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Hamaluba M, Sang S, Orindi B, Njau I, Karanja H, Kamau N, Gitonga JN, Mugo D, Wright D, Nyagwange J, Kutima B, Omuoyo D, Mwatasa M, Ngetsa C, Agoti C, Cheruiyot S, Nyaguara A, Munene M, Mturi N, Oloo E, Ochola-Oyier L, Mumba N, Mauncho C, Namayi R, Davies A, Tsofa B, Nduati EW, Aliyan N, Kasera K, Etyang A, Boyd A, Hill A, Gilbert S, Douglas A, Pollard A, Bejon P, Lambe T, Warimwe G. Safety and immunogenicity of ChAdOx1 nCoV-19 (AZD1222) vaccine in adults in Kenya: a phase 1/2 single-blind, randomised controlled trial. Wellcome Open Res 2023; 8:182. [PMID: 38707489 PMCID: PMC11066537 DOI: 10.12688/wellcomeopenres.19150.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/07/2024] Open
Abstract
Background There are limited data on the immunogenicity of coronavirus disease 2019 (COVID-19) vaccines in African populations. Here we report the immunogenicity and safety of the ChAdOx1 nCoV-19 (AZD1222) vaccine from a phase 1/2 single-blind, randomised, controlled trial among adults in Kenya conducted as part of the early studies assessing vaccine performance in different geographical settings to inform Emergency Use Authorisation. Methods We recruited and randomly assigned (1:1) 400 healthy adults aged ≥18 years in Kenya to receive ChAdOx1 nCoV-19 or control rabies vaccine, each as a two-dose schedule with a 3-month interval. The co-primary outcomes were safety, and immunogenicity assessed using total IgG enzyme-linked immunosorbent assay (ELISA) against SARS-CoV-2 spike protein 28 days after the second vaccination. Results Between 28 th October 2020 and 19 th August 2021, 400 participants were enrolled and assigned to receive ChAdOx1 nCoV-19 (n=200) or rabies vaccine (n=200). Local and systemic adverse events were self-limiting and mild or moderate in nature. Three serious adverse events were reported but these were deemed unrelated to vaccination. The geometric mean anti-spike IgG titres 28 days after second dose vaccination were higher in the ChAdOx1 group (2773 ELISA units [EU], 95% CI 2447, 3142) than in the rabies vaccine group (61 EU, 95% CI 45, 81) and persisted over the 12 months follow-up. We did not identify any symptomatic infections or hospital admissions with respiratory illness and so vaccine efficacy against clinically apparent infection could not be measured. Vaccine efficacy against asymptomatic SARS-CoV-2 infection was 38.4% (95% CI -26.8%, 70.1%; p=0.188). Conclusions The safety, immunogenicity and efficacy against asymptomatic infection of ChAdOx1 nCoV-19 among Kenyan adults was similar to that observed elsewhere in the world, but efficacy against symptomatic infection or severe disease could not be measured in this cohort. Pan-African Clinical Trials Registration PACTR202005681895696 (11/05/2020).
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Affiliation(s)
| | - Samuel Sang
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Irene Njau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Naomi Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daniel Wright
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
| | | | | | | | | | | | - Charles Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Amek Nyaguara
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Noni Mumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Alun Davies
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, England, UK
| | | | | | | | | | | | - Amy Boyd
- The Jenner Institute, University of Oxford, Oxford, England, UK
| | - Adrian Hill
- The Jenner Institute, University of Oxford, Oxford, England, UK
| | - Sarah Gilbert
- Pandemic Sciences Institute, University of Oxford, Oxford, England, UK
| | | | - Andrew Pollard
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, England, UK
| | - Teresa Lambe
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, England, UK
| | - George Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, England, UK
| | - COV004 Vaccine Trial Group
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, England, UK
- Ministry of Health, Nairobi, Kenya
- The Jenner Institute, University of Oxford, Oxford, England, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, England, UK
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2
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Otiende M, Nyaguara A, Bottomley C, Walumbe D, Mochamah G, Amadi D, Nyundo C, Kagucia EW, Etyang AO, Adetifa IMO, Brand SPC, Maitha E, Chondo E, Nzomo E, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Barasa E, Tsofa B, Mwangangi J, Bejon P, Agweyu A, Williams TN, Scott JAG. Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study. Nat Commun 2023; 14:6879. [PMID: 37898630 PMCID: PMC10613220 DOI: 10.1038/s41467-023-42615-6] [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: 02/06/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
The mortality impact of COVID-19 in Africa remains controversial because most countries lack vital registration. We analysed excess mortality in Kilifi Health and Demographic Surveillance System, Kenya, using 9 years of baseline data. SARS-CoV-2 seroprevalence studies suggest most adults here were infected before May 2022. During 5 waves of COVID-19 (April 2020-May 2022) an overall excess mortality of 4.8% (95% PI 1.2%, 9.4%) concealed a significant excess (11.6%, 95% PI 5.9%, 18.9%) among older adults ( ≥ 65 years) and a deficit among children aged 1-14 years (-7.7%, 95% PI -20.9%, 6.9%). The excess mortality rate for January 2020-December 2021, age-standardised to the Kenyan population, was 27.4/100,000 person-years (95% CI 23.2-31.6). In Coastal Kenya, excess mortality during the pandemic was substantially lower than in most high-income countries but the significant excess mortality in older adults emphasizes the value of achieving high vaccine coverage in this risk group.
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Affiliation(s)
- M Otiende
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya.
