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Jarju S, Wenlock RD, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA, Gaye H, Gaye B, Tunkara A, Kandeh S, Gomes M, Sylva EL, Toure F, Hornsby H, Lindsey BB, Nicklin MJ, Sayers JR, Sesay AK, Kucharski A, Hodgson D, Kampmann B, de Silva TI. High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia. Nat Commun 2024; 15:3814. [PMID: 38714680 PMCID: PMC11076623 DOI: 10.1038/s41467-024-48098-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study of 349 participants from 52 households in The Gambia between March 2021 and June 2022, with routine weekly SARS-CoV-2 RT-PCR and 6-monthly SARS-CoV-2 serology. Attack rates of 45% and 57% were seen during Delta and Omicron BA.1 waves respectively. Eighty-four percent of RT-PCR-positive infections were asymptomatic. Children under 5-years had a lower incidence of infection than 18-49-year-olds. One prior SARS-CoV-2 infection reduced infection risk during the Delta wave only, with immunity from ≥2 prior infections required to reduce the risk of infection with early Omicron lineage viruses. In an African population with high levels of infection-driven immunity and low vaccine coverage, we find high attack rates during SARS-CoV-2 waves, with a high proportion of asymptomatic infections and young children remaining relatively protected from infection.
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Affiliation(s)
- Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Rhys D Wenlock
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Madikoi Danso
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Dawda Jobe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Michelle Kumado
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Yusupha Jallow
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Mamlie Touray
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ebrima A Ceesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hoja Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Biran Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Abdoulie Tunkara
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Sheriff Kandeh
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Marie Gomes
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ellen Lena Sylva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Fatoumata Toure
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Benjamin B Lindsey
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Martin J Nicklin
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Jon R Sayers
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Abdul K Sesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Institute for International Health, Charité Universitätsmedizin, Berlin, Germany.
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK.
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK.
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Hookham L, Cantrell L, Cose S, Freyne B, Gadama L, Imede E, Kawaza K, Lissauer S, Musoke P, Nankabirwa V, Sekikubo M, Sommerfelt H, Voysey M, Le Doare K. Seroepidemiology of SARS-CoV-2 in a cohort of pregnant women and their infants in Uganda and Malawi. PLoS One 2024; 19:e0290913. [PMID: 38427691 PMCID: PMC10906847 DOI: 10.1371/journal.pone.0290913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/24/2023] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Data on SARS-CoV-2 infection in pregnancy and infancy has accumulated throughout the course of the pandemic, though evidence regarding asymptomatic SARS-CoV-2 infection and adverse birth outcomes are scarce. Limited information is available from countries in sub-Saharan Africa (SSA). The pregnant woman and infant COVID in Africa study (PeriCOVID Africa) is a South-South-North partnership involving hospitals and health centres in five countries: Malawi, Uganda, Mozambique, The Gambia, and Kenya. The study leveraged data from three ongoing prospective cohort studies: Preparing for Group B Streptococcal Vaccines (GBS PREPARE), SARS-CoV-2 infection and COVID-19 in women and their infants in Kampala and Mukono (COMAC) and Pregnancy Care Integrating Translational Science Everywhere (PRECISE). In this paper we describe the seroepidemiology of SARS-CoV-2 infection in pregnant women enrolled in sites in Uganda and Malawi, and the impact of SARS-CoV-2 infection on pregnancy and infant outcomes. OUTCOME Seroprevalence of SARS-CoV-2 antibodies in maternal blood, reported as the proportion of seropositive women by study site and wave of COVID-19 within each country. METHODS The PeriCOVID study was a prospective mother-infant cohort study that recruited pregnant women at any gestation antenatally or on the day of delivery. Maternal and cord blood samples were tested for SARS-CoV-2 antibodies using Wantai and Euroimmune ELISA. In periCOVID Uganda and Malawi nose and throat swabs for SARS-Cov-2 RT-PCR were obtained. RESULTS In total, 1379 women were enrolled, giving birth to 1387 infants. Overall, 63% of pregnant women had a SARS-CoV-2 positive serology. Over subsequent waves (delta and omicron), in the absence of vaccination, seropositivity rose from 20% to over 80%. The placental transfer GMR was 1.7, indicating active placental transfer of anti-spike IgG. There was no association between SARS-CoV-2 antibody positivity and adverse pregnancy or infancy outcomes.
