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Owuor DC, de Laurent ZR, Kikwai GK, Mayieka LM, Ochieng M, Müller NF, Otieno NA, Emukule GO, Hunsperger EA, Garten R, Barnes JR, Chaves SS, Nokes DJ, Agoti CN. Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018. Viruses 2021; 13:1956. [PMID: 34696386 PMCID: PMC8539974 DOI: 10.3390/v13101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.
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Affiliation(s)
- D. Collins Owuor
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Zaydah R. de Laurent
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Gilbert K. Kikwai
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Lillian M. Mayieka
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Melvin Ochieng
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Nicola F. Müller
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA;
| | - Nancy A. Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Gideon O. Emukule
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
| | - Elizabeth A. Hunsperger
- Centers for Disease Control and Prevention, Division of Global Health Protection, Nairobi 606-00621, Kenya;
- Centers for Disease Control and Prevention, Division of Global Health Protection, Atlanta, GA 30333, USA
| | - Rebecca Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - John R. Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - Sandra S. Chaves
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - D. James Nokes
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Public Health and Human Sciences, Pwani University, Kilifi 195-80108, Kenya
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Spatial clustering of livestock Anthrax events associated with agro-ecological zones in Kenya, 1957-2017. BMC Infect Dis 2021; 21:191. [PMID: 33602160 PMCID: PMC7890876 DOI: 10.1186/s12879-021-05871-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background Developing disease risk maps for priority endemic and episodic diseases is becoming increasingly important for more effective disease management, particularly in resource limited countries. For endemic and easily diagnosed diseases such as anthrax, using historical data to identify hotspots and start to define ecological risk factors of its occurrence is a plausible approach. Using 666 livestock anthrax events reported in Kenya over 60 years (1957–2017), we determined the temporal and spatial patterns of the disease as a step towards identifying and characterizing anthrax hotspots in the region. Methods Data were initially aggregated by administrative unit and later analyzed by agro-ecological zones (AEZ) to reveal anthrax spatio-temporal trends and patterns. Variations in the occurrence of anthrax events were estimated by fitting Poisson generalized linear mixed-effects models to the data with AEZs and calendar months as fixed effects and sub-counties as random effects. Results The country reported approximately 10 anthrax events annually, with the number increasing to as many as 50 annually by the year 2005. Spatial classification of the events in eight counties that reported the highest numbers revealed spatial clustering in certain administrative sub-counties, with 12% of the sub-counties responsible for over 30% of anthrax events, whereas 36% did not report any anthrax disease over the 60-year period. When segregated by AEZs, there was significantly greater risk of anthrax disease occurring in agro-alpine, high, and medium potential AEZs when compared to the agriculturally low potential arid and semi-arid AEZs of the country (p < 0.05). Interestingly, cattle were > 10 times more likely to be infected by B. anthracis than sheep, goats, or camels. There was lower risk of anthrax events in August (P = 0.034) and December (P = 0.061), months that follow long and short rain periods, respectively. Conclusion Taken together, these findings suggest existence of certain geographic, ecological, and demographic risk factors that promote B. anthracis persistence and trasmission in the disease hotspots.
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Ambrozaitis A, Radzišauskienė D, Žagminas K, Kuprevičienė N, Gravenstein S, Jančorienė L. Influenza A(H1N1)pdm09 and postpandemic influenza in Lithuania. Open Med (Wars) 2016; 11:341-353. [PMID: 28352819 PMCID: PMC5329851 DOI: 10.1515/med-2016-0064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/01/2016] [Indexed: 12/25/2022] Open
Abstract
The objective of this study is to describe the clinical and epidemiological characteristics of patients hospitalized in Lithuania who are infected with influenza A(H1N1)pdm09 and to compare pandemic A(H1N1) pdm09 infection with postpandemic. In total, 146 subjects hospitalized with influenza A(H1N1) pdm09 were identified from 2009–2011. There were 53 during the initial pandemic wave in the summer of 2009, 69 during the peak pandemic period, and 24 during the “postpandemic” period that we included in this study. There were 22 subjects who died after laboratory confirmation of influenza A(H1N1)pdm09. No deaths were documented during the first wave. Subjects presenting during the peak of pandemic influenza had a greater incidence of fever (100% vs 77.4%; p<0.001), dry cough (95.7% vs 82.7%; p=0.01), and vomiting (26.1% vs 1.9%, p<0.001) as compared with patients infected during the first wave. The rate of bacterial pneumonia was 18.8% (13/69) during the peak pandemic period and 12.5% (3/24, p=0.754) during the postpandemic period. None of the postpandemic influenza subjects’ intensive care unit stays were due to pneumonia. The hospitalized early 2009 H1N1 pandemic cases and postpandemic cases were milder compared with those at the peak of pandemic activity.
