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Nunes MC, Thommes E, Fröhlich H, Flahault A, Arino J, Baguelin M, Biggerstaff M, Bizel-Bizellot G, Borchering R, Cacciapaglia G, Cauchemez S, Barbier--Chebbah A, Claussen C, Choirat C, Cojocaru M, Commaille-Chapus C, Hon C, Kong J, Lambert N, Lauer KB, Lehr T, Mahe C, Marechal V, Mebarki A, Moghadas S, Niehus R, Opatowski L, Parino F, Pruvost G, Schuppert A, Thiébaut R, Thomas-Bachli A, Viboud C, Wu J, Crépey P, Coudeville L. Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report. Infect Dis Model 2024; 9:501-518. [PMID: 38445252 PMCID: PMC10912817 DOI: 10.1016/j.idm.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
In July 2023, the Center of Excellence in Respiratory Pathogens organized a two-day workshop on infectious diseases modelling and the lessons learnt from the Covid-19 pandemic. This report summarizes the rich discussions that occurred during the workshop. The workshop participants discussed multisource data integration and highlighted the benefits of combining traditional surveillance with more novel data sources like mobility data, social media, and wastewater monitoring. Significant advancements were noted in the development of predictive models, with examples from various countries showcasing the use of machine learning and artificial intelligence in detecting and monitoring disease trends. The role of open collaboration between various stakeholders in modelling was stressed, advocating for the continuation of such partnerships beyond the pandemic. A major gap identified was the absence of a common international framework for data sharing, which is crucial for global pandemic preparedness. Overall, the workshop underscored the need for robust, adaptable modelling frameworks and the integration of different data sources and collaboration across sectors, as key elements in enhancing future pandemic response and preparedness.
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Affiliation(s)
- Marta C. Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL) and Centre International de Recherche en Infectiologie (CIRI), Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Edward Thommes
- New Products and Innovation (NPI), Sanofi Vaccines (Global), Toronto, Ontario, Canada
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department of Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT (b-it), Bonn, Germany
| | - Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland and Swiss School of Public Health, Zürich, Switzerland
| | - Julien Arino
- Department of Mathematics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Matthew Biggerstaff
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Gaston Bizel-Bizellot
- Departement of Computational Biology, Departement of Global Health, Institut Pasteur, Paris, France
| | - Rebecca Borchering
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Giacomo Cacciapaglia
- Institut de Physique des Deux Infinis de Lyon (IP2I), UMR5822, IN2P3/CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000 CNRS, Paris, France
| | - Alex Barbier--Chebbah
- Decision and Bayesian Computation, Institut Pasteur, Université Paris Cité, CNRS UMR 3571, France
| | - Carsten Claussen
- Fraunhofer-Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Christine Choirat
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Monica Cojocaru
- Mathematics & Statistics Department, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Chitin Hon
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China
| | - Jude Kong
- Africa-Canada Artificial Intelligence and Data Innovation Consortium (ACADIC), Global South Artificial Intelligence for Pandemic and Epidemic Preparedness and Response Network (AI4PEP), Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
| | | | | | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | | | - Vincent Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, Paris, France
| | | | - Seyed Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Rene Niehus
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Lulla Opatowski
- UMR 1018, Team “Anti-infective Evasion and Pharmacoepidemiology”, Université Paris-Saclay, UVSQ, INSERM, France
- Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Université Paris Cité, Paris, France
| | - Francesco Parino
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | | | - Andreas Schuppert
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Rodolphe Thiébaut
- Bordeaux University, Department of Public Health, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France
| | | | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jianhong Wu
- York Emergency Mitigation, Engagement, Response, and Governance Institute, Laboratory for Industrial and Applied Mathematics, York University, Toronto, Ontario, Canada
| | - Pascal Crépey
- EHESP, Université de Rennes, CNRS, IEP Rennes, Arènes - UMR 6051, RSMS – Inserm U 1309, Rennes, France
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Ulrichs T, Rolland M, Wu J, Nunes MC, El Guerche-Séblain C, Chit A. Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies. Expert Rev Vaccines 2024. [PMID: 38656834 DOI: 10.1080/14760584.2024.2346589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION COVID-19 was an unprecedented challenge worldwide; however, disease epidemiology has evolved, and COVID-19 no longer constitutes a public health emergency of international concern. Nonetheless, COVID-19 remains a global threat and uncertainties remain, including definition of the end of the pandemic and transition to endemicity, and understanding true rates of SARS-CoV-2 infection/transmission. AREAS COVERED Six international experts convened (April 2023) to interpret changing COVID-19 epidemiology and public health challenges. We report the panel's recommendations and knowledge gaps in COVID-19 epidemiology, SARS-CoV-2 evolution, and future vaccination strategies, informed by peer-reviewed publications, surveillance data, health authority assessments, and clinical experience. EXPERT OPINION High population SARS-CoV-2 immunity indicates the likely end to the pandemic's acute phase. Continued emergence of variants/sublineages that can evade the vaccine-induced antibody response are likely, but widespread immunity reduces the risk of disease severity.Continued surveillance is required to capture transition to endemicity, seasonality, and emergence of novel variants/sublineages, to inform future vaccination strategies. COVID-19 vaccination should be integrated into routine vaccination programs throughout life.Co-circulation with other respiratory viruses should be monitored to avoid a combined peak, which could overrun healthcare systems. Effective, combined vaccines and improved education may help overcome vaccine hesitancy/booster fatigue and increase vaccination uptake.
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Affiliation(s)
- Timo Ulrichs
- Department of Global Health, Akkon University for Human Sciences, Berlin, Germany
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Jianhong Wu
- York Emergency Mitigation, Engagement, Response, and Governance Institute, York University, Toronto, Canada
| | - Marta C Nunes
- Université Claude Bernard Lyon, Lyon, France
- University of the Witwatersrand, Johannesburg, South Africa
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Cohen LE, Hansen CL, Andrew MK, McNeil SA, Vanhems P, Kyncl J, Domingo JD, Zhang T, Dbaibo G, Laguna-Torres VA, Draganescu A, Baumeister E, Gomez D, Raboni SM, Giamberardino HIG, Nunes MC, Burtseva E, Sominina A, Medić S, Coulibaly D, Salah AB, Otieno NA, Koul PA, Unal S, Tanriover MD, Mazur M, Bresee J, Viboud C, Chaves SS. Predictors of Severity of Influenza-Related Hospitalizations: Results From the Global Influenza Hospital Surveillance Network (GIHSN). J Infect Dis 2024; 229:999-1009. [PMID: 37527470 PMCID: PMC11011157 DOI: 10.1093/infdis/jiad303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The Global Influenza Hospital Surveillance Network (GIHSN) has since 2012 provided patient-level data on severe influenza-like-illnesses from >100 participating clinical sites worldwide based on a core protocol and consistent case definitions. METHODS We used multivariable logistic regression to assess the risk of intensive care unit admission, mechanical ventilation, and in-hospital death among hospitalized patients with influenza and explored the role of patient-level covariates and country income level. RESULTS The data set included 73 121 patients hospitalized with respiratory illness in 22 countries, including 15 660 with laboratory-confirmed influenza. After adjusting for patient-level covariates we found a 7-fold increase in the risk of influenza-related intensive care unit admission in lower middle-income countries (LMICs), compared with high-income countries (P = .01). The risk of mechanical ventilation and in-hospital death also increased by 4-fold in LMICs, though these differences were not statistically significant. We also find that influenza mortality increased significantly with older age and number of comorbid conditions. Across all severity outcomes studied and after controlling for patient characteristics, infection with influenza A/H1N1pdm09 was more severe than with A/H3N2. CONCLUSIONS Our study provides new information on influenza severity in underresourced populations, particularly those in LMICs.
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Affiliation(s)
- Lily E Cohen
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chelsea L Hansen
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- Brotman Baty Institute, University of Washington, Seattle, Washington, USA
- PandemiX Center, Department of Science & Environment, Roskilde University, Denmark
| | - Melissa K Andrew
- Canadian Center for Vaccinology, IWK Health Centre and Nova Scotia Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology, IWK Health Centre and Nova Scotia Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Jan Kyncl
- Department of Infectious Diseases Epidemiology, National Institute of Public Health, Prague, Czech Republic
- Department of Epidemiology and Biostatistics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Javier Díez Domingo
- Fundación Para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO–Public Health), Valencia, Spain
| | - Tao Zhang
- School of Public Health, Fudan University, Shanghai, China
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | | | - Anca Draganescu
- National Institute for Infectious Diseases “Prof Dr Matei Bals”, Bucharest, Romania
| | - Elsa Baumeister
- Respiratory Virus Laboratory, Virology Department, INEI-ANLIS, Buenos Aires, Argentina
| | - Doris Gomez
- Grupo de Investigación UNIMOL, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Sonia M Raboni
- Virology Laboratory, Infectious Diseases Division, Universidade Federal do Paraná, Hospital Pequeno Principe, Curitiba, Paraná, Brazil
| | - Heloisa I G Giamberardino
- Virology Laboratory, Infectious Diseases Division, Universidade Federal do Paraná, Hospital Pequeno Principe, Curitiba, Paraná, Brazil
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elena Burtseva
- Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Anna Sominina
- Smorodintsev Research Institute of Influenza, St Petersburg, Russia
| | - Snežana Medić
- Institute for Public Health of Vojvodina, Novi Sad, Serbia
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | | | - Afif Ben Salah
- Institut Pasteur de Tunis, Tunis, Tunisia
- Arabian Gulf University, Manama, Bahrain
| | - Nancy A Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Parvaiz A Koul
- Sheri Kashmir Institute of Medical Sciences, Srinagar, India
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
- Turkish Society of Internal Medicine, Ankara, Turkey
| | - Mine Durusu Tanriover
- Turkish Society of Internal Medicine, Ankara, Turkey
- Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Marie Mazur
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
| | - Joseph Bresee
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
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Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus. Nat Commun 2024; 15:3083. [PMID: 38600104 PMCID: PMC11006891 DOI: 10.1038/s41467-024-47118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also in great detail for SARS-CoV-2, a lack of global multi-annual sampling of complete RSV genomes limits our understanding of RSV molecular epidemiology. Here, we capitalise on the genomic surveillance by the INFORM-RSV study and apply phylodynamic approaches to uncover how selection and neutral epidemiological processes shape RSV diversity. Using complete viral genome sequences, we show similar patterns of site-specific diversifying selection among RSVA and RSVB and recover the imprint of non-neutral epidemic processes on their genealogies. Using a phylogeographic approach, we provide evidence for air travel governing the global patterns of RSVA and RSVB spread, which results in a considerable degree of phylogenetic mixing across countries. Our findings highlight the potential of systematic global RSV genomic surveillance for transforming our understanding of global RSV spread.
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Affiliation(s)
- Annefleur C Langedijk
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Deidre Wilkins
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Elizabeth J Kelly
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Eugenio Baraldi
- Department of Woman's and Child's Health, University Hospital of Padova, Padova, Italy
- ReSViNET Foundation, Zeist, the Netherlands
- Institute of Pediatric Research "Città della Speranza", Padova, Italy
| | | | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Eun Hwa Choi
- Seoul National University Children's Hospital, Seoul, South Korea
| | | | - Hsin Chi
- MacKay Children's Hospital, New Taipei, Taiwan, ROC
| | - Christian Keller
- Institute of Virology, University Hospital Giessen and Marburg, Marburg, Germany
| | | | | | | | - Anne Greenough
- ReSViNET Foundation, Zeist, the Netherlands
- King's College London, London, UK
| | | | - Federico Martinón-Torres
- ReSViNET Foundation, Zeist, the Netherlands
- Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Terho Heikkinen
- ReSViNET Foundation, Zeist, the Netherlands
- University of Turku and Turku University Hospital, Turku, Finland
| | - Renato T Stein
- ReSViNET Foundation, Zeist, the Netherlands
- Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Mitsuaki Hosoya
- Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Marta C Nunes
- ReSViNET Foundation, Zeist, the Netherlands
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Charl Verwey
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Hospices Civils de Lyon and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Anouk Evers
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | | | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, 801 N Broad St, Philadelphia, PA, 19122, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
| | - Louis J Bont
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands.
- ReSViNET Foundation, Zeist, the Netherlands.
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Schwalbe N, Nunes MC, Cutland C, Wahl B, Reidpath D. Assessing New York City's COVID-19 Vaccine Rollout Strategy: A Case for Risk-Informed Distribution. J Urban Health 2024:10.1007/s11524-024-00853-z. [PMID: 38578336 DOI: 10.1007/s11524-024-00853-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
This study reviews the impact of eligibility policies in the early rollout of the COVID-19 vaccine on coverage and probable outcomes, with a focus on New York City. We conducted a retrospective ecological study assessing age 65+, area-level income, vaccination coverage, and COVID-19 mortality rates, using linked Census Bureau data and New York City Health administrative data aggregated at the level of modified zip code tabulation areas (MODZCTA). The population for this study was all individuals in 177 MODZCTA in New York City. Population data were obtained from Census Bureau and New York City Health administrative data. The total mortality rate was examined through an ordinary least squares (OLS) regression model, using area-level wealth, the proportion of the population aged 65 and above, and the vaccination rate among this age group as predictors. Low-income areas with high proportions of older people demonstrated lower coverage rates (mean vaccination rate 52.8%; maximum coverage 67.9%) than wealthier areas (mean vaccination rate 74.6%; maximum coverage 99% in the wealthiest quintile) in the first 3 months of vaccine rollout and higher mortality over the year. Despite vaccine shortages, many younger people accessed vaccines ahead of schedule, particularly in high-income areas (mean coverage rate 60% among those 45-64 years in the wealthiest quintile). A vaccine program that prioritized those at greatest risk of COVID-19-associated morbidity and mortality would have prevented more deaths than the strategy that was implemented. When rolling out a new vaccine, policymakers must account for local contexts and conditions of high-risk population groups. If New York had focused limited vaccine supply on low-income areas with high proportions of residents 65 or older, overall mortality might have been lower.
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Affiliation(s)
- Nina Schwalbe
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, January 1 Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa.
- Heilbrunn Department of Population and Family Health, Columbia University, 722 W 168Th St, New York, NY, 10032, USA.
| | - Marta C Nunes
- Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL), and Centre International de Recherche en Infectiologie (CIRI), Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard Lyon 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Clare Cutland
- Wits African Leadership in Vaccinology Expertise (Wits-Alive), School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Brian Wahl
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Daniel Reidpath
- Institute for Global Health and Development, Queen Margaret University, Edinburgh, EH21 6UU, UK
- School of Social Sciences, Monash University, Clayton, VIC, 3125, Australia
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6
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Tomasicchio M, Jaumdally S, Wilson L, Kotze A, Semple L, Meier S, Pooran A, Esmail A, Pillay K, Roberts R, Kriel R, Meldau R, Oelofse S, Mandviwala C, Burns J, Londt R, Davids M, van der Merwe C, Roomaney A, Kühn L, Perumal T, Scott AJ, Hale MJ, Baillie V, Mahtab S, Williamson C, Joseph R, Sigal A, Joubert I, Piercy J, Thomson D, Fredericks DL, Miller MGA, Nunes MC, Madhi SA, Dheda K. SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset. Am J Respir Crit Care Med 2024; 209:840-851. [PMID: 38226855 PMCID: PMC10995573 DOI: 10.1164/rccm.202308-1438oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Rationale: In the upper respiratory tract, replicating (culturable) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recoverable for ∼4-8 days after symptom onset, but there is a paucity of data about the frequency and duration of replicating virus in the lower respiratory tract (i.e., the human lung).Objectives: We undertook lung tissue sampling (needle biopsy) shortly after death in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patients served as a control group.Methods: Lung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, and immunohistochemistry.Measurements and Main Results: Thirty-eight percent (16 of 42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 wk) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (P < 0.05). Nasopharyngeal culture was negative in 23.1% (6 of 26) of decedents despite lung culture positivity. This hitherto undescribed biophenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary proinflammatory response but with concurrent viral culture positivity.Conclusions: Concurrent rather than sequential active viral replication continues to drive a heightened proinflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe coronavirus disease (COVID-19).
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Affiliation(s)
- Michele Tomasicchio
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Shameem Jaumdally
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Lindsay Wilson
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Andrea Kotze
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Lynn Semple
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Stuart Meier
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Anil Pooran
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Komala Pillay
- Division of Anatomical Pathology, Department of Pathology, and
| | - Riyaadh Roberts
- Division of Anatomical Pathology, Department of Pathology, and
| | - Raymond Kriel
- Division of Anatomical Pathology, Department of Pathology, and
| | - Richard Meldau
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Suzette Oelofse
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Carley Mandviwala
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Jessica Burns
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Rolanda Londt
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Malika Davids
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Charnay van der Merwe
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Aqeedah Roomaney
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Louié Kühn
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Alex J. Scott
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sana Mahtab
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; and
| | - Ivan Joubert
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Jenna Piercy
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - David Thomson
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - David L. Fredericks
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Malcolm G. A. Miller
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Marta C. Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre of Excellence in Respiratory Pathogens, Hospices Civils de Lyon and Centre International de Recherche en Infectiologie, Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses, Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard – Lyon 1, Lyon, France
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
- Institute of Infectious Disease and Molecular Medicine
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Elias C, Nunes MC, Saadatian-Elahi M. Epidemiology of community-acquired pneumonia caused by S treptococcus pneumoniae in older adults: a narrative review. Curr Opin Infect Dis 2024; 37:144-153. [PMID: 38323404 DOI: 10.1097/qco.0000000000001005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
PURPOSE OF REVIEW This review covers updated perspectives on different aspects of pneumococcal community-acquired pneumonia (pCAP), including the epidemiology, clinical presentation, risk factors, antibiotic treatment, and existing preventive strategies in older adults. RECENT FINDINGS pCAP remains the most prevalent condition among lower respiratory tract infections in the older adults according to Global Burden of Diseases 2019. Older adults can display atypical symptoms such as confusion, general clinical deterioration, new onset of and exacerbation of underlying illness that might trigger clinical suspicion of pCAP. Older adults with pCAP often experience increased disease severity and a higher risk of pulmonary complications compared with younger individuals, owing to age-related changes in immunity and a higher prevalence of comorbidities. Vaccination stands fundamental for prevention, emphasizing the need for effective immunization strategies, specifically tailored for older adults. There is a pressing need to reinforce efforts aimed at boosting pneumococcal vaccination rates. SUMMARY Despite a high morbidity and mortality, the burden of pCAP, in particular hospital admission and occurrence of invasive infections, among the elderly population is not sufficiently documented. This review findings emphasize the substantial burden of pCAP in this vulnerable population, driven by factors such as advancing age and underlying comorbidities. The emergence of antibiotic-resistant pneumococcal strains further complicates treatment decisions and highlights the importance of tailored approaches for managing pCAP in older adults.
