Impact of the 1918 #Influenza #Pandemic in Coastal #Kenya (Trop Med Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Trop Med Infect Dis. 2019 Jun 8;4(2). pii: E91. doi: 10.3390/tropicalmed4020091.

Impact of the 1918 Influenza Pandemic in Coastal Kenya.

Andayi F1, Chaves SS2,3, Widdowson MA4,5.

Author information: 1 Influenza Program, Centers for Disease Control and Prevention-Kenya, Nairobi 00621, Kenya. 2 Influenza Program, Centers for Disease Control and Prevention-Kenya, Nairobi 00621, Kenya. 3 Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30333, USA. 4 Division of Global Health Protection, Centers for Disease Control and Prevention-Kenya, Nairobi 00621, Kenya. 5 Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.



The 1918 influenza pandemic was the most significant pandemic recorded in human history. Worldwide, an estimated half billion persons were infected and 20 to 100 million people died in three waves during 1918 to 1919. Yet the impact of this pandemic has been poorly documented in many countries especially those in Africa. We used colonial-era records to describe the impact of 1918 influenza pandemic in the Coast Province of Kenya. We gathered quantitative data on facility use and all-cause mortality from 1912 to 1925, and pandemic-specific data from active reporting from September 1918 to March 1919. We also extracted quotes from correspondence to complement the quantitative data and describe the societal impact of the pandemic. We found that crude mortality rates and healthcare utilization increased six- and three-fold, respectively, in 1918, and estimated a pandemic mortality rate of 25.3 deaths/1000 people/year. Impact to society and the health care system was dramatic as evidenced by correspondence. In conclusion, the 1918 pandemic profoundly affected Coastal Kenya. Preparation for the next pandemic requires continued improvement in surveillance, education about influenza vaccines, and efforts to prevent, detect and respond to novel influenza outbreaks.

KEYWORDS: 1918 pandemic; Africa; Kenya; Spanish flu; influenza pandemic

PMID: 31181715 DOI: 10.3390/tropicalmed4020091

Keywords: Influenza A; Pandemic Influenza; Spanish Flu; Society; Kenya.



#Serological #evidence of #Flavivirus #circulation in #human populations in Northern #Kenya: an assessment of disease risk 2016-2017 (Virol J., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Virol J. 2019 May 17;16(1):65. doi: 10.1186/s12985-019-1176-y.

Serological evidence of Flavivirus circulation in human populations in Northern Kenya: an assessment of disease risk 2016-2017.

Chepkorir E1,2, Tchouassi DP3, Konongoi SL4, Lutomiah J4, Tigoi C3, Irura Z5, Eyase F6, Venter M7, Sang R3.

Author information: 1 International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya. 2 Center for Viral Zoonoses, Department of Medical Virology, University of Pretoria, P. O. Box 323, Arcadia, 0007, South Africa. 3 International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya. 4 Center for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya. 5 Division of Disease Surveillance and Response, Ministry of Health, P. O. Box 20781-00202, Nairobi, Kenya. 6 Jomo Kenyatta University of Agriculture and Technology, P.O. Box 606, Village Market, Nairobi, Kenya. 7 Center for Viral Zoonoses, Department of Medical Virology, University of Pretoria, P. O. Box 323, Arcadia, 0007, South Africa.




Yellow fever, Dengue, West Nile and Zika viruses are re-emerging mosquito-borne Flaviviruses of public health concern. However, the extent of human exposure to these viruses and associated disease burden in Kenya and Africa at large remains unknown. We assessed the seroprevalence of Yellow fever and other Flaviviruses in human populations in West Pokot and Turkana Counties of Kenya. These areas border Uganda, South Sudan and Ethiopia where recent outbreaks of Yellow fever and Dengue have been reported, with possibility of spillover to Kenya.


Human serum samples collected through a cross-sectional survey in West Pokot and Turkana Counties were screened for neutralizing antibodies to Yellow fever, Dengue-2, West Nile and Zika virus using the Plaque Reduction Neutralization Test (PRNT). Seroprevalence was compared by county, site and important human demographic characteristics. Adjusted odds ratios (aOR) were estimated using Firth logistic regression model.