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Affiliation(s)
- Lauren Hookham
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Liberty Cantrell
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Stephen Cose
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Bridget Freyne
- Malawi Liverpool Wellcome Trust, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, United Kingdom
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Luis Gadama
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Esther Imede
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Samantha Lissauer
- Malawi Liverpool Wellcome Trust, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | - Phillipa Musoke
- Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Victoria Nankabirwa
- Department of Epidemiology & Biostatistics, School of Public Health, Makerere University, Kampala, Uganda
| | - Musa Sekikubo
- Department of Obstetrics & Gynaecology Makerere University, Kampala, Uganda
| | - Halvor Sommerfelt
- Centre for Intervention Science in Maternal and Child Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Norwegian Institute of Public Health, Bergen, Norway
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Kirsty Le Doare
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
- Makerere University, John’s Hopkins University, Kampala, Uganda
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Wariri O, Utazi CE, Okomo U, Sowe A, Sogur M, Fofanna S, Ezeani E, Saidy L, Sarwar G, Dondeh BL, Murray KA, Grundy C, Kampmann B. Impact of the COVID-19 pandemic on the coverage and timeliness of routine childhood vaccinations in the Gambia, 2015-2021. BMJ Glob Health 2023; 8:e014225. [PMID: 38148110 PMCID: PMC10753753 DOI: 10.1136/bmjgh-2023-014225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/10/2023] [Indexed: 12/28/2023] Open
Abstract
INTRODUCTION The COVID-19 pandemic caused widespread morbidity and mortality and resulted in the biggest setback in routine vaccinations in three decades. Data on the impact of the pandemic on immunisation in Africa are limited, in part, due to low-quality routine or administrative data. This study examined coverage and timeliness of routine childhood immunisation during the pandemic in The Gambia, a country with an immunisation system considered robust. METHODS We obtained prospective birth cohort data of 57 286 children in over 300 communities in two health and demographic surveillance system sites, including data from the pre-pandemic period (January 2015-February 2020) and the three waves of the pandemic period (March 2020-December 2021). We determined monthly coverage and timeliness (early and delayed) of the birth dose of hepatitis B vaccine (HepB0) and the first dose of pentavalent vaccine (Penta1) during the different waves of the pandemic relative to the pre-pandemic period. We implemented a binomial interrupted time-series regression model. RESULT We observed no significant change in the coverage of HepB0 and Penta1 vaccinations from the pre-pandemic period up until the periods before the peaks of the first and second waves of the pandemic in 2020. However, there was an increase in HepB0 coverage before as well as after the peak of the third wave in 2021 compared with the pre-pandemic period (pre-third wave peak OR = 1.83, 95% CI 1.06 to 3.14; post-third wave period OR=2.20, 95% CI 1.23 to 3.92). There was some evidence that vaccination timeliness changed during specific periods of the pandemic. Early Penta1 vaccination decreased by 70% (OR=0.30, 95% CI 0.12 to 0.78) in the period before the second wave, and delayed HepB0 vaccination decreased by 47% (OR=0.53, 95% CI 0.29 to 0.97) after the peak of the third wave in 2021. CONCLUSION Despite the challenges of the COVID-19 pandemic, The Gambia's routine vaccination programme has defied the setbacks witnessed in other settings and remained resilient, with coverage increasing and timeliness improving during the second and third waves. These findings highlight the importance of having adequate surveillance systems to monitor the impact of large shocks to vaccination coverage and timeliness.