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Affiliation(s)
- Christelle Elias
- Service d'Hygiène, Epidémiologie, Infectiovigilance et Prévention, Hospices Civils de Lyon
- Équipe Santé Publique, Epidémiologie et Eco-évolution des Maladies Infectieuses (PHE ID), Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon
| | - Marta C Nunes
- Équipe Santé Publique, Epidémiologie et Eco-évolution des Maladies Infectieuses (PHE ID), Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mitra Saadatian-Elahi
- Service d'Hygiène, Epidémiologie, Infectiovigilance et Prévention, Hospices Civils de Lyon
- Équipe Santé Publique, Epidémiologie et Eco-évolution des Maladies Infectieuses (PHE ID), Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon
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8
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Wang X, Li Y, Shi T, Bont LJ, Chu HY, Zar HJ, Wahi-Singh B, Ma Y, Cong B, Sharland E, Riley RD, Deng J, Figueras-Aloy J, Heikkinen T, Jones MH, Liese JG, Markić J, Mejias A, Nunes MC, Resch B, Satav A, Yeo KT, Simões EAF, Nair H. Global disease burden of and risk factors for acute lower respiratory infections caused by respiratory syncytial virus in preterm infants and young children in 2019: a systematic review and meta-analysis of aggregated and individual participant data. Lancet 2024; 403:1241-1253. [PMID: 38367641 DOI: 10.1016/s0140-6736(24)00138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Infants and young children born prematurely are at high risk of severe acute lower respiratory infection (ALRI) caused by respiratory syncytial virus (RSV). In this study, we aimed to assess the global disease burden of and risk factors for RSV-associated ALRI in infants and young children born before 37 weeks of gestation. METHODS We conducted a systematic review and meta-analysis of aggregated data from studies published between Jan 1, 1995, and Dec 31, 2021, identified from MEDLINE, Embase, and Global Health, and individual participant data shared by the Respiratory Virus Global Epidemiology Network on respiratory infectious diseases. We estimated RSV-associated ALRI incidence in community, hospital admission, in-hospital mortality, and overall mortality among children younger than 2 years born prematurely. We conducted two-stage random-effects meta-regression analyses accounting for chronological age groups, gestational age bands (early preterm, <32 weeks gestational age [wGA], and late preterm, 32 to <37 wGA), and changes over 5-year intervals from 2000 to 2019. Using individual participant data, we assessed perinatal, sociodemographic, and household factors, and underlying medical conditions for RSV-associated ALRI incidence, hospital admission, and three severity outcome groups (longer hospital stay [>4 days], use of supplemental oxygen and mechanical ventilation, or intensive care unit admission) by estimating pooled odds ratios (ORs) through a two-stage meta-analysis (multivariate logistic regression and random-effects meta-analysis). This study is registered with PROSPERO, CRD42021269742. FINDINGS We included 47 studies from the literature and 17 studies with individual participant-level data contributed by the participating investigators. We estimated that, in 2019, 1 650 000 (95% uncertainty range [UR] 1 350 000-1 990 000) RSV-associated ALRI episodes, 533 000 (385 000-730 000) RSV-associated hospital admissions, 3050 (1080-8620) RSV-associated in-hospital deaths, and 26 760 (11 190-46 240) RSV-attributable deaths occurred in preterm infants worldwide. Among early preterm infants, the RSV-associated ALRI incidence rate and hospitalisation rate were significantly higher (rate ratio [RR] ranging from 1·69 to 3·87 across different age groups and outcomes) than for all infants born at any gestational age. In the second year of life, early preterm infants and young children had a similar incidence rate but still a significantly higher hospitalisation rate (RR 2·26 [95% UR 1·27-3·98]) compared with all infants and young children. Although late preterm infants had RSV-associated ALRI incidence rates similar to that of all infants younger than 1 year, they had higher RSV-associated ALRI hospitalisation rate in the first 6 months (RR 1·93 [1·11-3·26]). Overall, preterm infants accounted for 25% (95% UR 16-37) of RSV-associated ALRI hospitalisations in all infants of any gestational age. RSV-associated ALRI in-hospital case fatality ratio in preterm infants was similar to all infants. The factors identified to be associated with RSV-associated ALRI incidence were mainly perinatal and sociodemographic characteristics, and factors associated with severe outcomes from infection were mainly underlying medical conditions including congenital heart disease, tracheostomy, bronchopulmonary dysplasia, chronic lung disease, or Down syndrome (with ORs ranging from 1·40 to 4·23). INTERPRETATION Preterm infants face a disproportionately high burden of RSV-associated disease, accounting for 25% of RSV hospitalisation burden. Early preterm infants have a substantial RSV hospitalisation burden persisting into the second year of life. Preventive products for RSV can have a substantial public health impact by preventing RSV-associated ALRI and severe outcomes from infection in preterm infants. FUNDING EU Innovative Medicines Initiative Respiratory Syncytial Virus Consortium in Europe.
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Affiliation(s)
- Xin Wang
- National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, China; Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - You Li
- National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, China; Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Ting Shi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Louis J Bont
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands; ReSViNET Foundation, Zeist, Netherlands
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Bhanu Wahi-Singh
- Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Yiming Ma
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Bingbing Cong
- National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Emma Sharland
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Richard D Riley
- Centre for Prognosis Research, School of Medicine, Keele University, Keele, UK
| | - Jikui Deng
- Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | | | - Terho Heikkinen
- Department of Pediatrics, Turku University Hospital, Turku, Finland; Department of Pediatrics, University of Turku, Turku, Finland
| | - Marcus H Jones
- Department of Pediatrics, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Johannes G Liese
- Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Joško Markić
- Department of Pediatrics, University Hospital Split, Split, Croatia; School of Medicine, University of Split, Split, Croatia
| | - Asuncion Mejias
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Marta C Nunes
- South African Medical Research Council, Wits Vaccines and Infectious Diseases Analytics Research Unit and Department of Science and Technology and National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Center of Excellence in Respiratory Pathogens, Hospices Civils de Lyon, and Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Bernhard Resch
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria; Division of Neonatology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Ashish Satav
- MAHAN Trust Mahatma Gandhi Tribal Hospital, District Amaravati, Maharashtra, India
| | - Kee Thai Yeo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Neonatology, KK Women's and Children's Hospital, Singapore; Duke-NUS Medical School, Singapore
| | - Eric A F Simões
- Department of Pediatrics, Section of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO, USA; Department of Epidemiology and Center for Global Health, Colorado School of Public Health, Aurora, CO, USA
| | - Harish Nair
- National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, China; Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK; MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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9
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Johnson M, Lazarus SK, Bennett AE, Tovar-Salazar A, Robertson CE, Kofonow JM, Li S, McCollister B, Nunes MC, Madhi SA, Frank DN, Weinberg A. Gut Microbiota and Other Factors Associated With Increased Regulatory T Cells in Hiv-exposed Uninfected Infants. Res Sq 2024:rs.3.rs-3909424. [PMID: 38352510 PMCID: PMC10862973 DOI: 10.21203/rs.3.rs-3909424/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
HIV-exposed uninfected infants (HEU) have higher infectious morbidity than HIV-unexposed infants (HUU). HEU have multiple immune defects of unknown origin. We hypothesized that HEU have higher regulatory T cells (Treg) than HUU, which may dampen their immune defenses against pathogens. We compared 25 Treg subsets between HEU and HUU and sought the factors that may affect Treg frequencies. At birth, 3 Treg subsets, including CD4 + FOXP3 + and CD4 + FOXP3 + CD25+, had higher frequencies in 123 HEU than 117 HUU and 3 subsets were higher in HUU. At 28 and 62 weeks of life, 5 Treg subsets were higher in HEU, and none were higher in HUU. The frequencies of the discrepant Treg subsets correlated at birth with differential abundances of bacterial taxas in maternal gut microbiome and at subsequent visits in infant gut microbiomes. In vitro, bacterial taxa most abundant in HEU expanded Treg subsets with higher frequencies in HEU, recapitulating the in vivo observations. Other factors that correlated with increased Treg were low maternal CD4 + T cells in HEU at birth and male sex in HUU at 28 weeks. We conclude that maternal and infant gut dysbiosis are central to the Treg increase in HEU and may be targeted by mitigating interventions.
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10
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Olwagen CP, Downs SL, Izu A, Tharasimbi L, Van Der Merwe L, Nunes MC, Madhi SA. Bacterial nasopharyngeal colonisation in children in South Africa before and during the COVID-19 pandemic: an observational study. Lancet Microbe 2024; 5:e34-e42. [PMID: 38048806 PMCID: PMC10789613 DOI: 10.1016/s2666-5247(23)00260-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Deployment of non-pharmaceutical interventions such as face masking and physical distancing during the COVID-19 pandemic could have altered the transmission dynamics and carriage of respiratory organisms. We evaluated colonisation with Streptococcus pneumoniae and other upper respiratory tract bacterial colonisers before and during the COVID-19 pandemic. METHODS We did two cross-sectional surveys in Soweto, South Africa from July 3 to Dec 13, 2018 (pre-COVID-19 period) and from Aug 4, 2021, to March 31, 2022 (COVID-19 period) in healthy children (aged ≤60 months) who had recorded HIV status and had not received antibiotics in the 21 days before enrolment. At enrolment, we collected nasopharyngeal swab samples from child participants. Following nucleic acid extraction, nanofluidic quantitative PCR was used to screen all samples for 92 S pneumoniae serotypes and 14 other bacteria. The primary objective was to compare the prevalence and density of pneumococcal nasopharyngeal colonisation, overall and stratified by 13-valent pneumococcal conjugate vaccine (PCV13) serotypes and non-vaccine serotypes. Secondary study objectives included a comparison of serotype-specific pneumococcal colonisation and density, as well as colonisation by the 14 other bacteria in the COVID-19 versus pre-COVID-19 period. We used an adjusted multiple logistic and linear regression model to compare the colonisation prevalence and density between study periods. FINDINGS We analysed nasopharyngeal swabs from 1107 children (n=571 in the pre-COVID-19 period; n=536 in the COVID-19 period). We observed no change in overall pneumococcal colonisation between periods (274 [51%] of 536 in the COVID-19 period vs 282 [49%] of 571 in the pre-COVID-19 period; adjusted odds ratio [aOR] 1·03 [95% CI 0·95-1·12]). The prevalence of PCV13 serotypes was lower in the COVID-19 than in the pre-COVID-19 period (72 [13%] vs 106 [19%]; 0·87 [0·78-0·97]), whereas the prevalence of non-typeable S pneumoniae was higher (34 [6%] vs 63 [12%]; 1·30 [1·12-1·50]). The mean log10 density for overall pneumococcal colonisation was lower in the COVID-19 period than in the pre-COVID-19 period (3·96 [95% CI 3·85-4·07] vs 4·72 [4·63-4·80] log10 genome equivalents per mL; p<0·0001). A lower density of non-vaccine serotypes (3·63 [3·51-3·74] vs 4·08 [3·95-4·22] log10 genome equivalents per mL; p<0·0001) and non-typeable S pneumoniae (3·11 [2·94-3·29] vs 4·41 [4·06-4·75] log10 genome equivalents per mL; p<0·00001) was also observed in the COVID-19 period. There was no difference in the density of PCV13 serotypes between the periods. The prevalence of colonisation during the COVID-19 versus pre-COVID-19 period was lower for non-typeable Haemophilus influenzae (280 [49%] vs 165 [31%]; aOR 0·77 [95% CI 0·71-0·84]), Moraxella catarrhalis (328 [57%] vs 242 [45%]; 0·85 [0·79-0·92]), and Neisseria lactamica (51 [9%] vs 13 [2%]; 0·64 [0·52-0·78]), but higher for Acinetobacter baumannii (34 [6%] vs 102 [19%]; 1·55 [1·35-1·77]) and Staphylococcus aureus (29 [5%] vs 52 [10%]; 1·28 [1·10-1·50]). INTERPRETATION There were variable effects on the colonisation prevalence and density of bacterial organisms during the COVID-19 compared with the pre-COVID-19 period. The lower prevalence of PCV13 serotype together with other respiratory organisms including non-typeable H influenzae and M catarrhalis could have in part contributed to a decrease in all-cause lower respiratory tract infections observed in South Africa during the initial stage of the COVID-19 pandemic. The pathophysiological mechanism for the increase in A baumannii and S aureus colonisation warrants further investigation, as does the clinical relevance of these findings. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Sarah L Downs
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Alane Izu
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Lebohang Tharasimbi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Lara Van Der Merwe
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Marta C Nunes
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Centre of Excellence in Respiratory Pathogens, Hospices Civils de Lyon, and Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Lyon, France
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science-National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Wits Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.
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11
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Olwagen CP, Jeche TR, Van Der Merwe L, Nunes MC, Madhi SA, Baillie VL. Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia. Sci Rep 2023; 13:21332. [PMID: 38049501 PMCID: PMC10695952 DOI: 10.1038/s41598-023-48045-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
Pneumonia is a major cause of death among adults living with HIV in South Africa, but the etiology of many cases remains unknown. This study evaluated the utility of a nanofluidic qPCR assay to detect and serotype Streptococcus pneumoniae in urine samples from patients hospitalized with community-acquired pneumonia (CAP). The nanofluidic qPCR assay was optimized to target 13 pneumococcal serotypes and 4 reference genes. Archived urine samples collected from patients > 15 years of age hospitalized with pneumonia between April 2018 and August 2019 were retrospectively tested using the nanofluidic qPCR assay, BinaxNOW urine antigen test, and standard LytA qPCR. Blood culture was undertaken on a subset of the samples at the discretion of the attending physician. Cohens' Kappa statistics were used to determine the concordance between the methods. Of the 828 adults hospitalized for CAP, urine samples were available in 53% (n = 439). Of those, a random subset of 96 (22%) samples underwent testing. Of the participants included in the final analysis, the mean age was 45.8 years (SD 16.2), 49% (n = 47) were female, 98% (n = 94) were black, and 66% (n = 63) were living with HIV infection. The nanofluidic qPCR method was able to detect PCV13 vaccine strains spiked into urine samples; however, the method failed to detect any pneumococcus in clinical samples. In comparison, 19% of the pneumonia cases were attributed to S. pneumoniae using urine antigen testing. Nanofluidic qPCR is unable to detect and serotype Streptococcus pneumoniae in urine samples of South Africans hospitalized with CAP.
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Affiliation(s)
- Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.
| | - Tariro R Jeche
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Lara Van Der Merwe
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Centre of Excellence in Respiratory Pathogens, Hospices Civils de Lyon, and Centre International de Recherche en Infectiologie (CIRI), Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, U1111, Lyon, France
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky L Baillie
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
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12
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Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom 2023; 9:001162. [PMID: 38117675 PMCID: PMC10763497 DOI: 10.1099/mgen.0.001162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.
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Affiliation(s)
- Fahima Moosa
- 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
| | - 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
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dineo Mogale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 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
| | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J. Zar
- Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - 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
| | - 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
| | - 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
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13
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Nunes MC, Tamblyn A, Jose L, Ntsimane M, Lerotholi N, Machimana C, Taylor A, Laher F, Madhi SA. Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV. AIDS 2023; 37:2305-2310. [PMID: 37773052 PMCID: PMC10653295 DOI: 10.1097/qad.0000000000003731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023]
Abstract
OBJECTIVE Vaccination during pregnancy with tetanus-diphtheria-acellular pertussis (Tdap) vaccine is recommended to protect the young infants against pertussis. There is a paucity of data on immune responses to Tdap in pregnant women with HIV (PWWH), and its impact on the protection of their infants has not been described. METHODS In an open label phase IV clinical trial in South Africa, we evaluated the immunogenicity and safety of Tdap in PWWH compared with HIV-uninfected women. Antigen-specific immunoglobulin G (IgG) to pertussis toxoid, filamentous haemagglutinin, pertactin, fimbriae, diphtheria and tetanus were measured by electrochemiluminescence-based multiplex assay. RESULTS Overall, 91 PWWH and 136 HIV-uninfected pregnant women were enrolled. All PWWH were on antiretroviral treatment and 94.5% had HIV viral loads <40 copies per millilitre. Antibody levels prevaccination were lower among PWWH compared with HIV-uninfected women for all antigens. At 1 month postvaccination PWWH compared with HIV-uninfected women had lower fold-increase and antibody concentrations for all epitopes. Also, a lower proportion of PWWH achieved ≥4-fold increase from pre to postvaccination for pertussis toxoid and pertactin, or diphtheria IgG levels ≥0.1 IU/ml and ≥1 IU/ml postvaccination. Adverse events postvaccination were similar in PWWH and HIV-uninfected. CONCLUSION Tdap vaccination was safe and immunogenic. PWHW had, however, attenuated humoral immune responses, which could affect the effectiveness of protecting their infants against pertussis compared with those born to women without HIV.ClinicalTrials.gov identifier: NCT05264662.
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Affiliation(s)
- Marta C. Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon and Centre International de Recherche en Infectiologie (CIRI), Équipe Santé publique, épidémiologie et écologie évolutive des maladies infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Amy Tamblyn
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Lisa Jose
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Mathapelo Ntsimane
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Ntoetse Lerotholi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Charmaine Machimana
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Ashleigh Taylor
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Farzanah Laher
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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14
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Wilson L, Chang JW, Meier S, Ganief T, Ganief N, Oelofse S, Baillie V, Nunes MC, Madhi SA, Blackburn J, Dheda K. Proteomic Profiling of Urine From Hospitalized Patients With Severe Pneumonia due to SARS-CoV-2 vs Other Causes: A Preliminary Report. Open Forum Infect Dis 2023; 10:ofad451. [PMID: 37799131 PMCID: PMC10549212 DOI: 10.1093/ofid/ofad451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
The pathogenesis of coronavirus disease 2019 (COVID-19) pneumonia remains poorly understood. The urine proteome of hospitalized patients with severe COVID-19 pneumonia, compared with severe non-COVID-19 pneumonia controls, was distinct and associated with lower abundance of several host proteins. Protein-specific machine learning analysis outlined biomarker combinations able to differentiate COVID-19 pneumonia from non-COVID-19 pneumonia controls.
