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Anywaine Z, Hansen C, Warimwe GM, Abu-Baker Mustapher G, Nyakarahuka L, Balinandi S, Ario AR, Lutwama JJ, Elliott A, Kaleebu P. Severe morbidity and hospital-based mortality from Rift Valley fever disease between November 2017 and March 2020 among humans in Uganda. Virol J 2024; 21:104. [PMID: 38702807 PMCID: PMC11069174 DOI: 10.1186/s12985-024-02377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Rift Valley fever (RVF) is a zoonotic viral disease of increasing intensity among humans in Africa and the Arabian Peninsula. In Uganda, cases reported prior to 2016 were mild or not fully documented. We report in this paper on the severe morbidity and hospital-based mortality of human cases in Uganda. METHODS Between November 2017 and March 2020 human cases reported to the Uganda Virus Research Institute (UVRI) were confirmed by polymerase chain reaction (PCR). Ethical and regulatory approvals were obtained to enrol survivors into a one-year follow-up study. Data were collected on socio-demographics, medical history, laboratory tests, potential risk factors, and analysed using Stata software. RESULTS Overall, 40 cases were confirmed with acute RVF during this period. Cases were not geographically clustered and nearly all were male (39/40; 98%), median age 32 (range 11-63). The median definitive diagnosis time was 7 days and a delay of three days between presumptive and definitive diagnosis. Most patients (31/40; 78%) presented with fever and bleeding at case detection. Twenty-eight (70%) cases were hospitalised, out of whom 18 (64%) died. Mortality was highest among admissions in regional referral (11/16; 69%) and district (4/5; 80%) hospitals, hospitalized patients with bleeding at case detection (17/27; 63%), and patients older than 44 years (9/9; 100%). Survivors mostly manifested a mild gastro-intestinal syndrome with nausea (83%), anorexia (75%), vomiting (75%), abdominal pain (50%), and diarrhoea (42%), and prolonged symptoms of severe disease including jaundice (67%), visual difficulties (67%), epistaxis (50%), haemoptysis (42%), and dysentery (25%). Symptom duration varied between two to 120 days. CONCLUSION RVF is associated with high hospital-based mortality, severe and prolonged morbidity among humans that present to the health care system and are confirmed by PCR. One-health composite interventions should be developed to improve environmental and livestock surveillance, prevent infections, promptly detect outbreaks, and improve patient outcomes.
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Affiliation(s)
- Zacchaeus Anywaine
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK.
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Christian Hansen
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Luke Nyakarahuka
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alex Riolexus Ario
- National Institute of Public Health, Ministry of Health, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alison Elliott
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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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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3
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Juan-Giner A, Namulwana ML, Kimathi D, Grantz KH, Fall G, Dia M, Bob NS, Sall AA, Nerima C, Sahani MK, Mulogo EM, Ampeire I, Hombach J, Nanjebe D, Mwanga-Amumpaire J, Cummings DAT, Bejon P, Warimwe GM, Grais RF. Immunogenicity and safety of fractional doses of 17D-213 yellow fever vaccine in children (YEFE): a randomised, double-blind, non-inferiority substudy of a phase 4 trial. Lancet Infect Dis 2023; 23:965-973. [PMID: 37127047 DOI: 10.1016/s1473-3099(23)00131-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Current supply shortages constrain yellow fever vaccination activities, particularly outbreak response. Although fractional doses of all WHO-prequalified yellow fever vaccines have been shown to be safe and immunogenic in a randomised controlled trial in adults, they have not been evaluated in a randomised controlled trial in young children (9-59 months old). We aimed to assess the immunogenicity and safety of fractional doses compared with standard doses of the WHO-prequalified 17D-213 vaccine in young children. METHODS This substudy of the YEFE phase 4 study was conducted at the Epicentre Mbarara Research Centre (Mbarara, Uganda). Eligible children were aged 9-59 months without contraindications for vaccination, without history of previous yellow fever vaccination or infection and not requiring yellow fever vaccination for travelling. Participants were randomly assigned, using block randomisation, 1:1 to standard or fractional (one-fifth) dose of yellow fever vaccine. Investigators, participants, and laboratory personnel were blinded to group allocation. Participants were followed for immunogenicity and safety at 10 days, 28 days, and 1 year after vaccination. The primary outcome was non-inferiority in seroconversion (-10 percentage point margin) 28 days after vaccination measured by 50% plaque reduction neutralisation test (PRNT50) in the per-protocol population. Safety and seroconversion at 10 days and 12-16 months after vaccination (given COVID-19 resctrictions) were secondary outcomes. This study is registered with ClinicalTrials.gov, NCT02991495. FINDINGS Between Feb 20, 2019, and Sept 9, 2019, 433 children were assessed, and 420 were randomly assigned to fractional dose (n=210) and to standard dose (n=210) 17D-213 vaccination. 28 days after vaccination, 202 (97%, 95% CI 95-99) of 207 participants in the fractional dose group and 191 (100%, 98-100) of 191 in the standard dose group seroconverted. The absolute difference in seroconversion between the study groups in the per-protocol population was -2 percentage points (95% CI -5 to 1). 154 (73%) of 210 participants in the fractional dose group and 168 (80%) of 210 in the standard dose group reported at least one adverse event 28 days after vaccination. At 10 days follow-up, seroconversion was lower in the fractional dose group than in the standard dose group. The most common adverse events were upper respiratory tract infections (n=221 [53%]), diarrhoea (n=68 [16%]), rhinorrhoea (n=49 [12%]), and conjunctivitis (n=28 [7%]). No difference was observed in incidence of adverse events and serious adverse events between study groups. CONCLUSIONS Fractional doses of the 17D-213 vaccine were non-inferior to standard doses in inducing seroconversion 28 days after vaccination in children aged 9-59 months when assessed with PRNT50, but we found fewer children seroconverted at 10 days. The results support consideration of the use of fractional dose of yellow fever vaccines in WHO recommendations for outbreak response in the event of a yellow fever vaccine shortage to include children. FUNDING Médecins Sans Frontières Foundation.
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Affiliation(s)
| | | | - Derick Kimathi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - Kyra H Grantz
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | | | | | | | - Edgar M Mulogo
- Department of Community Health, Mbarara University of Science & Technology, Mbarara, Uganda
| | | | - Joachim Hombach
- Immunization, Vaccines, and Biologicals, World Health Organization, Geneva, Switzerland
| | | | | | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
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4
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Kimathi D, Juan-Giner A, Orindi B, Grantz KH, Bob NS, Cheruiyot S, Hamaluba M, Kamau N, Fall G, Dia M, Mosobo M, Moki F, Kiogora K, Chirro O, Thiong'o A, Mwendwa J, Guantai A, Karanja HK, Gitonga J, Mugo D, Ramko K, Faye O, Sanders EJ, Grais RF, Bejon P, Warimwe GM. Immunogenicity and safety of fractional doses of 17D-213 yellow fever vaccine in HIV-infected people in Kenya (YEFE): a randomised, double-blind, non-inferiority substudy of a phase 4 trial. Lancet Infect Dis 2023; 23:974-982. [PMID: 37127045 PMCID: PMC10371873 DOI: 10.1016/s1473-3099(23)00114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Evidence indicates that fractional doses of yellow fever vaccine are safe and sufficiently immunogenic for use during yellow fever outbreaks. However, there are no data on the generalisability of this observation to populations living with HIV. Therefore, we aimed to evaluate the immunogenicity of fractional and standard doses of yellow fever vaccine in HIV-positive adults. METHODS We conducted a randomised, double-blind, non-inferiority substudy in Kilifi, coastal Kenya to compare the immunogenicity and safety of a fractional dose (one-fifth of the standard dose) versus the standard dose of 17D-213 yellow fever vaccine among HIV-positive volunteers. HIV-positive participants aged 18-59 years, with baseline CD4+ T-cell count of at least 200 cells per mL, and who were not pregnant, had no previous history of yellow fever vaccination or infection, and had no contraindication for yellow fever vaccination were recruited from the community. Participants were randomly assigned 1:1 in blocks (variable block sizes) to either a fractional dose or a standard dose of the 17D-213 yellow fever vaccine. Vaccines were administered subcutaneously by an unblinded nurse and pharmacist; all other study personnel were blinded to the vaccine allocation. The primary outcome of the study was the proportion of participants who seroconverted by the plaque reduction neutralisation test (PRNT50) 28 days after vaccination for the fractional dose versus the standard dose in the per-protocol population. Secondary outcomes were assessment of adverse events and immunogenicity during the 1-year follow-up period. Participants were considered to have seroconverted if the post-vaccination antibody titre was at least 4 times greater than the pre-vaccination titre. We set a non-inferiority margin of not less than a 17% decrease in seroconversion in the fractional dose compared with the standard dose. This study is registered with ClinicalTrials.gov, NCT02991495. FINDINGS Between Jan 29, 2019, and May 17, 2019, 303 participants were screened, and 250 participants were included and vaccinated; 126 participants were assigned to the fractional dose and 124 to the standard dose. 28 days after vaccination, 112 (96%, 95% CI 90-99) of 117 participants in the fractional dose group and 115 (98%, 94-100) of 117 in the standard dose group seroconverted by PRNT50. The difference in seroconversion between the fractional dose and the standard dose was -3% (95% CI -7 to 2). Fractional dosing therefore met the non-inferiority criterion, and non-inferiority was maintained for 1 year. The most common adverse events were headache (n=31 [12%]), fatigue (n=23 [9%]), myalgia (n=23 [9%]), and cough (n=14 [6%]). Reported adverse events were either mild (182 [97%] of 187 adverse events) or moderate (5 [3%]) and were self-limiting. INTERPRETATION Fractional doses of the 17D-213 yellow fever vaccine were sufficiently immunogenic and safe demonstrating non-inferiority to the standard vaccine dose in HIV-infected individuals with CD4+ T cell counts of at least 200 cells per mL. These results provide confidence that fractional dose recommendations are applicable to populations with high HIV prevalence. FUNDING Wellcome Trust, Médecins Sans Frontières Foundation, and the UK Department for International Development.
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Affiliation(s)
- Derick Kimathi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | | | - Benedict Orindi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kyra H Grantz
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Stanley Cheruiyot
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mainga Hamaluba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - Naomi Kamau
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Moses Mosobo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Felix Moki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kenneth Kiogora
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Oscar Chirro
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alexander Thiong'o
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Jane Mwendwa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Andrew Guantai
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry K Karanja
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John Gitonga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daisy Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kelly Ramko
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | | | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK.
