Dr.  Samoel Ashimosi Khamadi, BSc, MSc, MPH, PhD - Walter Reed Program Tanzania & Kenya Medical Research Institute  - Research Director & Senior Research Officer

Dr. Samoel Ashimosi Khamadi

BSc, MSc, MPH, PhD

Walter Reed Program Tanzania & Kenya Medical Research Institute

Research Director & Senior Research Officer

Mbeya, Mbeya | Afghanistan

Main Specialties: Biology

Additional Specialties: Molecular Biology, Diagnostics, Public Health, HIV/AIDS Research


Top Author

Dr.  Samoel Ashimosi Khamadi, BSc, MSc, MPH, PhD - Walter Reed Program Tanzania & Kenya Medical Research Institute  - Research Director & Senior Research Officer

Dr. Samoel Ashimosi Khamadi

BSc, MSc, MPH, PhD

Introduction

A seasoned Researcher with an interest in finding lasting solutions to Public Health Challenges that communities face using simple but effective methods. Trained in Molecular Biology Techniques, Laboratory Diagnostics and Public Health. Has published widely in areas of Parasitology, immunology, Molecular Biology, Laboratory Science and Public Health. Actively engaged in student mentorship involving lecturing, training on proposal and dissertation writing with over 40 students supervised at Masters and PhD levels with accompanying dissertations.

Primary Affiliation: Walter Reed Program Tanzania & Kenya Medical Research Institute - Mbeya, Mbeya , Afghanistan

Specialties:

Additional Specialties:

Research Interests:


View Dr. Samoel Ashimosi Khamadi’s Resume / CV

Education

Dec 2017
UNIVERSITY OF SALFORD
Master of Business Administration
Leadership and Sustainability
Dec 2016
University of Liverpool
Master of Public Health
International Public Health
Dec 2006
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
PhD in Molecular Medicine
Wrote a dissertation on HIV subtypes circulating in Northern Kenya, cross-border and Founder Effects
Dec 2006
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
PhD in Molecular Medicine
Wrote a dissertation on HIV subtypes circulating in Northern Kenya, cross-border and Founder Effects
Dec 2006
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
PhD in Molecular Medicine
Wrote a dissertation on HIV subtypes circulating in Northern Kenya, cross-border and Founder Effects
Dec 2000
University of Nairobi
Master of Science (Parasitology and Immunology)
Wrote a dissertation on "Characterization of Trypanosoma brucei T-lymphocyte Triggering Factor (TLTF)"
Dec 2000
University of Nairobi
Master of Science (Parasitology and Immunology)
Wrote a dissertation on Characterization of Trypanosoma brucei T-lymphocyte Triggering Factor (TLTF)
Dec 2000
University of Nairobi
Master of Science (Parasitology and Immunology)
Wrote a dissertation on Characterization of Trypanosoma brucei T-lymphocyte Triggering Factor (TLTF)
Dec 2000
University of Nairobi
Master of Science (Parasitology and Immunology)
Wrote a dissertation on Characterization of Trypanosoma brucei T-lymphocyte Triggering Factor (TLTF)
Apr 1996
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Bachelor of Science (Botany and Zoology)
Majored in Zoology and Botany with minor in Chemsitry
Apr 1996
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Bachelor of Science (Botany and Zoology)
Majored in Zoology and Botany with minor in Chemsitry
Apr 1996
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Bachelor of Science (Botany and Zoology)
Majored in Zoology and Botany with minor in Chemsitry
Apr 1996
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Bachelor of Science (Botany and Zoology)
Majored in Zoology and Botany with minor in Chemsitry
Apr 1996
Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Bachelor of Science (Botany and Zoology)
Majored in Zoology and Botany with minor in Chemsitry

Publications

60Publications

657Reads

1399Profile Views

284PubMed Central Citations

Predominance of Hepatitis B Virus Genotype A Among Treated HIV Infected Patients Experiencing High Hepatitis B Virus Drug Resistance in Nairobi, Kenya.

AIDS Res Hum Retroviruses 2017 Sep 18;33(9):966-969. Epub 2017 Apr 18.