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Affiliation(s)
- Arvydas Ambrozaitis
- Department of Infectious, Chest Diseases Dermatovenereology and Allergology, Vilnius University, Lithuania , Vilnius, LT-08117
| | - Daiva Radzišauskienė
- Department of Infectious, Chest Diseases Dermatovenereology and Allergology, Vilnius University, Lithuania , Vilnius, LT-08117
| | - Kęstutis Žagminas
- Public Health Institute, Vilnius University, Lithuania , Vilnius, LT-03101
| | | | - Stefan Gravenstein
- University Hospitals-Case Medical Center and Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America and Warren Alpert Medical School of Brown University
| | - Ligita Jančorienė
- Department of Infectious, Chest Diseases Dermatovenereology and Allergology, Vilnius University, Lithuania , Vilnius, LT-08117
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Fischer WA, Gong M, Bhagwanjee S, Sevransky J. Global burden of influenza as a cause of cardiopulmonary morbidity and mortality. Glob Heart 2014; 9:325-36. [PMID: 25667184 DOI: 10.1016/j.gheart.2014.08.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory infections, including influenza, are a leading cause of cardiopulmonary morbidity and mortality worldwide. Until recently, the epidemiology of influenza was limited to resource-rich countries. Emerging epidemiological reports characterizing the 2009 H1N1 pandemic, however, suggest that influenza exerts an even greater toll in low-income, resource-constrained environments where it is the cause of 5% to 27% of all severe acute respiratory infections. The increased burden of disease in this setting is multifactorial and likely is the result of higher rates of comorbidities such as human immunodeficiency virus, decreased access to health care, including vaccinations and antiviral medications, and limited healthcare infrastructure, including oxygen therapy or critical care support. Improved global epidemiology of influenza is desperately needed to guide allocation of life-saving resources, including vaccines, antiviral medications, and direct the improvement of basic health care to mitigate the impact of influenza infection on the most vulnerable populations.
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Affiliation(s)
- William A Fischer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; The Center for Environmental Medicine, Asthma and Lung Biology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | | | - Satish Bhagwanjee
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Jonathan Sevransky
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA, USA
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Lekana-Douki SE, Mouinga-Ondémé A, Nkoghe D, Drosten C, Drexler JF, Kazanji M, Leroy EM. Early introduction and delayed dissemination of pandemic influenza, Gabon. Emerg Infect Dis 2013; 19:644-7. [PMID: 23631999 PMCID: PMC3647404 DOI: 10.3201/eid1904.111925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Active surveillance in health care centers in Gabon during 2009–2011 detected 72 clinical cases of pandemic (H1N1) 2009 (pH1N1). We found that pH1N1 virus was introduced in mid-2009 but spread throughout the country in 2010. Thus, Gabon was also affected by pH1N1.
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Oria PA, Arunga G, Lebo E, Wong JM, Emukule G, Muthoka P, Otieno N, Mutonga D, Breiman RF, Katz MA. Assessing parents' knowledge and attitudes towards seasonal influenza vaccination of children before and after a seasonal influenza vaccination effectiveness study in low-income urban and rural Kenya, 2010-2011. BMC Public Health 2013; 13:391. [PMID: 23617891 PMCID: PMC3639236 DOI: 10.1186/1471-2458-13-391] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 04/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Influenza vaccine is rarely used in Kenya, and little is known about attitudes towards the vaccine. From June-September 2010, free seasonal influenza vaccine was offered to children between 6 months and 10 years old in two Population-Based Infectious Disease Surveillance (PBIDS) sites. This survey assessed attitudes about influenza, uptake of the vaccine and experiences with childhood influenza vaccination. Methods We administered a questionnaire and held focus group discussions with parents of children of enrollment age in the two sites before and after first year of the vaccine campaign. For pre-vaccination focus group discussions, we randomly selected mothers and fathers who had an eligible child from the PBIDS database to participate. For the post-vaccination focus group discussions we stratified parents whose children were eligible for vaccination into fully vaccinated, partially vaccinated and non-vaccinated groups. Results Overall, 5284 and 5755 people completed pre and post-vaccination questionnaires, respectively, in Kibera and Lwak. From pre-vaccination questionnaire results, among parents who were planning on vaccinating their children, 2219 (77.6%) in Kibera and 1780 (89.6%) in Lwak said the main reason was to protect the children from seasonal influenza. In the pre-vaccination discussions, no parent had heard of the seasonal influenza vaccine. At the end of the vaccine campaign, of 18,652 eligible children, 5,817 (31.2%) were fully vaccinated, 2,073 (11.1%) were partially vaccinated and, 10,762 (57.7%) were not vaccinated. In focus group discussions, parents who declined vaccine were concerned about vaccine safety or believed seasonal influenza illness was not severe enough to warrant vaccination. Parents who declined the vaccine were mainly too busy [251(25%) in Kibera and 95 (10.5%) in Lwak], or their child was away during the vaccination period [199(19.8%) in Kibera; 94(10.4%) in Lwak]. Conclusion If influenza vaccine were to be introduced more broadly in Kenya, effective health messaging will be needed on vaccine side effects and frequency and potential severity of influenza infection.
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Affiliation(s)
- Prisca Adhiambo Oria
- Kenya Medical Research Institute/Centers for Disease Control and Prevention (KEMRI/CDC), Nairobi, Kenya.