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5
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Jenkin D, Wright D, Folegatti PM, Platt A, Poulton I, Lawrie A, Tran N, Boyd A, Turner C, Gitonga JN, Karanja HK, Mugo D, Ewer KJ, Bowden TA, Gilbert SC, Charleston B, Kaleebu P, Hill AVS, Warimwe GM. Safety and immunogenicity of a ChAdOx1 vaccine against Rift Valley fever in UK adults: an open-label, non-randomised, first-in-human phase 1 clinical trial. Lancet Infect Dis 2023; 23:956-964. [PMID: 37060917 PMCID: PMC7614834 DOI: 10.1016/s1473-3099(23)00068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND Rift Valley fever is a viral epidemic illness prevalent in Africa that can be fatal or result in debilitating sequelae in humans. No vaccines are available for human use. We aimed to evaluate the safety and immunogenicity of a non-replicating simian adenovirus-vectored Rift Valley fever (ChAdOx1 RVF) vaccine in humans. METHODS We conducted a phase 1, first-in-human, open-label, dose-escalation trial in healthy adults aged 18-50 years at the Centre for Clinical Vaccinology and Tropical Medicine, Oxford, UK. Participants were required to have no serious comorbidities or previous history of receiving an adenovirus-based vaccine before enrolment. Participants were non-randomly allocated to receive a single ChAdOx1 RVF dose of either 5 × 109 virus particles (vp), 2·5 × 1010 vp, or 5 × 1010 vp administered intramuscularly into the deltoid of their non-dominant arm; enrolment was sequential and administration was staggered to allow for safety to be assessed before progression to the next dose. Primary outcome measures were assessment of adverse events and secondary outcome measures were Rift Valley fever neutralising antibody titres, Rift Valley fever GnGc-binding antibody titres (ELISA), and cellular response (ELISpot), analysed in all participants who received a vaccine. This trial is registered with ClinicalTrials.gov (NCT04754776). FINDINGS Between June 11, 2021, and Jan 13, 2022, 15 volunteers received a single dose of either 5 × 109 vp (n=3), 2·5 × 1010 vp (n=6), or 5 × 1010 vp (n=6) ChAdOx1 RVF. Nine participants were female and six were male. 14 (93%) of 15 participants reported solicited local adverse reactions; injection-site pain was the most frequent (13 [87%] of 15). Ten (67%) of 15 participants (from the 2·5 × 1010 vp and 5 × 1010 vp groups only) reported systemic symptoms, which were mostly mild in intensity, the most common being headache (nine [60%] of 15) and fatigue (seven [47%]). All unsolicited adverse events reported within 28 days were either mild or moderate in severity; gastrointestinal symptoms were the most common reaction (at least possibly related to vaccination), occurring in four (27%) of 15 participants. Transient decreases in total white cell, lymphocyte, or neutrophil counts occurred at day 2 in some participants in the intermediate-dose and high-dose groups. Lymphopenia graded as severe occurred in two participants in the 5 × 1010 vp group at a single timepoint, but resolved at the subsequent follow-up visit. No serious adverse events occurred. Rift Valley fever neutralising antibodies were detectable across all dose groups, with all participants in the 5 × 1010 vp dose group having high neutralising antibody titres that peaked at day 28 after vaccination and persisted through the 3-month follow-up. High titres of binding IgG targeting Gc glycoprotein were detected whereas those targeting Gn were comparatively low. IFNγ cellular responses against Rift Valley fever Gn and Gc glycoproteins were observed in all participants except one in the 5 × 1010 vp dose group. These IFNγ responses peaked at 2 weeks after vaccination, were highest in the 5 × 1010 vp dose group, and tended to be more frequent against the Gn glycoprotein. INTERPRETATION ChAdOx1 RVF was safe, well tolerated, and immunogenic when administered as a single dose in this study population. The data support further clinical development of ChAdOx1 RVF for human use. FUNDING UK Department of Health and Social Care through the UK Vaccines Network, Oak Foundation, and the Wellcome Trust. TRANSLATION For the Swahili translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Daniel Jenkin
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Daniel Wright
- The Jenner Institute, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Abigail Platt
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Ian Poulton
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Alison Lawrie
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nguyen Tran
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Amy Boyd
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Cheryl Turner
- The Jenner Institute, University of Oxford, Oxford, UK
| | - John N Gitonga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry K Karanja
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daisy Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Katie J Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Thomas A Bowden
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council-Uganda Virus Research Institute and The London School of Hygiene & Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | | | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.
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6
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Ramirez Valdez K, Nzau B, Dorey-Robinson D, Jarman M, Nyagwange J, Schwartz JC, Freimanis G, Steyn AW, Warimwe GM, Morrison LJ, Mwangi W, Charleston B, Bonnet-Di Placido M, Hammond JA. A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies. Vaccines (Basel) 2023; 11:1099. [PMID: 37376488 PMCID: PMC10302312 DOI: 10.3390/vaccines11061099] [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: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy-light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy-light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.
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Affiliation(s)
| | - Benjamin Nzau
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | | | - James Nyagwange
- The Pirbright Institute, Pirbright GU24 0NF, UK
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | | | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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Nyagwange J, Kutima B, Mwai K, Karanja HK, Gitonga JN, Mugo D, Sein Y, Wright D, Omuoyo DO, Nyiro JU, Tuju J, Nokes DJ, Agweyu A, Bejon P, Ochola-Oyier LI, Scott JAG, Lambe T, Nduati E, Agoti C, Warimwe GM. Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro. Int J Infect Dis 2023; 127:11-16. [PMID: 36476349 PMCID: PMC9721188 DOI: 10.1016/j.ijid.2022.11.041] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/10/2022] Open
Abstract
OBJECTIVES Many regions of Africa have experienced lower COVID-19 morbidity and mortality than Europe. Pre-existing humoral responses to endemic human coronaviruses (HCoV) may cross-protect against SARS-CoV-2. We investigated the neutralizing capacity of SARS-CoV-2 spike reactive and nonreactive immunoglobulin (Ig)G and IgA antibodies in prepandemic samples. METHODS To investigate the presence of pre-existing immunity, we performed enzyme-linked immunosorbent assay using spike antigens from reference SARS-CoV-2, HCoV HKU1, OC43, NL63, and 229E using prepandemic samples from Kilifi in coastal Kenya. In addition, we performed neutralization assays using pseudotyped reference SARS-CoV-2 to determine the functionality of the identified reactive antibodies. RESULTS We demonstrate the presence of HCoV serum IgG and mucosal IgA antibodies, which cross-react with the SARS-CoV-2 spike. We show pseudotyped reference SARS-CoV-2 neutralization by prepandemic serum, with a mean infective dose 50 of 1: 251, which is 10-fold less than that of the pooled convalescent sera from patients with COVID-19 but still within predicted protection levels. The prepandemic naso-oropharyngeal fluid neutralized pseudo-SARS-CoV-2 at a mean infective dose 50 of 1: 5.9 in the neutralization assay. CONCLUSION Our data provide evidence for pre-existing functional humoral responses to SARS-CoV-2 in Kilifi, coastal Kenya and adds to data showing pre-existing immunity for COVID-19 from other regions.
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Affiliation(s)
- James Nyagwange
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya.
| | | | - Kennedy Mwai
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, 27 St Andrews Road, Parktown 2193, Johannesburg, South Africa
| | - Henry K Karanja
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - John N Gitonga
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - Yiakon Sein
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - Daniel Wright
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | | | - Joyce U Nyiro
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - James Tuju
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4 7AL, United Kingdom; School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ambrose Agweyu
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | | | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street WC1E 7HT, London, United Kingdom
| | - Teresa Lambe
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Eunice Nduati
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - Charles Agoti
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme,PO Box 230, Kilifi, Kenya; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
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8
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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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9
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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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10
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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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11
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Nyamwaya DK, Otiende M, Mwango L, Kariuki SM, Otieno B, Omuoyo DO, Githinji G, Kitsao BS, Karanja HK, Gitonga JN, de Laurent ZR, Davies A, Mwarumba S, Agoti CN, Thumbi SM, Hamaluba MM, Newton CR, Bejon P, Warimwe GM. Incidence of chikungunya virus infections among Kenyan children with neurological disease, 2014-2018: A cohort study. PLoS Med 2022; 19:e1003994. [PMID: 35550620 PMCID: PMC9135332 DOI: 10.1371/journal.pmed.1003994] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Neurological complications due to chikungunya virus (CHIKV) infection have been described in different parts of the world, with children being disproportionately affected. However, the burden of CHIKV-associated neurological disease in Africa is currently unknown and given the lack of diagnostic facilities in routine care it is possible that CHIKV is an unrecognized etiology among children with encephalitis or other neurological illness. METHODS AND FINDINGS We estimated the incidence of CHIKV infection among children hospitalized with neurological disease in Kilifi County, coastal Kenya. We used reverse transcriptase polymerase chain reaction (RT-PCR) to systematically test for CHIKV in cerebrospinal fluid (CSF) samples from children aged <16 years hospitalized with symptoms of neurological disease at Kilifi County Hospital between January 2014 and December 2018. Clinical records were linked to the Kilifi Health and Demographic Surveillance System and population incidence rates of CHIKV infection estimated. There were 18,341 pediatric admissions for any reason during the 5-year study period, of which 4,332 (24%) had CSF collected. The most common clinical reasons for CSF collection were impaired consciousness, seizures, and coma (47%, 22%, and 21% of all collections, respectively). After acute investigations done for immediate clinical care, CSF samples were available for 3,980 admissions, of which 367 (9.2%) were CHIKV RT-PCR positive. Case fatality among CHIKV-positive children was 1.4% (95% CI 0.4, 3.2). The annual incidence of CHIKV-associated neurological disease varied between 13 to 58 episodes per 100,000 person-years among all children <16 years old. Among children aged <5 years, the incidence of CHIKV-associated neurological disease was 77 per 100,000 person-years, compared with 20 per 100,000 for cerebral malaria and 7 per 100,000 for bacterial meningitis during the study period. Because of incomplete case ascertainment due to children not presenting to hospital, or not having CSF collected, these are likely minimum estimates. Study limitations include reliance on hospital-based surveillance and limited CSF sampling in children in coma or other contraindications to lumbar puncture, both of which lead to under-ascertainment of incidence and of case fatality. CONCLUSIONS In this study, we observed that CHIKV infections are relatively more common than cerebral malaria and bacterial meningitis among children hospitalized with neurological disease in coastal Kenya. Given the wide distribution of CHIKV mosquito vectors, studies to determine the geographic extent of CHIKV-associated neurological disease in Africa are essential.