3 Department of Microbiology, Kenyatta University , Nairobi, Kenya .

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http://dx.doi.org/10.1089/AID.2017.0019DOI Listing
September 2017
6 Reads
1 Citation
2.330 Impact Factor

Genetic Polymorphisms of the CX3CR1 Gene Associated with HIV-1 Infections in Kenyan Population

J AIDS Clin Res 2017, 8: 712

Journal of AIDS and Clinical Research

Introduction: Repeated exposure to Human Immunodeficiency Virus (HIV) does not always result in infection. Understanding the mechanisms that confer protection against progressive infection with HIV-1 may be useful in the development of appropriate interventions. The impact of CX3CR1 polymorphisms on human immunodeficiency virus type 1 (HIV-1) pathogenesis is controversial, with conflicting reports of their role in disease progression in HIV-1 infected individuals. The aim of this study is to characterize polymorphisms of the CX3CR1 co-receptor gene among HIV infected adults and infants in a Kenyan Population. Methods: Clinical samples were obtained from 200 HIV infected infants and 200 HIV infected adults and genotyped for the CX3CR1 gene 280M and 249I mutations. These were identified by PCR–RFLP analysis after amplification of a 588 base pair sequence of CX3CR1 gene. Results: In determining the presence of T280M and V249I haplotypes it was found that overall, infants had higher percentages of the wild type alleles at (42% and 45%), respectively compared to adults (37% and 36%) respectively. In the case of heterozygous mutants, adults had higher percentages (11% and 12%), respectively than among infants (7% and 4%), respectively. Adults also had higher percentages of homozygous mutants of (2%) compared to infants (1%). This study showed that the differences in mutations of CX3CR1 gene allele in I249 and M280 was p=0.075 and p=0.215, respectively which was not statistically significant (p>0.05). Conclusion: This study showed that CX3CR1 gene polymorphisms exist in Kenya though the numbers of mutations are at very low levels to warrant any meaningful impact in the population in terms of HIV-1 disease progression. It is probable that alternative mechanisms are operating in conferring resistance to HIV-I infection. Further in vitro cellular studies need to be carried out to determine the exact role of CX3CR1 gene mutations in HIV/AIDS pathogenesis.

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August 2017
29 Reads

RANTES Gene Polymorphisms Associated with HIV-1 Infections in Kenyan Population.

Dis Markers 2016 16;2016:4703854. Epub 2016 Oct 16.

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1155/2016/4703854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5086385PMC
February 2017
6 Reads
1 Citation
2.174 Impact Factor

Chemokine Coreceptor-2 Gene Polymorphisms among HIV-1 Infected Individuals in Kenya.

Dis Markers 2015 2;2015:952067. Epub 2015 Aug 2.

Kenya Medical Research Institute, Nairobi 54628, Kenya.

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http://dx.doi.org/10.1155/2015/952067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537727PMC
April 2016
8 Reads
2.174 Impact Factor

Hepatitis B, Hepatitis C and HIV-1 Coinfection in Two Informal Urban Settlements in Nairobi, Kenya.

PLoS One 2015 12;10(6):e0129247. Epub 2015 Jun 12.

Centre for Infectious and Parasitic Disease Control Research, Kenya Medical Research Institute, Busia, Kenya.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129247PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466314PMC
April 2016
12 Reads
9 Citations
3.234 Impact Factor

Prevalence of Transmitted Drug Resistance Mutations in HIV-1-Infected Drug-Naive Patients from Urban and Suburban Regions of Kenya.

AIDS Res Hum Retroviruses 2016 Mar 24;32(3):220-5. Epub 2015 Sep 24.

1 Aga Khan University Hospital , Nairobi, Kenya .

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http://dx.doi.org/10.1089/aid.2015.0026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779969PMC
March 2016
14 Reads
1 Citation
2.330 Impact Factor

Genotyping of enteroviruses isolated in Kenya from pediatric patients using partial VP1 region.

Springerplus 2016 24;5:158. Epub 2016 Feb 24.

Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya, P.O. Box 606-00621, Nairobi, Kenya ; Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya.

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http://dx.doi.org/10.1186/s40064-016-1834-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766141PMC
March 2016
18 Reads
1 Citation

Genotyping of enteroviruses isolated in Kenya from pediatric patients using partial VP1 region