Of 877 samples tested, 127 neutralized with at least one of the four flaviviruses (14.5, 95% CI 12.3-17.0%), with a higher proportion in Turkana (21.1%, n = 87/413) than in West Pokot (8.6%, n = 40/464). Zika virus seroprevalence was significantly higher in West Pokot (7.11%) than in Turkana County (0.24%; χ2 P < 0.0001). A significantly higher Yellow fever virus seroprevalence was also observed in Turkana (10.7%) compared to West Pokot (1.29%; χ2 P < 0.0001). A high prevalence of West Nile virus was detected in Turkana County only (10.2%) while Dengue was only detected in one sample, from West Pokot. The odds of infection with West Nile virus was significantly higher in males than in females (aOR = 2.55, 95% CI 1.22-5.34). Similarly, the risk of Zika virus infection in West Pokot was twice higher in males than females (aOR = 2.01, 95% CI 0.91-4.41).


Evidence of neutralizing antibodies to West Nile and Zika viruses indicates that they have been circulating undetected in human populations in these areas. While the observed Yellow Fever prevalence in Turkana and West Pokot Counties may imply virus activity, we speculate that this could also be as a result of vaccination following the Yellow Fever outbreak in the Omo river valley, South Sudan and Uganda across the border.

KEYWORDS: Dengue virus; Flaviviruses risk assessment; Northern Kenya; Plaque reduction neutralization test; Seroprevalence; West Nile virus; Yellow fever virus; Zika virus

PMID: 31101058 DOI: 10.1186/s12985-019-1176-y

Keywords: Flavivirus; WNV; Zika Virus; Dengue Fever; Yellow Fever; Serology; Seroprevalence; Kenya.


Effect of 10-valent #PCV on #IPD and #nasopharyngeal carriage in #Kenya: a longitudinal surveillance study (Lancet, abstract)

[Source: The Lancet, full page: (LINK). Abstract, edited.]

Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study

Laura L Hammitt, MD, Anthony O Etyang, ChB, Susan C Morpeth, FRACP, John Ojal, PhD, Alex Mutuku, MSc, Neema Mturi, MRCPCH, Jennifer C Moisi, PhD, Ifedayo M Adetifa, PhD, Angela Karani, BSc, Donald O Akech, BSc, Mark Otiende, MSc, Tahreni Bwanaali, MBA, Jackline Wafula, BSN, Christine Mataza, KRCHN, Edward Mumbo, BSc, Collins Tabu, MPH, Maria Deloria Knoll, PhD, Evasius Bauni, PhD, Prof Kevin Marsh, FMedSci, Prof Thomas N Williams, FMedSci, Tatu Kamau, MPH, Shahnaaz K Sharif, MD, Prof Orin S Levine, PhD, Prof J Anthony G Scott, FRCP

Open Access / PublishedApril 15, 2019 / DOI:




Ten-valent pneumococcal conjugate vaccine (PCV10), delivered at 6, 10, and 14 weeks of age was introduced in Kenya in January, 2011, accompanied by a catch-up campaign in Kilifi County for children aged younger than 5 years. Coverage with at least two PCV10 doses in children aged 2–11 months was 80% in 2011 and 84% in 2016; coverage with at least one dose in children aged 12–59 months was 66% in 2011 and 87% in 2016. We aimed to assess PCV10 effect against nasopharyngeal carriage and invasive pneumococcal disease (IPD) in children and adults in Kilifi County.


This study was done at the KEMRI-Wellcome Trust Research Programme among residents of the Kilifi Health and Demographic Surveillance System, a rural community on the Kenyan coast covering an area of 891 km2. We linked clinical and microbiological surveillance for IPD among admissions of all ages at Kilifi County Hospital, Kenya, which serves the community, to the Kilifi Health and Demographic Surveillance System from 1999 to 2016. We calculated the incidence rate ratio (IRR) comparing the prevaccine (Jan 1, 1999–Dec 31, 2010) and postvaccine (Jan 1, 2012–Dec 31, 2016) eras, adjusted for confounding, and reported percentage reduction in IPD as 1 minus IRR. Annual cross-sectional surveys of nasopharyngeal carriage were done from 2009 to 2016.