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Affiliation(s)
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Lilian Mwango
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | | | | | | | | | | | | | | | | | - Alun Davies
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | | | | | - Samuel M. Thumbi
- Paul G Allen School for Global Animal Health, Washington State University, Washington, United States of America
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Center for Epidemiological Modelling and Analysis, Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | | | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- * E-mail:
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12
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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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13
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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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14
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Nyagwange J, Kutima B, Mwai K, Karanja HK, Gitonga JN, Mugo D, Uyoga S, Tuju J, Ochola-Oyier LI, Ndungu F, Bejon P, Agweyu A, Adetifa IMO, Scott JAG, Warimwe GM. Comparative performance of WANTAI ELISA for total immunoglobulin to receptor binding protein and an ELISA for IgG to spike protein in detecting SARS-CoV-2 antibodies in Kenyan populations. J Clin Virol 2022; 146:105061. [PMID: 34973474 PMCID: PMC8711170 DOI: 10.1016/j.jcv.2021.105061] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022]
Abstract
Many SARS-CoV-2 antibody detection assays have been developed but their differential performance is not well described. In this study we compared an in-house (KWTRP) ELISA which has been used extensively to estimate seroprevalence in the Kenyan population with WANTAI, an ELISA which has been approved for widespread use by the WHO. Using a wide variety of sample sets including pre-pandemic samples (negative gold standard), SARS-CoV-2 PCR positive samples (positive gold standard) and COVID-19 test samples from different periods (unknowns), we compared performance characteristics of the two assays. The overall concordance between WANTAI and KWTRP was 0.97 (95% CI, 0.95-0.98). For WANTAI and KWTRP, sensitivity was 0.95 (95% CI 0.90-0.98) and 0.93 (95% CI 0.87-0.96), respectively. Specificity for WANTAI was 0.98 (95% CI, 0.96-0.99) and 0.99 (95% CI 0.96-1.00) while KWTRP specificity was 0.99 (95% CI, 0.98-1.00) and 1.00 using pre-pandemic blood donors and pre-pandemic malaria cross-sectional survey samples respectively. Both assays show excellent characteristics to detect SARS-CoV-2 antibodies.
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Affiliation(s)
- James Nyagwange
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.
| | | | - Kennedy Mwai
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, 27 St Andrews Road, Parktown 2193, Johannesburg, South Africa
| | - Henry K Karanja
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - John N Gitonga
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - James Tuju
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Francis Ndungu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya; Nuffield Department of Medicine, Oxford University, OX3 7BN, Oxford, United Kingdom
| | - Ambrose Agweyu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, WC1E 7HT, Keppel Street, London, United Kingdom
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, WC1E 7HT, Keppel Street, London, United Kingdom
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya; Nuffield Department of Medicine, Oxford University, OX3 7BN, Oxford, United Kingdom
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15
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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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16
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Nyamwaya DK, Thumbi SM, Bejon P, Warimwe GM, Mokaya J. The global burden of Chikungunya fever among children: A systematic literature review and meta-analysis. PLOS Glob Public Health 2022; 2:e0000914. [PMID: 36962807 PMCID: PMC10022366 DOI: 10.1371/journal.pgph.0000914] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Chikungunya fever (CHIKF) is an arboviral illness that was first described in Tanzania (1952). In adults, the disease is characterised by debilitating arthralgia and arthritis that can persist for months, with severe illness including neurological complications observed in the elderly. However, the burden, distribution and clinical features of CHIKF in children are poorly described. We conducted a systematic literature review and meta-analysis to determine the epidemiology of CHIKF in children globally by describing its prevalence, geographical distribution, and clinical manifestations. We searched electronic databases for studies describing the epidemiology of CHIKF in children. We included peer-reviewed primary studies that reported laboratory confirmed CHIKF. We extracted information on study details, sampling approach, study participants, CHIKF positivity, clinical presentation and outcomes of CHIKF in children. The quality of included studies was assessed using Joanna Briggs Institute Critical Appraisal tool for case reports and National Institute of Health quality assessment tool for quantitative studies and case series. Random-effects meta-analysis was used to estimate the pooled prevalence of CHIKF among children by geographical location. We summarised clinical manifestations, laboratory findings, administered treatment and disease outcomes associated with CHIKF in children. We identified 2104 studies, of which 142 and 53 articles that met the inclusion criteria were included in the systematic literature review and meta-analysis, respectively. Most of the selected studies were from Asia (54/142 studies) and the fewest from Europe (5/142 studies). Included studies were commonly conducted during an epidemic season (41.5%) than non-epidemic season (5.1%). Thrombocytopenia was common among infected children and CHIKF severity was more prevalent in children <1 year. Children with undifferentiated fever before CHIKF was diagnosed were treated with antibiotics and/or drugs that managed specific symptoms or provided supportive care. CHIKF is a significant under-recognised and underreported health problem among children globally and development of drugs/vaccines should target young children.
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Affiliation(s)
- Doris K Nyamwaya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Samuel M Thumbi
- Paul G Allen School for Global Health, Washington State University, Pullman, Washington, United States of America
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Center for Epidemiological Modelling and Analysis, Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Jolynne Mokaya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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17
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Abstract
Since the initial use of vaccination in the eighteenth century, our understanding of human and animal immunology has greatly advanced and a wide range of vaccine technologies and delivery systems have been developed. The COVID-19 pandemic response leveraged these innovations to enable rapid development of candidate vaccines within weeks of the viral genetic sequence being made available. The development of vaccines to tackle emerging infectious diseases is a priority for the World Health Organization and other global entities. More than 70% of emerging infectious diseases are acquired from animals, with some causing illness and death in both humans and the respective animal host. Yet the study of critical host-pathogen interactions and the underlying immune mechanisms to inform the development of vaccines for their control is traditionally done in medical and veterinary immunology 'silos'. In this Perspective, we highlight a 'One Health vaccinology' approach and discuss some key areas of synergy in human and veterinary vaccinology that could be exploited to accelerate the development of effective vaccines against these shared health threats.
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Affiliation(s)
- George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- The Pirbright Institute, Woking, UK.
| | | | - Thomas A Bowden
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford, UK
| | - Samuel M Thumbi
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
- Center for Epidemiological Modelling and Analysis, Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
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18
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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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19
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Berg A, Wright D, Dulal P, Stedman A, Fedosyuk S, Francis MJ, Charleston B, Warimwe GM, Douglas AD. Stability of Chimpanzee Adenovirus Vectored Vaccines (ChAdOx1 and ChAdOx2) in Liquid and Lyophilised Formulations. Vaccines (Basel) 2021; 9:1249. [PMID: 34835180 PMCID: PMC8623940 DOI: 10.3390/vaccines9111249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/04/2022] Open
Abstract
Adenovirus vectored vaccines have entered global use during the COVID-19 pandemic, and are in development for multiple other human and veterinary applications. An attraction of the technology is the suitability of the vaccines for storage at 2-8 °C for months. Widely used COVID-19 vaccine ChAdOx1 nCoV-19 (University of Oxford/AstraZeneca) is based on a species E simian adenovirus. Species E simian serotypes have been used in a wide range of other development programs, but the stability of such vectors has not been extensively described in the peer-reviewed literature. Here, we explore the stability of two candidate vaccines based on two species E serotypes: a Rift Valley fever vaccine based upon the ChAdOx1 vector (Y25 serotype) used in ChAdOx1 nCoV-19, and a rabies vaccine based upon a ChAdOx2 vector (AdC68 serotype). We describe each vector's stability in liquid and lyophilised formulations using in vitro and in vivo potency measurements. Our data support the suitability of liquid formulations of these vectors for storage at 2-8 °C for up to 1 year, and potentially for nonrefrigerated storage for a brief period during last-leg distribution (perhaps 1-3 days at 20 °C-the precise definition of acceptable last-leg storage conditions would require further product-specific data). Depending upon the level of inprocess potency loss that is economically acceptable, and the level of instorage loss that is compatible with maintenance of acceptable end-of-storage potency, a previously reported lyophilised formulation may enable longer term storage at 20 °C or storage for a number of days at 30 °C.
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Affiliation(s)
- Adam Berg
- Wellcome Trust Centre for Human Genetics, Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (A.B.); (P.D.); (S.F.)
| | - Daniel Wright
- Wellcome Trust Centre for Human Genetics, Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (A.B.); (P.D.); (S.F.)
| | - Pawan Dulal
- Wellcome Trust Centre for Human Genetics, Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (A.B.); (P.D.); (S.F.)
| | - Anna Stedman
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (A.S.); (B.C.); (G.M.W.)
| | - Sofiya Fedosyuk
- Wellcome Trust Centre for Human Genetics, Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (A.B.); (P.D.); (S.F.)
| | - Michael J. Francis
- BioVacc Consulting Ltd., The Red House, 10 Market Square, Amersham HP7 0DQ, UK;
| | - Bryan Charleston
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (A.S.); (B.C.); (G.M.W.)
| | - George M. Warimwe
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (A.S.); (B.C.); (G.M.W.)
- KEMRI-Wellcome Trust Research Programme, Kilifi P.O. Box 230-80108, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford OX3 7LG, UK
| | - Alexander D. Douglas
- Wellcome Trust Centre for Human Genetics, Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (A.B.); (P.D.); (S.F.)
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20
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Bottomley C, Otiende M, Uyoga S, Gallagher K, Kagucia EW, Etyang AO, Mugo D, Gitonga J, Karanja H, Nyagwange J, Adetifa IMO, Agweyu A, Nokes DJ, Warimwe GM, Scott JAG. Quantifying previous SARS-CoV-2 infection through mixture modelling of antibody levels. Nat Commun 2021; 12:6196. [PMID: 34702829 PMCID: PMC8548402 DOI: 10.1038/s41467-021-26452-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022] Open
Abstract
As countries decide on vaccination strategies and how to ease movement restrictions, estimating the proportion of the population previously infected with SARS-CoV-2 is important for predicting the future burden of COVID-19. This proportion is usually estimated from serosurvey data in two steps: first the proportion above a threshold antibody level is calculated, then the crude estimate is adjusted using external estimates of sensitivity and specificity. A drawback of this approach is that the PCR-confirmed cases used to estimate the sensitivity of the threshold may not be representative of cases in the wider population-e.g., they may be more recently infected and more severely symptomatic. Mixture modelling offers an alternative approach that does not require external data from PCR-confirmed cases. Here we illustrate the bias in the standard threshold-based approach by comparing both approaches using data from several Kenyan serosurveys. We show that the mixture model analysis produces estimates of previous infection that are often substantially higher than the standard threshold analysis.