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Affiliation(s)
- Lindsay Wilson
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Ju-Wei Chang
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Stuart Meier
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Tariq Ganief
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Naadir Ganief
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Suzette Oelofse
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Vicky Baillie
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Blackburn
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
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15
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Downs SL, Olwagen CP, Van Der Merwe L, Nzenze SA, Nunes MC, Madhi SA. Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children. Int J Infect Dis 2023; 134:45-52. [PMID: 37209864 PMCID: PMC10404162 DOI: 10.1016/j.ijid.2023.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVES Pneumococcal conjugate vaccines (PCVs) reduce pneumococcal-associated disease by reducing vaccine-serotype (VT) acquisition in vaccinated children, thereby interrupting VT transmission. The 7-valent-PCV was introduced in the South African immunization program in 2009 (13-valent-PCV since 2011) using a 2+1 schedule (at 6, 14, and 40 weeks of age). We aimed to evaluate temporal changes in VT and non-vaccine-serotype (NVT) colonization after 9 years of childhood PCV immunization in South Africa. METHODS Nasopharyngeal swabs were collected from healthy children <60-month-old (n = 571) in 2018 (period-2) and compared with samples (n = 1135) collected during early PCV7-introduction (period-1, 2010-11) in an urban low-income setting (Soweto). Pneumococci were tested for using a multiplex quantitative-polymerase chain reaction serotyping reaction-set. RESULTS Overall pneumococcal colonization in period-2 (49.4%; 282/571) was 27.5% lower than period-1 (68.1%; 773/1135; adjusted odds ratio [aOR]: 0.66; 95% confidence interval [CI]: 0.54-0.88). Colonization by VT was reduced by 54.5% in period-2 (18.6%; 106/571) compared with period-1 (40.9%; 465/1135; aOR: 0.41; 95% CI: 0.3-0.56). Nevertheless, serotype 19F carriage prevalence was higher (8.1%; 46/571) in period-2 compared with period-1 (6.6%; 75/1135; aOR: 2.0; 95% CI: 1.09-3.56). NVT colonization prevalence was similar in period-2 and period-1 (37.8%; 216/571 and 42.4%; 481/1135). CONCLUSION There remains a high residual prevalence of VT, particularly 19F, colonization nine years post-introduction of PCV in the South African childhood immunization program.
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Affiliation(s)
- Sarah L Downs
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.
| | - Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Lara Van Der Merwe
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Susan A Nzenze
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C Nunes
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
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16
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Izu A, Nunes MC, Solomon F, Baillie V, Serafin N, Verwey C, Moore DP, Laubscher M, Ncube M, Olwagen C, Dangor Z, Madhi SA. All-cause and pathogen-specific lower respiratory tract infection hospital admissions in children younger than 5 years during the COVID-19 pandemic (2020-22) compared with the pre-pandemic period (2015-19) in South Africa: an observational study. Lancet Infect Dis 2023; 23:1031-1041. [PMID: 37141913 PMCID: PMC10151031 DOI: 10.1016/s1473-3099(23)00200-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Non-pharmaceutical interventions affected the circulation of and illness due to endemic respiratory pathogens during the COVID-19 pandemic. We investigated the incidence of admissions to hospital for overall and specific pathogen-associated lower respiratory tract infection (LRTI) during the COVID-19 pandemic compared with incidence in the pre-pandemic period. METHODS In this observational study, we analysed surveillance data for children younger than 5 years from two public hospitals in Soweto, South Africa, for all-cause LRTI, respiratory syncytial virus (RSV), influenza, human metapneumovirus, and Bordetella pertussis from Jan 1, 2015 to Dec 31, 2022. Data were obtained from an electronic database that includes information for all admissions to the general paediatric wards at the two hospitals, automatically identified by a computer program. We excluded children admitted to hospital with incidental SARS-CoV-2 infection or COVID-19 without LRTI diagnosis. Incidence during COVID-19 pandemic years (2020, 2021, and 2022) were compared with pre-pandemic rates (2015-19). FINDINGS Overall, there were 42 068 all-cause hospital admissions, including 18 303 all-cause LRTI hospital admissions, from Jan 1, 2015, to Dec 31, 2022, 17 822 (42·4%) of whom were female, 23 893 (57·0%) were male, and 353 (0·8%) had missing data. All-cause LRTI incidence risk ratio (IRR) was 30% lower in 2020 (IRR 0·70, 95% CI 0·67-0·74) and 13% lower in 2021 (0·87, 0·83-0·91), but 16% higher in 2022 (1·16, 1·11-1·21) compared with the pre-pandemic period. Furthermore, compared with the pre-pandemic period, incidence of RSV-associated LRTI (0·52, 0·45-0·58), influenza-associated LRTI (0·05, 0·02-0·11), and pulmonary tuberculosis (0·52, 0·41-0·65) were lower in 2020, with similar trends observed for human-metapneumovirus-associated LRTI, pertussis, and invasive pneumococcal disease (IPD). Compared with the pre-pandemic period, by 2022, RSV-associated LRTI incidence was similar (1·04, 0·95-1·14) and influenza-associated LRTI showed a non-significant increase (1·14, 0·92-1·39), whereas incidence remained lower for tuberculosis (0·79, 0·65-0·94) and IPD (0·51, 0·24-0·99). In 2022, the incidence of COVID-19-associated LRTI hospital admission (65 per 100 000 children younger than 5 years) was lower than pre-pandemic RSV-associated LRTI (0·23, 0·19-0·27) but higher than pre-pandemic influenza-associated LRTI (1·19, 0·97-1·45), although the difference was not significant. All-cause LRTI death in 2022 (57 per 100 000 children younger than 5 years) was 28% higher than in the pre-pandemic period (1·28, 1·03-1·58). INTERPRETATION The higher incidence of all-cause LRTI admissions to hospital in 2022 compared with the pre-pandemic period is partly due to ongoing COVID-19 admission to hospital, and could worsen if other endemic respiratory pathogens revert to pre-pandemic incidence. Interventions, including the introduction of vaccines for people who are pregnant that aim to prevent RSV and possibly COVID-19 in young children, are warranted. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Alane Izu
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa; Center of Excellence in Respiratory Pathogens, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale, Université Claude Bernard Lyon, Lyon, France
| | - Fatima Solomon
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky Baillie
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Charl Verwey
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - David P Moore
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Marius Laubscher
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Musawenkosi Ncube
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Courtney Olwagen
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Dangor
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, National Research Foundation: Vaccine Preventable Diseases, Department of Science, University of the Witwatersrand, Johannesburg, South Africa.
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17
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Saadatian-Elahi M, Henaff L, Elias C, Nunes MC, Hot A, Martin-Gaujard G, Escuret V, Amour S, Vanhems P. Patient influenza vaccination reduces the risk of hospital-acquired influenza: An incident test negative-case control study in Lyon university hospital, France (2004-2020). Vaccine 2023; 41:4341-4346. [PMID: 37321894 DOI: 10.1016/j.vaccine.2023.05.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/02/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Literature is limited on the impact of patient vaccination on the risk of hospital-acquired influenza (HAI). This test negative case-control study nested in a surveillance program aimed at evaluating the effectiveness of influenza vaccination in reducing the risk of HAI in hospitalized patients during 15 influenza seasons (2004-05 to 2019-20). METHODS HAI cases were those who developed influenza like illness (ILI) symptoms at least 72 h after hospitalization and had a positive reverse transcriptase-polymerase chain reaction (RT-PCR). Controls were those with ILI symptoms and a negative RT-PCR test. A nasal swab as well as socio-demographic, clinical data and information on influenza vaccination were collected. RESULTS Of the 296 patients included, 67 were confirmed HAI cases. Influenza vaccine coverage was significantly higher among controls compared to HAI cases (p = 0.002). The risk of HAI was reduced by almost 60 % in vaccinated patients. CONCLUSIONS A better control of HAI can be achieved by vaccinating hospitalized patients.
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Affiliation(s)
- Mitra Saadatian-Elahi
- Service Hygiène, Epidémiologie et Prévention, Centre Hospitalier Hôpital Eduard Herriot, Hospices Civils de Lyon, 69437 Lyon Cedex, France; CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Laetitia Henaff
- Service Hygiène, Epidémiologie et Prévention, Centre Hospitalier Hôpital Eduard Herriot, Hospices Civils de Lyon, 69437 Lyon Cedex, France; CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Christelle Elias
- Service Hygiène, Epidémiologie et Prévention, Centre Hospitalier Hôpital Eduard Herriot, Hospices Civils de Lyon, 69437 Lyon Cedex, France; CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Marta C Nunes
- CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; Centre for Excellence in Respiratory Pathogens, Hospices Civils de Lyon, Lyon, France; South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arnaud Hot
- Internal Medicine, University Hospital Edouard Herriot, Hospices Civils de Lyon, France
| | | | - Vanessa Escuret
- Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Virpath - Grippe, de l'émergence au contrôle, Centre International de Recherche en Infectiologie (CIRI), Inserm U111, CNRS 5308, ENS, UCBL1, Faculté de Médecine RTH Laënnec, Lyon, France
| | - Selilah Amour
- Service Hygiène, Epidémiologie et Prévention, Centre Hospitalier Hôpital Eduard Herriot, Hospices Civils de Lyon, 69437 Lyon Cedex, France; CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Philippe Vanhems
- Service Hygiène, Epidémiologie et Prévention, Centre Hospitalier Hôpital Eduard Herriot, Hospices Civils de Lyon, 69437 Lyon Cedex, France; CIRI, Centre International de Recherche en Infectiologie, (Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
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18
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Wilkins D, Langedijk AC, Lebbink RJ, Morehouse C, Abram ME, Ahani B, Aksyuk AA, Baraldi E, Brady T, Chen AT, Chi H, Choi EH, Cohen R, Danilenko DM, Gopalakrishnan V, Greenough A, Heikkinen T, Hosoya M, Keller C, Kelly EJ, Kragten-Tabatabaie L, Martinón-Torres F, de Los Santos AHM, Nunes MC, Palomino MA, Papenburg J, Pernica JM, Richmond P, Stein RT, Tuffy KM, Verwey C, Esser MT, Tabor DE, Bont LJ. Nirsevimab binding-site conservation in respiratory syncytial virus fusion glycoprotein worldwide between 1956 and 2021: an analysis of observational study sequencing data. Lancet Infect Dis 2023; 23:856-866. [PMID: 36940703 DOI: 10.1016/s1473-3099(23)00062-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Nirsevimab is an extended half-life monoclonal antibody to the respiratory syncytial virus (RSV) fusion protein that has been developed to protect infants for an entire RSV season. Previous studies have shown that the nirsevimab binding site is highly conserved. However, investigations of the geotemporal evolution of potential escape variants in recent (ie, 2015-2021) RSV seasons have been minimal. Here, we examine prospective RSV surveillance data to assess the geotemporal prevalence of RSV A and B, and functionally characterise the effect of the nirsevimab binding-site substitutions identified between 2015 and 2021. METHODS We assessed the geotemporal prevalence of RSV A and B and nirsevimab binding-site conservation between 2015 and 2021 from three prospective RSV molecular surveillance studies (the US-based OUTSMART-RSV, the global INFORM-RSV, and a pilot study in South Africa). Nirsevimab binding-site substitutions were assessed in an RSV microneutralisation susceptibility assay. We contextualised our findings by assessing fusion-protein sequence diversity from 1956 to 2021 relative to other respiratory-virus envelope glycoproteins using RSV fusion protein sequences published in NCBI GenBank. FINDINGS We identified 5675 RSV A and RSV B fusion protein sequences (2875 RSV A and 2800 RSV B) from the three surveillance studies (2015-2021). Nearly all (25 [100%] of 25 positions of RSV A fusion proteins and 22 [88%] of 25 positions of RSV B fusion proteins) amino acids within the nirsevimab binding site remained highly conserved between 2015 and 2021. A highly prevalent (ie, >40·0% of all sequences) nirsevimab binding-site Ile206Met:Gln209Arg RSV B polymorphism arose between 2016 and 2021. Nirsevimab neutralised a diverse set of recombinant RSV viruses, including new variants containing binding-site substitutions. RSV B variants with reduced susceptibility to nirsevimab neutralisation were detected at low frequencies (ie, prevalence <1·0%) between 2015 and 2021. We used 3626 RSV fusion-protein sequences published in NCBI GenBank between 1956 and 2021 (2024 RSV and 1602 RSV B) to show that the RSV fusion protein had lower genetic diversity than influenza haemagglutinin and SARS-CoV-2 spike proteins. INTERPRETATION The nirsevimab binding site was highly conserved between 1956 and 2021. Nirsevimab escape variants were rare and have not increased over time. FUNDING AstraZeneca and Sanofi.
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Affiliation(s)
- Deidre Wilkins
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Annefleur C Langedijk
- Division of Paediatric Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, Netherlands
| | | | - Michael E Abram
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Bahar Ahani
- Bioinformatics, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Anastasia A Aksyuk
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Eugenio Baraldi
- Woman's and Child's Health, Neonatal Intensive Care Unit, University of Padova, Padova, Italy; Institute of Pediatric Research, Città della Speranza, Padova, Italy
| | - Tyler Brady
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Albert Tian Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Hsin Chi
- Department of Paediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, South Korea
| | - Robert Cohen
- Université Paris XII, Créteil, FranceAssociation Clinique et Thérapeutique Infantile du Val-de-Marne (ACTIV), Créteil, France; Clinical Research Center, Centre Hospitalier Intercommunal de Créteil (CHIC), Créteil, France
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | | | - Anne Greenough
- Department of Women and Children's Health, King's College London, London, UK; ReSViNET foundation, Zeist, Netherlands
| | - Terho Heikkinen
- ReSViNET foundation, Zeist, Netherlands; Department of Pediatrics, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Mitsuaki Hosoya
- School of Medicine, Fukushima Medical University, Fukushima, Japan
| | | | - Elizabeth J Kelly
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Federico Martinón-Torres
- ReSViNET foundation, Zeist, Netherlands; Translational Paediatrics and Infectious Diseases, Paediatrics Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Pediatrics and Infectious Diseases Section, Pediatrics Department, Hospital Clínico Universitario de Santiago, Galicia, Spain
| | | | - Marta C Nunes
- ReSViNET foundation, Zeist, Netherlands; South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Jesse Papenburg
- Department of Pediatrics, McGill University Health Centre, Montreal, QC, Canada
| | - Jeffrey M Pernica
- Division of Infectious Diseases, McMaster University, Hamilton, ON, Canada
| | - Peter Richmond
- Division of Pediatrics, School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Renato T Stein
- ReSViNET foundation, Zeist, Netherlands; Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Kevin M Tuffy
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Charl Verwey
- Department of Paediatrics and Child Health, School of Clinical Medicine and South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark T Esser
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
| | - David E Tabor
- Translational Medicine, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Louis J Bont
- Department of Paediatrics, University Medical Centre Utrecht, Utrecht, Netherlands; ReSViNET foundation, Zeist, Netherlands
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Andrew MK, Pott H, Staadegaard L, Paget J, Chaves SS, Ortiz JR, McCauley J, Bresee J, Nunes MC, Baumeister E, Raboni SM, Giamberardino HIG, McNeil SA, Gomez D, Zhang T, Vanhems P, Koul PA, Coulibaly D, Otieno NA, Dbaibo G, Almeida MLG, Laguna-Torres VA, Drăgănescu AC, Burtseva E, Sominina A, Danilenko D, Medić S, Diez-Domingo J, Lina B. Age Differences in Comorbidities, Presenting Symptoms, and Outcomes of Influenza Illness Requiring Hospitalization: A Worldwide Perspective From the Global Influenza Hospital Surveillance Network. Open Forum Infect Dis 2023; 10:ofad244. [PMID: 37383245 PMCID: PMC10296081 DOI: 10.1093/ofid/ofad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/26/2023] [Indexed: 06/30/2023] Open
Abstract
Background The Global Influenza Hospital Surveillance Network (GIHSN) was established in 2012 to conduct coordinated worldwide influenza surveillance. In this study, we describe underlying comorbidities, symptoms, and outcomes in patients hospitalized with influenza. Methods Between November 2018 and October 2019, GIHSN included 19 sites in 18 countries using a standardized surveillance protocol. Influenza infection was laboratory-confirmed with reverse-transcription polymerase chain reaction. A multivariate logistic regression model was utilized to analyze the extent to which various risk factors predict severe outcomes. Results Of 16 022 enrolled patients, 21.9% had laboratory-confirmed influenza; 49.2% of influenza cases were A/H1N1pdm09. Fever and cough were the most common symptoms, although they decreased with age (P < .001). Shortness of breath was uncommon among those <50 years but increased with age (P < .001). Middle and older age and history of underlying diabetes or chronic obstructive pulmonary disease were associated with increased odds of death and intensive care unit (ICU) admission, and male sex and influenza vaccination were associated with lower odds. The ICU admissions and mortality occurred across the age spectrum. Conclusions Both virus and host factors contributed to influenza burden. We identified age differences in comorbidities, presenting symptoms, and adverse clinical outcomes among those hospitalized with influenza and benefit from influenza vaccination in protecting against adverse clinical outcomes. The GIHSN provides an ongoing platform for global understanding of hospitalized influenza illness.
