Bio

Prof. Bulimo's Bio

Is an Associate Professor of Biochemistry at the Department of Biochemistry, School of Medicine in the University of Nairobi. He is a leading Virologist in Kenya and Africa on response to viral respiratory pathogens causing influenza, influenza-like-illnesses (ILI) and, Severe Acute Respiratory Infections (SARI). He is currently involved with response and Research on the ongoing COVID-19 pandemic in Kenya.

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Publications


Submitted

Bulimo, W.  Submitted.  Uniprot Protein Sequences. Abstract
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Bulimo, W.  Submitted.  NCBI Protein Sequences. Abstract
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Bulimo, W.  Submitted.  NCBI Nucleotide Sequences. Abstract
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  Submitted.  . Abstract
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2021

Ogana, W, Juma VO, Bulimo WD.  2021.  A {SIRD} model applied to {COVID}-19 dynamics and intervention strategies during the first wave in Kenya, mar. : Cold Spring Harbor Laboratory AbstractWebsite
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Bahati, V, Bulimo W, Gachara G.  2021.  Comparative Seroprevalence of Hepatitis B Virus among in-Mates and Low Risk Voluntary Blood Donors in Garissa, Kenya. Journal of Biosciences and Medicines. 09:85–95., Number 07: Scientific Research Publishing, Inc. AbstractWebsite
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Ngayo, MO, Oluka M, Bulimo WD, Okalebo FA.  2021.  Influence of Social Psychological Status On Efavirenz And Nevirapine Plasma Concentration Among {HIV} Patients In Kenya, jul. : Research Square Platform {LLC} AbstractWebsite
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Chikwana, N, Maina EN, Gavamukulya Y, Bulimo W, Wamunyokoli F.  2021.  Antiproliferative Activity, c-Myc and {FGFR}1 Genes Expression Profiles and Safety of Annona muricata Fruit Extract on Rhabdomyosarcoma and {BALB}/c Mice, jul. Journal of Complementary and Alternative Medical Research. :30–46.: Sciencedomain International AbstractWebsite
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MM, B, M B, J F, EA L, A A, K A, GA B, WD B, E B, C C, H D, P D'A, L DC, N F, A M.  2021.  Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa., 10. EClinicalMedicine. Abstract
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Langat, SK, Eyase F, Bulimo W, Lutomiah J, Oyola SO, Imbuga M, Sang R.  2021.  Profiling of {RNA} Viruses in Biting Midges ( Ceratopogonidae ) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis, oct. (Benhur Lee, Ed.).: American Society for Microbiology AbstractWebsite
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Baba, MM, Bitew M, Fokam J, Lelo EA, Ahidjo A, Asmamaw K, Beloumou GA, Bulimo WD, Buratti E, Chenwi C, Dadi H, D'Agaro P, De Conti L, Fainguem N, Gadzama G, Maiuri P, Majanja J, Meshack W, Ndjolo A, Nkenfou C, Oderinde BS, Opanda SM, Segat L, Stuani C, Symekher SL, Takou D, Tesfaye K, Triolo G, Tuki K, Zacchigna S, Marcello A.  2021.  Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa, 2021. 40:101101. Abstract1-s2.0-s2589537021003813-main-1.pdf1-s2.0-s2589537021003813-main-1.pdfWebsite

BackgroundManagement and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS.
Methods
This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR).
Findings
The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35.
Interpretation
In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output.

Ogana, W, Juma VO, Bulimo WD.  2021.  A SIRD model applied to COVID-19 dynamics and intervention strategies during the first wave in Kenya, 2021/01/01. medRxiv. :2021.03.17.21253626. AbstractWebsite

The first case of COVID-19 was reported in Kenya in March 2020 and soon after non-pharmaceutical interventions (NPIs) were established to control the spread of the disease. The NPIs consisted, and continue to consist, of mitigation measures followed by a period of relaxation of some of the measures. In this paper, we use a deterministic mathematical model to analyze the dynamics of the disease, during the first wave, and relate it to the intervention measures. In the process, we develop a new method for estimating the disease parameters. Our solutions yield a basic reproduction number, R0 = 2.76, which is consistent with other solutions. The results further show that the initial mitigation reduced disease transmission by 40% while the subsequent relaxation increased transmission by 25%. We also propose a mathematical model on how interventions of known magnitudes collectively affect disease transmission rates. The modelled positivity rate curve compares well with observations. If interventions of unknown magnitudes have occurred, and data is available on the positivity rate, we use the method of planar envelopes around a curve to deduce the modelled positivity rate and the magnitudes of the interventions. Our solutions deduce mitigation and relaxation effects of 42.5% and 26%, respectively; these percentages are close to values obtained by the solution of the SIRD system. Our methods so far apply to a single wave; there is a need to investigate the possibility of extending them to handle multiple waves.Competing Interest StatementThe authors have declared no competing interest.Clinical TrialNot a clinical trialFunding StatementNo funding supportAuthor DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:KNH-UoN Ethics and Research Committee https://erc.uonbi.ac.keAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData sources: All the data used is in the public domain [1, 44, 56, 57]

Ngayo, MO, Oluka M, Bulimo WD, Okalebo FA.  2021.  Influence of Social Psychological Status On Efavirenz And Nevirapine Plasma Concentration Among HIV Patients In Kenya, 2021. : Research Square Abstract