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Affiliation(s)
- Oghenebrume Wariri
- Vaccines and Immunity Theme, MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Chigozie Edson Utazi
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Southampton Statistical Sciences Research Institute, , University of Southampton, Southampton, UK
| | - Uduak Okomo
- Vaccines and Immunity Theme, MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- MARCH Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Alieu Sowe
- Expanded Programme on Immunization, Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Malick Sogur
- Expanded Programme on Immunization, Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Sidat Fofanna
- Expanded Programme on Immunization, Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Esu Ezeani
- Health and Demographic Surveillance System (HDSS), MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Lamin Saidy
- Data Management & Architecture, MRC Unit The Gambia a London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Golam Sarwar
- Health and Demographic Surveillance System (HDSS), MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Bai-Lamin Dondeh
- Data Management & Architecture, MRC Unit The Gambia a London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Kris A Murray
- Centre on Climate Change and Planetary Health, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chris Grundy
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Global Health, Charité Universitatsmedizin Berlin, Berlin, Germany
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4
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Janha RE, Bah A, Jah H, Touray F, Idris Y, Keita S, Gaye Y, Jallow S, Faye-Joof T, Njie B, Craik R, Mohammed NI, von Dadelszen P, D'Alessandro U, Roca A. SARS-CoV-2 seroprevalence in pregnant women during the first three COVID-19 waves in The Gambia. Int J Infect Dis 2023; 135:109-117. [PMID: 37586660 DOI: 10.1016/j.ijid.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023] Open
Abstract
OBJECTIVES SARS-CoV-2 transmission in sub-Saharan Africa has probably been underestimated. Population-based seroprevalence studies are needed to determine the extent of transmission in the continent. METHODS Blood samples from a cohort of Gambian pregnant women were tested for SARS-CoV-2 total receptor binding domain (RBD) immunoglobulin (Ig) M/IgG before (Pre-pandemic: October-December 2019) and during the pandemic (Pre-wave 1: February-June 2020; Post-wave 1: October-December 2020, Post-wave 2: May-June 2021; and Post-wave 3: October-December 2021). Samples reactive for SARS-CoV-2 total RBD IgM/IgG were tested in specific S1- and nucleocapsid (NCP) IgG assays. RESULTS SARS-CoV-2 total RBD IgM/IgG seroprevalence was 0.9% 95% confidence interval (0.2, 4.9) in Pre-pandemic; 4.1% (1.4, 11.4) in Pre-wave 1; 31.1% (25.2, 37.7) in Post-wave 1; 62.5% (55.8, 68.8) in Post-wave 2 and 90.0% (85.1, 93.5) in Post-wave 3. S-protein IgG and NCP-protein IgG seroprevalence also increased at each Post-wave period. Although S-protein IgG and NCP-protein IgG seroprevalence was similar at Post-wave 1, S-protein IgG seroprevalence was higher at Post-wave 2 and Post-wave 3, (prevalence difference 13.5 [0.1, 26.8] and prevalence ratio 1.5 [1.0, 2.3] in Post-wave 2; and 22.9 [9.2, 36.6] and 1.4 [1.1, 1.8] in Post-wave 3 respectively, P <0.001). CONCLUSION SARS-CoV-2 transmission in The Gambia during the first 3 COVID-19 waves was high, differing significantly from official numbers of COVID-19 cases reported. Our findings are important for policy makers in managing the near-endemic COVID-19.
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Affiliation(s)
- Ramatoulie E Janha
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Hawanatu Jah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Fatima Touray
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Yahaya Idris
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Saikou Keita
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Yassin Gaye
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Tisbeh Faye-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Baboucarr Njie
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Rachel Craik
- Department of Women and Children's Health, School of Life Course Science, Faculty of Life Sciences and Medicine, King's College London, London, UK; Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Peter von Dadelszen
- Department of Women and Children's Health, School of Life Course Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia.
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5
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Bah A, Russo G. Factors that influenced utilization of antenatal and immunization services in two local government areas in The Gambia during COVID-19: An interview-based qualitative study. PLoS One 2023; 18:e0276357. [PMID: 37384645 PMCID: PMC10309596 DOI: 10.1371/journal.pone.0276357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
INTRODUCTION Evidence is being consolidated that shows that the utilization of antenatal and immunization services has declined in low-income countries (LICs) during the COVID-19 pandemic. Very little is known about the effects of the pandemic on antenatal and immunization service utilization in The Gambia. We set out to explore the COVID-19-related factors affecting the utilization of antenatal and immunization services in two Local Government Areas (LGAs) in The Gambia. METHODS A qualitative methodology was used to explore patients' and providers' experiences of antenatal and immunization services during the pandemic in two LGAs in The Gambia. Thirty-one study participants were recruited from four health facilities, applying a theory-driven sampling framework, including health workers as well as female patients. Qualitative evidence was collected through theory-driven semi-structured interviews, and was recorded, translated into English, transcribed, and analysed thematically, applying a social-ecological framework. RESULTS In our interviews, we identified themes at five different levels: individual, interpersonal, community, institutional and policy factors. Individual factors revolved around patients' fear of being infected in the facilities, and of being quarantined, and their anxiety about passing on infections to family members. Interpersonal factors involved the reluctance of partners and family members, as well as perceived negligence and disrespect by health workers. Community factors included misinformation within the community and mistrust of vaccines. Institutional factors included the shortage of health workers, closures of health facilities, and the lack of personal protective equipment (PPEs) and essential medicines. Finally, policy factors revolved around the consequences of COVID-19 prevention measures, particularly the shortage of transport options and mandatory wearing of face masks. CONCLUSIONS Our findings suggest that patients' fears of contagion, perceptions of poor treatment in the health system, and a general anxiety around the imposing of prevention measures, undermined the uptake of services. In future emergencies, the government in The Gambia, and governments in other LICs, will need to consider the unintended consequences of epidemic control measures on the uptake of antenatal and immunization services.