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Affiliation(s)
- Melissa K Andrew
- Correspondence: Melissa K. Andrew, MD, PhD, Department of Medicine (Geriatrics), Dalhousie University, 5955 Veterans Memorial Lane, Halifax, NS B3H 2E1, Canada (); Bruno Lina, Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, 103 Grande Rue de la Croix-Rousse, Lyon, 69317 CEDEX 04, France ()
| | - Henrique Pott
- Dalhousie University and Canadian Center for Vaccinology, Halifax, Canada
- Department of Medicine, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Lisa Staadegaard
- Netherlands Institute for Health Care Research (Nivel), Utrecht, Netherlands
| | - John Paget
- Netherlands Institute for Health Care Research (Nivel), Utrecht, Netherlands
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
| | - Justin R Ortiz
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - John McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Institute, London, United Kingdom
| | - Joseph Bresee
- Centre for Vaccine Equity, Task Force for Global Health, Atlanta, Georgia, USA
| | - Marta C Nunes
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa
| | - Elsa Baumeister
- National Reference Laboratory for Viral Respiratory Diseases, Virology Department, INEI-ANLIS, Buenos Aires, Argentina
| | - Sonia Mara Raboni
- Molecular Biology/Microbiology Research Laboratory, Universidade Federal do Paraná, Curitiba, Brazil
| | - Heloisa I G Giamberardino
- Epidemiology, Immunization and Infection Control Department—Hospital Pequeno Principe, Curitiba, Paraná, Brazil
| | - Shelly A McNeil
- Dalhousie University and Canadian Center for Vaccinology, Halifax, Canada
| | - Doris Gomez
- Grupo de Investigación UNIMOL, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Tao Zhang
- School of Public Health, Fudan University, Shanghai, China
| | | | | | - Daouda Coulibaly
- Institut National d'Hygiène Publique (INHP), Abidjan, Côte d’Ivoire
| | - Nancy A Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | | | | | | | - Elena Burtseva
- FSBI “N.F. Gamaleya NRCEM” Ministry of Health of the Russian Federation (Federal Research Budgetary Institute “National Research Center of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya), Moscow, Russia
| | - Anna Sominina
- Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Snežana Medić
- Institute of Public Health of Vojvodina, Novi Sad, Serbia
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | | | - Bruno Lina
- Correspondence: Melissa K. Andrew, MD, PhD, Department of Medicine (Geriatrics), Dalhousie University, 5955 Veterans Memorial Lane, Halifax, NS B3H 2E1, Canada (); Bruno Lina, Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, 103 Grande Rue de la Croix-Rousse, Lyon, 69317 CEDEX 04, France ()
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20
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Dunne EM, Nunes MC, Slack MPE, Theilacker C, Gessner BD. Effects of pneumococcal conjugate vaccines on reducing the risk of respiratory disease associated with coronavirus infection. Pneumonia (Nathan) 2023; 15:10. [PMID: 37226198 DOI: 10.1186/s41479-023-00112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/30/2023] [Indexed: 05/26/2023] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) provide protection against vaccine-type pneumococcal disease in both children and adults. Growing evidence suggests that PCVs also reduce pneumonia and lower respiratory tract infections (LRTIs) more broadly, including protecting against viral-associated respiratory diseases. In this short narrative review, we highlight clinical studies investigating whether PCVs might have a role in reducing coronavirus disease, both those caused by endemic human coronaviruses (HCoVs) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). These studies include two randomized controlled trials assessing HCoV-associated pneumonia, one each in children and older adults, and two observational studies of PCV13 effectiveness against HCoV-associated LRTI and COVID-19 in adults. We discuss possible mechanisms for PCV protection including preventing viral pneumococcal co-infections and the possibility that pneumococci in the upper respiratory tract might modify the host immune response to SARS-CoV-2. Lastly, we identify knowledge gaps and further questions on the potential role of PCVs during the COVID-19 pandemic.
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Affiliation(s)
| | - Marta C Nunes
- Center of Excellence in Respiratory Pathogens, Hospices Civils de Lyon and Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard, Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mary P E Slack
- School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, Australia
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21
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Hooli S, King C, McCollum ED, Colbourn T, Lufesi N, Mwansambo C, Gregory CJ, Thamthitiwat S, Cutland C, Madhi SA, Nunes MC, Gessner BD, Hazir T, Mathew JL, Addo-Yobo E, Chisaka N, Hassan M, Hibberd PL, Jeena P, Lozano JM, MacLeod WB, Patel A, Thea DM, Nguyen NTV, Zaman SM, Ruvinsky RO, Lucero M, Kartasasmita CB, Turner C, Asghar R, Banajeh S, Iqbal I, Maulen-Radovan I, Mino-Leon G, Saha SK, Santosham M, Singhi S, Awasthi S, Bavdekar A, Chou M, Nymadawa P, Pape JW, Paranhos-Baccala G, Picot VS, Rakoto-Andrianarivelo M, Rouzier V, Russomando G, Sylla M, Vanhems P, Wang J, Basnet S, Strand TA, Neuman MI, Arroyo LM, Echavarria M, Bhatnagar S, Wadhwa N, Lodha R, Aneja S, Gentile A, Chadha M, Hirve S, O'Grady KAF, Clara AW, Rees CA, Campbell H, Nair H, Falconer J, Williams LJ, Horne M, Qazi SA, Nisar YB. In-hospital mortality risk stratification in children aged under 5 years with pneumonia with or without pulse oximetry: A secondary analysis of the Pneumonia REsearch Partnership to Assess WHO REcommendations (PREPARE) dataset. Int J Infect Dis 2023; 129:240-250. [PMID: 36805325 PMCID: PMC10017350 DOI: 10.1016/j.ijid.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/01/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023] Open
Abstract
OBJECTIVES We determined the pulse oximetry benefit in pediatric pneumonia mortality risk stratification and chest-indrawing pneumonia in-hospital mortality risk factors. METHODS We report the characteristics and in-hospital pneumonia-related mortality of children aged 2-59 months who were included in the Pneumonia Research Partnership to Assess WHO Recommendations dataset. We developed multivariable logistic regression models of chest-indrawing pneumonia to identify mortality risk factors. RESULTS Among 285,839 children, 164,244 (57.5%) from hospital-based studies were included. Pneumonia case fatality risk (CFR) without pulse oximetry measurement was higher than with measurement (5.8%, 95% confidence interval [CI] 5.6-5.9% vs 2.1%, 95% CI 1.9-2.4%). One in five children with chest-indrawing pneumonia was hypoxemic (19.7%, 95% CI 19.0-20.4%), and the hypoxemic CFR was 10.3% (95% CI 9.1-11.5%). Other mortality risk factors were younger age (either 2-5 months [adjusted odds ratio (aOR) 9.94, 95% CI 6.67-14.84] or 6-11 months [aOR 2.67, 95% CI 1.71-4.16]), moderate malnutrition (aOR 2.41, 95% CI 1.87-3.09), and female sex (aOR 1.82, 95% CI 1.43-2.32). CONCLUSION Children with a pulse oximetry measurement had a lower CFR. Many children hospitalized with chest-indrawing pneumonia were hypoxemic and one in 10 died. Young age and moderate malnutrition were risk factors for in-hospital chest-indrawing pneumonia-related mortality. Pulse oximetry should be integrated in pneumonia hospital care for children under 5 years.
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Affiliation(s)
- Shubhada Hooli
- Division of Pediatric Emergency Medicine, Texas Children's Hospital/Baylor College of Medicine, Houston, United States of America
| | - Carina King
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden and Institute for Global Health, University College London, London, United Kingdom
| | - Eric D McCollum
- Global Program in Respiratory Sciences, Eudowood Division of Pediatric Respiratory Sciences, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, United States of America and Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States of America
| | - Tim Colbourn
- Institute for Global Health, University College London, London, United Kingdom
| | | | | | - Christopher J Gregory
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, United States of America
| | - Somsak Thamthitiwat
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Clare Cutland
- African Leadership in Vaccinology Expertise (Alive), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir Ahmed Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Tabish Hazir
- The Children's Hospital, (Retired), Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan (deceased)
| | - Joseph L Mathew
- Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Emmanuel Addo-Yobo
- Kwame Nkrumah University of Science & Technology/Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Noel Chisaka
- World Bank, Washington DC, United States of America
| | - Mumtaz Hassan
- The Children's Hospital, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan (deceased)
| | - Patricia L Hibberd
- Department of Global Health, Boston University School of Public Health, Boston, United States of America
| | | | - Juan M Lozano
- Florida International University, Miami, United States of America
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, United States of America
| | - Archana Patel
- Lata Medical Research Foundation, Nagpur and Datta Meghe Institute of Medical Sciences, Sawangi, India
| | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, United States of America
| | | | - Syed Ma Zaman
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Raul O Ruvinsky
- Dirección de Control de Enfermedades Inmunoprevenibles, Ministerio de Salud de la Nación, Buenos Aires, Argentina
| | - Marilla Lucero
- Research Institute for Tropical Medicine, Manila, Philippines
| | - Cissy B Kartasasmita
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | | | - Rai Asghar
- Rawalpindi Medical College, Rawalpindi, Pakistan
| | | | - Imran Iqbal
- Combined Military Hospital Institute of Medical Sciences, Multan, Pakistan
| | - Irene Maulen-Radovan
- Instituto Nacional de Pediatria Division de Investigacion Insurgentes, Mexico City, Mexico
| | - Greta Mino-Leon
- Children's Hospital Dr Francisco de Ycaza Bustamante, Head of Department, Infectious diseases, Guayaquil, Ecuador
| | - Samir K Saha
- Child Health Research Foundation and Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mathuram Santosham
- International Vaccine Access Center (IVAC), Department of International Health, Johns Hopkins University, Baltimore, United States of America
| | | | - Shally Awasthi
- King George's Medical University, Department of Pediatrics, Lucknow, India
| | | | - Monidarin Chou
- University of Health Sciences, Rodolph Mérieux Laboratory & Ministry of Environment, Phom Phen, Cambodia
| | - Pagbajabyn Nymadawa
- Mongolian Academy of Sciences, Academy of Medical Sciences, Ulaanbaatar, Mongolia
| | | | | | | | | | | | - Graciela Russomando
- Universidad Nacional de Asuncion, Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Asuncion, Paraguay
| | - Mariam Sylla
- Gabriel Touré Hospital, Department of Pediatrics, Bamako, Mali
| | - Philippe Vanhems
- Unité d'Hygiène, Epidémiologie, Infectiovigilance et Prévention, Hospices Civils de Lyon, Lyon, France and Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale U1111, CNRS Unité Mixte de Recherche 5308, École Nationale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Jianwei Wang
- Chinese Academy of Medical Sciences & Peking Union, Medical College Institute of Pathogen Biology, MOH Key Laboratory of Systems Biology of Pathogens and Dr Christophe Mérieux Laboratory, Beijing, China
| | - Sudha Basnet
- Center for Intervention Science in Maternal and Child Health, University of Bergen, Norway and Department of Pediatrics, Tribhuvan University Institute of Medicine, Nepal
| | - Tor A Strand
- Research Department, Innlandet Hospital Trust, Lillehammer, Norway
| | - Mark I Neuman
- Division of Emergency Medicine, Boston Children's Hospital, Harvard Medical School, Boston, United States of America
| | | | - Marcela Echavarria
- Clinical Virology Unit, Centro de Educación Médica e Investigaciones Clínicas, Mar del Plata, Argentina
| | | | - Nitya Wadhwa
- Translational Health Science and Technology Institute, Faridabad, India
| | - Rakesh Lodha
- All India Institute of Medical Sciences, New Delhi, India
| | - Satinder Aneja
- School of Medical Sciences & Research, Sharda University, Greater Noida, India
| | - Angela Gentile
- Department of Epidemiology, "R. Gutiérrez" Children's Hospital, Buenos Aires, Argentina
| | - Mandeep Chadha
- Former Scientist G, ICMR National Institute of Virology, Pune, India
| | | | - Kerry-Ann F O'Grady
- Australian Centre for Health Services Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Alexey W Clara
- Centers for Disease Control, Central American Region, Guatemala City, Guatemala
| | - Chris A Rees
- Division of Pediatric Emergency Medicine, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, United States of America
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Harish Nair
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Jennifer Falconer
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Linda J Williams
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Margaret Horne
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, Scotland
| | - Shamim A Qazi
- Department of Maternal, Newborn, Child, and Adolescent Health (Retired), World Health Organization, Geneva, Switzerland
| | - Yasir Bin Nisar
- Department of Maternal, Newborn, Child, and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland.
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Downs SL, Madhi SA, van der Merwe L, Nunes MC, Olwagen CP. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes. Sci Rep 2023; 13:4588. [PMID: 36944704 PMCID: PMC10030628 DOI: 10.1038/s41598-023-31820-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Sensitive tools for detecting concurrent colonizing pneumococcal serotypes are needed for detailed evaluation of the direct and indirect impact of routine pneumococcal conjugate vaccine (PCV) immunization. A high-throughput quantitative nanofluidic real-time PCR (Standard BioTools 'Fluidigm') reaction-set was developed to detect and quantify 92 pneumococcal serotypes in archived clinical samples. Nasopharyngeal swabs collected in 2009-2011 from South African children ≤ 5 years-old, previously serotyped with standard culture-based methods were used for comparison. The reaction-set within the 'Fluidigm' effectively amplified all targets with high efficiency (90-110%), reproducibility (R2 ≥ 0.98), and at low limit-of-detection (< 102 CFU/ml). A blind analysis of 1 973 nasopharyngeal swab samples showed diagnostic sensitivity > 80% and specificity > 95% compared with the referent standard, culture based Quellung method. The qPCR method was able to serotype pneumococcal types with good discrimination compared with Quellung (ROC-AUC: > 0.73). The high-throughput nanofluidic real-time PCR method simultaneously detects 57 individual serotypes, and 35 serotypes within 16 serogroups in 96 samples (including controls), within a single qPCR run. This method can be used to evaluate the impact of current PCV formulations on vaccine-serotype and non-vaccine-serotype colonization, including detection of multiple concurrently colonizing serotypes. Our qPCR method can allow for monitoring of serotype-specific bacterial load, as well as emergence or ongoing transmission of minor or co-colonizing serotypes that may have invasive disease potential.
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Affiliation(s)
- Sarah L Downs
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lara van der Merwe
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Courtney P Olwagen
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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23
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Ramocha LM, Dorfman JR, Groome M, Baillie V, Verwey C, Laubscher M, Nunes MC, Madhi SA. Human Metapneumovirus-Associated Hospitalization in HIV-1 Exposed Uninfected and HIV-1 Uninfected Children Less Than 5 Years in South Africa. J Pediatric Infect Dis Soc 2023; 12:53-55. [PMID: 36306473 DOI: 10.1093/jpids/piac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022]
Abstract
Using hospital surveillance data, we estimated Human metapneumovirus (hMPV) hospitalization incidence by age and HIV-exposure status. hMPV-associated hospitalization incidence was highest in <1-year children. Incidence rate ratios of HIV-exposed over unexposed children were 1.5 (95%CI 0.9-2.4) for <6-month children, 1.4 (95%CI 0.7-2.4) for 6- to 11-month children and 0.9 (95%CI 0.4-1.9) for 12- to 59-month children.
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Affiliation(s)
- Lesego M Ramocha
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Jeffrey R Dorfman
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,Division of Medical Virology, Department of Pathology, Stellenbosch University, Cape Town, South Africa
| | - Michelle Groome
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky Baillie
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Charl Verwey
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Pediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marius Laubscher
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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24
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Smith ER, Oakley E, Grandner GW, Rukundo G, Farooq F, Ferguson K, Baumann S, Adams Waldorf KM, Afshar Y, Ahlberg M, Ahmadzia H, Akelo V, Aldrovandi G, Bevilacqua E, Bracero N, Brandt JS, Broutet N, Carrillo J, Conry J, Cosmi E, Crispi F, Crovetto F, Del Mar Gil M, Delgado-López C, Divakar H, Driscoll AJ, Favre G, Fernandez Buhigas I, Flaherman V, Gale C, Godwin CL, Gottlieb S, Gratacós E, He S, Hernandez O, Jones S, Joshi S, Kalafat E, Khagayi S, Knight M, Kotloff KL, Lanzone A, Laurita Longo V, Le Doare K, Lees C, Litman E, Lokken EM, Madhi SA, Magee LA, Martinez-Portilla RJ, Metz TD, Miller ES, Money D, Moungmaithong S, Mullins E, Nachega JB, Nunes MC, Onyango D, Panchaud A, Poon LC, Raiten D, Regan L, Sahota D, Sakowicz A, Sanin-Blair J, Stephansson O, Temmerman M, Thorson A, Thwin SS, Tippett Barr BA, Tolosa JE, Tug N, Valencia-Prado M, Visentin S, von Dadelszen P, Whitehead C, Wood M, Yang H, Zavala R, Tielsch JM. Clinical risk factors of adverse outcomes among women with COVID-19 in the pregnancy and postpartum period: a sequential, prospective meta-analysis. Am J Obstet Gynecol 2023; 228:161-177. [PMID: 36027953 PMCID: PMC9398561 DOI: 10.1016/j.ajog.2022.08.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/07/2022] [Indexed: 01/28/2023]
Abstract
OBJECTIVE This sequential, prospective meta-analysis sought to identify risk factors among pregnant and postpartum women with COVID-19 for adverse outcomes related to disease severity, maternal morbidities, neonatal mortality and morbidity, and adverse birth outcomes. DATA SOURCES We prospectively invited study investigators to join the sequential, prospective meta-analysis via professional research networks beginning in March 2020. STUDY ELIGIBILITY CRITERIA Eligible studies included those recruiting at least 25 consecutive cases of COVID-19 in pregnancy within a defined catchment area. METHODS We included individual patient data from 21 participating studies. Data quality was assessed, and harmonized variables for risk factors and outcomes were constructed. Duplicate cases were removed. Pooled estimates for the absolute and relative risk of adverse outcomes comparing those with and without each risk factor were generated using a 2-stage meta-analysis. RESULTS We collected data from 33 countries and territories, including 21,977 cases of SARS-CoV-2 infection in pregnancy or postpartum. We found that women with comorbidities (preexisting diabetes mellitus, hypertension, cardiovascular disease) vs those without were at higher risk for COVID-19 severity and adverse pregnancy outcomes (fetal death, preterm birth, low birthweight). Participants with COVID-19 and HIV were 1.74 times (95% confidence interval, 1.12-2.71) more likely to be admitted to the intensive care unit. Pregnant women who were underweight before pregnancy were at higher risk of intensive care unit admission (relative risk, 5.53; 95% confidence interval, 2.27-13.44), ventilation (relative risk, 9.36; 95% confidence interval, 3.87-22.63), and pregnancy-related death (relative risk, 14.10; 95% confidence interval, 2.83-70.36). Prepregnancy obesity was also a risk factor for severe COVID-19 outcomes including intensive care unit admission (relative risk, 1.81; 95% confidence interval, 1.26-2.60), ventilation (relative risk, 2.05; 95% confidence interval, 1.20-3.51), any critical care (relative risk, 1.89; 95% confidence interval, 1.28-2.77), and pneumonia (relative risk, 1.66; 95% confidence interval, 1.18-2.33). Anemic pregnant women with COVID-19 also had increased risk of intensive care unit admission (relative risk, 1.63; 95% confidence interval, 1.25-2.11) and death (relative risk, 2.36; 95% confidence interval, 1.15-4.81). CONCLUSION We found that pregnant women with comorbidities including diabetes mellitus, hypertension, and cardiovascular disease were at increased risk for severe COVID-19-related outcomes, maternal morbidities, and adverse birth outcomes. We also identified several less commonly known risk factors, including HIV infection, prepregnancy underweight, and anemia. Although pregnant women are already considered a high-risk population, special priority for prevention and treatment should be given to pregnant women with these additional risk factors.