Surveillance identified 667 cases of IPD in 3 211 403 person-years of observation. Yearly IPD incidence in children younger than 5 years reduced sharply in 2011 following vaccine introduction and remained low (PCV10-type IPD: 60·8 cases per 100 000 in the prevaccine era vs 3·2 per 100 000 in the postvaccine era [adjusted IRR 0·08, 95% CI 0·03–0·22]; IPD caused by any serotype: 81·6 per 100 000 vs 15·3 per 100 000 [0·32, 0·17–0·60]). PCV10-type IPD also declined in the post-vaccination era in unvaccinated age groups (<2 months [no cases in the postvaccine era], 5–14 years [adjusted IRR 0·26, 95% CI 0·11–0·59], and ≥15 years [0·19, 0·07–0·51]). Incidence of non-PCV10-type IPD did not differ between eras. In children younger than 5 years, PCV10-type carriage declined between eras (age-standardised adjusted prevalence ratio 0·26, 95% CI 0·19–0·35) and non-PCV10-type carriage increased (1·71, 1·47–1·99).


Introduction of PCV10 in Kenya, accompanied by a catch-up campaign, resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. Although the catch-up campaign is likely to have brought forward the benefits by several years, the study suggests that routine infant PCV10 immunisation programmes will provide substantial direct and indirect protection in low-income settings in tropical Africa.


Gavi, The Vaccine Alliance and The Wellcome Trust of Great Britain.

Keywords: Streptococcus pneumoniae; Vaccines; IPD; Kenya.


#Bombali #Ebola Virus in Mops condylurus #Bat, #Kenya (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 5—May 2019 / Dispatch

Bombali Ebola Virus in Mops condylurus Bat, Kenya

Kristian M. Forbes1  , Paul W. Webala, Anne J. Jääskeläinen, Samir Abdurahman, Joseph Ogola, Moses M. Masika, Ilkka Kivistö, Hussein Alburkat, Ilya Plyusnin, Lev Levanov, Essi M. Korhonen, Eili Huhtamo, Dufton Mwaengo, Teemu Smura, Ali Mirazimi, Omu Anzala, Olli Vapalahti, and Tarja Sironen

Author affiliations: University of Helsinki, Helsinki, Finland (K.M. Forbes, A.J. Jääskeläinen, I. Kivistö, H. Alburkat, I. Pljusnin, L. Levanov, E.M. Korhonen, E. Huhtamo, T. Smura, O. Vapalahti, T. Sironen); Maasai Mara University, Narok, Kenya (P.W. Webala); Helsinki University Hospital, Helsinki (A.J. Jääskeläinen, O. Vapalahti); Public Health Agency of Sweden, Stockholm, Sweden (S. Abdurahman, A. Mirazimi); University of Nairobi, Nairobi, Kenya (J. Ogola, M.M. Masika, D. Mwaengo, O. Anzala); Karolinska University Hospital, Stockholm (A. Mirazimi); National Veterinary Institute, Uppsala, Sweden (A. Mirazimi)



Putatively named Bombali Ebola virus was identified in organs and excreta of an Angolan free-tailed bat (Mops condylurus) in Kenya. Complete genome analysis revealed 98% nucleotide sequence similarity to the prototype virus from Sierra Leone. No Ebola virus–specific RNA or antibodies were detected from febrile humans in the area who reported contact with bats.

Keywords: Ebola; Ebola-Bombali Virus; Bats; Kenya.


#SandFly–Associated #Phlebovirus with Evidence of Neutralizing #Antibodies in #Humans, #Kenya (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 4—April 2019 / Research

Sand Fly–Associated Phlebovirus with Evidence of Neutralizing Antibodies in Humans, Kenya

David P. Tchouassi  , Marco Marklewitz, Edith Chepkorir, Florian Zirkel1, Sheila B. Agha, Caroline C. Tigoi, Edith Koskei, Christian Drosten, Christian Borgemeister, Baldwyn Torto, Sandra Junglen2  , and Rosemary Sang2

Author affiliations: International Centre of Insect Physiology and Ecology, Nairobi, Kenya (D.P. Tchouassi, E. Chepkorir, S.B. Agha, C.C. Tigoi, B. Torto, R. Sang); Charité-Universitätsmedizin Berlin, Berlin, Germany (M. Marklewitz, F. Zirkel, C. Drosten, S. Junglen); German Center for Infection Research, Berlin (M. Marklewitz, F. Zirkel. C. Drosten, S. Junglen); Center for Virus Research, Kenya Medical Research Institute, Nairobi (E. Koskei, R. Sang); University of Bonn, Bonn, Germany (C. Borgemeister)