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Affiliation(s)
- Abdourahman Bah
- The Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
| | - Giuliano Russo
- The Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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7
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Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y, Sambou S, Jarju G, Manjang B, Jagne A, Bittaye SO, Bittaye M, Forrest K, Tiruneh DA, Samateh AL, Jagne S, Hué S, Mohammed N, Amambua-Ngwa A, Kampmann B, D'Alessandro U, de Silva TI, Roca A, Sesay AK. Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. Lancet Glob Health 2023; 11:e414-e424. [PMID: 36796985 PMCID: PMC9928486 DOI: 10.1016/s2214-109x(22)00553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
BACKGROUND COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. METHODS Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed. FINDINGS Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. INTERPRETATION More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. FUNDING Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
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Affiliation(s)
- Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Haruna S Jallow
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Jarra Manneh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sanyang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mariama A Kujabi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Laye Ndure
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alhagie Papa Sey
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Dabiri Damilare K
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Yaya Bah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | | | | | | | | | - Karen Forrest
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | - Sheriffo Jagne
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Nuredin Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Anna Roca
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Abdul Karim Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
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8
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Mohammed NI, Mackenzie G, Ezeani E, Sidibeh M, Jammeh L, Sarwar G, Saine AKF, Sonko B, Gomez P, Dondeh BL, Hossain MJ, Jasseh M, Usuf E, Prentice AM, Jeffries D, Dalessandro U, Roca A. Quantifying excess mortality during the COVID-19 pandemic in 2020 in The Gambia: a time-series analysis of three health and demographic surveillance systems. Int J Infect Dis 2023; 128:61-68. [PMID: 36566776 PMCID: PMC9780021 DOI: 10.1016/j.ijid.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Estimates for COVID-19-related excess mortality for African populations using local data are needed to design and implement effective control policies. METHODS We applied time-series analysis using data from three health and demographic surveillance systems in The Gambia (Basse, Farafenni, and Keneba) to examine pandemic-related excess mortality during 2020, when the first SARS-CoV-2 wave was observed, compared to the pre-pandemic period (2016-2019). RESULTS Across the three sites, average mortality during the pre-pandemic period and the total deaths during 2020 were 1512 and 1634, respectively (Basse: 1099 vs 1179, Farafenni: 316 vs 351, Keneba: 98 vs 104). The overall annual crude mortality rates per 100,000 (95% CI) were 589 (559, 619) and 599 (571, 629) for the pre-pandemic and 2020 periods, respectively. The adjusted excess mortality rate was 8.8 (-34.3, 67.6) per 100,000 person-month with the adjusted rate ratio (aRR) = 1.01 (0.94,1.11). The age-stratified analysis showed excess mortality in Basse for infants (aRR = 1.22 [1.04, 1.46]) and in Farafenni for the 65+ years age group (aRR = 1.19 [1, 1.44]). CONCLUSION We did not find significant excess overall mortality in 2020 in The Gambia. However, some age groups may have been at risk of excess death. Public health response in countries with weak health systems needs to consider vulnerable age groups and the potential for collateral damage.