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Affiliation(s)
- Emily R Smith
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC.
| | - Erin Oakley
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Gargi Wable Grandner
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Gordon Rukundo
- PeriCOVID (PREPARE)-Uganda Team, Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Fouzia Farooq
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Kacey Ferguson
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Sasha Baumann
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Kristina Maria Adams Waldorf
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA; Department of Global Health, University of Washington, Seattle, WA
| | - Yalda Afshar
- Division of Maternal-Fetal Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Mia Ahlberg
- Division of Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Homa Ahmadzia
- Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Victor Akelo
- Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Grace Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA
| | - Elisa Bevilacqua
- Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Nabal Bracero
- Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, San Juan, PR; Puerto Rico Obstetrics and Gynecology (PROGyn)
| | - Justin S Brandt
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Natalie Broutet
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Jorge Carrillo
- Departamento de Obstetricia y Ginecologia, Clinica Alemana de Santiago, Facultad de Medicina Clinica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Jeanne Conry
- International Federation of Gynecology and Obstetrics, London, United Kingdom
| | - Erich Cosmi
- Department of Women's and Children's Health, Obstetrics and Gynecology Clinic, University of Padua, Padua, Italy
| | - Fatima Crispi
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu Barcelona and Hospital Clínic de Barcelona, Universitat de Barcelona, and Center for Biomedical Research on Rare Diseases, Barcelona, Spain
| | - Francesca Crovetto
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu Barcelona and Hospital Clínic de Barcelona, Universitat de Barcelona, and Center for Biomedical Research on Rare Diseases, Barcelona, Spain
| | - Maria Del Mar Gil
- Department of Obstetrics and Gynecology, Hospital Universitario de Torrejón, Madrid, Spain; School of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Camille Delgado-López
- Surveillance for Emerging Threats to Mothers and Babies, Puerto Rico Department of Health, San Juan, PR
| | - Hema Divakar
- Asian Research & Training Institute for Skill Transfer, Bengaluru, India
| | - Amanda J Driscoll
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD
| | - Guillaume Favre
- Materno-fetal and Obstetrics Research Unit, Département Femme-Mère-Enfant, Lausanne University Hospital, Lausanne, Switzerland
| | - Irene Fernandez Buhigas
- Department of Obstetrics and Gynecology, Hospital Universitario de Torrejón, Madrid, Spain; School of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Valerie Flaherman
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA
| | - Christopher Gale
- Neonatal Medicine, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Christine L Godwin
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Sami Gottlieb
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Eduard Gratacós
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu Barcelona and Hospital Clínic de Barcelona, Universitat de Barcelona, and Center for Biomedical Research on Rare Diseases, Barcelona, Spain
| | - Siran He
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Olivia Hernandez
- Gynecology and Obstetrics, Félix Bulnes Hospital and RedSalud Clinic, Santiago, Chile
| | - Stephanie Jones
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sheetal Joshi
- Asian Research & Training Institute for Skill Transfer, Bengaluru, India
| | - Erkan Kalafat
- Department of Obstetrics and Gynecology, School of Medicine, Koç University, Istanbul, Turkey
| | - Sammy Khagayi
- Kenya Medical Research Institute-Centre for Global Health Research, Kisumu, Kenya
| | - Marian Knight
- National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD
| | - Antonio Lanzone
- Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy; Catholic University of Sacred Heart, Rome, Italy
| | - Valentina Laurita Longo
- Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy; Catholic University of Sacred Heart, Rome, Italy
| | - Kirsty Le Doare
- PeriCOVID (PREPARE)-Uganda Team, Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda; Medical Research Council /Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda; Paediatric Infectious Disease Research Group, St George's University of London, London, United Kingdom
| | - Christoph Lees
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Ethan Litman
- Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Erica M Lokken
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA; Department of Global Health, University of Washington, Seattle, WA
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura A Magee
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, United Kingdom; Institute of Women and Children's Health, King's College Hospital, London, United Kingdom
| | | | - Torri D Metz
- Division of Maternal-Fetal Medicine, The University of Utah Health, Salt Lake City, UT
| | - Emily S Miller
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Deborah Money
- Department of Obstetrics and Gynecology, The University of British Columbia, Vancouver, Canada
| | - Sakita Moungmaithong
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong
| | - Edward Mullins
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom; George Institute for Global Health, London, United Kingdom
| | - Jean B Nachega
- Department of Epidemiology and Center for Global Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA; Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Departments of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Alice Panchaud
- Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland; Service of Pharmacy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Liona C Poon
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong
| | - Daniel Raiten
- Pediatric Growth and Nutrition Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lesley Regan
- International Federation of Gynecology and Obstetrics, Imperial College London, London, United Kingdom
| | - Daljit Sahota
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong
| | - Allie Sakowicz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jose Sanin-Blair
- Maternal-Fetal Unit, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Olof Stephansson
- Division of Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marleen Temmerman
- Centre of Excellence in Women and Child Health, Aga Khan University, Nairobi, Kenya
| | - Anna Thorson
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Soe Soe Thwin
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Beth A Tippett Barr
- Centers for Disease Control and Prevention, Kisumu, Kenya; Nyanja Health Research Institute, Salima, Malawi
| | - Jorge E Tolosa
- Maternal-Fetal Unit, Universidad Pontificia Bolivariana, Medellín, Colombia; Department of Obstetrics and Gynecology, Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR; Department of Obstetrics and Gynecology, Maternal Fetal Medicine, St. Luke's University Health Network, Bethlehem, PA
| | - Niyazi Tug
- Department of Obstetrics and Gynecology, Sancaktepe Sehit Prof. Dr. Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Miguel Valencia-Prado
- Division of Children with Special Medical Needs, Puerto Rico Department of Health, San Juan, PR
| | - Silvia Visentin
- Department of Women's and Children's Health, Obstetrics and Gynecology Clinic, University of Padua, Padua, Italy
| | - Peter von Dadelszen
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, United Kingdom; Global Health Institute, King's College London, London, United Kingdom
| | - Clare Whitehead
- Department of Maternal Fetal Medicine, University of Melbourne, Royal Women's Hospital, Melbourne, Australia
| | - Mollie Wood
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Huixia Yang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
| | - Rebecca Zavala
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - James M Tielsch
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC
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25
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Smith ER, Oakley E, Grandner GW, Ferguson K, Farooq F, Afshar Y, Ahlberg M, Ahmadzia H, Akelo V, Aldrovandi G, Tippett Barr BA, Bevilacqua E, Brandt JS, Broutet N, Fernández Buhigas I, Carrillo J, Clifton R, Conry J, Cosmi E, Crispi F, Crovetto F, Delgado-López C, Divakar H, Driscoll AJ, Favre G, Flaherman VJ, Gale C, Gil MM, Gottlieb SL, Gratacós E, Hernandez O, Jones S, Kalafat E, Khagayi S, Knight M, Kotloff K, Lanzone A, Le Doare K, Lees C, Litman E, Lokken EM, Laurita Longo V, Madhi SA, Magee LA, Martinez-Portilla RJ, McClure EM, Metz TD, Miller ES, Money D, Moungmaithong S, Mullins E, Nachega JB, Nunes MC, Onyango D, Panchaud A, Poon LC, Raiten D, Regan L, Rukundo G, Sahota D, Sakowicz A, Sanin-Blair J, Söderling J, Stephansson O, Temmerman M, Thorson A, Tolosa JE, Townson J, Valencia-Prado M, Visentin S, von Dadelszen P, Adams Waldorf K, Whitehead C, Yassa M, Tielsch JM. Adverse maternal, fetal, and newborn outcomes among pregnant women with SARS-CoV-2 infection: an individual participant data meta-analysis. BMJ Glob Health 2023; 8:e009495. [PMID: 36646475 PMCID: PMC9895919 DOI: 10.1136/bmjgh-2022-009495] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Despite a growing body of research on the risks of SARS-CoV-2 infection during pregnancy, there is continued controversy given heterogeneity in the quality and design of published studies. METHODS We screened ongoing studies in our sequential, prospective meta-analysis. We pooled individual participant data to estimate the absolute and relative risk (RR) of adverse outcomes among pregnant women with SARS-CoV-2 infection, compared with confirmed negative pregnancies. We evaluated the risk of bias using a modified Newcastle-Ottawa Scale. RESULTS We screened 137 studies and included 12 studies in 12 countries involving 13 136 pregnant women.Pregnant women with SARS-CoV-2 infection-as compared with uninfected pregnant women-were at significantly increased risk of maternal mortality (10 studies; n=1490; RR 7.68, 95% CI 1.70 to 34.61); admission to intensive care unit (8 studies; n=6660; RR 3.81, 95% CI 2.03 to 7.17); receiving mechanical ventilation (7 studies; n=4887; RR 15.23, 95% CI 4.32 to 53.71); receiving any critical care (7 studies; n=4735; RR 5.48, 95% CI 2.57 to 11.72); and being diagnosed with pneumonia (6 studies; n=4573; RR 23.46, 95% CI 3.03 to 181.39) and thromboembolic disease (8 studies; n=5146; RR 5.50, 95% CI 1.12 to 27.12).Neonates born to women with SARS-CoV-2 infection were more likely to be admitted to a neonatal care unit after birth (7 studies; n=7637; RR 1.86, 95% CI 1.12 to 3.08); be born preterm (7 studies; n=6233; RR 1.71, 95% CI 1.28 to 2.29) or moderately preterm (7 studies; n=6071; RR 2.92, 95% CI 1.88 to 4.54); and to be born low birth weight (12 studies; n=11 930; RR 1.19, 95% CI 1.02 to 1.40). Infection was not linked to stillbirth. Studies were generally at low or moderate risk of bias. CONCLUSIONS This analysis indicates that SARS-CoV-2 infection at any time during pregnancy increases the risk of maternal death, severe maternal morbidities and neonatal morbidity, but not stillbirth or intrauterine growth restriction. As more data become available, we will update these findings per the published protocol.
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Affiliation(s)
- Emily R Smith
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | - Erin Oakley
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | - Gargi Wable Grandner
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | - Kacey Ferguson
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | - Fouzia Farooq
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | - Yalda Afshar
- Division of Maternal Fetal Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Mia Ahlberg
- Department of Medicine, Solna, Clinical Epidemiology Division, Karolinska Institute, Stockholm, Sweden
| | - Homa Ahmadzia
- Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Victor Akelo
- Office of the Director, US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Grace Aldrovandi
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Beth A Tippett Barr
- Office of the Director, US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Elisa Bevilacqua
- Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italy
| | - Justin S Brandt
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Nathalie Broutet
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneve, Switzerland
| | | | - Jorge Carrillo
- Departamento de Obstetricia y Ginecologia, Universidad del Desarrollo Facultad de Medicina Clinica Alemana, Santiago, Chile
| | - Rebecca Clifton
- The Biostatistics Center, The George Washington University Milken Institute School of Public Health, Rockville, Maryland, USA
| | - Jeanne Conry
- International Federation of Gynecology and Obstetrics, London, UK
| | - Erich Cosmi
- Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Fatima Crispi
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Francesca Crovetto
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Camille Delgado-López
- Surveillance for Emerging Threats to Mothers and Babies, Puerto Rico Department of Health, San Juan, Puerto Rico
| | - Hema Divakar
- Asian Research and Training Institute for Skill Transfer (ARTIST), Bengaluru, India
| | - Amanda J Driscoll
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Guillaume Favre
- Materno-Fetal and Obstetrics Research Unit, Department ‘Femme-Mère-Enfant’, Lausanne University Hospital, Lausanne, Switzerland
| | - Valerie J Flaherman
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Chris Gale
- Neonatal Medicine, School of Public Health, Imperial College London Faculty of Medicine, London, UK
| | - Maria M Gil
- Department of Obstetrics and Gynecology, Hospital Universitario de Torrejón, Madrid, Spain
| | - Sami L Gottlieb
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneve, Switzerland
| | - Eduard Gratacós
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Olivia Hernandez
- Gynecology and Obstetrics, Felix Bulnes Hospital and RedSalud Clinic, Santiago, Chile
| | - Stephanie Jones
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | - Erkan Kalafat
- Department of Obstetrics and Gynecology, Koç University School of Medicine, Istanbul, Turkey
| | - Sammy Khagayi
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Marian Knight
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karen Kotloff
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Antonio Lanzone
- Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italy
| | - Kirsty Le Doare
- Uganda Virus Institute and the London School of Hygiene & Tropical Medicine, Entebbe, Uganda,Pediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Christoph Lees
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ethan Litman
- Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Erica M Lokken
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Valentina Laurita Longo
- Institute of Obstetrics and Gynecology Clinic, Catholic University of Sacred Heart, Rome, Italy
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | - Laura A Magee
- Department of Women and Children’s Health, School of Life Course and Population Sciences, King's College London, London, UK
| | | | | | - Tori D Metz
- Departments of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake, Utah, USA
| | - Emily S Miller
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Deborah Money
- Department of Obstetrics and Gynecology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sakita Moungmaithong
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Edward Mullins
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jean B Nachega
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | | | - Alice Panchaud
- Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Liona C Poon
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Daniel Raiten
- Pediatric Growth and Nutrition Branch, National Institute of Health, Bethesda, Maryland, USA
| | - Lesley Regan
- International Federation of Gynecology and Obstetrics, London, UK
| | - Gordon Rukundo
- Uganda Virus Institute and the London School of Hygiene & Tropical Medicine, Entebbe, Uganda
| | - Daljit Sahota
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Allie Sakowicz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jose Sanin-Blair
- Universidad Pontificia Bolivariana, Medellin, Antioquia, Colombia
| | - Jonas Söderling
- Department of Medicine, Solna, Clinical Epidemiology Division, Karolinska Institute, Stockholm, Sweden
| | - Olof Stephansson
- Department of Medicine, Solna, Clinical Epidemiology Division, Karolinska Institute, Stockholm, Sweden
| | - Marleen Temmerman
- Centre of Excellence in Women and Child Health, Aga Khan University, Nairobi, Kenya
| | - Anna Thorson
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneve, Switzerland
| | - Jorge E Tolosa
- Department of Obstetrics and Gynecology, St Luke's University Health Network, Bethlehem, Pennsylvania, USA
| | - Julia Townson
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Miguel Valencia-Prado
- Children with Special Medical Needs Division, Puerto Rico Department of Health, San Juan, Puerto Rico
| | - Silvia Visentin
- Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Peter von Dadelszen
- Department of Women and Children's Health, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - Kristina Adams Waldorf
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Clare Whitehead
- Department of Maternal-Fetal Medicine, The Royal Women's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Murat Yassa
- Department of Obstetrics and Gynecology, Sancaktepe Sehit Prof Dr Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Jim M Tielsch
- Department of Global Health, The George Washington University Milken Institute School of Public Health, Washington, DC, USA
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26
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Mazur NI, Terstappen J, Baral R, Bardají A, Beutels P, Buchholz UJ, Cohen C, Crowe JE, Cutland CL, Eckert L, Feikin D, Fitzpatrick T, Fong Y, Graham BS, Heikkinen T, Higgins D, Hirve S, Klugman KP, Kragten-Tabatabaie L, Lemey P, Libster R, Löwensteyn Y, Mejias A, Munoz FM, Munywoki PK, Mwananyanda L, Nair H, Nunes MC, Ramilo O, Richmond P, Ruckwardt TJ, Sande C, Srikantiah P, Thacker N, Waldstein KA, Weinberger D, Wildenbeest J, Wiseman D, Zar HJ, Zambon M, Bont L. Respiratory syncytial virus prevention within reach: the vaccine and monoclonal antibody landscape. Lancet Infect Dis 2023; 23:e2-e21. [PMID: 35952703 PMCID: PMC9896921 DOI: 10.1016/s1473-3099(22)00291-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/12/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Respiratory syncytial virus is the second most common cause of infant mortality and a major cause of morbidity and mortality in older adults (aged >60 years). Efforts to develop a respiratory syncytial virus vaccine or immunoprophylaxis remain highly active. 33 respiratory syncytial virus prevention candidates are in clinical development using six different approaches: recombinant vector, subunit, particle-based, live attenuated, chimeric, and nucleic acid vaccines; and monoclonal antibodies. Nine candidates are in phase 3 clinical trials. Understanding the epitopes targeted by highly neutralising antibodies has resulted in a shift from empirical to rational and structure-based vaccine and monoclonal antibody design. An extended half-life monoclonal antibody for all infants is likely to be within 1 year of regulatory approval (from August, 2022) for high-income countries. Live-attenuated vaccines are in development for older infants (aged >6 months). Subunit vaccines are in late-stage trials for pregnant women to protect infants, whereas vector, subunit, and nucleic acid approaches are being developed for older adults. Urgent next steps include ensuring access and affordability of a respiratory syncytial virus vaccine globally. This review gives an overview of respiratory syncytial virus vaccines and monoclonal antibodies in clinical development highlighting different target populations, antigens, and trial results.