| | - A Nyaguara
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - C Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
| | - D Walumbe
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - G Mochamah
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - D Amadi
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - C Nyundo
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - E W Kagucia
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - A O Etyang
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - I M O Adetifa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
| | - S P C Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4 7AL, UK
| | - E Maitha
- Department of Health, Kilifi County, Kilifi, Kenya
| | - E Chondo
- Department of Health, Kilifi County, Kilifi, Kenya
| | - E Nzomo
- Kilifi County Hospital, Kilifi, Kenya
| | - R Aman
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - M Mwangangi
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - P Amoth
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - K Kasera
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - W Ng'ang'a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - E Barasa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - B Tsofa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - J Mwangangi
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - P Bejon
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7BN, UK
| | - A Agweyu
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - T N Williams
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Institute for Global Health Innovation, Imperial College, London, SW72AS, UK
| | - J A G Scott
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
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3
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Kagucia EW, Ziraba AK, Nyagwange J, Kutima B, Kimani M, Akech D, Ng'oda M, Sigilai A, Mugo D, Karanja H, Gitonga J, Karani A, Toroitich M, Karia B, Otiende M, Njeri A, Aman R, Amoth P, Mwangangi M, Kasera K, Ng'ang'a W, Voller S, Ochola‐Oyier LI, Bottomley C, Nyaguara A, Munywoki PK, Bigogo G, Maitha E, Uyoga S, Gallagher KE, Etyang AO, Barasa E, Mwangangi J, Bejon P, Adetifa IMO, Warimwe GM, Scott JAG, Agweyu A. SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February-December 2022. Influenza Other Respir Viruses 2023; 17:e13173. [PMID: 37752065 PMCID: PMC10522478 DOI: 10.1111/irv.13173] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND We sought to estimate SARS-CoV-2 antibody seroprevalence within representative samples of the Kenyan population during the third year of the COVID-19 pandemic and the second year of COVID-19 vaccine use. METHODS We conducted cross-sectional serosurveys among randomly selected, age-stratified samples of Health and Demographic Surveillance System (HDSS) residents in Kilifi and Nairobi. Anti-spike (anti-S) immunoglobulin G (IgG) serostatus was measured using a validated in-house ELISA and antibody concentrations estimated with reference to the WHO International Standard for anti-SARS-CoV-2 immunoglobulin. RESULTS HDSS residents were sampled in February-June 2022 (Kilifi HDSS N = 852; Nairobi Urban HDSS N = 851) and in August-December 2022 (N = 850 for both sites). Population-weighted coverage for ≥1 doses of COVID-19 vaccine were 11.1% (9.1-13.2%) among Kilifi HDSS residents by November 2022 and 34.2% (30.7-37.6%) among Nairobi Urban HDSS residents by December 2022. Population-weighted anti-S IgG seroprevalence among Kilifi HDSS residents increased from 69.1% (65.8-72.3%) by May 2022 to 77.4% (74.4-80.2%) by November 2022. Within the Nairobi Urban HDSS, seroprevalence by June 2022 was 88.5% (86.1-90.6%), comparable with seroprevalence by December 2022 (92.2%; 90.2-93.9%). For both surveys, seroprevalence was significantly lower among Kilifi HDSS residents than among Nairobi Urban HDSS residents, as were antibody concentrations (p < 0.001). CONCLUSION More than 70% of Kilifi residents and 90% of Nairobi residents were seropositive for anti-S IgG by the end of 2022. There is a potential immunity gap in rural Kenya; implementation of interventions to improve COVID-19 vaccine uptake among sub-groups at increased risk of severe COVID-19 in rural settings is recommended.
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Affiliation(s)
| | | | | | | | | | - Donald Akech
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
| | - Maurine Ng'oda
- African Population and Health Research CenterNairobiKenya
| | | | - Daisy Mugo
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
| | | | - John Gitonga
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
| | | | | | | | - Mark Otiende
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
| | - Anne Njeri
- African Population and Health Research CenterNairobiKenya
| | | | | | | | | | - Wangari Ng'ang'a
- Presidential Policy and Strategy UnitThe Presidency, Government of KenyaNairobiKenya
| | - Shirine Voller
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- London School of Hygiene and Tropical MedicineLondonUK
| | | | | | | | - Patrick K. Munywoki
- Division for Global Health ProtectionUS Centers of Disease Control and Prevention, Center for Global HealthNairobiKenya
| | | | | | - Sophie Uyoga
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
| | - Katherine E. Gallagher
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- London School of Hygiene and Tropical MedicineLondonUK
| | | | | | | | - Philip Bejon
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineOxford UniversityOxfordUK
| | - Ifedayo M. O. Adetifa
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- London School of Hygiene and Tropical MedicineLondonUK
| | - George M. Warimwe
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineOxford UniversityOxfordUK
| | - J. Anthony G. Scott
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- London School of Hygiene and Tropical MedicineLondonUK
| | - Ambrose Agweyu
- KEMRI‐Wellcome Trust Research ProgrammeKilifiKenya
- London School of Hygiene and Tropical MedicineLondonUK
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4
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Ngere P, Onsongo J, Langat D, Nzioka E, Mudachi F, Kadivane S, Chege B, Kirui E, Were I, Mutiso S, Kibisu A, Ihahi J, Mutethya G, Mochache T, Lokamar P, Boru W, Makayotto L, Okunga E, Ganda N, Haji A, Gathenji C, Kariuki W, Osoro E, Kasera K, Kuria F, Aman R, Nabyonga J, Amoth P. Characterization of COVID-19 cases in the early phase (March to July 2020) of the pandemic in Kenya. J Glob Health 2022; 12:15001. [PMID: 36583253 PMCID: PMC9801068 DOI: 10.7189/jogh.12.15001] [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: 12/31/2022] Open
Abstract
Background Kenya detected the first case of COVID-19 on March 13, 2020, and as of July 30, 2020, 17 975 cases with 285 deaths (case fatality rate (CFR) = 1.6%) had been reported. This study described the cases during the early phase of the pandemic to provide information for monitoring and response planning in the local context. Methods We reviewed COVID-19 case records from isolation centres while considering national representation and the WHO sampling guideline for clinical characterization of the COVID-19 pandemic within a country. Socio-demographic, clinical, and exposure data were summarized using median and mean for continuous variables and proportions for categorical variables. We assigned exposure variables to socio-demographics, exposure, and contact data, while the clinical spectrum was assigned outcome variables and their associations were assessed. Results A total of 2796 case records were reviewed including 2049 (73.3%) male, 852 (30.5%) aged 30-39 years, 2730 (97.6%) Kenyans, 636 (22.7%) transporters, and 743 (26.6%) residents of Nairobi City County. Up to 609 (21.8%) cases had underlying medical conditions, including hypertension (n = 285 (46.8%)), diabetes (n = 211 (34.6%)), and multiple conditions (n = 129 (21.2%)). Out of 1893 (67.7%) cases with likely sources of exposure, 601 (31.8%) were due to international travel. There were 2340 contacts listed for 577 (20.6%) cases, with 632 contacts (27.0%) being traced. The odds of developing COVID-19 symptoms were higher among case who were aged above 60 years (odds ratio (OR) = 1.99, P = 0.007) or had underlying conditions (OR = 2.73, P < 0.001) and lower among transport sector employees (OR = 0.31, P < 0.001). The odds of developing severe COVID-19 disease were higher among cases who had underlying medical conditions (OR = 1.56, P < 0.001) and lower among cases exposed through community gatherings (OR = 0.27, P < 0.001). The odds of survival of cases from COVID-19 disease were higher among transport sector employees (OR = 3.35, P = 0.004); but lower among cases who were aged ≥60 years (OR = 0.58, P = 0.034) and those with underlying conditions (OR = 0.58, P = 0.025). Conclusion The early phase of the COVID-19 pandemic demonstrated a need to target the elderly and comorbid cases with prevention and control strategies while closely monitoring asymptomatic cases.