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Affiliation(s)
- Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
| | - Grant Mackenzie
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Murdoch Children's Research Institute, Melbourne, Australia
| | - Esu Ezeani
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mamadi Sidibeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Lamin Jammeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Aji Kumba Folawiyo Saine
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sonko
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Pierre Gomez
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bai Lamin Dondeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Momodou Jasseh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
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9
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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10
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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11
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Alber D, Haidara FC, Luoma J, Adubra L, Ashorn P, Ashorn U, Badji H, Cloutman-Green E, Diallo F, Ihamuotila R, Klein N, Martell O, Onwuchekwa UU, Samaké O, Sow SO, Traore A, Wilson K, Ducker C, Fan YM. SARS-CoV-2 infection and antibody seroprevalence in routine surveillance patients, healthcare workers and general population in Kita region, Mali: an observational study 2020-2021. BMJ Open 2022; 12:e060367. [PMID: 35710236 PMCID: PMC9207578 DOI: 10.1136/bmjopen-2021-060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE To estimate the degree of SARS-CoV-2 transmission among healthcare workers (HCWs) and general population in Kita region of Mali. DESIGN Routine surveillance in 12 health facilities, HCWs serosurvey in five health facilities and community serosurvey in 16 villages in or near Kita town, Mali. SETTING Kita region, western Mali; local health centres around the central (regional) referral health centre. PARTICIPANTS Patients in routine surveillance, HCWs in local health centres and community members of all ages in populations associated with study health centres. MAIN OUTCOME MEASURES Seropositivity of ELISA test detecting SARS-CoV-2-specific total antibodies and real-time RT-PCR confirmed SARS-CoV-2 infection. RESULTS From 2392 routine surveillance samples, 68 (2.8%, 95% CI: 2.2% to 3.6%) tested positive for SARS-CoV-2 by RT-PCR. The monthly positivity rate was 0% in June-August 2020 and gradually increased to 6% by December 2020 and 6.2% by January 2021, then declined to 5.5%, 3.3%, 3.6% and 0.8% in February, March, April and May 2021, respectively. From 397 serum samples collected from 113 HCWs, 175 (44.1%, 95% CI: 39.1% to 49.1%) were positive for SARS-CoV-2 antibodies. The monthly seroprevalence was around 10% from September to November 2020 and increased to over 40% from December 2020 to May 2021. For community serosurvey in December 2020, overall seroprevalence of SARS-CoV-2 antibodies was 27.7%. The highest age-stratified seroprevalence was observed in participants aged 60-69 years (45.5%, 95% CI: 32.3% to 58.6%). The lowest was in children aged 0-9 years (14.0%, 95% CI: 7.4% to 20.6%). CONCLUSIONS SARS-CoV-2 in rural Mali is much more widespread than assumed by national testing data and particularly in the older population and frontline HCWs. The observation is contrary to the widely expressed view, based on limited data, that COVID-19 infection rates were lower in 2020-2021 in West Africa than in other settings.
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Affiliation(s)
- Dagmar Alber
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Juho Luoma
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Laura Adubra
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henry Badji
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Rikhard Ihamuotila
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | | | - Oumar Samaké
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Samba O Sow
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Awa Traore
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Kevin Wilson
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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12
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Diallo BA, Usuf E, Ceesay O, D'Alessandro U, Roca A, Martinez-Alvarez M. Clinical research on COVID-19: perceptions and barriers to participation in The Gambia. BMJ Glob Health 2022; 7:e007533. [PMID: 35190459 PMCID: PMC8861886 DOI: 10.1136/bmjgh-2021-007533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/29/2022] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION The need to rapidly identify safe and efficacious drug therapies for COVID-19 has resulted in the implementation of multiple clinical trials investigating potential treatment options. These are being undertaken in an unprecedented research environment and at a higher speed than ever before. It is unclear how West African communities perceive such activities and how such perceptions influence participation in COVID-19 clinical trials. This qualitative study was conducted to assess the level of acceptability of a clinical trial on the prevention and treatment of COVID-19 in The Gambia and identify strategies to better engage communities in participating in such a trial. METHODS Data were collected using digitally recorded semistructured interviews (SSIs) and focus group discussions (FGDs) in Brikama and Kanifing local government areas. These are two of the most densely populated administrative subdivisions in The Gambia, where the clinical trial was to be implemented by the MRC Unit The Gambia. 26 men and 22 women aged between 19 and 70 years, with diverse socioeconomic profiles, participated in 8 FGDs (n=36) and 12 SSIs (n=12). Thematic analysis was used to analyse the data. RESULTS Fear of stigmatisation of patients with COVID-19 was a recurring theme in most FGDs and SSIs, with detrimental effects on willingness to accept COVID-19 testing and home visits to follow up patients with COVID-19 and their household contacts. Preserving the privacy of individuals enrolled in the study was key to potentially increase trial participation. Trust in the implementing institution and its acknowledged expertise were facilitators to accepting the administration of investigational products to sick individuals and their close contacts. CONCLUSION COVID-19 is a stigmatising disease. Developing a research-participant collaboration through an ongoing engagement with community members is crucial to a successful enrolment in COVID-19 clinical trials. Trust and acknowledged expertise of the implementing institution are key facilitators to foster such collaboration.
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Affiliation(s)
- Brahima Amara Diallo
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Effua Usuf
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Omar Ceesay
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Anna Roca
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Melisa Martinez-Alvarez
- Disease Control and Elimination (DCE), Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
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13
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Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022. [PMID: 36726685 DOI: 10.17605/osf.io/tsf78] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrissa Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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