Springerplus. 2016 Feb 24;5:158

Springerplus

Enteroviruses (EV) are responsible for a wide range of clinical diseases in humans. Though studied broadly in several regions of the world, the genetic diversity of human enteroviruses (HEV) circulating in the sub-Saharan Africa remains under-documented. In the current study, we molecularly typed 61 HEV strains isolated in Kenya between 2008 and 2011 targeting the 3'-end of the VP1 gene. Viral RNA was extracted from the archived isolates and part of the VP1 gene amplified by RT-PCR, followed by sequence analysis. Twenty-two different EV types were detected. Majority (72.0 %) of these belonged to Enterovirus B species followed by Enterovirus D (21.3 %) and Enterovirus A (6.5 %). The most frequently detected types were Enterovirus-D68 (EV-D68), followed by Coxsackievirus B2 (CV-B2), CV-B1, CV-B4 and CV-B3. Phylogenetic analyses of these viruses revealed that Kenyan CV-B1 isolates were segregated among sequences of global CV-B1 strains. Conversely, the Kenyan CV-B2, CV-B3, CV-B4 and EV-D68 strains generally grouped together with those detected from other countries. Notably, the Kenyan EV-D68 strains largely clustered with sequences of global strains obtained between 2008 and 2010 than those circulating in recent years. Overall, our results indicate that HEV strains belonging to Enterovirus D and Enterovirus B species pre-dominantly circulated and played a significant role in pediatric respiratory infection in Kenya, during the study period. The Kenyan CV-B1 strains were genetically divergent from those circulating in other countries. Phylogenetic clustering of Kenyan EV-D68 strains with sequences of global strains circulating between 2008 and 2010 than those obtained in recent years suggests a high genomic variability associated with the surface protein encoding VP1 gene in these enteroviruses.

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February 2016
9 Reads

Lessons learned from implementing the HIV infant tracking system (HITSystem): A web-based intervention to improve early infant diagnosis in Kenya.

Healthc (Amst) 2015 Dec 14;3(4):190-5. Epub 2015 Aug 14.

Children's Mercy Hospital, Health Services and Outcomes Research, Kansas City, MO, USA.

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http://dx.doi.org/10.1016/j.hjdsi.2015.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690847PMC
December 2015
5 Reads
6 Citations

Trypanosoma Infection Rates in Glossina Species in Mtito Andei Division, Makueni County, Kenya.

J Parasitol Res 2015 4;2015:607432. Epub 2015 Nov 4.

Department of Agricultural Resource Management, Embu University College, P.O. Box 6, Embu 60100, Kenya.

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http://dx.doi.org/10.1155/2015/607432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649094PMC
November 2015
9 Reads

Chemokine Coreceptor-2 Gene Polymorphisms among HIV-1 Infected Individuals in Kenya

Volume 2015 (2015), Article ID 952067

Disease Markers

Chemokine Coreceptor-2 (CCR2) is an entry coreceptor for HIV-1. A mutation in the coding gene for this coreceptor, CCR2-64I, has been shown to be an important factor for delaying disease progression. In Kenya no studies have been done to determine the status of CCR2 gene polymorphisms among HIV-1 infected individuals. To determine the existence and distribution of CCR2 gene mutations and identify polymorphic groups of the coreceptor gene in the population, a cross-sectional study was conducted to analyze the differences in allelic frequencies of CCR2-64I among HIV-1 seropositive individuals. Blood samples were collected from HIV/AIDS screening centers and analyzed for the presence of CCR2-64I using restriction fragment length polymorphism (RFLP). One hundred and eighteen samples collected from different regions of the country were genotyped for the CCR2-64I mutation. Of these, 4 (3.4%) were homozygous mutants (I/I) and 21 (17.8%) were heterozygous (V/I). Ninety-three subjects (78.8%) were wild type (V/V). With the search for a preventive/therapeutic HIV vaccine elusive, the presence of CCR-2 gene polymorphisms that delay disease progression and prolong the lives of the infected in the Kenyan population may contribute to the growing evidence that host genetic factors are important in predicting susceptibility to HIV-1 infection.

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July 2015
5 Reads

HIV-1 Drug Resistance Mutations in Patients Failing 1st Line Therapy in a Comprehensive Care Center in Nairobi, Kenya

World Journal of AIDS, 2015, 5, 83-89

Wold Journal of AIDS

Background: HIV-1 drug resistance is an emerging challenge for HIV-1 infected clients who are on antiretroviral therapy (ART). In Kenya, as in many other developing countries, ART is now accessible to clients who need it. However, they must be done a CD4 test first and if the count is <300, then ART is commenced. With the initiation of ART comes the challenge of adherence to medication, a factor that is impacted greatly by the understanding of the client of the importance of adherence and the financial ability to keep their appointments, especially if the clients come from a distant location. Objective: To identify HIV-1 drug resistance mutations inclientsfailing1st line antiretroviral therapy in Nairobi, Kenya. Methodology: A cross-sectional study was carried out where whole blood samples were collected from clients attending a HIV care and treatment clinic in Nairobi. Clients who had been on ART for more than 6 months and had a viral load greater than 1000 were enrolled in the study. A total of 52 client samples were successfully sequenced in the reverse transcriptase region and analyzed. Results: After analysis of the generated sequences, it was seen that 43 (82.6%) of the clients had HIV-1 drug resistance mutations conferring resistance to one or more nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse-transcriptase inhibitors (NNRTIs). Majority of the clients (46%) were infected with HIV-1 subtype A viruses. Conclusion: The findings of the study showed that a significant proportion of the clients on ART had developed resistance mutations to one or more drugs that are used as 1st line therapy in Kenya. There is need for continuous education of the population on importance of adherence to medication. There is also need for clinicians to be trained on using viral load and HIV drug resistance testing, where available, as methods of monitoring treatment failure so that clients can be switched to alternative medication immediately the need arises, so as to improve their treatment outcomes.