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Affiliation(s)
- Philip Ngere
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Kenya,Washington State University, Global Health, Kenya
| | | | - Daniel Langat
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Kenya
| | - Elizabeth Nzioka
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | - Faith Mudachi
- Department of Promotive and Preventive Health, Ministry of Health, Kenya
| | - Samuel Kadivane
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Kenya
| | - Bernard Chege
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | - Elvis Kirui
- National Public Health Laboratory Services, Ministry of Health, Kenya
| | - Ian Were
- Office of the Director General, Ministry of Health, Kenya
| | - Stephen Mutiso
- Department of Promotive and Preventive Health, Ministry of Health, Kenya
| | - Amos Kibisu
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | - Josephine Ihahi
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | - Gladys Mutethya
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | | | - Peter Lokamar
- National Public Health Laboratory Services, Ministry of Health, Kenya
| | - Waqo Boru
- Field Epidemiology and Laboratory Training Program, Ministry of Health, Kenya
| | - Lyndah Makayotto
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Kenya
| | - Emmanuel Okunga
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Kenya
| | | | - Adam Haji
- World Health Organization, Nairobi Kenya
| | | | | | - Eric Osoro
- Washington State University, Global Health, Kenya
| | - Kadondi Kasera
- Public Health Emergency Operation Centre, Ministry of Health, Kenya
| | - Francis Kuria
- Directorate of Public Health, Ministry of Health, Kenya
| | - Rashid Aman
- Cabinet Administrative Secretary, Ministry of Health, Kenya
| | | | - Patrick Amoth
- Office of the Director General, Ministry of Health, Kenya
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5
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Herman-Roloff A, Aman R, Samandari T, Kasera K, Emukule GO, Amoth P, Chen TH, Kisivuli J, Weyenga H, Hunsperger E, Onyango C, Juma B, Munyua P, Wako D, Akelo V, Kimanga D, Ndegwa L, Mohamed AA, Okello P, Kariuki S, De Cock KM, Bulterys M. Adapting Longstanding Public Health Collaborations between Government of Kenya and CDC Kenya in Response to the COVID-19 Pandemic, 2020-2021. Emerg Infect Dis 2022; 28:S159-S167. [PMID: 36502403 DOI: 10.3201/eid2813.211550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Kenya's Ministry of Health (MOH) and the US Centers for Disease Control and Prevention in Kenya (CDC Kenya) have maintained a 40-year partnership during which measures were implemented to prevent, detect, and respond to disease threats. During the COVID-19 pandemic, the MOH and CDC Kenya rapidly responded to mitigate disease impact on Kenya's 52 million residents. We describe activities undertaken jointly by the MOH and CDC Kenya that lessened the effects of COVID-19 during 5 epidemic waves from March through December 2021. Activities included establishing national and county-level emergency operations centers and implementing workforce development and deployment, infection prevention and control training, laboratory diagnostic advancement, enhanced surveillance, and information management. The COVID-19 pandemic provided fresh impetus for the government of Kenya to establish a national public health institute, launched in January 2022, to consolidate its public health activities and counter COVID-19 and future infectious, vaccine-preventable, and emerging zoonotic diseases.
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6
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Ojal J, Brand SPC, Were V, Okiro EA, Kombe IK, Mburu C, Aziza R, Ogero M, Agweyu A, Warimwe GM, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Ochola-Oyier LI, Agoti CN, Kasera K, Amoth P, Mwangangi M, Aman R, Ng’ang’a W, Tsofa B, Bejon P, Barasa E, Keeling MJ, Nokes DJ. Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data. Wellcome Open Res 2022; 6:127. [PMID: 36187498 PMCID: PMC9511207 DOI: 10.12688/wellcomeopenres.16748.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 02/02/2023] Open
Abstract
Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.
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Affiliation(s)
- John Ojal
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Samuel P. C. Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vincent Were
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Emelda A. Okiro
- Population Health Unit, Kenya Medical Research Institute - Wellcome Trust Research programme, Nairobi, Kenya
| | - Ivy K. Kombe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Caroline Mburu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Rabia Aziza
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Morris Ogero
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Ambrose Agweyu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - George M. Warimwe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Sophie Uyoga
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Ifedayo M. O. Adetifa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - J. Anthony G. Scott
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Edward Otieno
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | | | - Charles N. Agoti
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Wangari Ng’ang’a
- Presidential Policy & Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edwine Barasa
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matt J. Keeling
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - D. James Nokes
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
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7
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Etyang AO, Adetifa I, Omore R, Misore T, Ziraba AK, Ng’oda MA, Gitau E, Gitonga J, Mugo D, Kutima B, Karanja H, Toroitich M, Nyagwange J, Tuju J, Wanjiku P, Aman R, Amoth P, Mwangangi M, Kasera K, Ng’ang’a W, Akech D, Sigilai A, Karia B, Karani A, Voller S, Agoti CN, Ochola-Oyier LI, Otiende M, Bottomley C, Nyaguara A, Uyoga S, Gallagher K, Kagucia EW, Onyango D, Tsofa B, Mwangangi J, Maitha E, Barasa E, Bejon P, Warimwe GM, Scott JAG, Agweyu A. SARS-CoV-2 seroprevalence in three Kenyan health and demographic surveillance sites, December 2020-May 2021. PLOS Glob Public Health 2022; 2:e0000883. [PMID: 36962821 PMCID: PMC10021917 DOI: 10.1371/journal.pgph.0000883] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/12/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. We conducted population-based serosurveys at three Health and Demographic Surveillance Systems (HDSSs) to determine the cumulative incidence of infection with SARS-CoV-2. METHODS We selected random age-stratified population-based samples at HDSSs in Kisumu, Nairobi and Kilifi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. No participant had received a COVID-19 vaccine. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally-validated assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. We adjusted prevalence estimates using classical methods and Bayesian modelling to account for the sampling scheme and assay performance. RESULTS We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27 (10-78) years and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kisumu, Nairobi and Kilifi, seroprevalences (95% CI) at the beginning of the study were 36.0% (28.2-44.4%), 32.4% (23.1-42.4%), and 14.5% (9.1-21%), and respectively; at the end they were 42.0% (34.7-50.0%), 50.2% (39.7-61.1%), and 24.7% (17.5-32.6%), respectively. Seroprevalence was substantially lower among children (<16 years) than among adults at all three sites (p≤0.001). CONCLUSION By May 2021 in three broadly representative populations of unvaccinated individuals in Kenya, seroprevalence of anti-SARS-CoV-2 IgG was 25-50%. There was wide variation in cumulative incidence by location and age.