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Affiliation(s)
- Natalie I Mazur
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jonne Terstappen
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ranju Baral
- PATH, Center for Vaccine Innovation & Access, Seattle, WA, USA
| | - Azucena Bardají
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain; Centro de Investigaçao em Saúde de Manhiça, Maputo, Mozambique; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Philippe Beutels
- Centre for Health Economics Research & Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; School of Public Health, The University of New South Wales, Sydney, NSW, Australia
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Cheryl Cohen
- University of the Witwatersrand, Centre for Respiratory Disease and Meningitis at the National Institute for Communicable Diseases, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - James E Crowe
- Vanderbilt Vaccine Center, Pediatrics & Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Clare L Cutland
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda Eckert
- Obstetrics & Gynecology, Global Health, University of Washington, Seattle, WA, USA
| | - Daniel Feikin
- Department of Immunisations, Vaccines & Biologicals, World Health Organization, Geneva, Switzerland
| | - Tiffany Fitzpatrick
- Yale School of Public Health Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
| | - Youyi Fong
- Vaccine & Infectious Disease Division, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Terho Heikkinen
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Deborah Higgins
- PATH, Center for Vaccine Innovation & Access, Seattle, WA, USA
| | | | - Keith P Klugman
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Philippe Lemey
- Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Yvette Löwensteyn
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Flor M Munoz
- Department of Pediatrics, Division of Infectious Disease, and Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick K Munywoki
- Kenyan Medical Research Institute-Wellcome Trust Research Program, Kilifi, Kenya
| | | | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Marta C Nunes
- South African Medical Research Council, Wits Vaccines & Infectious Diseases Analytics Research Unit and Department of Science and Technology and National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Octavio Ramilo
- Nationwide Children's Hospital Columbus, Columbus, OH, USA
| | - Peter Richmond
- School of Medicine, Division of Paediatrics, University of Western Australia, Perth, WA, Australia
| | - Tracy J Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Charles Sande
- Kenyan Medical Research Institute-Wellcome Trust Research Program, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - Padmini Srikantiah
- Respiratory Syncytial Virus Program and Global Health, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Naveen Thacker
- Deep Children Hospital & Research Centre, Gandhidham, India
| | - Kody A Waldstein
- Department of Microbiology and Immunology, University of Iowa, Iowa, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa, IA, USA
| | - Dan Weinberger
- Yale School of Public Health Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
| | - Joanne Wildenbeest
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Dexter Wiseman
- National Heart & Lung Institute, Imperial College, London, UK
| | - Heather J Zar
- Department of Pediatrics & Child Health, Red Cross Children's Hospital and SA-MRC unit of Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Maria Zambon
- Reference Microbiology, Public Health England, Faculty of Medicine, Imperial College, London, UK
| | - Louis Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands; ReSViNET Foundation, Julius Clinical, Zeist, Netherlands.
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27
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Martin H, Falconer J, Addo-Yobo E, Aneja S, Arroyo LM, Asghar R, Awasthi S, Banajeh S, Bari A, Basnet S, Bavdekar A, Bhandari N, Bhatnagar S, Bhutta ZA, Brooks A, Chadha M, Chisaka N, Chou M, Clara AW, Colbourn T, Cutland C, D'Acremont V, Echavarria M, Gentile A, Gessner B, Gregory CJ, Hazir T, Hibberd PL, Hirve S, Hooli S, Iqbal I, Jeena P, Kartasasmita CB, King C, Libster R, Lodha R, Lozano JM, Lucero M, Lufesi N, MacLeod WB, Madhi SA, Mathew JL, Maulen-Radovan I, McCollum ED, Mino G, Mwansambo C, Neuman MI, Nguyen NTV, Nunes MC, Nymadawa P, O'Grady KAF, Pape JW, Paranhos-Baccala G, Patel A, Picot VS, Rakoto-Andrianarivelo M, Rasmussen Z, Rouzier V, Russomando G, Ruvinsky RO, Sadruddin S, Saha SK, Santosham M, Singhi S, Soofi S, Strand TA, Sylla M, Thamthitiwat S, Thea DM, Turner C, Vanhems P, Wadhwa N, Wang J, Zaman SMA, Campbell H, Nair H, Qazi SA, Nisar YB. Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications. J Glob Health 2022; 12:04075. [PMID: 36579417 PMCID: PMC9798037 DOI: 10.7189/jogh.12.04075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The existing World Health Organization (WHO) pneumonia case management guidelines rely on clinical symptoms and signs for identifying, classifying, and treating pneumonia in children up to 5 years old. We aimed to collate an individual patient-level data set from large, high-quality pre-existing studies on pneumonia in children to identify a set of signs and symptoms with greater validity in the diagnosis, prognosis, and possible treatment of childhood pneumonia for the improvement of current pneumonia case management guidelines. Methods Using data from a published systematic review and expert knowledge, we identified studies meeting our eligibility criteria and invited investigators to share individual-level patient data. We collected data on demographic information, general medical history, and current illness episode, including history, clinical presentation, chest radiograph findings when available, treatment, and outcome. Data were gathered separately from hospital-based and community-based cases. We performed a narrative synthesis to describe the final data set. Results Forty-one separate data sets were included in the Pneumonia Research Partnership to Assess WHO Recommendations (PREPARE) database, 26 of which were hospital-based and 15 were community-based. The PREPARE database includes 285 839 children with pneumonia (244 323 in the hospital and 41 516 in the community), with detailed descriptions of clinical presentation, clinical progression, and outcome. Of 9185 pneumonia-related deaths, 6836 (74%) occurred in children <1 year of age and 1317 (14%) in children aged 1-2 years. Of the 285 839 episodes, 280 998 occurred in children 0-59 months old, of which 129 584 (46%) were 2-11 months of age and 152 730 (54%) were males. Conclusions This data set could identify an improved specific, sensitive set of criteria for diagnosing clinical pneumonia and help identify sick children in need of referral to a higher level of care or a change of therapy. Field studies could be designed based on insights from PREPARE analyses to validate a potential revised pneumonia algorithm. The PREPARE methodology can also act as a model for disease database assembly.
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Affiliation(s)
- Helena Martin
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer Falconer
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Emmanuel Addo-Yobo
- Kwame Nkrumah University of Science and Technology/Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Satinder Aneja
- School of Medical Sciences and Research, Sharda University, Greater Noida, India
| | | | - Rai Asghar
- Rawalpindi Medical College, Rawalpindi, Pakistan
| | - Shally Awasthi
- King George’s Medical University, Department of Pediatrics, Lucknow, India
| | - Salem Banajeh
- Department of Paediatrics and Child Health, University of Sana’a, Sana’a, Yemen
| | - Abdul Bari
- Independent newborn and child health consultant, Islamabad, Pakistan
| | - Sudha Basnet
- Center for Intervention Science in Maternal and Child Health, University of Bergen, Norway,Department of Pediatrics, Tribhuvan University Institute of Medicine, Nepal
| | - Ashish Bavdekar
- King Edward Memorial (KEM) Hospital Pune, Department of Pediatrics, Pune, India
| | - Nita Bhandari
- Center for Health Research and Development, Society for Applied Studies, India
| | | | - Zulfiqar A Bhutta
- Institute for Global Health and Development, Aga Khan University, Pakistan
| | - Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mandeep Chadha
- Former Scientist, Indian Council of Medical Research (ICMR), National Institute of Virology, Pune, India
| | | | - Monidarin Chou
- University of Health Sciences, Rodolphe Mérieux Laboratory, Phom Phen, Cambodia,Ministry of Environment, Phom Phen, Cambodia
| | - Alexey W Clara
- Centers for Disease Control, Central American Region, Guatemala City, Guatemala
| | - Tim Colbourn
- Institute for Global Health, University College London, London, United Kingdom
| | - Clare Cutland
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Marcela Echavarria
- Clinical Virology Unit, Centro de Educación Médica e Investigaciones Clínicas, Argentina
| | - Angela Gentile
- Department of Epidemiology, “R. Gutiérrez” Children's Hospital, Buenos Aires, Argentina
| | - Brad Gessner
- Pfizer Vaccines, Collegeville, Pennsylvania, USA
| | - Christopher J. Gregory
- Division of Vector-borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Tabish Hazir
- Retired from Children Hospital, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Patricia L. Hibberd
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Shubhada Hooli
- Section of Pediatric Emergency Medicine, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Imran Iqbal
- Department of Paediatrics, Combined Military Hospital Institute of Medical Sciences, Multan, Pakistan
| | | | - Cissy B Kartasasmita
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Carina King
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden,Institute for Global Health, University College London, London, United Kingdom
| | | | - Rakesh Lodha
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Marilla Lucero
- Research Institute for Tropical Medicine, Manila, Philippines
| | | | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Shabir Ahmed Madhi
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Joseph L Mathew
- Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Irene Maulen-Radovan
- Instituto Nactional de Pediatria Division de Investigacion Insurgentes, Mexico City, Mexico
| | - Eric D McCollum
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,Global Program in Respiratory Sciences, Eudowood Division of Pediatric Respiratory Sciences, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
| | - Greta Mino
- Department of Infectious diseases, Guayaquil, Ecuador
| | | | - Mark I Neuman
- Division of Emergency Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pagbajabyn Nymadawa
- Mongolian Academy of Sciences, Academy of Medical Sciences, Ulaanbaatar, Mongolia
| | - Kerry-Ann F O'Grady
- Australian Centre for Health Services Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | | | | | - Archana Patel
- Lata Medical Research Foundation, Nagpur and Datta Meghe Institute of Medical Sciences, Sawangi, India
| | | | | | - Zeba Rasmussen
- Division of International Epidemiology and Population Studies (DIEPS), Fogarty International Center (FIC), National Institute of Health (NIH), USA
| | | | - Graciela Russomando
- Universidad Nacional de Asuncion, Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Asuncion, Paraguay
| | - Raul O Ruvinsky
- Dirección de Control de Enfermedades Inmunoprevenibles, Ministerio de Salud de la Nación, Buenos Aires, Argentina
| | - Salim Sadruddin
- Consultant/Retired World Health Organization (WHO) Staff, Geneva, Switzerland
| | - Samir K. Saha
- Child Health Research Foundation, Dhaka, Bangladesh,Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mathuram Santosham
- International Vaccine Access Center (IVAC), Department of International Health, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Sajid Soofi
- Department of Pediatrics and Child Health, Aga Khan University, Pakistan
| | - Tor A Strand
- Research Department, Innlandet Hospital Trust, Lillehammer, Norway
| | - Mariam Sylla
- Gabriel Touré Hospital, Department of Pediatrics, Bamako, Mali
| | - Somsak Thamthitiwat
- Division of Global Health Protection, Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Philippe Vanhems
- Unité d'Hygiène, Epidémiologie, Infectiovigilance et Prévention, Hospices Civils de Lyon, Lyon, France,Centre International de Recherche en Infectiologie, École Nationale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Nitya Wadhwa
- Translational Health Science and Technology Institute, Faridabad, India
| | - Jianwei Wang
- Chinese Academy of Medical Sciences & Peking Union, Medical College Institute of Pathogen Biology, MOH Key Laboratory of Systems Biology of Pathogens and Dr Christophe Mérieux Laboratory, Beijing, China
| | - Syed MA Zaman
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Harry Campbell
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Harish Nair
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Shamim Ahmad Qazi
- Consultant/Retired World Health Organization (WHO) Staff, Geneva, Switzerland
| | - Yasir Bin Nisar
- Department of Maternal, Newborn, Child and Adolescent Health and Ageing, World Health Organization (WHO), Geneva, Switzerland
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28
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Nunes MC, Jones S, Strehlau R, Baba V, Ditse Z, da Silva K, Bothma L, Serafin N, Baillie VL, Kwatra G, Burke M, Wise A, Adam M, Mlandu P, Melamu M, Phelp J, Fraser W, Wright C, Zell E, Adam Y, Madhi SA. Antepartum SARS-CoV-2 infection and adverse birth outcomes in South African women. J Glob Health 2022; 12:05050. [DOI: 10.7189/jogh.12.05050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Marta C Nunes
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Jones
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- Nkanyezi Research Unit sub-division of VIDA, Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vuyelwa Baba
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly da Silva
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lané Bothma
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky L Baillie
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- Nkanyezi Research Unit sub-division of VIDA, Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Wise
- Department of Obstetrics and Gynecology, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mary Adam
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philiswa Mlandu
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mpolokeng Melamu
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliette Phelp
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Colleen Wright
- Lancet Laboratories, Johannesburg, South Africa
- Division of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elizabeth Zell
- Stat-Epi Associates, Inc., Ponte Vedra Beach, Florida, USA
| | - Yasmin Adam
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Nunes MC, Jones S, Strehlau R, Baba V, Ditse Z, da Silva K, Bothma L, Serafin N, Baillie VL, Kwatra G, Burke M, Wise A, Adam M, Mlandu P, Melamu M, Phelp J, Fraser W, Wright C, Zell E, Adam Y, Madhi SA. Active Intrapartum SARS-CoV-2 Infection and Pregnancy Outcomes. Am J Perinatol 2022; 39:S42-S48. [PMID: 36307090 DOI: 10.1055/s-0042-1757274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection during pregnancy has been associated with poor pregnancy outcomes. There is, however, not much information on the impact of the timing of SARS-CoV-2 infection on pregnancy outcomes, and studies from low-middle income settings are also scarce. STUDY DESIGN We conducted a cross-sectional study from April to December 2020, in South Africa, to assess the association of SARS-CoV-2 infection on a nasal swab at the time of labor with fetal death, preterm birth, low birth weight, or pregnancy-induced complications. When possible, maternal blood, cord blood, and placenta were collected. SARS-CoV-2 infection was investigated by a nucleic acid amplification test (NAAT). RESULTS Overall, 3,117 women were tested for SARS-CoV-2 on a nasal swab, including 1,562 (50%) healthy women with uncomplicated term delivery. A positive NAAT was detected among 132 (4%) women. Adverse birth outcomes or pregnancy-related complications were not associated with SARS-CoV-2 infection at the time of labor. Among SARS-CoV-2-infected women, an NAAT-positive result was also obtained from 6 out of 98 (6%) maternal blood samples, 8 out of 93 (9%) cord-blood samples, 14 out of 54 (26%) placentas, and 3 out of 22 (14%) nasopharyngeal swabs from newborns collected within 72 hours of birth. Histological assessment of placental tissue revealed that women with SARS-CoV-2 nasal infection had a higher odds (3.82, 95% confidence interval: 1.20, 12.19) of chronic chorioamnionitis compared with those without SARS-CoV-2 infection. CONCLUSION Our study demonstrates that intrapartum, SARS-CoV-2 infection was not associated with evaluated poor outcomes. In utero fetal and placental infections and possible vertical and/or horizontal viral transfer to the newborn were detected among women with nasal SARS-CoV-2 infection. KEY POINTS · Intrapartum SARS-CoV-2 infection was not associated with evaluated poor outcomes.. · In utero fetal and placental infections were detected among women with nasal SARS-CoV-2 infection.. · Women with SARS-CoV-2 nasal infection had a higher odds of chronic chorioamnionitis..
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Affiliation(s)
- Marta C Nunes
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Jones
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- Nkanyezi Research Unit Sub-Division of VIDA, Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vuyelwa Baba
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly da Silva
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lané Bothma
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky L Baillie
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- Nkanyezi Research Unit Sub-Division of VIDA, Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Wise
- Department of Obstetrics and Gynecology, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mary Adam
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philiswa Mlandu
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mpolokeng Melamu
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliette Phelp
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Fraser
- Lancet Laboratories, Johannesburg, Gauteng, South Africa
| | - Colleen Wright
- Lancet Laboratories, Johannesburg, Gauteng, South Africa.,Division of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | | | - Yasmin Adam
- Department of Obstetrics and Gynecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines, and Infectious Diseases Analytics (VIDA) Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Nunes MC, Walaza S, Meiring S, Zar HJ, Reubenson G, McMorrow M, Tempia S, Rossi L, Itzikowitz R, Bishop K, Mathunjwa A, Wise A, Treurnicht FK, Hellferscee O, Laubscher M, Serafin N, Cutland CL, Madhi SA, Cohen C. Effectiveness of Influenza Vaccination of Pregnant Women for Prevention of Maternal and Early Infant Influenza-Associated Hospitalizations in South Africa: A Prospective Test-Negative Study. Open Forum Infect Dis 2022; 9:ofac552. [PMID: 36447608 PMCID: PMC9697604 DOI: 10.1093/ofid/ofac552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Influenza vaccination during pregnancy reduces influenza-associated illness in the women and their infants, but effectiveness estimates against influenza-associated hospitalization are limited and lacking from settings with high human immunodeficiency virus (HIV) infection prevalence. We assessed the effect of maternal vaccination in HIV-uninfected women and women with HIV in preventing influenza-associated hospitalizations in infants and the women. METHODS During 2015-2018, influenza vaccination campaigns targeting pregnant women were augmented at selected antenatal clinics; these were coupled with prospective hospital-based surveillance for acute respiratory or febrile illness in infants aged <6 months and cardiorespiratory illness among pregnant or postpartum women. Vaccine effectiveness (VE) was assessed using a test-negative case-control study. RESULTS Overall, 71 influenza-positive and 371 influenza-negative infants were included in the analysis; mothers of 26.8% of influenza-positive infants were vaccinated during pregnancy compared with 35.6% of influenza-negative infants, corresponding to an adjusted VE (aVE) of 29.0% (95% confidence interval [CI], -33.6% to 62.3%). When limited to vaccine-matched strains, aVE was 65.2% (95% CI, 11.7%-86.3%). For maternal hospitalizations, 56 influenza-positive and 345 influenza-negative women were included in the analysis, with 28.6% of influenza-positive women being vaccinated compared with 38.3% of influenza-negatives, for an aVE of 46.9% (95% CI, -2.8% to 72.5%). Analysis restricted to HIV-uninfected women resulted in 82.8% (95% CI, 40.7%-95.0%) aVE. No significant aVE (-32.5% [95% CI, -208.7% to 43.1%]) was detected among women with HIV. CONCLUSIONS Influenza vaccination during pregnancy prevented influenza-associated hospitalizations among young infants when infected with vaccine strains and among HIV-uninfected women.
