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Otiende M, Nyaguara A, Bottomley C, Walumbe D, Mochamah G, Amadi D, Nyundo C, Kagucia EW, Etyang AO, Adetifa IMO, Brand SPC, Maitha E, Chondo E, Nzomo E, Aman R, Mwangangi M, Amoth P, Kasera K, Ng'ang'a W, Barasa E, Tsofa B, Mwangangi J, Bejon P, Agweyu A, Williams TN, Scott JAG. Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study. Nat Commun 2023; 14:6879. [PMID: 37898630 PMCID: PMC10613220 DOI: 10.1038/s41467-023-42615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
The mortality impact of COVID-19 in Africa remains controversial because most countries lack vital registration. We analysed excess mortality in Kilifi Health and Demographic Surveillance System, Kenya, using 9 years of baseline data. SARS-CoV-2 seroprevalence studies suggest most adults here were infected before May 2022. During 5 waves of COVID-19 (April 2020-May 2022) an overall excess mortality of 4.8% (95% PI 1.2%, 9.4%) concealed a significant excess (11.6%, 95% PI 5.9%, 18.9%) among older adults ( ≥ 65 years) and a deficit among children aged 1-14 years (-7.7%, 95% PI -20.9%, 6.9%). The excess mortality rate for January 2020-December 2021, age-standardised to the Kenyan population, was 27.4/100,000 person-years (95% CI 23.2-31.6). In Coastal Kenya, excess mortality during the pandemic was substantially lower than in most high-income countries but the significant excess mortality in older adults emphasizes the value of achieving high vaccine coverage in this risk group.
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Affiliation(s)
- M Otiende
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya.
| | - A Nyaguara
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - C Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
| | - D Walumbe
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - G Mochamah
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - D Amadi
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - C Nyundo
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - E W Kagucia
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - A O Etyang
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - I M O Adetifa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
| | - S P C Brand
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4 7AL, UK
| | - E Maitha
- Department of Health, Kilifi County, Kilifi, Kenya
| | - E Chondo
- Department of Health, Kilifi County, Kilifi, Kenya
| | - E Nzomo
- Kilifi County Hospital, Kilifi, Kenya
| | - R Aman
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - M Mwangangi
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - P Amoth
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - K Kasera
- Ministry of Health, Government of Kenya; Afya House, Cathedral Road, Nairobi, Kenya
| | - W Ng'ang'a
- Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya
| | - E Barasa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - B Tsofa
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - J Mwangangi
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - P Bejon
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7BN, UK
| | - A Agweyu
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
| | - T N Williams
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Institute for Global Health Innovation, Imperial College, London, SW72AS, UK
| | - J A G Scott
- KEMRI-Wellcome Research Trust Programme, PO Box 230, Kilifi, 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street London, London, WC1E 7HT, UK
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Kwambana-Adams BA, Clark SA, Tay N, Agbla S, Chaguza C, Kagucia EW, Borrow R, Heyderman RS. Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease. Int J Mol Sci 2022; 23:ijms231911879. [PMID: 36233182 PMCID: PMC9569512 DOI: 10.3390/ijms231911879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
To improve the storage and transport of clinical specimens for the diagnosis of Neisseria meningitidis (Nm) infections in resource-limited settings, we have evaluated the performance of dried blood spot (DBS) and dried cerebrospinal fluid spot (DCS) assays. DBS and DCS were prepared on filter paper from liquid specimens previously tested for Nm in the United Kingdom. Nm was detected and genogrouped by real-time PCR performed on crude genomic DNA extracted from the DBS (n = 226) and DCS (n = 226) specimens. Targeted whole-genome sequencing was performed on a subset of specimens, DBS (n = 4) and DCS (n = 6). The overall agreement between the analysis of liquid and dried specimens was (94.2%; 95% CI 90.8−96.7) for blood and (96.4%; 95% CI 93.5−98.0) for cerebrospinal fluid. Relative to liquid specimens as the reference, the DBS and DCS assays had sensitivities of (89.1%; 95% CI 82.7−93.8) and (94.2%; 95% CI 88.9−97.5), respectively, and both assays had specificities above 98%. A genogroup was identified by dried specimen analysis for 81.9% of the confirmed meningococcal infections. Near full-length Nm genome sequences (>86%) were obtained for all ten specimens tested which allowed determination of the sequence type, clonal complex, presence of antimicrobial resistance and other meningococcal genotyping. Dried blood and CSF filter spot assays offer a practical alternative to liquid specimens for the molecular and genomic characterisation of invasive meningococcal diseases in low-resource settings.