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Matheka DM, Mokaya J, Maritim M. Overview of influenza virus infections in Kenya: past, present and future. Pan Afr Med J 2013; 14:138. [PMID: 23785543 PMCID: PMC3683518 DOI: 10.11604/pamj.2013.14.138.2612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/06/2013] [Indexed: 11/11/2022] Open
Abstract
The World Health Organization (WHO) estimates that acute lower respiratory infections account for 4 million deaths per year. The rates are even higher in developing countries. Influenza, a virus causing respiratory infections, has widely been studied in developed countries. However, there is paucity of data on its epidemiology, seasonality and burden in most developing countries. In the contrary, Kenya (a developing country) has an elaborate national epidemio-surveillance network for influenza, where a lot of data is generated on the epidemiology and seasonality of influenza in Kenya and the East African region. Several steps have been taken to control influenza in Kenya, including vaccination and surveillance programs. However, some challenges still exist. This article explores the pattern of influenza and existing interventions in Kenya, and highlights suggestions on what can be done to adequately control this virus in future.
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Wane J, Nyatanyi T, Nkunda R, Rukelibuga J, Ahmed Z, Biedron C, Kabeja A, Muhimpundu MA, Kabanda A, Antara S, Briet O, Koama JB, Rusanganwa A, Mukabayire O, Karema C, Raghunathan P, Lowrance D. 2009 pandemic influenza A (H1N1) virus outbreak and response--Rwanda, October, 2009-May, 2010. PLoS One 2012; 7:e31572. [PMID: 22745652 PMCID: PMC3383749 DOI: 10.1371/journal.pone.0031572] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 01/11/2012] [Indexed: 11/18/2022] Open
Abstract
Background In October 2009, the first case of pandemic influenza A(H1N1)pdm09 (pH1N1) was confirmed in Kigali, Rwanda and countrywide dissemination occurred within several weeks. We describe clinical and epidemiological characteristics of this epidemic. Methods From October 2009 through May 2010, we undertook epidemiologic investigations and response to pH1N1. Respiratory specimens were collected from all patients meeting the WHO case definition for pH1N1, which were tested using CDC’s real time RT-PCR protocol at the Rwandan National Reference Laboratory (NRL). Following documented viral transmission in the community, testing focused on clinically severe and high-risk group suspect cases. Results From October 9, 2009 through May 31, 2010, NRL tested 2,045 specimens. In total, 26% (n = 532) of specimens tested influenza positive; of these 96% (n = 510) were influenza A and 4% (n = 22) were influenza B. Of cases testing influenza A positive, 96.8% (n = 494), 3% (n = 15), and 0.2% (n = 1) were A(H1N1)pdm09, Seasonal A(H3) and Seasonal A(non-subtyped), respectively. Among laboratory-confirmed cases, 263 (53.2%) were children <15 years and 275 (52%) were female. In total, 58 (12%) cases were hospitalized with mean duration of hospitalization of 5 days (Range: 2–15 days). All cases recovered and there were no deaths. Overall, 339 (68%) confirmed cases received oseltamivir in any setting. Among all positive cases, 26.9% (143/532) were among groups known to be at high risk of influenza-associated complications, including age <5 years 23% (122/532), asthma 0.8% (4/532), cardiac disease 1.5% (8/532), pregnancy 0.6% (3/532), diabetes mellitus 0.4% (2/532), and chronic malnutrition 0.8% (4/532). Conclusions Rwanda experienced a PH1N1 outbreak which was epidemiologically similar to PH1N1 outbreaks in the region. Unlike seasonal influenza, children <15 years were the most affected by pH1N1. Lessons learned from the outbreak response included the need to strengthen integrated disease surveillance, develop laboratory contingency plans, and evaluate the influenza sentinel surveillance system.
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Affiliation(s)
| | - Thierry Nyatanyi
- Center of Treatment and Research on HIV/AIDS, Malaria, Tuberculosis and Other Epidemic Diseases, Ministry of Health, Kigali, Rwanda
| | | | - Joseph Rukelibuga
- Influenza Division, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
| | - Zara Ahmed
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
| | - Caitlin Biedron
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
| | - Adeline Kabeja
- Center of Treatment and Research on HIV/AIDS, Malaria, Tuberculosis and Other Epidemic Diseases, Ministry of Health, Kigali, Rwanda
| | - Marie Aimée Muhimpundu
- Center of Treatment and Research on HIV/AIDS, Malaria, Tuberculosis and Other Epidemic Diseases, Ministry of Health, Kigali, Rwanda
| | | | - Simon Antara
- African Field Epidemiology Network, Kigali, Rwanda
| | - Olivier Briet
- Center of Treatment and Research on HIV/AIDS, Malaria, Tuberculosis and Other Epidemic Diseases, Ministry of Health, Kigali, Rwanda
| | - Jean Baptiste Koama
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
| | | | | | - Corine Karema
- Center of Treatment and Research on HIV/AIDS, Malaria, Tuberculosis and Other Epidemic Diseases, Ministry of Health, Kigali, Rwanda
| | - Pratima Raghunathan
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
| | - David Lowrance
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention (CDC), Kigali, Rwanda
- * E-mail:
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