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June 2015
5 Reads

Genetic diversity of human enterovirus 68 strains isolated in Kenya using the hypervariable 3'-end of VP1 gene.

PLoS One 2014 23;9(7):e102866. Epub 2014 Jul 23.

Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Unit-Kenya (USAMRU-K), Nairobi, Kenya.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102866PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108357PMC
April 2015
20 Reads
10 Citations
3.234 Impact Factor

Progress Toward Eliminating Mother to Child Transmission of HIV in Kenya: Review of Treatment Guideline Uptake and Pediatric Transmission at Four Government Hospitals Between 2010 and 2012.

AIDS Behav. 2015 Apr 23.

AIDS and Behaviour

We analyzed prevention of mother-to-child transmission (PMTCT) data from a retrospective cohort of n = 1365 HIV+ mothers who enrolled their HIV-exposed infants in early infant diagnosis services in four Kenyan government hospitals from 2010 to 2012. Less than 15 and 20 % of mother-infant pairs were provided with regimens that met WHO Option A and B/B+ guidelines, respectively. Annually, the gestational age at treatment initiation decreased, while uptake of Option B/B+ increased (all p's < 0.001). Pediatric HIV infection was halved (8.6-4.3 %), yet varied significantly by hospital. In multivariable analyses, HIV-exposed infants who received no PMTCT (AOR 4.6 [2.49, 8.62], p < 0.001), mixed foods (AOR 5.0 [2.77, 9.02], p < 0.001), and care at one of the four hospitals (AOR 3.0 [1.51, 5.92], p = 0.002) were more likely to be HIV-infected. While the administration and uptake of WHO PMTCT guidelines is improving, an expanded focus on retention and medication adherence will further reduce pediatric HIV transmission

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April 2015
7 Reads

HIV-1 drug resistance mutations among infants born to HIV-positive mothers in Busia, Kenya.

AIDS Res Hum Retroviruses 2014 Dec;30(12):1236-8

1 Centre for Virus Research, Kenya Medical Research Institute , Nairobi, Kenya .

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http://dx.doi.org/10.1089/AID.2014.0158DOI Listing
December 2014
5 Reads
1 Citation
2.330 Impact Factor

HIV type 1 drug resistance patterns among patients failing first and second line antiretroviral therapy in Nairobi, Kenya.

BMC Res Notes 2014 Dec 9;7:890. Epub 2014 Dec 9.

Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1186/1756-0500-7-890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295353PMC
December 2014
7 Reads
1 Citation

HIV type 1 drug resistance patterns among patients failing first and second line antiretroviral therapy in Nairobi, Kenya.

BMC Res Notes. 2014 Dec 9;7:890.

BMC Research Notes

BACKGROUND: The ever-expanding rollout of antiretroviral therapy in poor resource settings without routine virological monitoring has been accompanied with development of drug resistance that has resulted in limited treatment success. METHODS: A cross-sectional study with one time viral load was conducted during the period between 2012 and 2013 to determine treatment failure and drug resistance mutations among adults receiving first-line (44) (3TC_d4T/AZT_NVP/EFV) and second-line (20) (3TC/AZT/LPV/r) in Nairobi, Kenya. HIV-1 pol-RT genotyping for drug resistance was performed using an in-house protocol. RESULTS: A total of 64 patients were recruited (mean age 36.9 yrs.) during the period between 2012 and 2013 of the 44 adult patients failing first-line 24 (40.9%) had drug resistance mutations. Eight (8) patients had NRTI resistance mutations with NAMS M184V (54.2%) and K65R (8.4%) mutations being the highest followed by TAMs T215Y and K70R (12.5%). In addition, among patients failing second-line (20), six patients (30%) had NNRTI resistance; two patients on K103N and G190A mutations while V106A, Y184V, A98G, Y181C mutations per patient were also detected. However, for NRTI two patients had TAM T215Y. M184V mutation occurred in one patient. CONCLUSIONS: The study findings showed that HIV-1 drug resistance was significantly high in the study population. The detected accumulated resistance strains show that emergence of HIV drug resistance will continue to be a big challenge and should be given more attention as the scale up of treatment in the country continues.

