic functions were fit to describe the correlation of CoV2-S-IgG measured before a wave and the probability for seroconversion/boosting thereafter for unvaccinated and vaccinated adults. FINDINGS Despite little disease, 176/339 (51·9%) participants were seropositive following wave 1, rising to 74%, 89·8% and 97·3% after waves 2, 3 and 4 respectively. CoV2-S-IgG induced by natural exposure protected against subsequent SARS-CoV-2 infection with the greatest protection for beta and least for omicron. Vaccination induced higher CoV2-S-IgG in seropositive compared to naïve vaccinees. Amongst seropositive participants, proportions above the 50% protection against infection threshold were 69% (95% CrI: 62, 72) following 1 vaccine dose, 63% (95% CrI: 63, 75) following 2 doses and only 11% (95% CrI: 7, 14) in unvaccinated during the omicron wave. INTERPRETATION Naturally induced CoV2-S-IgG do not achieve high enough levels to prevent omicron infection in most exposed individuals but are substantially boosted by vaccination leading to significant protection. A single vaccination in those with prior immunity is more immunogenic than 2 doses in a naïve vaccinee and may provide adequate protection. FUNDING UK NIH GECO award (GEC111), Wellcome Trust Centre for Infectious Disease Research in Africa (CIDRI), Bill & Melinda Gates Foundation, USA (OPP1017641, OPP1017579) and NIH H3 Africa (U54HG009824, U01AI110466]. HZ is supported by the SA-MRC. MPN is supported by an Australian National Health and Medical Research Council Investigator Grant (APP1174455). BJQ is supported by a grant from the Bill and Melinda Gates Foundation (OPP1139859). Stefan Flasche is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant number 208812/Z/17/Z).
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Affiliation(s)
- Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Rae MacGinty
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Marina Johnson
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK
| | - Adam Hunt
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK
| | - Tiffany Burd
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Stefan Flasche
- Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, UK
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK
- Corresponding author at: Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK.
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Gao Q, Shang WP, Jing MX. Effect of Nucleic Acid Screening Measures on COVID-19 Transmission in Cities of Different Scales and Assessment of Related Testing Resource Demands-Evidence from China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13343. [PMID: 36293923 PMCID: PMC9602617 DOI: 10.3390/ijerph192013343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND COVID-19 is in its epidemic period, and China is still facing the dual risks of import and domestic rebound. To better control the COVID-19 pandemic under the existing conditions, the focus of this study is to simulate the nucleic acid testing for different population size cities in China to influence the spread of COVID-19, assess the situation under different scenarios, the demand for the laboratory testing personnel, material resources, for the implementation of the nucleic acid screening measures, emergency supplies, and the configuration of human resources to provide decision-making basis. METHODS According to the transmission characteristics of COVID-19 and the current prevention and control strategies in China, four epidemic scenarios were assumed. Based on the constructed SVEAIiQHR model, the number of people infected with COVID-19 in cities with populations of 10 million, 5 million, and 500,000 was analyzed and predicted under the four scenarios, and the demand for laboratory testing resources was evaluated, respectively. RESULTS For large, medium, and small cities, whether full or regional nucleic acid screening can significantly reduce the epidemic prevention and control strategy of different scenarios laboratory testing resource demand difference is bigger, implement effective non-pharmaceutical interventions and regional nucleic acid screening measures to significantly reduce laboratory testing related resources demand, but will cause varying degrees of inspection staff shortages. CONCLUSION There is still an urgent need for laboratory testing manpower in China to implement effective nucleic acid screening measures in the event of an outbreak. Cities or regions with different population sizes and levels of medical resources should flexibly implement prevention and control measures according to specific conditions after the outbreak, assess laboratory testing and human resource need as soon as possible, and prepare and allocate materials and personnel.