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Affiliation(s)
| | - Ifedayo Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard Omore
- Kenya Medical Research Institute Centre for Global Health Research, Kisumu, Kenya
| | - Thomas Misore
- Kenya Medical Research Institute Centre for Global Health Research, Kisumu, Kenya
| | | | | | - Evelyn Gitau
- African Population and Health Research Center, Nairobi, Kenya
| | - John Gitonga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Wangari Ng’ang’a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Donald Akech
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Shirine Voller
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Amek Nyaguara
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | | | - Edwine Barasa
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - J. Anthony G. Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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8
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Orangi S, Ojal J, Brand SP, Orlendo C, Kairu A, Aziza R, Ogero M, Agweyu A, Warimwe GM, Uyoga S, Otieno E, Ochola-Oyier LI, Agoti CN, Kasera K, Amoth P, Mwangangi M, Aman R, Ng'ang'a W, Adetifa IM, Scott JAG, Bejon P, Keeling MJ, Flasche S, Nokes DJ, Barasa E. Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya. BMJ Glob Health 2022; 7:e009430. [PMID: 35914832 PMCID: PMC9344598 DOI: 10.1136/bmjgh-2022-009430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 04/22/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND A few studies have assessed the epidemiological impact and the cost-effectiveness of COVID-19 vaccines in settings where most of the population had been exposed to SARS-CoV-2 infection. METHODS We conducted a cost-effectiveness analysis of COVID-19 vaccine in Kenya from a societal perspective over a 1.5-year time frame. An age-structured transmission model assumed at least 80% of the population to have prior natural immunity when an immune escape variant was introduced. We examine the effect of slow (18 months) or rapid (6 months) vaccine roll-out with vaccine coverage of 30%, 50% or 70% of the adult (>18 years) population prioritising roll-out in those over 50-years (80% uptake in all scenarios). Cost data were obtained from primary analyses. We assumed vaccine procurement at US$7 per dose and vaccine delivery costs of US$3.90-US$6.11 per dose. The cost-effectiveness threshold was US$919.11. FINDINGS Slow roll-out at 30% coverage largely targets those over 50 years and resulted in 54% fewer deaths (8132 (7914-8373)) than no vaccination and was cost saving (incremental cost-effectiveness ratio, ICER=US$-1343 (US$-1345 to US$-1341) per disability-adjusted life-year, DALY averted). Increasing coverage to 50% and 70%, further reduced deaths by 12% (810 (757-872) and 5% (282 (251-317) but was not cost-effective, using Kenya's cost-effectiveness threshold (US$919.11). Rapid roll-out with 30% coverage averted 63% more deaths and was more cost-saving (ICER=US$-1607 (US$-1609 to US$-1604) per DALY averted) compared with slow roll-out at the same coverage level, but 50% and 70% coverage scenarios were not cost-effective. INTERPRETATION With prior exposure partially protecting much of the Kenyan population, vaccination of young adults may no longer be cost-effective.
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Affiliation(s)
- Stacey Orangi
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme Nairobi, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
| | - John Ojal
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel Pc Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Cameline Orlendo
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Angela Kairu
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme Nairobi, Nairobi, Kenya
| | - Rabia Aziza
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Morris Ogero
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ambrose Agweyu
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George M Warimwe
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Uyoga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edward Otieno
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Lynette I Ochola-Oyier
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Wangari Ng'ang'a
- Presidential Policy & Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Ifedayo Mo Adetifa
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - J Anthony G Scott
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matt J Keeling
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | - Stefan Flasche
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Edwine Barasa
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme Nairobi, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Agoti CN, Ochola-Oyier LI, Dellicour S, Mohammed KS, Lambisia AW, de Laurent ZR, Morobe JM, Mburu MW, Omuoyo DO, Ongera EM, Ndwiga L, Maitha E, Kitole B, Suleiman T, Mwakinangu M, Nyambu JK, Otieno J, Salim B, Musyoki J, Murunga N, Otieno E, Kiiru JN, Kasera K, Amoth P, Mwangangi M, Aman R, Kinyanjui S, Warimwe G, Phan M, Agweyu A, Cotten M, Barasa E, Tsofa B, Nokes DJ, Bejon P, Githinji G. Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study. eLife 2022; 11:71703. [PMID: 35699426 PMCID: PMC9282859 DOI: 10.7554/elife.71703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/27/2021] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. Methods Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis. Results During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. Conclusions Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission. Funding This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.
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Affiliation(s)
- Charles N Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University, Kilifi, Kenya
| | | | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.,Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Khadija Said Mohammed
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Arnold W Lambisia
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John M Morobe
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Maureen W Mburu
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Donwilliams O Omuoyo
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edidah M Ongera
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Leonard Ndwiga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | | | | | - Jennifer Musyoki
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edward Otieno
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Samson Kinyanjui
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - George Warimwe
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - My Phan
- Medical Research Centre (MRC)/ Uganda Virus Research Institute, Entebbe, Uganda
| | - Ambrose Agweyu
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matthew Cotten
- Medical Research Centre (MRC)/ Uganda Virus Research Institute, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Edwine Barasa
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,University of Warwick, Coventry, United Kingdom
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - George Githinji
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University, Kilifi, Kenya
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10
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Ojal J, Brand SPC, Were V, Okiro EA, Kombe IK, Mburu C, Aziza R, Ogero M, Agweyu A, Warimwe GM, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Ochola-Oyier LI, Agoti CN, Kasera K, Amoth P, Mwangangi M, Aman R, Ng’ang’a W, Tsofa B, Bejon P, Barasa E, Keeling MJ, Nokes DJ. Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data. Wellcome Open Res 2022; 6:127. [PMID: 36187498 PMCID: PMC9511207 DOI: 10.12688/wellcomeopenres.16748.2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/02/2023] Open
Abstract
Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.