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Affiliation(s)
- Marta C Nunes
- South African Medical Research Council, Faculty of Health Sciences, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, Faculty of Health Sciences, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Stefano Tempia
- 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, USA
| | - Liza Rossi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Raphaela Itzikowitz
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Kate Bishop
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Amy Wise
- Department of Obstetrics and Gynaecology, Rahima Moosa Mother and Child Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Matt Laubscher
- South African Medical Research Council, Faculty of Health Sciences, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, Faculty of Health Sciences, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Faculty of Health Sciences, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, Faculty of Health Sciences, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare L Cutland
- South African Medical Research Council, Faculty of Health Sciences, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, Faculty of Health Sciences, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Faculty of Health Sciences, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, Faculty of Health Sciences, South African Research Chair Initiative in Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Vanhems P, Nunes MC. Further Cautions When Modeling the Public Health Impact of Infectious Diseases. Am J Public Health 2022; 112:e1-e2. [DOI: 10.2105/ajph.2022.307086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Philippe Vanhems
- Philippe Vanhems is with the Service d’Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France, and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France. Marta C. Nunes is with the Hospices Civils de Lyon, Lyon, France, and the South African Medical Research Council, Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, and the Department of Science and Technology/National
| | - Marta C. Nunes
- Philippe Vanhems is with the Service d’Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France, and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France. Marta C. Nunes is with the Hospices Civils de Lyon, Lyon, France, and the South African Medical Research Council, Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, and the Department of Science and Technology/National
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Schwalbe N, Hanbali L, Nunes MC, Lehtimaki S. Use of financial incentives to increase adult vaccination coverage: A narrative review of lessons learned from COVID-19 and other adult vaccination efforts. Vaccine X 2022; 12:100225. [PMID: 36217357 PMCID: PMC9535879 DOI: 10.1016/j.jvacx.2022.100225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/29/2022] [Accepted: 09/29/2022] [Indexed: 10/25/2022] Open
Abstract
To encourage COVID-19 vaccination, governments have offered a wide range of incentives to their populations ranging from cash to cows. Often these programs were rolled out at scale before assessing potential effectiveness. To inform future policy, we conducted a narrative review to understand the evidence base informing these programs and the extent to which they are effective. While we found evidence on cash transfers increasing both the coverage and intention to be vaccinated for COVID-19 and other adult vaccines, improvements in coverage were limited. With mixed evidence, lottery programs did not appear to have a consistent meaningful impact on vaccination for COVID-19, and no evidence was identified on the positive effects of other non-cash incentives for COVID-19 or other adult vaccines. We conclude that the impact of cash transfers in incentivizing adult vaccination is marginal and their effectiveness in addressing vaccine hesitancy remains inconclusive.
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Affiliation(s)
- Nina Schwalbe
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Spark Street Advisors, New York, NY, United States,Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, NY, United States,Corresponding author at: 722 W 168th St, New York, NY 10032, USA.
| | | | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases; and South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Nunes MC, Johnson MJ, Kwatra G, Weinberg A, Madhi SA. T-cell responses to SARS-CoV-2 in unexposed South African women. Gates Open Res 2022; 5:150. [PMID: 35903460 PMCID: PMC9279637 DOI: 10.12688/gatesopenres.13373.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Background: A potential explanation for the fact that the high rate of infection of SARS-CoV-2 in South Africa did not translate into high rates of severe illness and death may be the presence of cross-reactive immunity induced by common cold coronaviruses (CCoV). Methods: We used SARS-CoV-2 peptide pools and whole virus antigen to stimulate peripheral blood mononuclear cells collected pre-2020 from South African women. Dual-colour FluoroSpot assay was used to measure interferon gamma (IFNγ) and interleukin 2 (IL2) production. Results: Among the 97 study participants, IFNγ responses were observed in 29.9% of the women and IL2 among 39.2%. Overall, 51.6% of women demonstrated response to at least one stimulant. Conclusion: We demonstrate the presence of cross-reactive immunity to SARS-CoV-2, which might have been induced by past exposure to CCoV.
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Affiliation(s)
- Marta C. Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael J. Johnson
- Department of Pediatrics, Medicine and Pathology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adriana Weinberg
- Department of Pediatrics, Medicine and Pathology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Motsoeneng BM, Dhar N, Nunes MC, Krammer F, Madhi SA, Moore PL, Richardson SI. Influenza Vaccination Results in Differential Hemagglutinin Stalk-Specific Fc-Mediated Functions in Individuals Living With or Without HIV. Front Immunol 2022; 13:873191. [PMID: 35514992 PMCID: PMC9062095 DOI: 10.3389/fimmu.2022.873191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 11/22/2022] Open
Abstract
Influenza virus hemagglutinin (HA) stalk-specific antibodies have been shown to potently induce Fc-mediated effector functions which are important in protection from disease. In placebo-controlled maternal influenza (MatFlu) vaccination trials of pregnant women living with or without HIV, reduced risk of influenza illness was associated with high HA stalk antibody titers following trivalent inactivated vaccination (TIV). However, the mechanisms of immunity conferred by the HA stalk antibodies were not well understood. Here, we investigated HA stalk-specific Fc effector functions including antibody-dependent cellular phagocytosis (ADCP), antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent complement deposition (ADCD), and FcγRIIa and FcγRIIIa binding in response to seasonal influenza vaccination. These were measured pre- and 1-month post-vaccination in 141 HIV-uninfected women (67 TIV and 74 placebo recipients) and 119 women living with HIV (WLWH; 66 TIV and 53 placebo recipients). In contrast to HIV-uninfected women, where HA stalk-specific ADCP and FcγRIIa binding were significantly boosted, WLWH showed no increase in response to vaccination. HA stalk-specific ADCC potential and FcγRIIIa binding were not boosted regardless of HIV status but were higher in WLWH compared with HIV-uninfected women prior to vaccination. HA stalk-specific ADCD was significantly increased by vaccination in all women, but was significantly lower in the WLWH both pre- and post- vaccination. Co-ordination between HA stalk-specific ADCP and ADCD in WLWH was improved by vaccination. Fc polyfunctionality was enhanced by vaccination in HIV-uninfected women and driven by the HA stalk antibody titers. However, in the WLWH, higher pre-vaccination Fc polyfunctionality was maintained post-vaccination but was decoupled from titer. Overall, we showed differential regulation of Fc effector HA stalk responses, suggesting that HIV infection results in unique humoral immunity in response to influenza vaccination, with relevance for future strategies that aim to target the HA stalk in this population.
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Affiliation(s)
- Boitumelo M Motsoeneng
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of The National Health Laboratory Services, Johannesburg, South Africa.,South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nisha Dhar
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Innovation/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Innovation/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Innovation/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of The National Health Laboratory Services, Johannesburg, South Africa.,South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Simone I Richardson
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of The National Health Laboratory Services, Johannesburg, South Africa.,South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Nunes MC, Mbotwe-Sibanda S, Baillie VL, Kwatra G, Aguas R, Madhi SA. SARS-CoV-2 Omicron Symptomatic Infections in Previously Infected or Vaccinated South African Healthcare Workers. Vaccines (Basel) 2022; 10:vaccines10030459. [PMID: 35335091 PMCID: PMC8951475 DOI: 10.3390/vaccines10030459] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
We investigated Omicron infections among healthcare workers (HCW) presenting with symptoms of SARS-CoV-2 infection and evaluated the protective effect of vaccination or prior infection. Between 24 November and 31 December 2021, HCW in Johannesburg, South Africa, were tested for SARS-CoV-2 infection by Nucleic Acid Amplification Test (NAAT). Blood samples collected either at the symptomatic visit or in the 3 months prior, were tested for spike protein immunoglobulin G (IgG). Overall, 433 symptomatic HCW were included in the analysis, with 190 (43.9%) having an Omicron infection; 69 (16.7%) were unvaccinated and 270 (62.4%) received a single dose of the Ad26.COV.2 vaccine. There was no difference in the odds of identifying Omicron between unvaccinated and Ad26.COV.2 vaccinated HCW (adjusted odds ratio (aOR) 0.81, 95% confidence interval (CI): 0.46, 1.43). One-hundred and fifty-four (35.3%) HCW had at least one SARS-CoV-2 NAAT-confirmed prior infection; these had lower odds of Omicron infection compared with those without past infection (aOR 0.55, 95%CI: 0.36, 0.84). Anti-spike IgG concentration of 1549 binding antibody unit/mL was suggestive of significant reduction in the risk of symptomatic Omicron infection. We found high reinfection and vaccine breakthrough infection rates with the Omicron variant among HCW. Prior infection and high anti-spike IgG concentration were protective against Omicron infection.
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Affiliation(s)
- Marta C. Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa; (S.M.-S.); (V.L.B.); (G.K.); (S.A.M.)
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa
- Correspondence: ; Tel.: +27-11-983-4263
| | - Sthembile Mbotwe-Sibanda
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa; (S.M.-S.); (V.L.B.); (G.K.); (S.A.M.)
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa
| | - Vicky L. Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa; (S.M.-S.); (V.L.B.); (G.K.); (S.A.M.)
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa; (S.M.-S.); (V.L.B.); (G.K.); (S.A.M.)
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK;
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa; (S.M.-S.); (V.L.B.); (G.K.); (S.A.M.)
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1862, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 2022; 185:467-484.e15. [PMID: 35081335 PMCID: PMC8723827 DOI: 10.1016/j.cell.2021.12.046] [Citation(s) in RCA: 600] [Impact Index Per Article: 300.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022]
Abstract
On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nicola Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kuan-Ying A Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital and Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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Nunes MC, Hale MJ, Mahtab S, Mabena FC, Dludlu N, Baillie VL, Thwala BN, Els T, du Plessis J, Laubscher M, Mckenzie S, Mtshali S, Menezes C, Serafin N, van Blydenstein S, Tsitsi M, Dulisse B, Madhi SA. Clinical characteristics and histopathology of COVID-19 related deaths in South African adults. PLoS One 2022; 17:e0262179. [PMID: 35051205 PMCID: PMC8775212 DOI: 10.1371/journal.pone.0262179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Comparisons of histopathological features and microbiological findings between decedents with respiratory symptoms due to SARS-CoV-2 infection or other causes, in settings with high prevalence of HIV and Mycobacterium tuberculosis (MTB) infections have not been reported. Deaths associated with a positive ante-mortem SARS-CoV-2 PCR test and/or respiratory disease symptoms at Chris Hani Baragwanath Academic Hospital in Soweto, South Africa from 15th April to 2nd November 2020, during the first wave of the South African COVID-19 epidemic, were investigated. Deceased adult patients had post-mortem minimally-invasive tissue sampling (MITS) performed to investigate for SARS-CoV-2 infection and molecular detection of putative pathogens on blood and lung samples, and histopathology examination of lung, liver and heart tissue. During the study period MITS were done in patients displaying symptoms of respiratory disease including 75 COVID-19-related deaths (COVID+) and 42 non-COVID-19-related deaths (COVID-). The prevalence of HIV-infection was lower in COVID+ (27%) than in the COVID- (64%), MTB detection was also less common among COVID+ (3% vs 13%). Lung histopathology findings showed differences between COVID+ and COVID- in the severity of the morphological appearance of Type-II pneumocytes, alveolar injury and repair initiated by SARS-CoV-2 infection. In the liver necrotising granulomatous inflammation was more common among COVID+. No differences were found in heart analyses. The prevalence of bacterial co-infections was higher in COVID+. Most indicators of respiratory distress syndrome were undifferentiated between COVID+ and COVID- except for Type-II pneumocytes. HIV or MTB infection does not appear in these data to have a meaningful correspondence with COVID-related deaths.
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Affiliation(s)
- Marta C. Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Martin J. Hale
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sana Mahtab
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Fikile C. Mabena
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Noluthando Dludlu
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky L. Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bukiwe N. Thwala
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Toyah Els
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeanine du Plessis
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marius Laubscher
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shakeel Mckenzie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sihle Mtshali
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Colin Menezes
- Department of Internal Medicine, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah van Blydenstein
- Department of Internal Medicine, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Merika Tsitsi
- Department of Internal Medicine, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Brian Dulisse
- BDII Analytics, Atlanta, GA, United States of America
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Carbonell-Estrany X, Simões EAF, Bont LJ, Gentile A, Homaira N, Scotta MC, Stein RT, Torres JP, Sheikh J, Broor S, Khuri-Bulos N, Nokes DJ, Munywoki PK, Bassat Q, Sharma AK, Basnet S, Garba M, De Jesus-Cornejo J, Lupisan SP, Nunes MC, Divarathna M, Fullarton JR, Rodgers-Gray BS, Keary I, Reñosa MDC, Verwey C, Moore DP, Noordeen F, Kabra S, do Vale MS, Paternina-De La Ossa R, Mariño C, Figueras-Aloy J, Krilov L, Berezin E, Zar HJ, Paudel K, Safadi MAP, Dbaibo G, Jroundi I, Jha R, Rafeek RAM, Pinheiro RDS, Bracht M, Muthugala R, Lanari M, Martinón-Torres F, Mitchell I, Irimu G, Pandey A, Krishnan A, Mejias A, da Costa MSC, Shrestha S, Pernica JM, de Carvalho FC, Jalango RE, Ibrahim H, Ewa A, Ensinck G, Ulloa-Gutierrez R, Miralha AL, Lucion MF, Hassan MZ, Akhtar Z, Aleem MA, Chowdhury F, Rojo P, Sande C, Musau A, Zaman K, Helena L, Arlant F, Ghimire P, Price A, Subedi KU, Brenes-Chacon H, Goswami DR, Rahman MZ, Hossain ME, Chisti MJ, Vain NE, Lim A, Chiu A, Papenburg J, Juarez MDV, Senaratne T, Arunasalam S, Strand TA, Ayuk A, Ogunrinde O, Tavares LVDS, Garba C, Garba BI, Dawa J, Gordon M, Osoro E, Agoti CN, Nyawanda B, Ngama M, Tabu C, Mathew JL, Cornacchia A, Rai GK, Jain A, Giongo MS, Paes BA. Identifying the research, advocacy, policy and implementation needs for the prevention and management of respiratory syncytial virus lower respiratory tract infection in low- and middle-income countries. Front Pediatr 2022; 10:1033125. [PMID: 36440349 PMCID: PMC9682277 DOI: 10.3389/fped.2022.1033125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION The high burden of respiratory syncytial virus (RSV) infection in young children disproportionately occurs in low- and middle-income countries (LMICs). The PROUD (Preventing RespiratOry syncytial virUs in unDerdeveloped countries) Taskforce of 24 RSV worldwide experts assessed key needs for RSV prevention in LMICs, including vaccine and newer preventive measures. METHODS A global, survey-based study was undertaken in 2021. An online questionnaire was developed following three meetings of the Taskforce panellists wherein factors related to RSV infection, its prevention and management were identified using iterative questioning. Each factor was scored, by non-panellists interested in RSV, on a scale of zero (very-low-relevance) to 100 (very-high-relevance) within two scenarios: (1) Current and (2) Future expectations for RSV management. RESULTS Ninety questionnaires were completed: 70 by respondents (71.4% physicians; 27.1% researchers/scientists) from 16 LMICs and 20 from nine high-income (HI) countries (90.0% physicians; 5.0% researchers/scientists), as a reference group. Within LMICs, RSV awareness was perceived to be low, and management was not prioritised. Of the 100 factors scored, those related to improved diagnosis particularly access to affordable point-of-care diagnostics, disease burden data generation, clinical and general education, prompt access to new interventions, and engagement with policymakers/payers were identified of paramount importance. There was a strong need for clinical education and local data generation in the lowest economies, whereas upper-middle income countries were more closely aligned with HI countries in terms of current RSV service provision. CONCLUSION Seven key actions for improving RSV prevention and management in LMICs are proposed.