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Affiliation(s)
- Qian Gao
- Department of Public Health, Shihezi University School of Medicine, Shihezi 832000, China
| | - Wen-Peng Shang
- Shihezi City Center for Disease Control and Prevention, Eighth Division, Xinjiang Production and Construction Corps, Shihezi 832000, China
| | - Ming-Xia Jing
- Department of Public Health, Shihezi University School of Medicine, Shihezi 832000, China
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Flacco ME, Acuti Martellucci C, Baccolini V, De Vito C, Renzi E, Villari P, Manzoli L. Risk of reinfection and disease after SARS-CoV-2 primary infection: Meta-analysis. Eur J Clin Invest 2022; 52:e13845. [PMID: 35904405 PMCID: PMC9353414 DOI: 10.1111/eci.13845] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/09/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION A precise estimate of the frequency and severity of SARS-CoV-2 reinfections would be critical to optimize restriction and vaccination policies for the hundreds of millions previously infected subjects. We performed a meta-analysis to evaluate the risk of reinfection and COVID-19 following primary infection. METHODS We searched MedLine, Scopus and preprint repositories for cohort studies evaluating the onset of new infections among baseline SARS-CoV-2-positive subjects. Random-effect meta-analyses of proportions were stratified by gender, exposure risk, vaccination status, viral strain, time between episodes, and reinfection definition. RESULTS Ninety-one studies, enrolling 15,034,624 subjects, were included. Overall, 158,478 reinfections were recorded, corresponding to a pooled rate of 0.97% (95% CI: 0.71%-1.27%), with no substantial differences by definition criteria, exposure risk or gender. Reinfection rates were still 0.66% after ≥12 months from first infection, and the risk was substantially lower among vaccinated subjects (0.32% vs. 0.74% for unvaccinated individuals). During the first 3 months of Omicron wave, the reinfection rates reached 3.31%. Overall rates of severe/lethal COVID-19 were very low (2-7 per 10,000 subjects according to definition criteria) and were not affected by strain predominance. CONCLUSIONS A strong natural immunity follows the primary infection and may last for more than one year, suggesting that the risk and health care needs of recovered subjects might be limited. Although the reinfection rates considerably increased during the Omicron wave, the risk of a secondary severe or lethal disease remained very low. The risk-benefit profile of multiple vaccine doses for this subset of population needs to be carefully evaluated.
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Affiliation(s)
- Maria Elena Flacco
- Department of Environmental and Preventive Sciences, University of Ferrara, Ferrara, Italy
| | | | - Valentina Baccolini
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Erika Renzi
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Lamberto Manzoli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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Guevara R, Prado-Vivar B, Márquez S, Muñoz EB, Carvajal M, Guadalupe JJ, Becerra-Wong M, Proaño S, Bayas-Rea R, Coloma J, Grunauer M, Trueba G, Rojas-Silva P, Barragán V, Cárdenas P. Occurrence of SARS-CoV-2 reinfections at regular intervals in Ecuador. Front Cell Infect Microbiol 2022; 12:951383. [PMID: 36164552 PMCID: PMC9507970 DOI: 10.3389/fcimb.2022.951383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their incidence has fluctuated with specific SARS-CoV-2 variant waves. Initially, reinfections were estimated to represent less than 1% of total COVID-19 infections. With the advent of the Omicron variant, reinfections became more frequent, representing up to 10% of cases (based on data from developed countries). The frequency of reinfections in Latin America has been scarcely reported. The current study shows that in Ecuador, the frequency of reinfections has increased 10-fold following the introduction of Omicron, after 22 months of surveillance in a single center of COVID-19 diagnostics. Suspected reinfections were identified retrospectively from a database of RT-qPCR-positive patients. Cases were confirmed by sequencing viral genomes from the first and second infections using the ONT MinION platform. Monthly surveillance showed that the main incidence peaks of reinfections were reached within four to five months, coinciding with the increase of COVID-19 cases in the country, suggesting that the emergence of reinfections is related to higher exposure to the virus during outbreaks. This study performed the longest monitoring of SARS-CoV-2 reinfections, showing an occurrence at regular intervals of 4-5 months and confirming a greater propensity of Omicron to cause reinfections.
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Affiliation(s)
- Rommel Guevara
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Erika B. Muñoz
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Mateo Carvajal
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Stefanie Proaño
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Rosa Bayas-Rea
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, United States
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- *Correspondence: Paúl Cárdenas,
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Kleynhans J, Walaza S, Martinson NA, Neti M, von Gottberg A, Bhiman JN, Toi D, Amoako DG, Buys A, Ndlangisa K, Wolter N, Genade L, Maloma L, Chewparsad J, Lebina L, de Gouveia L, Kotane R, Tempia S, Cohen C. Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 From Adult Index Cases With and Without Human Immunodeficiency Virus in South Africa, 2020-2021: A Case-Ascertained, Prospective, Observational Household Transmission Study. Clin Infect Dis 2022; 76:e71-e81. [PMID: 35925613 PMCID: PMC9384657 DOI: 10.1093/cid/ciac640] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In South Africa, 19% of adults are living with human immunodeficiency virus (HIV; LWH). Few data on the influence of HIV on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission are available. METHODS We performed a case-ascertained, prospective household transmission study of symptomatic adult index SARS-CoV-2 cases LWH and not living with HIV (NLWH) and their contacts from October 2020 to September 2021. Households were followed up 3 times a week for 6 weeks to collect nasal swabs for SARS-CoV-2 testing. We estimated household cumulative infection risk (HCIR) and duration of SARS-CoV-2 positivity (at a cycle threshold value <30 as proxy for high viral load). RESULTS HCIR was 59% (220 of 373), not differing by index HIV status (60% LWH vs 58% NLWH). HCIR increased with index case age (35-59 years: adjusted OR [aOR], 3.4; 95% CI, 1.5-7.8 and ≥60 years: aOR, 3.1; 95% CI, 1.0-10.1) compared with 18-34 years and with contacts' age, 13-17 years (aOR, 7.1; 95% CI, 1.5-33.9) and 18-34 years (aOR, 4.4; 95% CI, 1.0-18.4) compared with <5 years. Mean positivity was longer in cases LWH (adjusted hazard ratio, 0.4; 95% CI, .1-.9). CONCLUSIONS Index HIV status was not associated with higher HCIR, but cases LWH had longer positivity duration. Adults aged >35 years were more likely to transmit and individuals aged 13-34 to be infected SARS-CoV-2 in the household. As HIV infection may increase transmission, health services must maintain HIV testing and antiretroviral therapy initiation.