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Affiliation(s)
- C Bottomley
- International Statistics and Epidemiology Group, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - M Otiende
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - S Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - K Gallagher
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - E W Kagucia
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - A O Etyang
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Gitonga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - H Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Nyagwange
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - I M O Adetifa
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - A Agweyu
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - D J Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences, University of Warwick, Coventry, UK
| | - G M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - J A G Scott
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Oxford University, Oxford, UK
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21
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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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22
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Uyoga S, Adetifa IMO, Otiende M, Yegon C, Agweyu A, Warimwe GM, Scott JAG. Prevalence of SARS-CoV-2 Antibodies From a National Serosurveillance of Kenyan Blood Donors, January-March 2021. JAMA 2021; 326:1436-1438. [PMID: 34473191 PMCID: PMC8414357 DOI: 10.1001/jama.2021.15265] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
This study examines the prevalence of SARS-CoV-2 antibodies among blood donors aged 16 to 64 years in Kenya from January to March 2021.
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Affiliation(s)
- Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Christine Yegon
- Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya
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23
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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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24
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Mokaya J, Kimathi D, Lambe T, Warimwe GM. What Constitutes Protective Immunity Following Yellow Fever Vaccination? Vaccines (Basel) 2021; 9:vaccines9060671. [PMID: 34207358 PMCID: PMC8235545 DOI: 10.3390/vaccines9060671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 06/16/2021] [Indexed: 01/08/2023] Open
Abstract
Yellow fever (YF) remains a threat to global health, with an increasing number of major outbreaks in the tropical areas of the world over the recent past. In light of this, the Eliminate Yellow Fever Epidemics Strategy was established with the aim of protecting one billion people at risk of YF through vaccination by the year 2026. The current YF vaccine gives excellent protection, but its use is limited by shortages in supply due to the difficulties in producing the vaccine. There are good grounds for believing that alternative fractional dosing regimens can produce strong protection and overcome the problem of supply shortages as less vaccine is required per person. However, immune responses to these vaccination approaches are yet to be fully understood. In addition, published data on immune responses following YF vaccination have mostly quantified neutralising antibody titers. However, vaccine-induced antibodies can confer immunity through other antibody effector functions beyond neutralisation, and an effective vaccine is also likely to induce strong and persistent memory T cell responses. This review highlights the gaps in knowledge in the characterisation of YF vaccine-induced protective immunity in the absence or presence of neutralising antibodies. The assessment of biophysical antibody characteristics and cell-mediated immunity following YF vaccination could help provide a comprehensive landscape of YF vaccine-induced immunity and a better understanding of correlates of protective immunity.
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Affiliation(s)
- Jolynne Mokaya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX1 3SU, UK; (D.K.); (G.M.W.)
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi 8010, Kenya
- Correspondence:
| | - Derick Kimathi
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX1 3SU, UK; (D.K.); (G.M.W.)
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi 8010, Kenya
| | - Teresa Lambe
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK;
| | - George M. Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX1 3SU, UK; (D.K.); (G.M.W.)
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi 8010, Kenya
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25
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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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26
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Nyamwaya DK, Otiende M, Omuoyo DO, Githinji G, Karanja HK, Gitonga JN, R de Laurent Z, Otieno JR, Sang R, Kamau E, Cheruiyot S, Otieno E, Agoti CN, Bejon P, Thumbi SM, Warimwe GM. Endemic chikungunya fever in Kenyan children: a prospective cohort study. BMC Infect Dis 2021; 21:186. [PMID: 33602147 PMCID: PMC7889702 DOI: 10.1186/s12879-021-05875-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Background Chikungunya fever (CHIKF) was first described in Tanzania in 1952. Several epidemics including East Africa have occurred, but there are no descriptions of longitudinal surveillance of endemic disease. Here, we estimate the incidence of CHIKF in coastal Kenya and describe the associated viral phylogeny. Methods We monitored acute febrile illnesses among 3500 children visiting two primary healthcare facilities in coastal Kenya over a 5-year period (2014–2018). Episodes were linked to a demographic surveillance system and blood samples obtained. Cross-sectional sampling in a community survey of a different group of 435 asymptomatic children in the same study location was done in 2016. Reverse-transcriptase PCR was used for chikungunya virus (CHIKV) screening, and viral genomes sequenced for phylogenetic analyses. Results We found CHIKF to be endemic in this setting, associated with 12.7% (95% CI 11.60, 13.80) of all febrile presentations to primary healthcare. The prevalence of CHIKV infections among asymptomatic children in the community survey was 0.7% (95% CI 0.22, 2.12). CHIKF incidence among children < 1 year of age was 1190 cases/100,000-person years and 63 cases/100,000-person years among children aged ≥10 years. Recurrent CHIKF episodes, associated with fever and viraemia, were observed among 19 of 170 children with multiple febrile episodes during the study period. All sequenced viral genomes mapped to the ECSA genotype albeit distinct from CHIKV strains associated with the 2004 East African epidemic. Conclusions CHIKF may be a substantial public health burden in primary healthcare on the East African coast outside epidemic years, and recurrent infections are common. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05875-5.
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Affiliation(s)
- Doris K Nyamwaya
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Henry K Karanja
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - John N Gitonga
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | | | - James R Otieno
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | | | - Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Stanley Cheruiyot
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, NDM Research Building, Oxford, OX3 7FZ, UK
| | - Samuel M Thumbi
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164-7090, USA.,Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-4100, Kisumu, Kenya.,Institute of Tropical and Infectious Diseases, University of Nairobi, P.O Box 19676, Nairobi, 00202, Kenya
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya. .,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, NDM Research Building, Oxford, OX3 7FZ, UK.
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Juan-Giner A, Kimathi D, Grantz KH, Hamaluba M, Kazooba P, Njuguna P, Fall G, Dia M, Bob NS, Monath TP, Barrett AD, Hombach J, Mulogo EM, Ampeire I, Karanja HK, Nyehangane D, Mwanga-Amumpaire J, Cummings DAT, Bejon P, Warimwe GM, Grais RF. Immunogenicity and safety of fractional doses of yellow fever vaccines: a randomised, double-blind, non-inferiority trial. Lancet 2021; 397:119-127. [PMID: 33422245 PMCID: PMC7794660 DOI: 10.1016/s0140-6736(20)32520-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 11/04/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Stocks of yellow fever vaccine are insufficient to cover exceptional demands for outbreak response. Fractional dosing has shown efficacy, but evidence is limited to the 17DD substrain vaccine. We assessed the immunogenicity and safety of one-fifth fractional dose compared with standard dose of four WHO-prequalified yellow fever vaccines produced from three substrains. METHODS We did this randomised, double-blind, non-inferiority trial at research centres in Mbarara, Uganda, and Kilifi, Kenya. Eligible participants were aged 18-59 years, had no contraindications for vaccination, were not pregnant or lactating, had no history of yellow fever vaccination or infection, and did not require yellow fever vaccination for travel. Eligible participants were recruited from communities and randomly assigned to one of eight groups, corresponding to the four vaccines at standard or fractional dose. The vaccine was administered subcutaneously by nurses who were not masked to treatment, but participants and other study personnel were masked to vaccine allocation. The primary outcome was proportion of participants with seroconversion 28 days after vaccination. Seroconversion was defined as post-vaccination neutralising antibody titres at least 4 times pre-vaccination measurement measured by 50% plaque reduction neutralisation test (PRNT50). We defined non-inferiority as less than 10% decrease in seroconversion in fractional compared with standard dose groups 28 days after vaccination. The primary outcome was measured in the per-protocol population, and safety analyses included all vaccinated participants. This trial is registered with ClinicalTrials.gov, NCT02991495. FINDINGS Between Nov 6, 2017, and Feb 21, 2018, 1029 participants were assessed for inclusion. 69 people were ineligible, and 960 participants were enrolled and randomly assigned to vaccine manufacturer and dose (120 to Bio-Manguinhos-Fiocruz standard dose, 120 to Bio-Manguinhos-Fiocruz fractional dose, 120 to Chumakov Institute of Poliomyelitis and Viral Encephalitides standard dose, 120 to Chumakov Institute of Poliomyelitis and Viral Encephalitides fractional dose, 120 to Institut Pasteur Dakar standard dose, 120 to Institut Pasteur Dakar fractional dose, 120 to Sanofi Pasteur standard dose, and 120 to Sanofi Pasteur fractional dose). 49 participants had detectable PRNT50 at baseline and 11 had missing PRNT50 results at baseline or 28 days. 900 were included in the per-protocol analysis. 959 participants were included in the safety analysis. The absolute difference in seroconversion between fractional and standard doses by vaccine was 1·71% (95% CI -2·60 to 5·28) for Bio-Manguinhos-Fiocruz, -0·90% (-4·24 to 3·13) for Chumakov Institute of Poliomyelitis and Viral Encephalitides, 1·82% (-2·75 to 5·39) for Institut Pasteur Dakar, and 0·0% (-3·32 to 3·29) for Sanofi Pasteur. Fractional doses from all four vaccines met the non-inferiority criterion. The most common treatment-related adverse events were headache (22·2%), fatigue (13·7%), myalgia (13·3%) and self-reported fever (9·0%). There were no study-vaccine related serious adverse events. INTERPRETATION Fractional doses of all WHO-prequalified yellow fever vaccines were non-inferior to the standard dose in inducing seroconversion 28 days after vaccination, with no major safety concerns. These results support the use of fractional dosage in the general adult population for outbreak response in situations of vaccine shortage. FUNDING The study was funded by Médecins Sans Frontières Foundation, Wellcome Trust (grant no. 092654), and the UK Department for International Development. Vaccines were donated in kind.