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Affiliation(s)
| | - Eric A F Simões
- Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO, United States.,Department of Epidemiology, Center for Global Health, Colorado School of Public Health, University of Colorado, Aurora, CO, United States
| | - Louis J Bont
- Laboratory of Translational Immunology and Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Angela Gentile
- Epidemiology Department, Austral University, Buenos Aires, Argentina.,Ricardo Gutiérrez Children Hospital, Buenos Aires, Argentina
| | - Nusrat Homaira
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Respiratory Department, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Marcelo Comerlato Scotta
- Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Renato T Stein
- Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Juan P Torres
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jarju Sheikh
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Shobha Broor
- All India Institute of Medical Sciences, New Delhi, India
| | | | - D James Nokes
- Centre for Geographic Medicine Research-Coast, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Patrick K Munywoki
- Centre for Geographic Medicine Research-Coast, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,Institución Catalana de Investigación y Estudios Avanzados (ICREA), Barcelona, Spain.,Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain.,Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Arun K Sharma
- Department of Paediatrics, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Sudha Basnet
- Department of Paediatrics, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal.,University of Bergen, Bergen, Norway
| | - Maria Garba
- Ahmadu Bello University/Teaching Hospital, Zaria, Nigeria
| | | | - Socorro P Lupisan
- RITM-Tohoku Research Collaborating Center for Emerging Infections, Manila, Philippines
| | - Marta C Nunes
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maduja Divarathna
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | | | | | - Ian Keary
- Violicom Medical Limited, Aldermaston, United Kingdom
| | | | - Charl Verwey
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David P Moore
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Faseeha Noordeen
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Sushil Kabra
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Rolando Paternina-De La Ossa
- Hospital Santa Casa de Ribeirão Preto, São Paulo, Brazil.,Centro Universitário Barão de Mauá, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Leonard Krilov
- NYU Long Island School of Medicine, Mineola, NY, United States
| | | | - Heather J Zar
- Child Health and the SA-MRC Unit on Child and Adolescent Health, Department of Paediatrics, University of Cape Town (UCT), Cape Town, South Africa
| | | | | | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Imane Jroundi
- School of Medicine and Pharmacy, University Mohamed V, Rabat, Morocco
| | - Runa Jha
- National Public Health Laboratory, Ministry of Health & Population, Teku, Kathmandu, Nepal
| | - Rukshan A M Rafeek
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | | | | | | | | | | | | | - Grace Irimu
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Apsara Pandey
- Department of Pediatric Nursing, Maharajgunj Nursing Campus, Institute of Medicine, Tribhuwan University, Kathmandu, Nepal.,Pediatric Nurses Association of Nepal, Kathmandu, Nepal
| | - Anand Krishnan
- All India Institute of Medical Sciences, New Delhi, India
| | - Asuncion Mejias
- Nationwide Childrens Hospital, Columbus, OH, USA.,The Ohio State University, Columbus, OH, USA
| | | | | | | | | | | | - Hafsat Ibrahim
- Bayero University/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Atana Ewa
- University of Calabar/University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Gabriela Ensinck
- Hospital de Niños Víctor J. Vilela de Rosario, Santa Fe, Argentina
| | - Rolando Ulloa-Gutierrez
- Hospital Nacional de Niños "Dr. Carlos Sáenz Herrera", Caja Costarricense del Seguro Social (CCSS), San José, Costa Rica
| | | | - Maria Florencia Lucion
- Epidemiology Department, Austral University, Buenos Aires, Argentina.,Ricardo Gutiérrez Children Hospital, Buenos Aires, Argentina
| | - Md Zakiul Hassan
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Zubair Akhtar
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Fahmida Chowdhury
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pablo Rojo
- University Hospital October 12, Madrid, Spain
| | - Charles Sande
- Centre for Geographic Medicine Research-Coast, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Khalequ Zaman
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Luiza Helena
- Metropolitan University of Santos, São Paulo, Brazil
| | | | - Prakash Ghimire
- Department of Paediatrics, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - April Price
- London Health Sciences Centre, London, ON, Canada
| | | | - Helena Brenes-Chacon
- Hospital Nacional de Niños "Dr. Carlos Sáenz Herrera", Caja Costarricense del Seguro Social (CCSS), San José, Costa Rica
| | - Doli Rani Goswami
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Nestor E Vain
- Hospital Sanatorio Trinidad, Buenos Aires, Argentina
| | - Audrey Lim
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Aaron Chiu
- The Children's Hospital of Winnipeg, Winnipeg, MB, Canada
| | | | - Maria Del Valle Juarez
- Epidemiology Department, Austral University, Buenos Aires, Argentina.,Ricardo Gutiérrez Children Hospital, Buenos Aires, Argentina
| | | | - Shiyamalee Arunasalam
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Adaeze Ayuk
- University of Nigeria Teaching Hospital, Enugu, Nigeria
| | | | | | - Comfort Garba
- Ahmadu Bello University/Teaching Hospital, Zaria, Nigeria
| | - Bilkisu I Garba
- Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria
| | - Jeanette Dawa
- Washington State University - Global Health Kenya, Nairobi, Kenya
| | - Michelle Gordon
- Orillia Soldiers' Memorial Hospital, Orillia, Ontario, Canada
| | - Eric Osoro
- Washington State University - Global Health Kenya, Nairobi, Kenya
| | - Charles N Agoti
- Centre for Geographic Medicine Research-Coast, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Bryan Nyawanda
- Kenya Medical Research Institute- Center for Global Health Research, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Mwanajuma Ngama
- Centre for Geographic Medicine Research-Coast, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joseph L Mathew
- Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | | | - Ganesh Kumar Rai
- Nepal Pediatric Society (NEPAS), Kanti Children's Hospital, Kathmandu, Nepal
| | - Amita Jain
- King George's Medical University, Uttar Pradesh, India
| | | | - Bosco A Paes
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
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40
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HM, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter T, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Clemens SAC, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Ditse Z, Da Silva K, Madhi S, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. bioRxiv 2021:2021.12.03.471045. [PMID: 34981049 PMCID: PMC8722586 DOI: 10.1101/2021.12.03.471045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M.E. Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M. Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
- Department of Respiratory Sciences, University of Leicester
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Nikki Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios- IOC/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Kuan-Ying A. Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J. Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Neil G. Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A. Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R. Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
- corresponding authors: , , , ,
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- corresponding authors: , , , ,
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- corresponding authors: , , , ,
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
- corresponding authors: , , , ,
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- corresponding authors: , , , ,
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41
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Downs SL, Madhi SA, Van der Merwe L, Nunes MC, Olwagen CP. High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides. Sci Rep 2021; 11:23728. [PMID: 34887480 PMCID: PMC8660885 DOI: 10.1038/s41598-021-03127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/18/2021] [Indexed: 12/03/2022] Open
Abstract
Current real-time high-throughput Polymerase Chain Reaction (qPCR) methods do not distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009–2011), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/mL of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.
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Affiliation(s)
- S L Downs
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - S A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L Van der Merwe
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C P Olwagen
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Navarro Alonso JA, Bont LJ, Bozzola E, Herting E, Lega F, Mader S, Nunes MC, Ramilo O, Valiotis G, Olivier CW, Yates A, Faust SN. RSV: perspectives to strengthen the need for protection in all infants. Emerg Themes Epidemiol 2021; 18:15. [PMID: 34674730 PMCID: PMC8529565 DOI: 10.1186/s12982-021-00104-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Respiratory syncytial virus (RSV)-the most common viral cause of bronchiolitis-is a significant cause of serious illness among young children between the ages of 0-5 years and is especially concerning in the first year of life. Globally, RSV is a common cause of childhood acute lower respiratory illness (ALRI) and a major cause of hospital admissions in young children and infants and represents a substantial burden for health-care systems. This burden is strongly felt as there are currently no effective preventative options that are available for all infants. However, a renaissance in RSV prevention strategies is unfolding, with several new prophylactic options such as monoclonal antibodies and maternal vaccinations that are soon to be available. A key concern is that health decision makers and systems may not be ready to take full advantage of forthcoming technological innovations. A multi-stakeholder approach is necessary to bridge data gaps to fully utilise upcoming options. Knowledge must be made available at multiple levels to ensure that parents and doctors are aware of preventative options, but also to ensure that stakeholders and policymakers are given the necessary information to best advise implementation strategies.
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Affiliation(s)
| | - Louis J Bont
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Elena Bozzola
- Pediatric and Infectious Diseases Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - Egbert Herting
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Federico Lega
- Centre for Research on Healthcare Management, Bocconi University, Milan, Italy
| | - Silke Mader
- European Foundation for the Care of Newborn Infants (EFCNI), Munich, Germany
| | - Marta C Nunes
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Room WA4021, 700 Children's Drive, Columbus, OH, 43205, USA
| | - George Valiotis
- European Health Management Association (EHMA), Brussels, Belgium
| | - Catherine Weil Olivier
- University of Paris, 7 Denis Diderot, 28 rue Parmentier, Neuilly sur Seine, 92200, Paris, France
| | - Ann Yates
- International Confederation of Midwives (ICM), The Hague, The Netherlands
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Hampshire, Southampton, UK. .,NIHR Southampton Clinical Research Facility and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Hampshire, Southampton, UK.
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43
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Nunes MC, Johnson MJ, Kwatra G, Weinberg A, Madhi SA. T-cell responses to SARS-CoV-2 in unexposed South African women. Gates Open Res 2021; 5:150. [DOI: 10.12688/gatesopenres.13373.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 11/20/2022] Open
Abstract
Background: A potential explanation for the fact that the high rate of infection of SARS-CoV-2 in South Africa did not translate into high rates of severe illness and death may be the presence of cross-reactive immunity induced by common cold coronaviruses (CCoV). Methods: We used SARS-CoV-2 peptide pools and whole virus antigen to stimulate peripheral blood mononuclear cells collected pre-2020 from South African women. Dual-colour FluoroSpot assay was used to measure interferon gamma (IFNγ) and interleukin 2 (IL2) production. Results: Among the 97 study participants, IFNγ responses were observed in 29.9% of the women and IL2 among 39.2%. Overall, 51.6% of women demonstrated response to at least one stimulant. Conclusion: We demonstrate the presence of cross-reactive immunity to SARS-CoV-2, which might have been induced by past exposure to CCoV.
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44
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Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang B, Tuekprakhon A, Nutalai R, Zhou D, Mentzer AJ, Zhao Y, Duyvesteyn HME, López-Camacho C, Slon-Campos J, Walter TS, Skelly D, Johnson SA, Ritter TG, Mason C, Costa Clemens SA, Gomes Naveca F, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Dold C, Temperton N, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert SC, Malik T, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Baillie V, Serafin N, Ditse Z, Da Silva K, Paterson NG, Williams MA, Hall DR, Madhi S, Nunes MC, Goulder P, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 2021; 184:4220-4236.e13. [PMID: 34242578 PMCID: PMC8218332 DOI: 10.1016/j.cell.2021.06.020] [Citation(s) in RCA: 501] [Impact Index Per Article: 167.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.
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Affiliation(s)
- Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas S Walter
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Clutterbuck
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sagida Bibi
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mustapha Bittaye
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - David I Stuart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK; Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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Löwensteyn YN, Nair H, Nunes MC, van Roessel I, Vernooij FS, Willemsen J, Bont LJ, Mazur NI. Estimated impact of maternal vaccination on global paediatric influenza-related in-hospital mortality: A retrospective case series. EClinicalMedicine 2021; 37:100945. [PMID: 34386739 PMCID: PMC8343247 DOI: 10.1016/j.eclinm.2021.100945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/30/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Influenza virus infection is an important cause of under-five mortality. Maternal vaccination protects children younger than 3 months of age from influenza infection. However, it is unknown to what extent paediatric influenza-related mortality may be prevented by a maternal vaccine since global age-stratified mortality data are lacking. METHODS We invited clinicians and researchers to share clinical and demographic characteristics from children younger than 5 years who died with laboratory-confirmed influenza infection between January 1, 1995 and March 31, 2020. We evaluated the potential impact of maternal vaccination by estimating the number of children younger than 3 months with in-hospital influenza-related death using published global mortality estimates. FINDINGS We included 314 children from 31 countries. Comorbidities were present in 166 (53%) children and 41 (13%) children were born prematurely. Median age at death was 8·6 (IQR 4·5-16·6), 11·5 (IQR 4·3-24·0), and 15·5 (IQR 7·4-27·0) months for children from low- and lower-middle-income countries (LMICs), upper-middle-income countries (UMICs), and high-income countries (HICs), respectively. The proportion of children younger than 3 months at time of death was 17% in LMICs, 12% in UMICs, and 7% in HICs. We estimated that 3339 annual influenza-related in-hospital deaths occur in the first 3 months of life globally. INTERPRETATION In our study, less than 20% of children is younger than 3 months at time of influenza-related death. Although maternal influenza vaccination may impact maternal and infant influenza disease burden, additional immunisation strategies are needed to prevent global influenza-related childhood mortality. The missing data, global coverage, and data quality in this study should be taken into consideration for further interpretation of the results. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Yvette N Löwensteyn
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Harish Nair
- Respiratory Syncytial Virus Network (ReSViNET) Foundation, Zeist, the Netherlands
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Marta C Nunes
- Respiratory Syncytial Virus Network (ReSViNET) Foundation, Zeist, the Netherlands
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand; and Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Ichelle van Roessel
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Femke S Vernooij
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Joukje Willemsen
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Louis J Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
- Respiratory Syncytial Virus Network (ReSViNET) Foundation, Zeist, the Netherlands
| | - Natalie I Mazur
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, the Netherlands
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Nunes MC, Baillie VL, Kwatra G, Bhikha S, Verwey C, Menezes C, Cutland CL, Moore DP, Dangor Z, Adam Y, Mathivha R, Velaphi SC, Tsitsi M, Aguas R, Madhi SA. SARS-CoV-2 infection among healthcare workers in South Africa: a longitudinal cohort study. Clin Infect Dis 2021; 73:1896-1900. [PMID: 33949670 PMCID: PMC8135922 DOI: 10.1093/cid/ciab398] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
From April to September 2020, we investigated severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) infections in a cohort of 396 healthcare workers
(HCWs) from 5 departments at Chris Hani Baragwanath Hospital, South Africa.
Overall, 34.6% of HCWs had polymerase chain reaction–confirmed SARS-CoV-2
infection (132.1 [95% confidence interval, 111.8–156.2] infections per
1000 person-months); an additional 27 infections were identified by serology.
HCWs in the internal medicine department had the highest rate of infection
(61.7%). Among polymerase chain reaction–confirmed cases, 10.4% remained
asymptomatic, 30.4% were presymptomatic, and 59.3% were symptomatic.
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Affiliation(s)
- Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky L Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sutika Bhikha
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Charl Verwey
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Colin Menezes
- Department of Internal Medicine, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare L Cutland
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David P Moore
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Dangor
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yasmin Adam
- Department of Obstetrics & Gynaecology, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rudo Mathivha
- Department of Intensive Care, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sithembiso C Velaphi
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Merika Tsitsi
- Department of Internal Medicine, Chris Hani Baragwanath Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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47
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Dhar N, Kwatra G, Nunes MC, Cutland C, Izu A, Nachbagauer R, Krammer F, Madhi SA. Hemagglutinin Stalk Antibody Responses Following Trivalent Inactivated Influenza Vaccine Immunization of Pregnant Women and Association With Protection From Influenza Virus Illness. Clin Infect Dis 2021; 71:1072-1079. [PMID: 31565750 PMCID: PMC7428398 DOI: 10.1093/cid/ciz927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/17/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The conserved, immuno-subdominant influenza virus hemagglutinin (HA) stalk region is a potential universal group-specific influenza virus vaccine epitope. We analyzed antibody responses to H1 hemagglutinin stalk domain (H1/stalk) following trivalent influenza inactivated vaccine (IIV3) immunization in pregnant women, and association with protection against influenza virus illness. METHODS One hundred forty-five human immunodeficiency virus (HIV)-uninfected pregnant women (68 IIV3 and 77 placebo recipients) and 140 pregnant women with HIV infection (72 IIV3 and 68 placebo recipients) were independently randomized in placebo-controlled efficacy trials of IIV3. Plasma samples were tested for H1/stalk immunoglobulin G (IgG) and hemagglutination inhibition (HAI) antibodies prevaccination and 1 month postvaccination. Women had weekly surveillance for influenza illness, confirmed by polymerase chain reaction. RESULTS Increases in H1/stalk IgG (and HAI) antibody levels were elicited post-IIV3, with responses being higher in HIV-uninfected women than in women living with HIV. Among HIV-uninfected vaccinees, there was no correlation (postvaccination) between H1/stalk and HAI antibody responses, whereas a strong correlation was observed in vaccinees with HIV. The H1/stalk IgG concentration was lower among women developing A/H1N1 illness (85.3 arbitrary units [AU]/mL) than those without A/H1N1 illness (219.6 AU/mL; P = .001). H1/stalk IgG concentration ≥215 AU/mL was associated with 90% lower odds (odds ratio, 0.09; P = .005) of A/H1N1 illness. Also, H1/stalk IgG was significantly lower among women with influenza B illness (93.9 AU/mL) than among their counterparts (215.5 AU/mL) (P = .04); however, no association was observed after adjusting for HAI titers. CONCLUSIONS H1/stalk IgG concentration was associated with lower odds for A/H1N1 influenza virus illness, indicating its potential as an epitope for a universal vaccine against group 1 influenza virus.
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Affiliation(s)
- Nisha Dhar
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare Cutland
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alane Izu
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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48
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Nunes MC, Moreira M, Koen A, van Niekerk N, Jose L, Cutland CL, François N, Schoonbroodt S, Ruiz-Guiñazú J, Yarzabal JP, Borys D, Schuerman L, Madhi SA. Bacterial nasopharyngeal carriage following infant immunization with pneumococcal conjugate vaccines according to a 2+1 schedule in children in South Africa: an exploratory analysis of two clinical trials. Expert Rev Vaccines 2020; 19:1177-1189. [PMID: 33245004 DOI: 10.1080/14760584.2020.1853533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: We evaluated bacterial nasopharyngeal carriage (NPC) prevalence and cumulative acquisition following 7-valent pneumococcal conjugate vaccine (PCV7) or pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) administration. Methods: Participants were children from two clinical trials in a South African center who received PCV7 (n = 250) or PHiD-CV (n = 100) at ~6 weeks, ~14 weeks, and ~9-10 months of age, and were enrolled between Dec2009-Apr2010 and Mar2009-May2010 in the PCV7 and PHiD-CV studies, respectively. Sample collection, most microbiological assessments, and data re-analysis methods were identical. Results: NPC prevalence of any pneumococcal serotype was 18.5% and 17.0% at pre-vaccination, and 63.1% and 67.3% in 24-27 month-old children among PCV7 and PHiD-CV recipients, respectively. In 24-27 month-old children, 96.1% and 99.0% of PCV7 and PHiD-CV recipients had acquired ≥1 pneumococcal serotype, 53.7% and 62.9% ≥1 PCV7 serotype, 1.5%, and 3.1% ≥1 of serotypes 1, 5 or 7F, 23.2% and 19.6% serotype 6A, 23.2% and 21.7% serotype 19A, 88.7%, and 91.0% H. influenzae, and 50.3% and 62.9% Staphylococcus aureus, respectively. Conclusions: This analysis of two concurrent clinical trials did not reveal differences in bacterial NPC prevalence or acquisition in PCV7- and PHiD-CV-vaccinated children. Trial registration: South African National Clinical Trial Register (NHREC DOH-27-0511-299); ClinicalTrials.gov (NCT00829010).
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Affiliation(s)
- Marta C Nunes
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | | | - Anthonet Koen
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Nadia van Niekerk
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Lisa Jose
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Clare L Cutland
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | | | | | | | | | | | | | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
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49
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Macias AE, McElhaney JE, Chaves SS, Nealon J, Nunes MC, Samson SI, Seet BT, Weinke T, Yu H. The disease burden of influenza beyond respiratory illness. Vaccine 2020; 39 Suppl 1:A6-A14. [PMID: 33041103 PMCID: PMC7545338 DOI: 10.1016/j.vaccine.2020.09.048] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/10/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
Although influenza is primarily considered a respiratory infection and causes significant respiratory mortality, evidence suggests that influenza has an additional burden due to broader consequences of the illness. Some of these broader consequences include cardiovascular events, exacerbations of chronic underlying conditions, increased susceptibility to secondary bacterial infections, functional decline, and poor pregnancy outcomes, all of which may lead to an increased risk for hospitalization and death. Although it is methodologically difficult to measure these impacts, epidemiological and interventional study designs have evolved over recent decades to better take them into account. Recognizing these broader consequences of influenza virus infection is essential to determine the full burden of influenza among different subpopulations and the value of preventive approaches. In this review, we outline the main influenza complications and societal impacts beyond the classical respiratory symptoms of the disease.
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Affiliation(s)
- Alejandro E Macias
- Department of Medicine and Nutrition, University of Guanajuato, Guanajuato, Mexico.
| | | | | | | | - Marta C Nunes
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | | | - Bruce T Seet
- Sanofi Pasteur, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | | | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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50
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Verwey C, Nunes MC. RSV lower respiratory tract infection and lung health in the first 2 years of life. Lancet Glob Health 2020; 8:e1247-e1248. [PMID: 32971046 DOI: 10.1016/s2214-109x(20)30303-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Charl Verwey
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Chris Hani Baragwanath Academic Hospital, and Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Chris Hani Baragwanath Academic Hospital, and Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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