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Affiliation(s)
- Jackie Kleynhans
- Correspondence: J. Kleynhans, Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, 1 Modderfontein Road, Sandringham, 2192, Johannesburg, South Africa ()
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa,Center for TB Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mzimasi Neti
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dylan Toi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Kedibone Ndlangisa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Leisha Genade
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Lucia Maloma
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Juanita Chewparsad
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa,Africa Health Research Institute, Durban, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Retshidisitswe Kotane
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Tyrosine Kinase Inhibitors Do Not Promote a Decrease in SARS-CoV-2 Anti-Spike IgG after BNT162b2 Vaccination in Chronic Myeloid Leukemia: A Prospective Observational Study. Vaccines (Basel) 2022; 10:vaccines10091404. [PMID: 36146482 PMCID: PMC9501552 DOI: 10.3390/vaccines10091404] [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: 07/26/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
We performed a prospective observational study of chronic myeloid leukemia (CML) patients after anti-SARS-CoV-2 BNT162b2 vaccination (VC). In total, 32 CML patients with tyrosine kinase inhibitor (TKI) therapy, 10 CML patients with treatment-free remission, and 16 healthy subjects participated in the study. From April 2021 to September 2021, all cases (median age = 58 years) were vaccinated twice. Immunoglobulin G for SARS-CoV-2 spike protein (S-IgG) was measured at three timepoints (before the first VC, 1−5 weeks after the second VC (T1), and approximately 6 months after the second VC (T2)). S-IgG was not observed before the first VC in any participant. At T1, all cases had acquired S-IgG. There were no significant differences in S-IgG levels among groups. A paired sample comparison of median S-IgG titers between T1 and T2 in all groups showed a significant reduction in T2 S-IgG titers. There were no significant differences in S-IgG levels among groups. When all patients were analyzed, those aged ≥58 years had significantly lower S-IgG levels than those aged <58 years at T1. The BNT162b2 vaccine was highly effective in CML patients with or without TKIs, and S-IgG levels were as persistent as those in healthy individuals.
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48
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Sun K, Tempia S, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit JD, Gómez-Olivé FX, Mkhencele T, Viboud C, Cohen C. SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron's impact in South African population cohorts. Sci Transl Med 2022; 14:eabo7081. [PMID: 35638937 PMCID: PMC9161370 DOI: 10.1126/scitranslmed.abo7081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022]
Abstract
Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa's high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jinal N. Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, 21287, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Jacques D. du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
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49
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Sun K, Tempia S, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, Carrim M, Martinson NA, Kahn K, Lebina L, du Toit JD, Mkhencele T, Viboud C, Cohen C. Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.08.19.22278993. [PMID: 36032973 PMCID: PMC9413704 DOI: 10.1101/2022.08.19.22278993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. Propelled by increased transmissibility and immune escape properties, Omicron displaced other globally circulating variants within 3 months of its emergence. Due to limited testing, Omicron's attenuated clinical severity, and an increased risk of reinfection, the size of the Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood in South Africa and in many other countries. Using South African data from urban and rural cohorts closely monitored since the beginning of the pandemic, we analyzed sequential serum samples collected before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. Omicron BA.1/2 infection attack rates reached 65% (95% CI, 60% - 69%) in the rural cohort and 58% (95% CI, 61% - 74%) in the urban cohort, with repeat infections and vaccine breakthroughs accounting for >60% of all infections at both sites. Combined with previously collected data on pre-Omicron variant infections within the same cohorts, we identified 14 distinct categories of SARS-CoV-2 antigen exposure histories in the aftermath of the Omicron BA.1/2 wave, indicating a particularly fragmented immunologic landscape. Few individuals (<6%) remained naïve to SARS-CoV-2 and no exposure history category represented over 25% of the population at either cohort site. Further, cohort participants were more than twice as likely to get infected during the Omicron BA.1/2 wave, compared to the Delta wave. Prior infection with the ancestral strain (with D614G mutation), Beta, and Delta variants provided 13% (95% CI, -21% - 37%), 34% (95% CI, 17% - 48%), and 51% (95% CI, 39% - 60%) protection against Omicron BA.1/2 infection, respectively. Hybrid immunity (prior infection and vaccination) and repeated prior infections (without vaccination) reduced the risks of Omicron BA.1/2 infection by 60% (95% CI, 42% - 72%) and 85% (95% CI, 76% - 92%) respectively. Reinfections and vaccine breakthroughs had 41% (95% CI, 26% - 53%) lower risk of onward transmission than primary infections. Our study sheds light on a rapidly shifting landscape of population immunity, along with the changing characteristics of SARS-CoV-2, and how these factors interact to shape the success of emerging variants. Our findings are especially relevant to populations similar to South Africa with low SARS-CoV-2 vaccine coverage and a dominant contribution of immunity from prior infection. Looking forward, the study provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, South Africa