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Affiliation(s)
| | - Derick Kimathi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - Kyra H Grantz
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mainga Hamaluba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | | | - Patricia Njuguna
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | - Alan D Barrett
- Sealy Institute for Vaccines Sciences and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Joachim Hombach
- Immunization, Vaccines & Biologicals, WHO, Geneva, Switzerland
| | - Edgar M Mulogo
- Department of Community Health, Mbarara University of Science & Technology, Mbarara, Uganda
| | | | - Henry K Karanja
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
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28
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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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29
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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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30
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Wright D, Allen ER, Clark MH, Gitonga JN, Karanja HK, Hulswit RJ, Taylor I, Biswas S, Marshall J, Mwololo D, Muriuki J, Bett B, Bowden TA, Warimwe GM. Naturally Acquired Rift Valley Fever Virus Neutralizing Antibodies Predominantly Target the Gn Glycoprotein. iScience 2020; 23:101669. [PMID: 33134899 PMCID: PMC7588868 DOI: 10.1016/j.isci.2020.101669] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 11/30/2022] Open
Abstract
Rift Valley fever (RVF) is a viral hemorrhagic disease first discovered in Kenya in 1930. Numerous animal studies have demonstrated that protective immunity is acquired following RVF virus (RVFV) infection and that this correlates with acquisition of virus-neutralizing antibodies (nAbs) that target the viral envelope glycoproteins. However, naturally acquired immunity to RVF in humans is poorly described. Here, we characterized the immune response to the viral envelope glycoproteins, Gn and Gc, in RVFV-exposed Kenyan adults. Long-lived IgG (dominated by IgG1 subclass) and T cell responses were detected against both Gn and Gc. However, antigen-specific antibody depletion experiments showed that Gn-specific antibodies dominate the RVFV nAb response. IgG avidity against Gn, but not Gc, correlated with nAb titers. These data are consistent with the greater level of immune accessibility of Gn on the viral envelope surface and confirm the importance of Gn as an integral component for RVF vaccine development.
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Affiliation(s)
- Daniel Wright
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Elizabeth R. Allen
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | | | - John N. Gitonga
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya
| | - Henry K. Karanja
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya
| | - Ruben J.G. Hulswit
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Iona Taylor
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Sumi Biswas
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Damaris Mwololo
- International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya
| | - John Muriuki
- International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya
| | - Bernard Bett
- International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya
| | - Thomas A. Bowden
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7FZ, UK
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31
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Barsosio HC, Gitonga JN, Karanja HK, Nyamwaya DK, Omuoyo DO, Kamau E, Hamaluba MM, Nyiro JU, Kitsao BS, Nyaguara A, Mwakio S, Newton CR, Sang R, Wright D, Sanders EJ, Seale AC, Agoti CN, Berkley JA, Bejon P, Warimwe GM. Congenital microcephaly unrelated to flavivirus exposure in coastal Kenya. Wellcome Open Res 2020; 4:179. [PMID: 32175480 PMCID: PMC7059837 DOI: 10.12688/wellcomeopenres.15568.1] [Citation(s) in RCA: 8] [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] [Accepted: 11/13/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Zika virus (ZIKV) was first discovered in East Africa in 1947. ZIKV has caused microcephaly in the Americas, but it is not known whether ZIKV is a cause of microcephaly in East Africa. Methods: We used surveillance data from 11,061 live births at Kilifi County Hospital in coastal Kenya between January 2012 and October 2016 to identify microcephaly cases and conducted a nested case-control study to determine risk factors for microcephaly. Gestational age at birth was estimated based on antenatal ultrasound scanning ('Scanned cohort') or last menstrual period ('LMP cohort', including births ≥37 weeks' gestation only). Controls were newborns with head circumference Z scores between >-2 and ≤2 SD that were compared to microcephaly cases in relation to ZIKV exposure and other maternal and newborn factors. Results: Of the 11,061 newborns, 214 (1.9%, 95%CI 1.69, 2.21) had microcephaly. Microcephaly prevalence was 1.0% (95%CI 0.64, 1.70, n=1529) and 2.1% (95%CI 1.81, 2.38, n=9532) in the scanned and LMP cohorts, respectively. After excluding babies <2500 g (n=1199) in the LMP cohort the prevalence was 1.1% (95%CI 0.93, 1.39). Microcephaly showed an association with being born small for gestational age (p<0.001) but not with ZIKV neutralising antibodies (p=0.6) or anti-ZIKV NS1 IgM response (p=0.9). No samples had a ZIKV neutralising antibody titre that was at least fourfold higher than the corresponding dengue virus (DENV) titre. No ZIKV or other flavivirus RNA was detected in cord blood from cases or controls. Conclusions: Microcephaly was prevalent in coastal Kenya, but does not appear to be related to ZIKV exposure; the ZIKV response observed in our study population was largely due to cross-reactive responses to DENV or other related flaviviruses. Further research into potential causes and the clinical consequences of microcephaly in this population is urgently needed.
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Affiliation(s)
- Hellen C Barsosio
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | | | | | - Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joyce U Nyiro
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Amek Nyaguara
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles R Newton
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - Daniel Wright
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,The Jenner Institute, University of Oxford, Oxford, UK
| | | | - Anna C Seale
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,London School of Hygiene & Tropical Medicine, London, UK
| | | | - James A Berkley
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
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Allen ER, Krumm SA, Raghwani J, Halldorsson S, Elliott A, Graham VA, Koudriakova E, Harlos K, Wright D, Warimwe GM, Brennan B, Huiskonen JT, Dowall SD, Elliott RM, Pybus OG, Burton DR, Hewson R, Doores KJ, Bowden TA. A Protective Monoclonal Antibody Targets a Site of Vulnerability on the Surface of Rift Valley Fever Virus. Cell Rep 2019; 25:3750-3758.e4. [PMID: 30590046 PMCID: PMC6315105 DOI: 10.1016/j.celrep.2018.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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] [Received: 08/23/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
The Gn subcomponent of the Gn-Gc assembly that envelopes the human and animal pathogen, Rift Valley fever virus (RVFV), is a primary target of the neutralizing antibody response. To better understand the molecular basis for immune recognition, we raised a class of neutralizing monoclonal antibodies (nAbs) against RVFV Gn, which exhibited protective efficacy in a mouse infection model. Structural characterization revealed that these nAbs were directed to the membrane-distal domain of RVFV Gn and likely prevented virus entry into a host cell by blocking fusogenic rearrangements of the Gn-Gc lattice. Genome sequence analysis confirmed that this region of the RVFV Gn-Gc assembly was under selective pressure and constituted a site of vulnerability on the virion surface. These data provide a blueprint for the rational design of immunotherapeutics and vaccines capable of preventing RVFV infection and a model for understanding Ab-mediated neutralization of bunyaviruses more generally.
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Affiliation(s)
- Elizabeth R Allen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stefanie A Krumm
- Kings College London, Department of Infectious Diseases, 2nd Floor, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road, Oxford OX3 7LF, UK
| | - Steinar Halldorsson
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angela Elliott
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Victoria A Graham
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Elina Koudriakova
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Wright
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7FZ, UK; Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stuart D Dowall
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Roger Hewson
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Katie J Doores
- Kings College London, Department of Infectious Diseases, 2nd Floor, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Kimathi D, Juan A, Bejon P, Grais RF, Warimwe GM. Randomized, double-blinded, controlled non-inferiority trials evaluating the immunogenicity and safety of fractional doses of Yellow Fever vaccines in Kenya and Uganda. Wellcome Open Res 2019; 4:182. [PMID: 31984244 PMCID: PMC6971842 DOI: 10.12688/wellcomeopenres.15579.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/14/2019] [Indexed: 01/22/2023] Open
Abstract
Introduction: Yellow fever is endemic in specific regions of sub-Saharan Africa and the Americas, with recent epidemics occurring on both continents. The yellow fever vaccine is effective, affordable and safe, providing life-long immunity following a single dose vaccination. However, the vaccine production process is slow and cannot be readily scaled up during epidemics. This has led the World Health Organization (WHO) to recommend the use of fractional doses as a dose-sparing strategy during epidemics, but there are no randomized controlled trials of fractional yellow fever vaccine doses in Africa. Methods and analysis: We will recruit healthy adult volunteers, adults living with HIV, and children to a series of randomized controlled trials aiming to determine the immunogenicity and safety of fractional vaccine doses in comparison to the standard vaccine dose. The trials will be conducted across two sites; Kilifi, Kenya and Mbarara, Uganda. Recruited participants will be randomized to receive fractional or standard doses of yellow fever vaccine. Scheduled visits will include blood collection for serum and peripheral blood mononuclear cells (PBMCs) before vaccination and on various days - up to 2 years - post-vaccination. The primary outcome is the rate of seroconversion as measured by the plaque reduction neutralization test (PRNT 50) at 28 days post-vaccination. Secondary outcomes include antibody titre changes, longevity of the immune response, safety assessment using clinical data, the nature and magnitude of the cellular immune response and post-vaccination control of viremia by vaccine dose. Ethics and dissemination: The clinical trial protocols have received approval from the relevant institutional ethics and regulatory review committees in Kenya and Uganda, and the WHO Ethics Review Committee. The research findings will be disseminated through open-access publications and presented at relevant conferences and workshops. Registration: ClinicalTrials.gov NCT02991495 (registered on 13 December 2016) and NCT04059471 (registered on 15 August 2019).
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Affiliation(s)
- Derick Kimathi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - YEFE and NIFTY vaccine trials teams
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Epicentre, Paris, France
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Stedman A, Wright D, Wichgers Schreur PJ, Clark MHA, Hill AVS, Gilbert SC, Francis MJ, van Keulen L, Kortekaas J, Charleston B, Warimwe GM. Safety and efficacy of ChAdOx1 RVF vaccine against Rift Valley fever in pregnant sheep and goats. NPJ Vaccines 2019; 4:44. [PMID: 31646004 PMCID: PMC6802222 DOI: 10.1038/s41541-019-0138-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus that was first discovered in Kenya in 1930 and has since spread to become endemic in much of Africa and the Arabian Peninsula. Rift Valley fever (RVF) causes recurrent outbreaks of febrile illness associated with high levels of mortality and poor outcomes during pregnancy-including foetal malformations, spontaneous abortion and stillbirths-in livestock, and associated with miscarriage in humans. No vaccines are available for human use and those licensed for veterinary use have potential drawbacks, including residual virulence that may contraindicate their use in pregnancy. To address this gap, we previously developed a simian adenovirus vectored vaccine, ChAdOx1 RVF, that encodes RVFV envelope glycoproteins. ChAdOx1 RVF is fully protective against RVF in non-pregnant livestock and is also under development for human use. Here, we now demonstrate that when administered to pregnant sheep and goats, ChAdOx1 RVF is safe, elicits high titre RVFV neutralizing antibody, and provides protection against viraemia and foetal loss, although this protection is not as robust for the goats. In addition, we provide a description of RVFV challenge in pregnant goats and contrast this to the pathology observed in pregnant sheep. Together, our data further support the ongoing development of ChAdOx1 RVF vaccine for use in livestock and humans.