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December 2014
5 Reads

Diversity of Human Immunodeficiency Virus Type-1 Subtypes in Western Kenya

10.4236/wja.2014.44043

World Journal of AIDS

Background: HIV/AIDS is the principal pandemic in the world today. Two viral types (HIV-1 and HIV-2), with numerous groups (M, N and O for HIV-1 and A through H for HIV-2) have emerged. These have further proliferated into numerous subtypes, sub-subtypes and circulating recombinant forms (CRF) over the last 30 years. HIV-1 variants circulate together within a geographical region providing an opportunity for recombination of viral strains within infected individuals. In Kenya, at least nine different genetic HIV-1 subtypes and several recombinant forms have been defined within group M, which accounts for the majority of cases in the AIDS pandemic. Objective: To determine the genetic diversity of HIV-1 in the western region of Kenya bordering Uganda. Methodology: A cross sectional study was carried out at Busia District Hospital between 2007 and 2009. A total of 75 patients were sampled randomly from a cohort of 1000 clients on antiretroviral therapy. Blood samples were analysed at the HIV Laboratory, Kenya Medical Research Institute, Nairobi, Kenya. PCR was carried out on the Pol region of HIV, sequenced and analysed by BLAST for subtypes. Results: BLAST analysis revealed the following circulating subtypes: 40/75 (53.30%) were HIV-1 group M subtype A1; 21/75 (28.0%) were subtype D; 5/75 (6.7%) were subtype G; 4/75 (5.30%) were subtype C; and 2/75 (2.70%) were subtype A2. Only one isolate was identified for the other subtypes viz: 1/75 (1.30%) resembled subtype B; 1/75 (1.30%) was A1/C, and 1/75 (1.30%) was A1/D. Conclusion: The study showed increasing HIV-1 diversity along the Kenya-Uganda border with the emergence of A1/C and A1/D recombinants. Such HIV-1 diversityvis a vis the recent expanded access to antiretroviral therapy in resource limited settings calls for continuous evaluation of anti-HIV regimens. There is need therefore, for regular surveillance and monitoring for mutations that are likely to lead to drug resistance if we have to achieve successful treatment outcomes.

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November 2014
8 Reads

HIV-1 Drug Resistance Mutations Among Infants Born to HIV-Positive Mothers in Busia, Kenya.

AIDS Res Hum Retroviruses. 2014 Sep 30.

AIDS Research and Human Retroviruses

Abstract To determine HIV-1 subtypes and transmitted HIV-1 drug-resistant mutations among HIV-1-positive children born to HIV-positive mothers in Busia County, blood samples were collected from 53 children aged between 6 weeks and 5 years in 2011. Their mothers were HIV-1 positive and on antiretroviral therapy at the time the children were born. The samples were analyzed for HIV-1 drug resistance and subtypes through sequencing of portions of the HIV-1 pol gene. The generated sequences were analyzed for subtype diversity using the REGA and BLAST subtyping tools. HIV-1 drug resistance was determined using the Stanford University HIV database. Of the 53 samples that were successfully amplified and sequenced, 69.8% (37/53) were determined to be HIV-1 subtype A, 22.6% (12/53) were subtype D, 5.6% (3/53) were subtype C, and 1.8% (1/53) were subtype A1C. The prevalence of HIV-1 drug resistance mutations of any kind was 22.6% (12/53).

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September 2014
7 Reads

If you text them, they will come: using the HIV infant tracking system to improve early infant diagnosis quality and retention in Kenya.

AIDS 2014 Jul;28 Suppl 3:S313-21

aUniversity of Kansas Medical Center, Department of Family Medicine, Kansas City, Kansas bGlobal Health Innovations, Kansas City, Missouri, USA cKenya Medical Research Institute, Nairobi, Kenya dHealth Services and Outcomes Research, Children's Mercy Hospital, Kansas City, Missouri eTexas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital fDepartment of Pathology & Immunology, Baylor College of Medicine gHealth Empowering Humanity, Houston, Texas, USA hKenya Ministries of Health, National AIDS and STI Control Programme, Nairobi, Kenya iUniversity of Kansas, Department of Global Studies, Lawrence, Kansas jDepartment of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1097/QAD.0000000000000332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226133PMC
July 2014
11 Reads
24 Citations
5.554 Impact Factor

Genetic diversity of human enterovirus 68 strains isolated in Kenya using the hypervariable 3'-end of VP1 gene.

PLoS One. 2014 Jul 23;9(7):e102866.