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Affiliation(s)
- Brenda A. Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Malawi-Liverpool-Wellcome Clinical Research Programme (MLW), Blantyre P.O. Box 30096, Malawi
- Correspondence: (B.A.K.-A.); (S.A.C.)
| | - Stephen A. Clark
- Meningococcal Reference Unit, United Kingdom Health Security Agency (UKHSA), Manchester M13 9WL, UK
- Correspondence: (B.A.K.-A.); (S.A.C.)
| | - Nicole Tay
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Schadrac Agbla
- Department of Health Data Science, University of Liverpool, Liverpool L69 3GF, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Chrispin Chaguza
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Eunice W. Kagucia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi P.O. Box 230-8010, Kenya
| | - Ray Borrow
- Meningococcal Reference Unit, United Kingdom Health Security Agency (UKHSA), Manchester M13 9WL, UK
| | - Robert S. Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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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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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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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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6
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Bennett JC, Hetrich MK, Garcia Quesada M, Sinkevitch JN, Deloria Knoll M, Feikin DR, Zeger SL, Kagucia EW, Cohen AL, Ampofo K, Brandileone MCC, Bruden D, Camilli R, Castilla J, Chan G, Cook H, Cornick JE, Dagan R, Dalby T, Danis K, de Miguel S, De Wals P, Desmet S, Georgakopoulou T, Gilkison C, Grgic-Vitek M, Hammitt LL, Hilty M, Ho PL, Jayasinghe S, Kellner JD, Kleynhans J, Knol MJ, Kozakova J, Kristinsson KG, Ladhani SN, MacDonald L, Mackenzie GA, Mad’arová L, McGeer A, Mereckiene J, Morfeldt E, Mungun T, Muñoz-Almagro C, Nuorti JP, Paragi M, Pilishvili T, Puentes R, Saha SK, Sahu Khan A, Savrasova L, Scott JA, Skoczyńska A, Suga S, van der Linden M, Verani JR, von Gottberg A, Winje BA, Yildirim I, Zerouali K, Hayford K. Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project. Microorganisms 2021; 9:microorganisms9040696. [PMID: 33801760 PMCID: PMC8066231 DOI: 10.3390/microorganisms9040696] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04–0.06) for all ages, 0.05 (0.04–0.05) for <5 years of age, 0.08 (0.06–0.09) for 5–17 years, 0.06 (0.05–0.08) for 18–49 years, 0.06 (0.05–0.07) for 50–64 years, and 0.05 (0.04–0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3 + 0 schedule constrains generalizability and data from these settings are needed.
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Affiliation(s)
- Julia C. Bennett
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- Correspondence: (J.C.B.); (M.D.K.)
| | - Marissa K. Hetrich
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Maria Garcia Quesada
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Jenna N. Sinkevitch
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Maria Deloria Knoll
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- Correspondence: (J.C.B.); (M.D.K.)
| | | | - Scott L. Zeger
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Eunice W. Kagucia
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Adam L. Cohen
- World Health Organization, 1202 Geneva, Switzerland;
| | - Krow Ampofo
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA;
| | - Maria-Cristina C. Brandileone
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo 01246-902, Brazil;
| | - Dana Bruden
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Anchorage, AK 99508, USA;
| | - Romina Camilli
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), 00161 Rome, Italy;
| | - Jesús Castilla
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.C.); (C.M.-A.)