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Affiliation(s)
- Anna Stedman
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF UK
| | - Daniel Wright
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | | | - Madeleine H. A. Clark
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Adrian V. S. Hill
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Sarah C. Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Michael J. Francis
- BioVacc Consulting Ltd, The Red House, 10 Market Square, Amersham, HP7 0DQ UK
| | - Lucien van Keulen
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bryan Charleston
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF UK
| | - George M. Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ UK
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108 Kenya
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35
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Kivisi CA, Muthui M, Hunt M, Fegan G, Otto TD, Githinji G, Warimwe GM, Rance R, Marsh K, Bull PC, Abdi AI. Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy. Front Immunol 2019; 10:2328. [PMID: 31681266 PMCID: PMC6798654 DOI: 10.3389/fimmu.2019.02328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 11/13/2022] Open
Abstract
In sub-Saharan Africa, children below 5 years bear the greatest burden of severe malaria because they lack naturally acquired immunity that develops following repeated exposure to infections by Plasmodium falciparum. Antibodies to the surface of P. falciparum infected erythrocytes (IE) play an important role in this immunity. In children under the age of 6 months, relative protection from severe malaria is observed and this is thought to be partly due to trans-placental acquired protective maternal antibodies. However, the protective effect of maternal antibodies has not been fully established, especially the role of antibodies to variant surface antigens (VSA) expressed on IE. Here, we assessed the immune pressure on parasites infecting infants using markers associated with the acquisition of naturally acquired immunity to surface antigens. We hypothesized that, if maternal antibodies to VSA imposed a selection pressure on parasites, then the expression of a relatively conserved subset of var genes called group A var genes in infants should change with waning maternal antibodies. To test this, we compared their expression in parasites from children between 0 and 12 months and above 12 months of age. The transcript quantity and the proportional expression of group A var subgroup, including those containing domain cassette 13, were positively associated with age during the first year of life, which contrasts with above 12 months. This was accompanied by a decline in infected erythrocyte surface antibodies and an increase in parasitemia during this period. The observed increase in group A var gene expression with age in the first year of life, when the maternal antibodies are waning and before acquisition of naturally acquired antibodies with repeated exposure, is consistent with the idea that maternally acquired antibodies impose a selection pressure on parasites that infect infants and may play a role in protecting these infants against severe malaria.
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Affiliation(s)
- Cheryl A Kivisi
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.,Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | | | - Martin Hunt
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Greg Fegan
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - George M Warimwe
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Richard Rance
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | - Kevin Marsh
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Abdirahman I Abdi
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
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36
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Abstract
Rift Valley fever (RVF) is a mosquito-borne viral zoonosis that was first discovered in Kenya in 1930 and is now endemic throughout multiple African countries and the Arabian Peninsula. RVF virus primarily infects domestic livestock (sheep, goats, cattle) causing high rates of neonatal mortality and abortion, with human infection resulting in a wide variety of clinical outcomes, ranging from self-limiting febrile illness to life-threatening haemorrhagic diatheses, and miscarriage in pregnant women. Since its discovery, RVF has caused many outbreaks in Africa and the Arabian Peninsula with major impacts on human and animal health. However, options for the control of RVF outbreaks are limited by the lack of licensed human vaccines or therapeutics. For this reason, RVF is prioritized by the World Health Organization for urgent research and development of countermeasures for the prevention and control of future outbreaks. In this review, we highlight the current understanding of RVF, including its epidemiology, pathogenesis, clinical manifestations and status of vaccine development.
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Affiliation(s)
- Daniel Wright
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- The Jenner Institute, University of Oxford, Oxford OX1 2JD, UK
| | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Thomas A. Bowden
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford OX1 2JD, UK
| | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX1 2JD, UK
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37
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Tuju J, Mackinnon MJ, Abdi AI, Karanja H, Musyoki JN, Warimwe GM, Gitau EN, Marsh K, Bull PC, Urban BC. Antigenic cartography of immune responses to Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). PLoS Pathog 2019; 15:e1007870. [PMID: 31260501 PMCID: PMC6625739 DOI: 10.1371/journal.ppat.1007870] [Citation(s) in RCA: 5] [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: 01/24/2019] [Revised: 07/12/2019] [Accepted: 05/24/2019] [Indexed: 12/15/2022] Open
Abstract
Naturally acquired clinical immunity to Plasmodium falciparum is partly mediated by antibodies directed at parasite-derived antigens expressed on the surface of red blood cells which mediate disease and are extremely diverse. Unlike children, adults recognize a broad range of variant surface antigens (VSAs) and are protected from severe disease. Though crucial to the design and feasibility of an effective malaria vaccine, it is not yet known whether immunity arises through cumulative exposure to each of many antigenic types, cross-reactivity between antigenic types, or some other mechanism. In this study, we measured plasma antibody responses of 36 children with symptomatic malaria to a diverse panel of 36 recombinant proteins comprising part of the DBLα domain (the 'DBLα-tag') of PfEMP1, a major class of VSAs. We found that although plasma antibody responses were highly specific to individual antigens, serological profiles of responses across antigens fell into one of just two distinct types. One type was found almost exclusively in children that succumbed to severe disease (19 out of 20) while the other occurred in all children with mild disease (16 out of 16). Moreover, children with severe malaria had serological profiles that were narrower in antigen specificity and shorter-lived than those in children with mild malaria. Borrowing a novel technique used in influenza-antigenic cartography-we mapped these dichotomous serological profiles to amino acid sequence variation within a small sub-region of the PfEMP1 DBLα domain. By applying our methodology on a larger scale, it should be possible to identify epitopes responsible for eliciting the protective version of serological profiles to PfEMP1 thereby accelerating development of a broadly effective anti-disease malaria vaccine.
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Affiliation(s)
- James Tuju
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Chemistry and Biochemistry, Pwani University, Kilifi, Kenya
| | | | | | | | | | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Evelyn N. Gitau
- African Population and Health Research Center, Nairobi, Kenya
| | - Kevin Marsh
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Britta C. Urban
- Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Pembroke Place, Liverpool, United Kingdom
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38
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Fedosyuk S, Merritt T, Peralta-Alvarez MP, Morris SJ, Lam A, Laroudie N, Kangokar A, Wright D, Warimwe GM, Angell-Manning P, Ritchie AJ, Gilbert SC, Xenopoulos A, Boumlic A, Douglas AD. Simian adenovirus vector production for early-phase clinical trials: A simple method applicable to multiple serotypes and using entirely disposable product-contact components. Vaccine 2019; 37:6951-6961. [PMID: 31047679 PMCID: PMC6949866 DOI: 10.1016/j.vaccine.2019.04.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 01/04/2019] [Revised: 04/14/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022]
Abstract
A variety of Good Manufacturing Practice (GMP) compliant processes have been reported for production of non-replicating adenovirus vectors, but important challenges remain. Most clinical development of adenovirus vectors now uses simian adenoviruses or rare human serotypes, whereas reported manufacturing processes mainly use serotypes such as AdHu5 which are of questionable relevance for clinical vaccine development. Many clinically relevant vaccine transgenes interfere with adenovirus replication, whereas most reported process development uses selected antigens or even model transgenes such as fluorescent proteins which cause little such interference. Processes are typically developed for a single adenovirus serotype - transgene combination, requiring extensive further optimization for each new vaccine. There is a need for rapid production platforms for small GMP batches of non-replicating adenovirus vectors for early-phase vaccine trials, particularly in preparation for response to emerging pathogen outbreaks. Such platforms must be robust to variation in the transgene, and ideally also capable of producing adenoviruses of more than one serotype. It is also highly desirable for such processes to be readily implemented in new facilities using commercially available single-use materials, avoiding the need for development of bespoke tools or cleaning validation, and for them to be readily scalable for later-stage studies. Here we report the development of such a process, using single-use stirred-tank bioreactors, a transgene-repressing HEK293 cell - promoter combination, and fully single-use filtration and ion exchange components. We demonstrate applicability of the process to candidate vaccines against rabies, malaria and Rift Valley fever, each based on a different adenovirus serotype. We compare performance of a range of commercially available ion exchange media, including what we believe to be the first published use of a novel media for adenovirus purification (NatriFlo® HD-Q, Merck). We demonstrate the need for minimal process individualization for each vaccine, and that the product fulfils regulatory quality expectations. Cell-specific yields are at the upper end of those previously reported in the literature, and volumetric yields are in the range 1 × 1013 - 5 × 1013 purified virus particles per litre of culture, such that a 2-4 L process is comfortably adequate to produce vaccine for early-phase trials. The process is readily transferable to any GMP facility with the capability for mammalian cell culture and aseptic filling of sterile products.