PLoS One

Reports of increasing worldwide circulation of human enterovirus-68 (EV68) are well documented. Despite health concerns posed by resurgence of these viruses, little is known about EV68 strains circulating in Kenya. In this study, we characterized 13 EV68 strains isolated in Kenya between 2008 and 2011 based on the Hypervariable 3'-end of the VP1 gene. Viral RNA was extracted from the isolates and partial VP1 gene amplified by RT-PCR, followed by nucleotide sequencing. Alignment of deduced amino acid sequences revealed substitutions in Kenyan EV68 isolates absent in the prototype reference strain (Fermon). The majority of these changes were present in the BC and DE-loop regions, which are associated with viral antigenicity and virulence. The Kenyan strains exhibited high sequence homology with respect to those from other countries. Natural selection analysis based on the VP1 region showed that the Kenyan EV68 isolates were under purifying selection. Phylogenetic analysis revealed that majority (84.6%) of the Kenyan strains belonged to clade A, while a minority belonged to clades B and C. Overall, our results illustrate that although EV68 strains isolated in Kenya were genetically and antigenically divergent from the prototype strain (Fermon), they were closely related to those circulating in other countries, suggesting worldwide transmissibility. Further, the presence of shared mutations by Kenyan EV68 strains and those isolated in other countries, indicates evolution in the VP1 region may be contributing to increased worldwide detection of the viruses. This is the first study to document circulation of EV68 in Kenya.

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July 2014
5 Reads

If you text them, they will come: using the HIV infant tracking system to improve early infant diagnosis quality and retention in Kenya.

AIDS. 2014 Jul;28 Suppl 3:S313-21

AIDS

Abstract OBJECTIVE: The objective of this study is to evaluate the impact of the HIV Infant Tracking System (HITSystem) for quality improvement of early infant diagnosis (EID) of HIV services. DESIGN AND SETTING: This observational pilot study compared 12 months of historical preintervention EID outcomes at one urban and one peri-urban government hospital in Kenya to 12 months of intervention data to assess retention and time throughout the EID cascade of care. PARTICIPANTS: Mother-infant pairs enrolled in EID at participating hospitals before (n = 320) and during (n = 523) the HITSystem pilot were eligible to participate. INTERVENTION: The HITSystem utilizes Internet-based coordination of the multistep PCR cycle, automated alerts to trigger prompt action from providers and laboratory technicians, and text messaging to notify mothers when results are ready or additional action is needed. MAIN OUTCOME MEASURES: The main outcome measures were retention throughout EID services, meeting time-sensitive targets and improving results turn-around time, and increasing early antiretroviral therapy (ART) initiation among HIV-infected infants. RESULTS: The HITSystem was associated with an increase in the proportion of HIV-exposed infants retained in EID care at 9 months postnatal (45.1-93.0% urban; 43.2-94.1% peri-urban), a decrease in turn-around times between sample collection, PCR results and notification of mothers in both settings, and a significant increase in the proportion of HIV-infected infants started on antiretroviral therapy at each hospital(14 vs. 100% urban; 64 vs. 100% peri-urban). CONCLUSION: The HITSystem maximizes the use of easily accessible technology to improve the quality and efficiency of EID services in resource-limited settings.

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July 2014
6 Reads

Ticks and tick-borne viruses from livestock hosts in arid and semiarid regions of the eastern and northeastern parts of Kenya.

J Med Entomol 2014 Jan;51(1):269-77

Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628, Nairobi 00100, Kenya.

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January 2014
23 Reads
4 Citations
1.953 Impact Factor

Occurrence of etravirine/rilpivirine-specific resistance mutations selected by efavirenz and nevirapine in Kenyan patients with non-B HIV-1 subtypes failing antiretroviral therapy.

AIDS 2014 Jan;28(3):442-5

aU.S. Military HIV Research Program, Global Health Programs, Walter Reed Army Institute of Research, Silver Spring bHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA cKenya Defense Forces (KDF), United States Army Medical Research Unit - Kenya (USAMRU-K), Nairobi, Kenya dKenya Medical Research Institute (KEMRI)/Walter Reed Program, South Rift Valley (SRV), US Army Medical Research Unit-Kenya (USAMRU-K), Kerich, Kenya eSouthern Highlands Walter Reed Program, Mbeya, Tanzania.

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http://dx.doi.org/10.1097/QAD.0000000000000140DOI Listing
January 2014
81 Reads
4 Citations
5.554 Impact Factor

Occurrence of etravirine/rilpivirine-specific resistance mutations selected by efavirenz and nevirapine in Kenyan patients with non-B HIV-1 subtypes failing antiretroviral therapy.