We describe a novel virus, designated Ntepes virus (NPV), isolated from sand flies in Kenya. NPV has the characteristic phlebovirus trisegmented genome architecture and is related to, but distinct from, Gabek Forest phlebovirus. Diverse cell cultures derived from wildlife, livestock, and humans were susceptible to NPV, with pronounced permissiveness in swine and rodent cells. NPV infection of newborn mice caused rapid and fatal illness. Permissiveness for NPV replication in sand fly cells, but not mosquito cells, suggests a vector-specific adaptation. Specific neutralizing antibodies were found in 13.9% (26/187) of human serum samples taken at the site of isolation of NPV as well as a disparate site in northeastern Kenya, suggesting a wide distribution. We identify a novel human-infecting arbovirus and highlight the importance of rural areas in tropical Africa for arbovirus surveillance as well as extending arbovirus surveillance to include hematophagous arthropods other than mosquitoes.

Keywords: Phlebovirus; Human; Ntepes virus; Kenya.


#Streptococcus pneumoniae Serotype #Epidemiology among #PCV-10 Vaccinated and Unvaccinated #Children at Gertrude’s Children’s Hospital, #Nairobi County: A Cross-Sectional Study (F1000Res., abstract)

[Source: F1000 Research, full page: (LINK). Abstract, edited.]

Streptococcus pneumoniae Serotype Epidemiology among PCV-10 Vaccinated and Unvaccinated Children at Gertrude’s Children’s Hospital, Nairobi County: A Cross-Sectional Study [version 2; referees: 2 approved, 1 not approved]

Michael Walekhwa 1, Margaret Muturi1, Revathi Gunturu2, Eucharia Kenya3, Beatrice Kabera4

Author details: 1 Department of Pathology, Gertrude’s Children’s Hospital, Nairobi, Kenya; 2 School of Medicine, Aga Khan University Hospital, Nairobi, Kenya; 3 Department of Biological Sciences, University of Embu, Embu, Kenya; 4 Department of Medicine, Kenyatta University, Nairobi, Kenya




Serotype replacement and emergence of multidrug resistant S. pneumoniae has exacerbated the need for continuous regional serotype surveillance especially in the developing world. We investigated S. pneumoniae serotypes circulating among vaccinated and unvaccinated children ≤5 years in Nairobi County post PCV10 era.


A total of 206 vaccinated and unvaccinated children attending Gertrude’s Children’s Hospital (GCH) were recruited for this study. Nasopharyngeal swabs collected using Copan Flocked Swabs were the main study specimen. Culturing and isolation of S. pneumoniae was done on BA with gentamicin and BA plates respectively at the GCH main laboratory. Serotyping was done using the Quellung reaction at the KEMRI-Wellcome Trust, Kilifi.


Out of the 206 subjects sampled, 20.39% (42) were found to be carriers of S. pneumoniae. About 52% (n=22) of the S. pneumoniae carriers had received the recommended dose of PCV-10, while 48% (n=20) of the carriers had not. Almost all (n=41; 19.90% of subjects) isolates contained non-vaccine type S. pneumoniae serotypes, while n=1 of the serotypes (in 0.49% of subjects) were untypeable. Serotypes 28F, 6A, 11A, 3 and 7C were prevalent in both vaccinated and unvaccinated children, whereas serotypes 23A, 17F, 35F, 48, 13 and 35B, and 23B, 20, 19B, 21, untypeable, 15B and 39 were found among unvaccinated and vaccinated groups, respectively.


All S. pneumoniae serotypes isolated from the subjects sampled were non PCV-10 vaccine type. These results therefore highlight the importance of monitoring and evaluation to provide epidemiological information to determine the effectiveness of PCV10 in Kenya’s Public health services.

Keywords: Streptococcus pneumoniae, serotypes, Nairobi, Quellung reaction, Optochin test, Bile solubility

Corresponding authors: Margaret Muturi, Revathi Gunturu, Eucharia Kenya, Beatrice Kabera

Competing interests: No competing interests were disclosed.