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Affiliation(s)
- John Ojal
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Samuel P. C. Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vincent Were
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Emelda A. Okiro
- Population Health Unit, Kenya Medical Research Institute - Wellcome Trust Research programme, Nairobi, Kenya
| | - Ivy K. Kombe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Caroline Mburu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Rabia Aziza
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Morris Ogero
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Ambrose Agweyu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - George M. Warimwe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Sophie Uyoga
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Ifedayo M. O. Adetifa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - J. Anthony G. Scott
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Edward Otieno
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | | | - Charles N. Agoti
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Wangari Ng’ang’a
- Presidential Policy & Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edwine Barasa
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matt J. Keeling
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - D. James Nokes
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
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11
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Nyagwange J, Ndwiga L, Muteru K, Wamae K, Tuju J, testing team COVID, Kutima B, Gitonga J, Karanja H, Mugo D, Kasera K, Amoth P, Murunga N, Babu L, Otieno E, Githinji G, Nokes D, Tsofa B, Orindi B, Barasa E, Warimwe G, Agoti CN, Bejon P, Ochola-Oyier LI. Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya. Wellcome Open Res 2022; 7:69. [PMID: 35505772 PMCID: PMC9034174 DOI: 10.12688/wellcomeopenres.17661.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Accepted: 02/16/2022] [Indexed: 01/08/2023] Open
Abstract
Background: There are limited studies in Africa describing the epidemiology, clinical characteristics and serostatus of individuals tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We tested routine samples from the Coastal part of Kenya between 17 th March 2020 and 30 th June 2021. Methods: SARS-CoV-2 infections identified using reverse transcription polymerase chain reaction (RT-PCR) and clinical surveillance data at the point of sample collection were used to classify as either symptomatic or asymptomatic. IgG antibodies were measured in sera samples, using a well validated in-house enzyme-linked immunosorbent assay (ELISA). Results: Mombasa accounted for 56.2% of all the 99,694 naso-pharyngeal/oro-pharyngeal swabs tested, and males constituted the majority tested (73.4%). A total of 7737 (7.7%) individuals were SARS-CoV-2 positive by RT-PCR. The majority (i.e., 92.4%) of the RT-PCR positive individuals were asymptomatic. Testing was dominated by mass screening and travellers, and even at health facility level 91.6% of tests were from individuals without symptoms. Out of the 97,124 tests from asymptomatic individuals 7,149 (7%) were positive and of the 2,568 symptomatic individuals 588 (23%) were positive. In total, 2458 serum samples were submitted with paired naso-pharyngeal/oro-pharyngeal samples and 45% of the RT-PCR positive samples and 20% of the RT-PCR negative samples were paired with positive serum samples. Symptomatic individuals had significantly higher antibody levels than asymptomatic individuals and become RT-PCR negative on repeat testing earlier than asymptomatic individuals. Conclusions: In conclusion, the majority of SARS-CoV-2 infections identified by routine testing in Coastal Kenya were asymptomatic. This reflects the testing practice of health services in Kenya, but also implies that asymptomatic infection is very common in the population. Symptomatic infection may be less common, or it may be that individuals do not present for testing when they have symptoms.
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Affiliation(s)
| | | | | | - Kevin Wamae
- Kenya Medical Research Institute, Kilifi, Kenya
| | - James Tuju
- Kenya Medical Research Institute, Kilifi, Kenya
| | | | | | | | | | - Daisy Mugo
- Kenya Medical Research Institute, Kilifi, Kenya
| | | | | | | | | | | | | | - D.J. Nokes
- Kenya Medical Research Institute, Kilifi, Kenya
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12
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Etyang AO, Lucinde R, Karanja H, Kalu C, Mugo D, Nyagwange J, Gitonga J, Tuju J, Wanjiku P, Karani A, Mutua S, Maroko H, Nzomo E, Maitha E, Kamuri E, Kaugiria T, Weru J, Ochola LB, Kilimo N, Charo S, Emukule N, Moracha W, Mukabi D, Okuku R, Ogutu M, Angujo B, Otiende M, Bottomley C, Otieno E, Ndwiga L, Nyaguara A, Voller S, Agoti CN, Nokes DJ, Ochola-Oyier LI, Aman R, Amoth P, Mwangangi M, Kasera K, Ng’ang’a W, Adetifa IMO, Wangeci Kagucia E, Gallagher K, Uyoga S, Tsofa B, Barasa E, Bejon P, Scott JAG, Agweyu A, Warimwe GM. Seroprevalence of Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 Among Healthcare Workers in Kenya. Clin Infect Dis 2022; 74:288-293. [PMID: 33893491 PMCID: PMC8135298 DOI: 10.1093/cid/ciab346] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Few studies have assessed the seroprevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among healthcare workers (HCWs) in Africa. We report findings from a survey among HCWs in 3 counties in Kenya. METHODS We recruited 684 HCWs from Kilifi (rural), Busia (rural), and Nairobi (urban) counties. The serosurvey was conducted between 30 July and 4 December 2020. We tested for immunoglobulin G antibodies to SARS-CoV-2 spike protein, using enzyme-linked immunosorbent assay. Assay sensitivity and specificity were 92.7 (95% CI, 87.9-96.1) and 99.0% (95% CI, 98.1-99.5), respectively. We adjusted prevalence estimates, using bayesian modeling to account for assay performance. RESULTS The crude overall seroprevalence was 19.7% (135 of 684). After adjustment for assay performance, seroprevalence was 20.8% (95% credible interval, 17.5%-24.4%). Seroprevalence varied significantly (P < .001) by site: 43.8% (95% credible interval, 35.8%-52.2%) in Nairobi, 12.6% (8.8%-17.1%) in Busia and 11.5% (7.2%-17.6%) in Kilifi. In a multivariable model controlling for age, sex, and site, professional cadre was not associated with differences in seroprevalence. CONCLUSION These initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.