AIDS. 2014 Jan 28;28(3):442-5

AIDS

Resistance to efavirenz and nevirapine has not been associated with mutations at position 138 of reverse transcriptase. In an evaluation of virologic suppression rates in PEPFAR (President's Emergency Plan For AIDS Relief) clinics in Kenya among patients on first-line therapy (RV288), 63% (617/975) of randomly selected patients on antiretroviral therapy were suppressed (HIV RNA<400 copies/ml). Among those with non-nucleoside reverse transcriptase inhibitor resistance (n = 101), 14 (13.8%) had substitutions at 138 (A, G, K or Q), mutations selected only by etravirine and rilpivirine in subtype B viruses. All 14 patients received efavirenz or nevirapine, not etravirine or rilpivirine, and were predominantly subtype A1. This may be the first report of efavirenz and nevirapine selecting these mutations in these subtypes.

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January 2014
6 Reads

Population specific reference ranges of CD3, CD4 and CD8 lymphocyte subsets among healthy Kenyans.

AIDS Res Ther 2013 Nov 7;10(1):24. Epub 2013 Nov 7.

Department of Zoological Science, Kenyatta University, P,O, Box 43844-0100, Nairobi, Kenya.

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http://dx.doi.org/10.1186/1742-6405-10-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827884PMC
November 2013
11 Reads
1 Citation
1.841 Impact Factor

Prevalence of hepatitis B and C viral co-infections among HIV-1 infected individuals in Nairobi, Kenya.

BMC Res Notes 2013 Sep 9;6:363. Epub 2013 Sep 9.

Department of Plant and Microbial sciences, Kenyatta University, Nairobi, Kenya.

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http://dx.doi.org/10.1186/1756-0500-6-363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844558PMC
September 2013
12 Reads
16 Citations

Profile of HIV type 1 coreceptor tropism among Kenyan patients from 2009 to 2010.

AIDS Res Hum Retroviruses 2013 Aug 21;29(8):1105-9. Epub 2013 May 21.

Department of Plant and Microbial Sciences, Kenyatta University, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2012.0284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715788PMC
August 2013
7 Reads
1 Citation
2.330 Impact Factor

Circulating trends of non-B HIV type 1 subtypes among Kenyan individuals.

AIDS Res Hum Retroviruses 2013 Feb 4;29(2):400-3. Epub 2012 Oct 4.

Department of Plant and Microbial Sciences, Kenyatta University, 00100 Nairobi, Kenya.

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http://dx.doi.org/10.1089/AID.2012.0213DOI Listing
February 2013
8 Reads
6 Citations
2.330 Impact Factor

Evaluation of blood collection filter papers for HIV-1 DNA PCR.

J Clin Virol 2012 Oct 7;55(2):101-6. Epub 2012 Jul 7.

International Laboratory Branch, Division of Global HIV/AIDS, Centers for Disease Control and Prevention, USA.

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http://dx.doi.org/10.1016/j.jcv.2012.06.010DOI Listing
October 2012
34 Reads
4 Citations
3.020 Impact Factor

Are slum dwellers at heightened risk of HIV infection than other urban residents? Evidence from population-based HIV prevalence surveys in Kenya.

Health Place 2012 Sep 26;18(5):1144-52. Epub 2012 Apr 26.

University of Southampton, Division of Social Statistics and Centre for Global Health, Population, Poverty, and Policy, University of Southampton, Southampton SO17 1BJ, United Kingdom.

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http://dx.doi.org/10.1016/j.healthplace.2012.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427858PMC
September 2012
23 Reads
27 Citations
2.810 Impact Factor

Discrepant test findings in early infant diagnosis of HIV in a national reference laboratory in Kenya: challenges and opportunities for programs.

J Trop Pediatr 2012 Aug 3;58(4):247-52. Epub 2011 Nov 3.

Centre for Virus Research, Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya.

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http://dx.doi.org/10.1093/tropej/fmr076DOI Listing
August 2012
8 Reads
5 Citations
0.860 Impact Factor

HIV Type 1 genetic diversity and naturally occurring polymorphisms in HIV type 1 Kenyan isolates: implications for integrase inhibitors.

AIDS Res Hum Retroviruses 2012 Aug 16;28(8):933-6. Epub 2011 Dec 16.

Department of Plant and Microbial Sciences, Kenyatta University, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2011.0122DOI Listing
August 2012
6 Reads
3 Citations
2.330 Impact Factor

HIV type 1 subtype surveillance in central Kenya.

AIDS Res Hum Retroviruses 2012 Feb 8;28(2):228-31. Epub 2011 Jul 8.

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2011.0089DOI Listing
February 2012
8 Reads
7 Citations
2.330 Impact Factor

Production of congopain, the major cysteine protease of Trypanosoma (Nannomonas) congolense, in Pichia pastoris reveals unexpected dimerisation at physiological pH.

Protein Expr Purif 2011 Jan 7;75(1):95-103. Epub 2010 Sep 7.