| | - Jacques D du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Lewis HC, Ware H, Whelan M, Subissi L, Li Z, Ma X, Nardone A, Valenciano M, Cheng B, Noel K, Cao C, Yanes-Lane M, Herring BL, Talisuna A, Ngoy N, Balde T, Clifton D, Van Kerkhove MD, Buckeridge D, Bobrovitz N, Okeibunor J, Arora RK, Bergeri I. SARS-CoV-2 infection in Africa: a systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021. BMJ Glob Health 2022; 7:e008793. [PMID: 35998978 PMCID: PMC9402450 DOI: 10.1136/bmjgh-2022-008793] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Estimating COVID-19 cumulative incidence in Africa remains problematic due to challenges in contact tracing, routine surveillance systems and laboratory testing capacities and strategies. We undertook a meta-analysis of population-based seroprevalence studies to estimate SARS-CoV-2 seroprevalence in Africa to inform evidence-based decision making on public health and social measures (PHSM) and vaccine strategy. METHODS We searched for seroprevalence studies conducted in Africa published 1 January 2020-30 December 2021 in Medline, Embase, Web of Science and Europe PMC (preprints), grey literature, media releases and early results from WHO Unity studies. All studies were screened, extracted, assessed for risk of bias and evaluated for alignment with the WHO Unity seroprevalence protocol. We conducted descriptive analyses of seroprevalence and meta-analysed seroprevalence differences by demographic groups, place and time. We estimated the extent of undetected infections by comparing seroprevalence and cumulative incidence of confirmed cases reported to WHO. PROSPERO CRD42020183634. RESULTS We identified 56 full texts or early results, reporting 153 distinct seroprevalence studies in Africa. Of these, 97 (63%) were low/moderate risk of bias studies. SARS-CoV-2 seroprevalence rose from 3.0% (95% CI 1.0% to 9.2%) in April-June 2020 to 65.1% (95% CI 56.3% to 73.0%) in July-September 2021. The ratios of seroprevalence from infection to cumulative incidence of confirmed cases was large (overall: 100:1, ranging from 18:1 to 954:1) and steady over time. Seroprevalence was highly heterogeneous both within countries-urban versus rural (lower seroprevalence for rural geographic areas), children versus adults (children aged 0-9 years had the lowest seroprevalence)-and between countries and African subregions. CONCLUSION We report high seroprevalence in Africa suggesting greater population exposure to SARS-CoV-2 and potential protection against COVID-19 severe disease than indicated by surveillance data. As seroprevalence was heterogeneous, targeted PHSM and vaccination strategies need to be tailored to local epidemiological situations.
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Affiliation(s)
- Hannah C Lewis
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Harriet Ware
- Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mairead Whelan
- Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lorenzo Subissi
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Zihan Li
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Xiaomeng Ma
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Anthony Nardone
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
- Department of Epidemiology, Epiconcept, Paris, France
| | - Marta Valenciano
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
- Department of Epidemiology, Epiconcept, Paris, France
| | - Brianna Cheng
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
- School of Population and Global Health, McGill University, Montreal, Québec, Canada
| | - Kim Noel
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada
| | - Christian Cao
- Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mercedes Yanes-Lane
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada
- COVID-19 Immunity Task Force Secreteriat, McGill University, Montreal, Québec, Canada
| | - Belinda L Herring
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Ambrose Talisuna
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Nsenga Ngoy
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Thierno Balde
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - David Clifton
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Maria D Van Kerkhove
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - David Buckeridge
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada
- Division of Infectious Diseases and Medical Microbiology, McGill University Health Centre, Montreal, Québec, Canada
| | - Niklas Bobrovitz
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Okeibunor
- Emergency Preparedness and Response Programme, World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Rahul K Arora
- Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Isabel Bergeri
- WHO Health Emergencies Programme, World Health Organization, Geneva, Switzerland
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