- Instituto de Salud Pública de Navarra—IdiSNA, 31003 Pamplona, Navarra, Spain
| | - Guanhao Chan
- Singapore Ministry of Health, Communicable Diseases Division, Singapore 308442, Singapore;
| | - Heather Cook
- Centre for Disease Control, Department of Health and Community Services, Darwin, NT 8000, Australia;
| | - Jennifer E. Cornick
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK;
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, P.O. Box 30096 Blantyre, Malawi
| | - Ron Dagan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | - Tine Dalby
- Bacteria, Parasites and Fungi, Statens Serum Institut, DK-2300 Copenhagen, Denmark;
| | - Kostas Danis
- Santé Publique France, the French National Public Health Agency, Saint Maurice CEDEX, 94415 Paris, France;
| | - Sara de Miguel
- Epidemiology Department, Dirección General de Salud Pública, 28009 Madrid, Spain;
| | - Philippe De Wals
- Department of Social and Preventive Medicine, Laval University, Québec, QC G1V 0A6, Canada;
| | - Stefanie Desmet
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium;
- National Reference Centre for Streptococcus Pneumoniae, University Hospitals Leuven, 3000 Leuven, Belgium
| | | | - Charlotte Gilkison
- Epidemiology Team, Institute of Environmental Science and Research, Porirua, Wellington 5240, New Zealand;
| | - Marta Grgic-Vitek
- Communicable Diseases Centre, National Institute of Public Health, 1000 Ljubljana, Slovenia;
| | - Laura L. Hammitt
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Markus Hilty
- Swiss National Reference Centre for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland;
| | - Pak-Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China;
| | - Sanjay Jayasinghe
- National Centre for Immunisation Research and Surveillance and Discipline of Child and Adolescent Health, Children’s Hospital Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia;
| | - James D. Kellner
- Department of Pediatrics, University of Calgary, and Alberta Health Services, Calgary, AB T3B 6A8, Canada;
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (J.K.); (A.v.G.)
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Mirjam J. Knol
- National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands;
| | - Jana Kozakova
- National Institute of Public Health (NIPH), 100 42 Praha, Czech Republic;
| | - Karl G. Kristinsson
- Department of Clinical Microbiology, Landspitali—The National University Hospital, Hringbraut, 101 Reykjavik, Iceland;
| | - Shamez N. Ladhani
- Immunisation and Countermeasures Division, Public Health England, London NW9 5EQ, UK;
| | | | - Grant A. Mackenzie
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London WC1E 7HT, UK;
- Medical Research Council Unit the Gambia at London School of Hygiene & Tropical Medicine, P.O. Box 273 Banjul, The Gambia
- New Vaccines Group, Murdoch Children’s Research Institute, Parkville, Melbourne, VIC 3052, Australia
| | - Lucia Mad’arová
- National Reference Centre for Pneumococcal and Haemophilus Diseases, Regional Authority of Public Health, 975 56 Banská Bystrica, Slovakia;
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Jolita Mereckiene
- HSE Health Protection Surveillance Centre, Mountjoy, Dublin D01 A4A3, Ireland;
| | - Eva Morfeldt
- Department of Microbiology, Public Health Agency of Sweden, 171 82 Solna, Sweden;
| | - Tuya Mungun
- National Center of Communicable Diseases (NCCD), Ministry of Health, Bayanzurkh District, Ulaanbaatar 13336, Mongolia;
| | - Carmen Muñoz-Almagro
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.C.); (C.M.-A.)
- Medicine Department, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
- Molecular Microbiology Department, Hospital Sant Joan de Déu Research Institute, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - J. Pekka Nuorti
- Department of Health Security, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland;
- Health Sciences Unit, Faculty of Social Sciences, University of Tampere, 33100 Tampere, Finland
| | - Metka Paragi
- Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, 2000 Maribor, Slovenia;
| | - Tamara Pilishvili
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (T.P.); (J.R.V.)
| | - Rodrigo Puentes
- Instituto de Salud Pública de Chile, Santiago 7780050, Santiago Metropolitan, Chile;
| | - Samir K. Saha
- Child Health Research Foundation, Dhaka 1207, Bangladesh;
| | | | - Larisa Savrasova
- Centre for Disease Prevention and Control of Latvia, 1005 Riga, Latvia;
- Doctoral Studies Department, Riga Stradinš University, 1007 Riga, Latvia
| | - J. Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Shigeru Suga
- Infectious Disease Center and Department of Clinical Research, National Hospital Organization Mie Hospital, Tsu, Mie 514-0125, Japan;
| | - Mark van der Linden
- National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, 52074 Aachen, Germany;
| | - Jennifer R. Verani
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (T.P.); (J.R.V.)