UMR 17 IRD-CIRAD Trypanosomes, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1016/j.pep.2010.09.002DOI Listing
January 2011
6 Reads
2 Citations
1.700 Impact Factor

Reverse transcriptase inhibitors drug resistance mutations In drug-naive HIV type 1 positive Kenyans.

East African Medical Journal Vol. 88 No. 1 January 2011

East African Medical Journal

Objective: To evaluate the extent of HIV-1 drug resistance among drug naïve Kenyan individuals. Design: Cross-sectional study. Setting: Kenya Medical Research Institute HIV laboratory Nairobi, Kenya. Subjects: A total of seventy eight HIV-1 positive drug naïve subjects randomised from five Kenyan provincial hospitals between April and June 2004. Results: A major non-nucleoside reverse transcriptase (NNRTI) an associated mutation was found in one patient (1.3%). NNRTI associated resistance mutations were present at amino acid codon sites G98A (2.56%); K103E (1.3%) and L100F (3.57%) prevalences. Baseline resistance may compromise the response to standard NNRTI-based first-line ART in 1.3 % of the study subjects. Conclusion: This indicates in general, that drug resistance among HIV-1 positive drug naïve individual is at low thresholds (1.3%) but the problem could be more serious than reported here. Continuous resistance monitoring is therefore warranted to maintain individual and population-level ART effectiveness.

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January 2011
5 Reads

The effect of participant nonresponse on HIV prevalence estimates in a population-based survey in two informal settlements in Nairobi city.

Popul Health Metr 2010 Jul 22;8:22. Epub 2010 Jul 22.

African Population and Health Research Center, Shelter Afrique Centre, 2nd Floor, Longonot Road, Upper Hill P, O, Box 10787, 00100, Nairobi Kenya.

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http://dx.doi.org/10.1186/1478-7954-8-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918531PMC
July 2010
12 Reads
10 Citations

HIV type 1 subtype diversity and drug resistance among HIV type 1-infected Kenyan patients initiating antiretroviral therapy.

AIDS Res Hum Retroviruses 2009 Dec;25(12):1211-7

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2009.0007DOI Listing
December 2009
9 Reads
10 Citations
2.330 Impact Factor

Molecular genetic diversity of hepatitis B virus in Kenya.

Intervirology 2008 4;51(6):417-21. Epub 2009 Mar 4.

Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1159/000205526DOI Listing
September 2009
10 Reads
8 Citations
1.773 Impact Factor

Genetic diversity of HIV type 1 along the coastal strip of Kenya.

AIDS Res Hum Retroviruses 2009 Sep;25(9):919-23

Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2009.0005DOI Listing
September 2009
8 Reads
7 Citations
2.330 Impact Factor

The changing trend of HIV type 1 subtypes in Nairobi.

AIDS Res Hum Retroviruses 2009 Mar;25(3):337-42

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2008.0228DOI Listing
March 2009
13 Reads
5 Citations
2.330 Impact Factor

HIV type 1 genetic diversity in Moyale, Mandera, and Turkana based on env-C2-V3 sequences.

AIDS Res Hum Retroviruses 2008 Dec;24(12):1561-4

Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2008.0085DOI Listing
December 2008
8 Reads
5 Citations
2.330 Impact Factor

Rapid identification of infants for antiretroviral therapy in a resource poor setting: the Kenya experience.

J Trop Pediatr 2008 Dec 29;54(6):370-4. Epub 2008 May 29.

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.

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http://dx.doi.org/10.1093/tropej/fmn036DOI Listing
December 2008
9 Reads
19 Citations
0.860 Impact Factor

HIV type 1 subtypes among STI patients in Nairobi: a genotypic study based on partial pol gene sequencing.

AIDS Res Hum Retroviruses 2006 Nov;22(11):1172-7

Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya., KEMRI/JICA Project, Nairobi, Kenya.

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http://dx.doi.org/10.1089/aid.2006.22.1172DOI Listing
November 2006
27 Reads
6 Citations
2.330 Impact Factor

7 Reads

Top co-authors

Vincent Okoth
Vincent Okoth

Kenya Medical Research Institute

15
Raphael W Lihana
Raphael W Lihana

Center for Virus Research

11
Elijah M Songok
Elijah M Songok

Graduate School of Medical Science

8
Matilu Mwau
Matilu Mwau

Kenya Medical Research Institute

8
Anthony Kebira Nyamache
Anthony Kebira Nyamache

Kenyatta University

7
Kathy Goggin
Kathy Goggin

Children's Mercy Hospitals and Clinics

7
Nancy Lagat
Nancy Lagat

Center for Virus Research

7

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