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Affiliation(s)
| | - Ruth Lucinde
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry Karanja
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Daisy Mugo
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - John Gitonga
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | - James Tuju
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Angela Karani
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Hosea Maroko
- KEMRI Center for Infectious and Parasitic Diseases Control Research, Alupe, Kenya
| | | | | | | | | | | | | | | | | | | | | | - David Mukabi
- Department of Health, Busia County, Busia, Kenya
| | | | | | | | - Mark Otiende
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christian Bottomley
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Edward Otieno
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Amek Nyaguara
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Shirine Voller
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | | | - Wangari Ng’ang’a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Ifedayo M O Adetifa
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Katherine Gallagher
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sophie Uyoga
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Edwine Barasa
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - J Anthony G Scott
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - George M Warimwe
- KEMRI–Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
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13
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Lucinde RK, Mugo D, Bottomley C, Karani A, Gardiner E, Aziza R, Gitonga JN, Karanja H, Nyagwange J, Tuju J, Wanjiku P, Nzomo E, Kamuri E, Thuranira K, Agunda S, Nyutu G, Etyang AO, Adetifa IMO, Kagucia E, Uyoga S, Otiende M, Otieno E, Ndwiga L, Agoti CN, Aman RA, Mwangangi M, Amoth P, Kasera K, Nyaguara A, Ng’ang’a W, Ochola LB, Namdala E, Gaunya O, Okuku R, Barasa E, Bejon P, Tsofa B, Ochola-Oyier LI, Warimwe GM, Agweyu A, Scott JAG, Gallagher KE. Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals: Repeated cross-sectional surveys 2020-21. PLoS One 2022; 17:e0265478. [PMID: 36240176 PMCID: PMC9565697 DOI: 10.1371/journal.pone.0265478] [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: 03/01/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION The high proportion of SARS-CoV-2 infections that have remained undetected presents a challenge to tracking the progress of the pandemic and estimating the extent of population immunity. METHODS We used residual blood samples from women attending antenatal care services at three hospitals in Kenya between August 2020 and October 2021and a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. We fitted a two-component mixture model as an alternative to the threshold analysis to estimate of the proportion of individuals with past SARS-CoV-2 infection. RESULTS We estimated seroprevalence in 2,981 women; 706 in Nairobi, 567 in Busia and 1,708 in Kilifi. By October 2021, 13% of participants were vaccinated (at least one dose) in Nairobi, 2% in Busia. Adjusted seroprevalence rose in all sites; from 50% (95%CI 42-58) in August 2020, to 85% (95%CI 78-92) in October 2021 in Nairobi; from 31% (95%CI 25-37) in May 2021 to 71% (95%CI 64-77) in October 2021 in Busia; and from 1% (95% CI 0-3) in September 2020 to 63% (95% CI 56-69) in October 2021 in Kilifi. Mixture modelling, suggests adjusted cross-sectional prevalence estimates are underestimates; seroprevalence in October 2021 could be 74% in Busia and 72% in Kilifi. CONCLUSIONS There has been substantial, unobserved transmission of SARS-CoV-2 in Nairobi, Busia and Kilifi Counties. Due to the length of time since the beginning of the pandemic, repeated cross-sectional surveys are now difficult to interpret without the use of models to account for antibody waning.
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Affiliation(s)
- Ruth K. Lucinde
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- * E-mail:
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christian Bottomley
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Rabia Aziza
- School of Life Sciences and the Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom
| | | | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Edward Nzomo
- Kilifi County Hospital, Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Evans Kamuri
- Kenyatta National Hospital, Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Kaugiria Thuranira
- Kenyatta National Hospital, Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Sarah Agunda
- Kenyatta National Hospital, Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Gideon Nyutu
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Ifedayo M. O. Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Amek Nyaguara
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Wangari Ng’ang’a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | | | | | - Oscar Gaunya
- Busia Country Teaching & Referral Hospital, Busia, Kenya
| | - Rosemary Okuku
- Busia Country Teaching & Referral Hospital, Busia, Kenya
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | | | | | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | | | - J. Anthony G. Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Katherine E. Gallagher
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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14
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Brand SPC, Ojal J, Aziza R, Were V, Okiro EA, Kombe IK, Mburu C, Ogero M, Agweyu A, Warimwe GM, Nyagwange J, Karanja H, Gitonga JN, Mugo D, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Murunga N, Otiende M, Ochola-Oyier LI, Agoti CN, Githinji G, Kasera K, Amoth P, Mwangangi M, Aman R, Ng’ang’a W, Tsofa B, Bejon P, Keeling MJ, Nokes DJ, Barasa E. COVID-19 transmission dynamics underlying epidemic waves in Kenya. Science 2021; 374:989-994. [PMID: 34618602 PMCID: PMC7612211 DOI: 10.1126/science.abk0414] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 06/17/2021] [Accepted: 10/04/2021] [Indexed: 01/16/2023]
Abstract
Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or infection spreads to susceptible subpopulations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model, we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of higher-transmissibility variants. Reopening schools led to a minor increase in transmission between the second and third waves. Socioeconomic and urban–rural population structure are critical determinants of viral transmission in Kenya.
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Affiliation(s)
- Samuel P. C. Brand
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Warwick, UK
- School of Life Sciences, University of Warwick, Warwick, UK
| | - John Ojal
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Rabia Aziza
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Warwick, UK
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Vincent Were
- Health Economics Research Unit, KEMRI–Wellcome Trust Research Programme, Nairobi, Kenya
| | - Emelda A. Okiro
- Population Health Unit, Kenya Medical Research Institute–Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivy K Kombe
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Caroline Mburu
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Morris Ogero
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Ambrose Agweyu
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George M. Warimwe
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Nyagwange
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Henry Karanja
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - John N. Gitonga
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Daisy Mugo
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Sophie Uyoga
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Ifedayo M. O. Adetifa
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - J. Anthony G. Scott
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Edward Otieno
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Mark Otiende
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Lynette I. Ochola-Oyier
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - George Githinji
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Wangari Ng’ang’a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matt. J. Keeling
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Warwick, UK
- School of Life Sciences, University of Warwick, Warwick, UK
- Mathematics Institute, University of Warwick, Warwick, UK
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Warwick, UK
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Edwine Barasa
- Health Economics Research Unit, KEMRI–Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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15
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Kagucia EW, Gitonga JN, Kalu C, Ochomo E, Ochieng B, Kuya N, Karani A, Nyagwange J, Karia B, Mugo D, Karanja HK, Tuju J, Mutiso A, Maroko H, Okubi L, Maitha E, Ajuck H, Mukabi D, Moracha W, Bulimu D, Andanje N, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Nyaguara A, Voller S, Otiende M, Bottomley C, Agoti CN, Ochola-Oyier LI, Adetifa IMO, Etyang AO, Gallagher KE, Uyoga S, Barasa E, Bejon P, Tsofa B, Agweyu A, Warimwe GM, Scott JAG. Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Immunoglobulin G Antibody Seroprevalence Among Truck Drivers and Assistants in Kenya. Open Forum Infect Dis 2021; 8:ofab314. [PMID: 34660838 PMCID: PMC8519263 DOI: 10.1093/ofid/ofab314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 11/14/2022] Open
Abstract
In October 2020, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among healthcare workers and blood donors. Truck drivers and their assistants transport essential supplies during the coronavirus disease 2019 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 over a wide geographical area.