- Centers for Disease Control and Prevention (CDC), Center for Global Health (CGH), Division of Global Health Protection (DGHP), P.O. Box 606-00621 Nairobi, Kenya
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (J.K.); (A.v.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa
| | - Brita A. Winje
- Department of Infection Control and Vaccine, Norwegian Institute of Public Health, 0456 Oslo, Norway;
| | - Inci Yildirim
- Department of Pediatrics, Yale New Haven Children’s Hospital, New Haven, CT 06504, USA;
| | - Khalid Zerouali
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca 20250, Morocco;
- Department of Microbiology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca 20000, Morocco
| | - Kyla Hayford
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
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7
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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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8
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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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9
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Gibson DG, Ochieng B, Kagucia EW, Obor D, Odhiambo F, O’Brien KL, Feikin DR. Individual level determinants for not receiving immunization, receiving immunization with delay, and being severely underimmunized among rural western Kenyan children. Vaccine 2015; 33:6778-85. [DOI: 10.1016/j.vaccine.2015.10.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/22/2015] [Accepted: 10/06/2015] [Indexed: 11/15/2022]
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Feikin DR, Kagucia EW, Loo JD, Link-Gelles R, Puhan MA, Cherian T, Levine OS, Whitney CG, O’Brien KL, Moore MR. Serotype-specific changes in invasive pneumococcal disease after pneumococcal conjugate vaccine introduction: a pooled analysis of multiple surveillance sites. PLoS Med 2013; 10:e1001517. [PMID: 24086113 PMCID: PMC3782411 DOI: 10.1371/journal.pmed.1001517] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/12/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Vaccine-serotype (VT) invasive pneumococcal disease (IPD) rates declined substantially following introduction of 7-valent pneumococcal conjugate vaccine (PCV7) into national immunization programs. Increases in non-vaccine-serotype (NVT) IPD rates occurred in some sites, presumably representing serotype replacement. We used a standardized approach to describe serotype-specific IPD changes among multiple sites after PCV7 introduction. METHODS AND FINDINGS Of 32 IPD surveillance datasets received, we identified 21 eligible databases with rate data ≥ 2 years before and ≥ 1 year after PCV7 introduction. Expected annual rates of IPD absent PCV7 introduction were estimated by extrapolation using either Poisson regression modeling of pre-PCV7 rates or averaging pre-PCV7 rates. To estimate whether changes in rates had occurred following PCV7 introduction, we calculated site specific rate ratios by dividing observed by expected IPD rates for each post-PCV7 year. We calculated summary rate ratios (RRs) using random effects meta-analysis. For children <5 years old, overall IPD decreased by year 1 post-PCV7 (RR 0.55, 95% CI 0.46-0.65) and remained relatively stable through year 7 (RR 0.49, 95% CI 0.35-0.68). Point estimates for VT IPD decreased annually through year 7 (RR 0.03, 95% CI 0.01-0.10), while NVT IPD increased (year 7 RR 2.81, 95% CI 2.12-3.71). Among adults, decreases in overall IPD also occurred but were smaller and more variable by site than among children. At year 7 after introduction, significant reductions were observed (18-49 year-olds [RR 0.52, 95% CI 0.29-0.91], 50-64 year-olds [RR 0.84, 95% CI 0.77-0.93], and ≥ 65 year-olds [RR 0.74, 95% CI 0.58-0.95]). CONCLUSIONS Consistent and significant decreases in both overall and VT IPD in children occurred quickly and were sustained for 7 years after PCV7 introduction, supporting use of PCVs. Increases in NVT IPD occurred in most sites, with variable magnitude. These findings may not represent the experience in low-income countries or the effects after introduction of higher valency PCVs. High-quality, population-based surveillance of serotype-specific IPD rates is needed to monitor vaccine impact as more countries, including low-income countries, introduce PCVs and as higher valency PCVs are used. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Daniel R. Feikin
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- National Center for Emerging and Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Eunice W. Kagucia
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jennifer D. Loo
- Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ruth Link-Gelles
- Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Milo A. Puhan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Thomas Cherian
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland
| | - Orin S. Levine
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Cynthia G. Whitney
- Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Katherine L. O’Brien
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Matthew R. Moore
- Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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