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Affiliation(s)
- Sofiya Fedosyuk
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Thomas Merritt
- Clinical Biomanufacturing Facility, University of Oxford, Roosevelt Drive, Oxford OX3 7JT, UK
| | | | - Susan J Morris
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ada Lam
- Millipore (UK) Ltd. Bedfont Cross, Stanwell Road, TW14 8NX Feltham, UK
| | - Nicolas Laroudie
- Millipore SAS, 39 Route Industrielle de la Hardt, Molsheim 67120, France
| | | | - Daniel Wright
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; KEMRI-Wellcome Trust Research Programme, P.O. 230-80108 Kilifi, Kenya
| | - Phillip Angell-Manning
- Clinical Biomanufacturing Facility, University of Oxford, Roosevelt Drive, Oxford OX3 7JT, UK
| | - Adam J Ritchie
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah C Gilbert
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alex Xenopoulos
- EMD Millipore Corporation, 80 Ashby Road, Bedford, MA 01730, USA
| | - Anissa Boumlic
- Millipore SAS, 39 Route Industrielle de la Hardt, Molsheim 67120, France
| | - Alexander D Douglas
- Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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39
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Kamau E, Agoti CN, Ngoi JM, de Laurent ZR, Gitonga J, Cotten M, Phan MVT, Nokes DJ, Delwart E, Sanders E, Warimwe GM. Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya. Microbiol Resour Announc 2019; 8:e01566-18. [PMID: 30701251 PMCID: PMC6346200 DOI: 10.1128/mra.01566-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue infection remains poorly characterized in Africa and little is known regarding its associated viral genetic diversity. Here, we report dengue virus type 2 (DENV-2) sequence data from 10 clinical samples, including 5 complete genome sequences of the cosmopolitan genotype, obtained from febrile adults seeking outpatient care in coastal Kenya.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joyce M Ngoi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - John Gitonga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matthew Cotten
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences, Zeeman Institute, University of Warwick, Coventry, United Kingdom
| | - Eric Delwart
- Blood Systems Research Institute, University of California, San Francisco, California, USA
| | - Eduard Sanders
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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40
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Warimwe GM, Purushotham J, Perry BD, Hill AV, Gilbert SC, Dungu B, Charleston B. Tackling human and animal health threats through innovative vaccinology in Africa. AAS Open Res 2018; 1:18. [PMID: 32259020 PMCID: PMC7118973 DOI: 10.12688/aasopenres.12877.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 11/14/2018] [Indexed: 07/27/2023] Open
Abstract
Africa bears the brunt of many of the world's most devastating human and animal infectious diseases, a good number of which have no licensed or effective vaccines available. The continent's potential to generate novel interventions against these global health threats is however largely untapped. Strengthening Africa's vaccine research and development (R&D) sector could accelerate discovery, development and deployment of effective countermeasures against locally prevalent infectious diseases, many of which are neglected and have the capacity to spread to new geographical settings. Here, we review Africa's human and veterinary vaccine R&D sectors and identify key areas that should be prioritized for investment, and synergies that could be exploited from Africa's veterinary vaccine industry, which is surprisingly strong and has close parallels with human vaccine R&D.
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Affiliation(s)
- George M. Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- The Pirbright Institute, Woking, GU24 0NF, UK
| | | | - Brian D. Perry
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
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41
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Warimwe GM, Purushotham J, Perry BD, Hill AVS, Gilbert SC, Dungu B, Charleston B. Tackling human and animal health threats through innovative vaccinology in Africa. AAS Open Res 2018; 1:18. [PMID: 32259020 PMCID: PMC7118973 DOI: 10.12688/aasopenres.12877.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 11/14/2018] [Indexed: 11/20/2022] Open
Abstract
Africa bears the brunt of many of the world's most devastating human and animal infectious diseases, a good number of which have no licensed or effective vaccines available. The continent's potential to generate novel interventions against these global health threats is however largely untapped. Strengthening Africa's vaccine research and development (R&D) sector could accelerate discovery, development and deployment of effective countermeasures against locally prevalent infectious diseases, many of which are neglected and have the capacity to spread to new geographical settings. Here, we review Africa's human and veterinary vaccine R&D sectors and identify key areas that should be prioritized for investment, and synergies that could be exploited from Africa's veterinary vaccine industry, which is surprisingly strong and has close parallels with human vaccine R&D.
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Affiliation(s)
- George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,The Pirbright Institute, Woking, GU24 0NF, UK
| | | | - Brian D Perry
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | - Adrian V S Hill
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sarah C Gilbert
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
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Clark MHA, Warimwe GM, Di Nardo A, Lyons NA, Gubbins S. Systematic literature review of Rift Valley fever virus seroprevalence in livestock, wildlife and humans in Africa from 1968 to 2016. PLoS Negl Trop Dis 2018; 12:e0006627. [PMID: 30036382 PMCID: PMC6072204 DOI: 10.1371/journal.pntd.0006627] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [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: 10/09/2017] [Revised: 08/02/2018] [Accepted: 06/22/2018] [Indexed: 02/03/2023] Open
Abstract
Background Rift Valley fever virus (RVFV) is a zoonotic arbovirus that causes severe disease in livestock and humans. The virus has caused recurrent outbreaks in Africa and the Arabian Peninsula since its discovery in 1931. This review sought to evaluate RVFV seroprevalence across the African continent in livestock, wildlife and humans in order to understand the spatio-temporal distribution of RVFV seroprevalence and to identify knowledge gaps and areas requiring further research. Risk factors associated with seropositivity were identified and study designs evaluated to understand the validity of their results. Methodology The Preferred Reporting of Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were used to produce a protocol to systematically search for RVFV seroprevalence studies in PubMed and Web of Science databases. The Strengthening the Reporting of Observational studies in Epidemiology (STROBE) statement guided the evaluation of study design and analyses. Principal findings A total of 174 RVFV seroprevalence studies in 126 articles fulfilled the inclusion criteria. RVFV seroprevalence was recorded in 31 African countries from 1968 to 2016 and varied by time, species and country. RVFV seroprevalence articles including either livestock and humans or livestock and wildlife seroprevalence records were limited in number (8/126). No articles considered wildlife, livestock and human seroprevalence concurrently, nor wildlife and humans alone. Many studies did not account for study design bias or the sensitivity and specificity of diagnostic tests. Conclusions Future research should focus on conducting seroprevalence studies at the wildlife, livestock and human interface to better understand the nature of cross-species transmission of RVFV. Reporting should be more transparent and biases accounted for in future seroprevalence research to understand the true burden of disease on the African continent. Rift Valley fever virus (RVFV) is a vector-borne virus that infects wildlife and livestock, and can subsequently spread to humans. Due to the nature of the disease it has the potential to cause substantial economic and public health impacts. Rift Valley Fever (RVF) has been identified in Africa and the Arabian Peninsula, but has the potential to spread more widely. This systematic review assessed the distribution of RVF in livestock and humans in Africa by collating all the relevant studies we could find, extracting the data and critically evaluating them. Understanding when and where RVF has occurred in Africa and why some animals and humans get disease helps target control strategies and, in particular, those that reduce spread from livestock to humans. Furthermore, by evaluating past studies we can ensure that future ones are more robust and reproducible, so they can help us better understand the disease.
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Affiliation(s)
- Madeleine H. A. Clark
- Transmission Biology Group, The Pirbright Institute, Pirbright, Woking, United Kingdom
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - George M. Warimwe
- Biosciences Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Antonello Di Nardo
- Vesicular Disease Reference Laboratories, The Pirbright Institute, Pirbright, Woking, United Kingdom
| | - Nicholas A. Lyons
- Vesicular Disease Reference Laboratories, The Pirbright Institute, Pirbright, Woking, United Kingdom
| | - Simon Gubbins
- Transmission Biology Group, The Pirbright Institute, Pirbright, Woking, United Kingdom
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Abstract
Replication-deficient adenoviruses are potent vaccine development platforms used extensively for human and animal candidate vaccines, largely due to their very good safety and immunogenicity profile. In this chapter we describe a method that can be used in any laboratory for the scalable production of replication-deficient adenovirus vector vaccines to GLP for preclinical studies in animal models, including definitive experimental studies in large target animal species for veterinary applications. We use human adenovirus serotype 5 (HAdV5) as an example, but the method can be easily adapted for use with other adenovirus serotypes from different species of origin.
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Affiliation(s)
- Susan J Morris
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| | - Alison V Turner
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nicola Green
- The Clinical Biomanufacturing Facility, University of Oxford, Churchill Drive, Headington, Oxford, OX3 7JT, UK
| | - George M Warimwe
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
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Lorenzo G, López-Gil E, Warimwe GM, Brun A. Understanding Rift Valley fever: contributions of animal models to disease characterization and control. Mol Immunol 2015; 66:78-88. [PMID: 25725948 DOI: 10.1016/j.molimm.2015.02.001] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 12/26/2014] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
Abstract
Rift Valley fever (RVF) is a mosquito-borne viral zoonosis with devastating health impacts in domestic ruminants and humans. Effective vaccines and accurate disease diagnostic tools are key components in the control of RVF. Animal models reproducing infection with RVF virus are of upmost importance in the development of these disease control tools. Rodent infection models are currently used in the initial steps of vaccine development and for the study of virus induced pathology. Translation of data obtained in these animal models to target species (ruminants and humans) is highly desirable but does not always occur. Small ruminants and non-human primates have been used for pathogenesis and transmission studies, and for testing the efficacy of vaccines and therapeutic antiviral compounds. However, the molecular mechanisms of the immune response elicited by RVF virus infection or vaccination are still poorly understood. The paucity of data in this area offers opportunities for new research activities and programs. This review summarizes our current understanding with respect to immunity and pathogenesis of RVF in animal models with a particular emphasis on small ruminants and non-human primates, including recent experimental infection data in sheep.
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Affiliation(s)
- Gema Lorenzo
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación Agraria y Alimentaria (INIA-CISA), Valdeolmos, Madrid, Spain
| | - Elena López-Gil
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación Agraria y Alimentaria (INIA-CISA), Valdeolmos, Madrid, Spain
| | - George M Warimwe
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación Agraria y Alimentaria (INIA-CISA), Valdeolmos, Madrid, Spain.
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Warimwe GM, Fegan G, Kiragu EW, Musyoki JN, Macharia AW, Marsh K, Williams TN, Bull PC. An assessment of the impact of host polymorphisms on Plasmodium falciparum var gene expression patterns among Kenyan children. BMC Infect Dis 2014; 14:524. [PMID: 25267261 PMCID: PMC4262213 DOI: 10.1186/1471-2334-14-524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 09/24/2014] [Indexed: 11/16/2022] Open
Abstract
Background Host genotype accounts for a component of the variability in susceptibility to childhood Plasmodium falciparum malaria. However, despite numerous examples of host polymorphisms associated with tolerance or resistance to infection, direct evidence for an impact of host genetic polymorphisms on the in vivo parasite population is difficult to obtain. Parasite molecules whose expression is most likely to be associated with such adaptation are those that are directly involved in the host-parasite interaction. A prime candidate is the family of parasite var gene-encoded molecules on P. falciparum-infected erythrocytes, PfEMP1, which binds various host molecules and facilitates parasite sequestration in host tissues to avoid clearance by the spleen. Methods To assess the impact of host genotype on the infecting parasite population we used a published parasite var gene sequence dataset to compare var gene expression patterns between parasites from children with polymorphisms in molecules thought to interact with or modulate display of PfEMP1 on the infected erythrocyte surface: ABO blood group, haemoglobin S, alpha-thalassaemia, the T188G polymorphism of CD36 and the K29M polymorphism of ICAM1. Results Expression levels of ‘group A-like’ var genes, which encode a specific group of PfEMP1 variants previously associated with low host immunity and severe malaria, showed signs of elevation among children of blood group AB. No other host factor tested showed evidence for an association with var expression. Conclusions Our preliminary findings suggest that host ABO blood group may have a measurable impact on the infecting parasite population. This needs to be verified in larger studies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-524) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.