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Affiliation(s)
| | | | | | - Eric Ochomo
- KEMRI Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Benard Ochieng
- KEMRI Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Nickline Kuya
- KEMRI Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Agnes Mutiso
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hosea Maroko
- KEMRI Centre for Infectious and Parasitic Diseases Control Research, Busia, Kenya
| | - Lucy Okubi
- KEMRI Centre for Infectious and Parasitic Diseases Control Research, Busia, Kenya
| | | | | | | | | | | | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Wangari Ng'ang'a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Amek Nyaguara
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Shirine Voller
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Katherine E Gallagher
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
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16
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Githinji G, de Laurent ZR, Mohammed KS, Omuoyo DO, Macharia PM, Morobe JM, Otieno E, Kinyanjui SM, Agweyu A, Maitha E, Kitole B, Suleiman T, Mwakinangu M, Nyambu J, Otieno J, Salim B, Kasera K, Kiiru J, Aman R, Barasa E, Warimwe G, Bejon P, Tsofa B, Ochola-Oyier LI, Nokes DJ, Agoti CN. Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nat Commun 2021; 12:4809. [PMID: 34376689 PMCID: PMC8355311 DOI: 10.1038/s41467-021-25137-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 10/16/2020] [Accepted: 07/27/2021] [Indexed: 01/13/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.
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Affiliation(s)
- George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
| | | | | | | | - Peter M Macharia
- Population Health Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - John M Morobe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Samson M Kinyanjui
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - John Kiiru
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Edwine Barasa
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - George Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
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17
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Barasa E, Kazungu J, Orangi S, Kabia E, Ogero M, Kasera K. Indirect health effects of the COVID-19 pandemic in Kenya: a mixed methods assessment. BMC Health Serv Res 2021; 21:740. [PMID: 34311716 PMCID: PMC8311400 DOI: 10.1186/s12913-021-06726-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic and country measures to control it can lead to negative indirect health effects. Understanding these indirect health effects is important in informing strategies to mitigate against them. This paper presents an analysis of the indirect health effects of the pandemic in Kenya. METHODS We employed a mixed-methods approach, combining the analysis of secondary quantitative data obtained from the Kenya Health Information System database (from January 2019 to November 2020) and a qualitative inquiry involving key informant interviews (n = 12) and document reviews. Quantitative data were analysed using an interrupted time series analysis (using March 2020 as the intervention period). Thematic analysis approach was employed to analyse qualitative data. RESULTS Quantitative findings show mixed findings, with statistically significant reduction in inpatient utilization, and increase in the number of sexual violence cases per OPD visit that could be attributed to COVID-19 and its mitigation measures. Key informants reported that while financing of essential health services and domestic supply chains were not affected, international supply chains, health workforce, health infrastructure, service provision, and patient access were disrupted. However, the negative effects were thought to be transient, with mitigation measures leading to a bounce back. CONCLUSION Finding from this study provide some insights into the effects of the pandemic and its mitigation measures in Kenya. The analysis emphasizes the value of strategies to minimize these undesired effects, and the critical role that routine health system data can play in monitoring continuity of service delivery.
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Affiliation(s)
- Edwine Barasa
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield department of Medicine, University of Oxford, Oxford, UK.
| | - Jacob Kazungu
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Stacey Orangi
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Evelyn Kabia
- Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Morris Ogero
- Health Services Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
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18
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Adetifa IMO, Uyoga S, Gitonga JN, Mugo D, Otiende M, Nyagwange J, Karanja HK, Tuju J, Wanjiku P, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Rombo C, Yegon C, Kithi K, Odhiambo E, Rotich T, Orgut I, Kihara S, Bottomley C, Kagucia EW, Gallagher KE, Etyang A, Voller S, Lambe T, Wright D, Barasa E, Tsofa B, Bejon P, Ochola-Oyier LI, Agweyu A, Scott JAG, Warimwe GM. Temporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya. Nat Commun 2021; 12:3966. [PMID: 34172732 PMCID: PMC8233334 DOI: 10.1038/s41467-021-24062-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 02/19/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
Observed SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality.
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Affiliation(s)
- Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom.
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | | | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Wangari Ng'ang'a
- Presidential Policy & Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Charles Rombo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Christine Yegon
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Khamisi Kithi
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Elizabeth Odhiambo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Thomas Rotich
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Irene Orgut
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Sammy Kihara
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Christian Bottomley
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | | | - Katherine E Gallagher
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | | | - Shirine Voller
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Teresa Lambe
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Daniel Wright
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | | | | | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
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19
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Ojal J, Brand SPC, Were V, Okiro EA, Kombe IK, Mburu C, Aziza R, Ogero M, Agweyu A, Warimwe GM, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Ochola-Oyier LI, Agoti CN, Kasera K, Amoth P, Mwangangi M, Aman R, Ng’ang’a W, Tsofa B, Bejon P, Barasa E, Keeling MJ, Nokes DJ. Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data. Wellcome Open Res 2021; 6:127. [PMID: 36187498 PMCID: PMC9511207 DOI: 10.12688/wellcomeopenres.16748.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 02/02/2023] Open
Abstract
Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.