Grant information: The study was in part funded by the National Commission of Science Technology & Innovation (NACOSTI) Kenya. Ref Nos. NACOSTI/RCD/ST & I/7TH CALL/PhD/148.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright:  © 2019 Walekhwa M et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).

How to cite: Walekhwa M, Muturi M, Gunturu R et al.Streptococcus pneumoniae Serotype Epidemiology among PCV-10 Vaccinated and Unvaccinated Children at Gertrude’s Children’s Hospital, Nairobi County: A Cross-Sectional Study [version 2; referees: 2 approved, 1 not approved]. F1000Research 2019, 7:879 (

First published: 22 Jun 2018, 7:879 (

Latest published: 31 Jan 2019, 7:879 (

Keywords: Antibiotics; Drugs Resistance; Streptococcus pneumoniae; Vaccines; Kenya.


Genetic #Evidence of #MERS #Coronavirus and Widespread #Seroprevalence among #Camels in #Kenya (Virol Sin., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Virol Sin. 2018 Dec 20. doi: 10.1007/s12250-018-0076-4. [Epub ahead of print]

Genetic Evidence of Middle East Respiratory Syndrome Coronavirus (MERS-Cov) and Widespread Seroprevalence among Camels in Kenya.

Ommeh S1, Zhang W2, Zohaib A2, Chen J2, Zhang H2, Hu B2, Ge XY3, Yang XL2, Masika M4, Obanda V5, Luo Y2, Li S2, Waruhiu C2, Li B2, Zhu Y2, Ouma D6, Odendo V6, Wang LF7, Anderson DE7, Lichoti J8, Mungube E6, Gakuya F5, Zhou P2, Ngeiywa KJ8,9, Yan B2, Agwanda B10, Shi ZL11.

Author information: 1 Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya. 2 CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. 3 College of Biology, Hunan University, Changsha, 410006, China. 4 Department of Medical Microbiology, University of Nairobi, Nairobi, 30197-00100, Kenya. 5 Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya. 6 Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi, 57811-00200, Kenya. 7 Veterinary Services Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857,  Singapore. 8 Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock Fisheries and Irrigation, Nairobi, 34188-00100, Kenya. 9 Kenya Camel Association, Nairobi, 30095-00100, Kenya. 10 Department of Zoology, National Museums of Kenya, Nairobi, 40658-00100, Kenya. 11 CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.



We describe the first genome isolation of Middle East respiratory syndrome coronavirus (MERS-CoV) in Kenya. This fatal zoonotic pathogen was first described in the Kingdom of Saudi Arabia in 2012. Epidemiological and molecular evidence revealed zoonotic transmission from camels to humans and between humans. Currently, MERS-CoV is classified by the WHO as having high pandemic potential requiring greater surveillance. Previous studies of MERS-CoV in Kenya mainly focused on site-specific and archived camel and human serum samples for antibodies. We conducted active nationwide cross-sectional surveillance of camels and humans in Kenya, targeting both nasal swabs and plasma samples from 1,163 camels and 486 humans collected from January 2016 to June 2018. A total of 792 camel plasma samples were positive by ELISA. Seroprevalence increased with age, and the highest prevalence was observed in adult camels (82.37%, 95% confidence interval (CI) 79.50-84.91). More female camels were significantly seropositive (74.28%, 95% CI 71.14-77.19) than male camels (P < 0.001) (53.74%, 95% CI 48.48-58.90). Only 11 camel nasal swabs were positive for MERS-CoV by reverse transcription-quantitative PCR. Phylogenetic analysis of whole genome sequences showed that Kenyan MERS-CoV clustered within sub-clade C2, which is associated with the African clade, but did not contain signature deletions of orf4b in African viruses. None of the human plasma screened contained neutralizing antibodies against MERS-CoV. This study confirms the geographically widespread occurrence of MERS-CoV in Kenyan camels. Further one-health surveillance approaches in camels, wildlife, and human populations are needed.

KEYWORDS: Kenya; Middle East respiratory syndrome coronavirus (MERS-CoV); One-health; Public health; Zoonosis

PMID: 30570714 DOI: 10.1007/s12250-018-0076-4

Keywords: MERS-CoV; Human; Camels; Seroprevalence; Kenya.