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Abdi AI, Fegan G, Muthui M, Kiragu E, Musyoki JN, Opiyo M, Marsh K, Warimwe GM, Bull PC. Plasmodium falciparum antigenic variation: relationships between widespread endothelial activation, parasite PfEMP1 expression and severe malaria. BMC Infect Dis 2014; 14:170. [PMID: 24674301 PMCID: PMC3986854 DOI: 10.1186/1471-2334-14-170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 03/19/2014] [Indexed: 12/01/2022] Open
Abstract
Background Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) is a family of variant surface antigens (VSA) that mediate the adhesion of parasite infected erythrocytes to capillary endothelial cells within host tissues. Opinion is divided over the role of PfEMP1 in the widespread endothelial activation associated with severe malaria. In a previous study we found evidence for differential associations between defined VSA subsets and specific syndromes of severe malaria: group A-like PfEMP1 expression and the “rosetting” phenotype were associated with impaired consciousness and respiratory distress, respectively. This study explores the involvement of widespread endothelial activation in these associations. Methods We used plasma angiopoietin-2 as a marker of widespread endothelial activation. Using logistic regression analysis, we explored the relationships between plasma angiopoietin-2 levels, parasite VSA expression and the two syndromes of severe malaria, impaired consciousness and respiratory distress. Results Plasma angiopoietin-2 was associated with both syndromes. The rosetting phenotype did not show an independent association with respiratory distress when adjusted for angiopoietin-2, consistent with a single pathogenic mechanism involving widespread endothelial activation. In contrast, group A-like PfEMP1 expression and angiopoietin-2 maintained independent associations with impaired consciousness when adjusted for each other. Conclusion The results are consistent with multiple pathogenic mechanisms leading to severe malaria and heterogeneity in the pathophysiology of impaired consciousness. The observed association between group A-like PfEMP1 and impaired consciousness does not appear to involve widespread endothelial activation.
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Affiliation(s)
- Abdirahman I Abdi
- KEMRI-Wellcome Trust Research Programme, P,O, Box 230-80108, Kilifi, Kenya.
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Warimwe GM, Lorenzo G, Lopez-Gil E, Reyes-Sandoval A, Cottingham MG, Spencer AJ, Collins KA, Dicks MDJ, Milicic A, Lall A, Furze J, Turner AV, Hill AVS, Brun A, Gilbert SC. Immunogenicity and efficacy of a chimpanzee adenovirus-vectored Rift Valley fever vaccine in mice. Virol J 2013; 10:349. [PMID: 24304565 PMCID: PMC4235025 DOI: 10.1186/1743-422x-10-349] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/29/2013] [Indexed: 02/07/2023] Open
Abstract
Background Rift Valley Fever (RVF) is a viral zoonosis that historically affects livestock production and human health in sub-Saharan Africa, though epizootics have also occurred in the Arabian Peninsula. Whilst an effective live-attenuated vaccine is available for livestock, there is currently no licensed human RVF vaccine. Replication-deficient chimpanzee adenovirus (ChAd) vectors are an ideal platform for development of a human RVF vaccine, given the low prevalence of neutralizing antibodies against them in the human population, and their excellent safety and immunogenicity profile in human clinical trials of vaccines against a wide range of pathogens. Methods Here, in BALB/c mice, we evaluated the immunogenicity and efficacy of a replication-deficient chimpanzee adenovirus vector, ChAdOx1, encoding the RVF virus envelope glycoproteins, Gn and Gc, which are targets of virus neutralizing antibodies. The ChAdOx1-GnGc vaccine was assessed in comparison to a replication-deficient human adenovirus type 5 vector encoding Gn and Gc (HAdV5-GnGc), a strategy previously shown to confer protective immunity against RVF in mice. Results A single immunization with either of the vaccines conferred protection against RVF virus challenge eight weeks post-immunization. Both vaccines elicited RVF virus neutralizing antibody and a robust CD8+ T cell response. Conclusions Together the results support further development of RVF vaccines based on replication-deficient adenovirus vectors, with ChAdOx1-GnGc being a potential candidate for use in future human clinical trials.
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Naranbhai V, Hill AVS, Abdool Karim SS, Naidoo K, Abdool Karim Q, Warimwe GM, McShane H, Fletcher H. Ratio of monocytes to lymphocytes in peripheral blood identifies adults at risk of incident tuberculosis among HIV-infected adults initiating antiretroviral therapy. J Infect Dis 2013; 209:500-9. [PMID: 24041796 PMCID: PMC3903371 DOI: 10.1093/infdis/jit494] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [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] [Indexed: 12/13/2022] Open
Abstract
Background. Eight decades ago, the ratio of monocytes to lymphocytes (hereafter, the “ML ratio”) was noted to affect outcomes of mycobacterial infection in rabbits. Recent transcriptomic studies support a role for relative proportions of myeloid and lymphoid transcripts in tuberculosis outcomes. The ML ratio in peripheral blood is known to be governed by hematopoietic stem cells with distinct biases. Methods. The predictive value of the baseline ML ratio was modeled in 2 prospective cohorts of HIV-infected adults starting cART in South Africa (primary cohort, 1862 participants; replication cohort, 345 participants). Incident tuberculosis was diagnosed with clinical, radiographic, and microbiologic methods per contemporary guidelines. Kaplan-Meier survival analyses and Cox proportional hazards modeling were conducted. Results. The incidence rate of tuberculosis differed significantly by baseline ML ratio: 32.61 (95% confidence interval [CI], 15.38–61.54), 16.36 (95% CI, 12.39–21.23), and 51.80 (95% CI, 23.10–101.71) per 1000 patient-years for ML ratios of less than the 5th percentile, between the 5th and 95th percentiles, and greater than the 95th percentile, respectively (P = .007). Neither monocyte counts nor lymphocyte counts alone were associated with tuberculosis. After adjustment for sex, World Health Organization human immunodeficiency virus disease stage, CD4+ T-cell counts, and previous history of tuberculosis, hazards of disease were significantly higher for patients with ML ratios of less than the 5th percentile or greater than the 95th percentile (adjusted hazard ratio, 2.47; 95% CI, 1.39–4.40; P = .002). Conclusions. The ML ratio may be a useful, readily available tool to stratify the risk of tuberculosis and suggests involvement of hematopoietic stem cell bias in tuberculosis pathogenesis.
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Warimwe GM, Fletcher HA, Olotu A, Agnandji ST, Hill AVS, Marsh K, Bejon P. Peripheral blood monocyte-to-lymphocyte ratio at study enrollment predicts efficacy of the RTS,S malaria vaccine: analysis of pooled phase II clinical trial data. BMC Med 2013; 11:184. [PMID: 23962071 PMCID: PMC3765422 DOI: 10.1186/1741-7015-11-184] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RTS,S is the most advanced candidate malaria vaccine but it is only partially protective and the causes of inter-individual variation in efficacy are poorly understood. Here, we investigated whether peripheral blood monocyte-to-lymphocyte ratios (ML ratio), previously shown to correlate with clinical malaria risk, could account for differences in RTS,S efficacy among phase II trial participants in Africa. METHODS Of 11 geographical sites where RTS,S has been evaluated, pre-vaccination ML ratios were only available for trial participants in Kilifi, Kenya (N = 421) and Lambarene, Gabon (N = 189). Using time to first clinical malaria episode as the primary endpoint we evaluated the effect of accounting for ML ratio on RTS,S vaccine efficacy against clinical malaria by Cox regression modeling. RESULTS The unadjusted efficacy of RTS,S in this combined dataset was 47% (95% confidence interval (CI) 26% to 62%, P <0.001). However, RTS,S efficacy decreased with increasing ML ratio, ranging from 67% (95% CI 64% to 70%) at an ML ratio of 0.1 to 5% (95% CI -3% to 13%) at an ML ratio of 0.6. The statistical interaction between RTS,S vaccination and ML ratio was still evident after adjustment for covariates associated with clinical malaria risk in this dataset. CONCLUSION The results suggest that stratification of study participants by ML ratio, easily measured from full differential blood counts before vaccination, might help identify children who are highly protected and those that are refractory to protection with the RTS,S vaccine. Identifying causes of low vaccine efficacy among individuals with high ML ratio could inform strategies to improve overall RTS,S vaccine efficacy. TRIAL REGISTRATION ClinicalTrials.Gov numbers NCT00380393 and NCT00436007.
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Affiliation(s)
- George M Warimwe
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom.
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Warimwe GM, Recker M, Kiragu EW, Buckee CO, Wambua J, Musyoki JN, Marsh K, Bull PC. Plasmodium falciparum var gene expression homogeneity as a marker of the host-parasite relationship under different levels of naturally acquired immunity to malaria. PLoS One 2013; 8:e70467. [PMID: 23922996 PMCID: PMC3726600 DOI: 10.1371/journal.pone.0070467] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 04/12/2013] [Accepted: 06/19/2013] [Indexed: 11/19/2022] Open
Abstract
Acquired immunity to Plasmodium falciparum infection causes a change from frequent, sometimes life-threatening, malaria in young children to asymptomatic, chronic infections in older children and adults. Little is known about how this transition occurs but antibodies to the extremely diverse PfEMP1 parasite antigens are thought to play a role. PfEMP1 is encoded by a family of 60 var genes that undergo clonal antigenic variation, potentially creating an antigenically heterogeneous infecting population of parasites within the host. Previous theoretical work suggests that antibodies to PfEMP1 may play a role in "orchestrating" their expression within infections leading to sequential, homogeneous expression of var genes, and prolonged infection chronicity. Here, using a cloning and sequencing approach we compare the var expression homogeneity (VEH) between isolates from children with asymptomatic and clinical infections. We show that asymptomatic infections have higher VEH than clinical infections and a broader host antibody response. We discuss this in relation to the potential role of host antibodies in promoting chronicity of infection and parasite survival through the low transmission season.
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Affiliation(s)
- George M. Warimwe
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Mario Recker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Esther W. Kiragu
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Caroline O. Buckee
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Juliana Wambua
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Jennifer N. Musyoki
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kevin Marsh
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter C. Bull
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
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