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Affiliation(s)
- John Ojal
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Samuel P. C. Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vincent Were
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Emelda A. Okiro
- Population Health Unit, Kenya Medical Research Institute - Wellcome Trust Research programme, Nairobi, Kenya
| | - Ivy K. Kombe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Caroline Mburu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Rabia Aziza
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Morris Ogero
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Ambrose Agweyu
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - George M. Warimwe
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Sophie Uyoga
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Ifedayo M. O. Adetifa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - J. Anthony G. Scott
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Edward Otieno
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
| | | | - Charles N. Agoti
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Wangari Ng’ang’a
- Presidential Policy & Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edwine Barasa
- Health Economics Research Unit, Kenya Medical Research Institute - Wellcome Trust Research Programme, Nairobi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matt J. Keeling
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - D. James Nokes
- Kenya Medical Research Institute - Wellcome Trust Research programme, Kilifi, Kenya
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
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20
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Uyoga S, Adetifa IMO, Karanja HK, Nyagwange J, Tuju J, Wanjiku P, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Rombo C, Yegon C, Kithi K, Odhiambo E, Rotich T, Orgut I, Kihara S, Otiende M, Bottomley C, Mupe ZN, Kagucia EW, Gallagher KE, Etyang A, Voller S, Gitonga JN, Mugo D, Agoti CN, Otieno E, Ndwiga L, Lambe T, Wright D, Barasa E, Tsofa B, Bejon P, Ochola-Oyier LI, Agweyu A, Scott JAG, Warimwe GM. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors. Science 2021; 371:79-82. [PMID: 33177105 PMCID: PMC7877494 DOI: 10.1126/science.abe1916] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [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: 08/20/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa.
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Affiliation(s)
- Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Wangari Ng'ang'a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Charles Rombo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Christine Yegon
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Khamisi Kithi
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Elizabeth Odhiambo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Thomas Rotich
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Irene Orgut
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Sammy Kihara
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christian Bottomley
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Zonia N Mupe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Katherine E Gallagher
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | - Shirine Voller
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Teresa Lambe
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Daniel Wright
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | | | | | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
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21
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Uyoga S, Adetifa IMO, Karanja HK, Nyagwange J, Tuju J, Wanjiku P, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Rombo C, Yegon C, Kithi K, Odhiambo E, Rotich T, Orgut I, Kihara S, Otiende M, Bottomley C, Mupe ZN, Kagucia EW, Gallagher KE, Etyang A, Voller S, Gitonga JN, Mugo D, Agoti CN, Otieno E, Ndwiga L, Lambe T, Wright D, Barasa E, Tsofa B, Bejon P, Ochola-Oyier LI, Agweyu A, Scott JAG, Warimwe GM. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors. Science 2021; 371:79-82. [PMID: 33177105 DOI: 10.1101/2020.07.27.20162693] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/06/2020] [Indexed: 05/24/2023]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa.
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Affiliation(s)
- Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | | | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Rashid Aman
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | | | - Wangari Ng'ang'a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - Charles Rombo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Christine Yegon
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Khamisi Kithi
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Elizabeth Odhiambo
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Thomas Rotich
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Irene Orgut
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Sammy Kihara
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christian Bottomley
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Zonia N Mupe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Katherine E Gallagher
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | - Shirine Voller
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | | | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Teresa Lambe
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Daniel Wright
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | | | | | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
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22
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Enos M, Sitienei J, Ong’ang’o J, Mungai B, Kamene M, Wambugu J, Kipruto H, Manduku V, Mburu J, Nyaboke D, Ngari F, Omesa E, Omale N, Mwirigi N, Okallo G, Njoroge J, Githiomi M, Mwangi M, Kirathe D, Kiplimo R, Ndombi A, Odeny L, Mailu E, Kandie T, Maina M, Kasera K, Mulama B, Mugi B, Weyenga H. Kenya tuberculosis prevalence survey 2016: Challenges and opportunities of ending TB in Kenya. PLoS One 2018; 13:e0209098. [PMID: 30586448 PMCID: PMC6306266 DOI: 10.1371/journal.pone.0209098] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [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: 08/08/2018] [Accepted: 11/28/2018] [Indexed: 11/19/2022] Open
Abstract
Background We aimed to determine the prevalence of pulmonary TB amongst the adult population (≥15 years) in 2016 in Kenya. Method A nationwide cross-sectional survey where participants first underwent TB symptom screening and chest x-ray. Subsequently, participants who reported cough >2weeks and/or had a chest x-ray suggestive of TB, submitted sputum specimen for laboratory examination by smear microscopy, culture and Xpert MTB/RIF. Result The survey identified 305 prevalent TB cases translating to a prevalence of 558 [95%CI 455–662] per 100,000 adult population. The highest disease burden was reported among people aged 25–34 years (716 [95% CI 526–906]), males (809 [(95% CI 656–962]) and those who live in urban areas (760 [95% CI 539–981]). Compared to the reported TB notification rate for Kenya in 2016, the prevalence to notification ratio was 2.5:1. The gap between the survey prevalence and notification rates was highest among males, age groups 25–34, and the older age group of 65 years and above. Only 48% of the of the survey prevalent cases reported cough >2weeks. In addition, only 59% of the identified cases had the four cardinal symptoms for TB (cough ≥2 weeks, fever, night sweat and weight loss. However, 88.2% had an abnormal chest x-ray suggestive of TB. The use of Xpert MTB/RIF identified 77.7% of the cases compared to smear microscopy’s 46%. Twenty-one percent of the survey participants with respiratory symptoms reported to have sought prior health care at private clinics and chemists. Among the survey prevalent cases who reported TB related symptoms, 64.9% had not sought any health care prior to the survey. Conclusion This survey established that TB prevalence in Kenya is higher than had been estimated, and about half of the those who fall ill with the disease each year are missed.
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Affiliation(s)
- Masini Enos
- Ministry of Health, Nairobi, Republic of Kenya
- * E-mail:
| | | | | | | | | | | | - Hillary Kipruto
- World Health Organization Kenya country office, Nairobi, Kenya
| | | | | | | | - Faith Ngari
- Ministry of Health, Nairobi, Republic of Kenya
| | | | | | | | | | | | | | - Mike Mwangi
- Ministry of Health, Nairobi, Republic of Kenya
| | | | | | - Amos Ndombi
- Ministry of Health, Nairobi, Republic of Kenya
| | | | | | | | - Maurice Maina
- United States Agency for International Development, Nairobi, Kenya
| | | | | | | | - Herman Weyenga
- US Centers of Disease Control and Prevention, Nairobi, Kenya
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