HIV-related stigma, lack of disclosure and social support are still a hindrance to HIV testing, care, and prevention. We evaluated the influence of these socio-phycological status on nevirapine (NVP) and efavirenz (EFV) plasma concentrations among HIV patients in Kenya. Blood samples were obtained from 254 and 312 consenting HIV patients on NVP and EFV based first-line Antiretroviral therapy (ART) respectively and a detailed structured questionnaire was administered. The NVP and EFV plasma level was measured by liquid chromatography - tandem mass spectrometry (LC-MS/MS). The median duration of living with HIV infection was 5 years (IQR = 1–11years) and a median duration since ART initiation was 3 years (IQR = 1–8 years). There were 68.1% and 65.4% of the patients on NVP and EFV respectively who did not feel guilty for being HIV positive. The disclosure rate was about 96.1% and 94.6% of patients on NVP and EFV respectively. About 85% and 78.2% of patients on NVP and EFV respectively who got social support as much as needed. The non-adherence to ART in the past 30 days was 64.6% and 66.3% patients on NVP and EFV respectively. The median (IQR) plasma concentration were [6237.5 ng/mL, IQR 45188–8964 ng/mL] for NVP and [2739.5 ng/mL, IQR 1878 –4891.5 ng/mL] for EFV. There were 14.2% and 4.5% patients on NVP and EFV respectively with suboptimal plasma concertation associated with poor viral suppression. Multivariate linear regression analysis showed feeling guilty for being HIV positive (adjusted β = 954 , 95% CI = 192.7 to 2156.6 ; p =0.014) or feeling worthless for being HIV positive (adjusted β = 852 , 95% CI = 64.3 to 1639.7 ; p =0.034); being certain of telling the primary sexual partner about HIV positive status (adjusted β 363, 95% CI, 97.9 to 628.1; p = 0.007); disclosing HIV status to neighbors (adjusted β = 1731 , 95% CI = 376 to 3086 ; p =0.012) and getting transportation to hospital whenever needed (adjusted β = -1143.3, 95% CI = -1914.3 to -372.4 ; p =0.004) were associated with NVP/EFV plasma levels. The NVP and EFV plasma level was highly heterogenous with a significant proportion of patients reporting levels correlated with poor viral suppression. The patient’s stigma, lack of disclosure and social support contributes significantly on the overall ART treatment outcome. Taking these factors into consideration, HIV treatment may be personalized to achieve optimal treatment success

Chikwana, N, Maina EN, Gavamukulya Y, Bulimo W, Wamunyokoli F.  2021.  Antiproliferative Activity, c-Myc and FGFR1 Genes Expression Profiles and Safety of Annona muricata Fruit Extract on Rhabdomyosarcoma and BALB/c Mice. Journal of Complementary and Alternative Medical Research. 14(4):30-46.
Umuhoza, T, Bulimo WD, Julius Oyugi, Musabyimana JP, Kinengyere AA, Mancuso JD.  2021.  Prevalence of human respiratory syncytial virus, parainfluenza and adenoviruses in East Africa Community partner states of Kenya, Tanzania, and Uganda: A systematic review and meta-analysis (2007–2020), 2021/04/27. PLOS ONE. 16(4):e0249992-.: Public Library of Science Abstractjournal.pone_.0249992.pdfjournal.pone_.0249992.pdfWebsite

Background Viruses are responsible for a large proportion of acute respiratory tract infections (ARTIs). Human influenza, parainfluenza, respiratory-syncytial-virus, and adenoviruses are among the leading cause of ARTIs. Epidemiological evidence of those respiratory viruses is limited in the East Africa Community (EAC) region. This review sought to identify the prevalence of respiratory syncytial virus, parainfluenza, and adenoviruses among cases of ARTI in the EAC from 2007 to 2020. Methods A literature search was conducted in Medline, Global Index Medicus, and the grey literature from public health institutions and programs in the EAC. Two independent reviewers performed data extraction. We used a random effects model to pool the prevalence estimate across studies. We assessed heterogeneity with the I2 statistic, and Cochran’s Q test, and further we did subgroup analysis. This review was registered with PROSPERO under registration number CRD42018110186. Results A total of 12 studies met the eligibility criteria for the studies documented from 2007 to 2020. The overall pooled prevalence of adenoviruses was 13% (95% confidence interval [CI]: 6–21, N = 28829), respiratory syncytial virus 11% (95% CI: 7–15, N = 22627), and parainfluenza was 9% (95% CI: 7–11, N = 28363). Pooled prevalence of reported ARTIs, all ages, and locality varied in the included studies. Studies among participants with severe acute respiratory disease had a higher pooled prevalence of all the three viruses. Considerable heterogeneity was noted overall and in subgroup analysis. Conclusion Our findings indicate that human adenoviruses, respiratory syncytial virus and parainfluenza virus are prevalent in Kenya, Tanzania, and Uganda. These three respiratory viruses contribute substantially to ARTIs in the EAC, particularly among those with severe disease and those aged five and above.

2020

Kivata, MW, Mbuchi M, Eyase F, Bulimo WD, Kyanya CK, Oundo V, Mbinda WM, Sang W, Andagalu B, Soge OO, McClelland RS, Distelhorst J.  2020.  Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya. BMC Infectious Diseases. 20, Number 1 Abstract
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Nambati, EA, Njoka M, Eyase F, Majanja J, Njuguna N, Gitonga SM, Mwikwabe N, Lelo E, Mwangi M, kingoro A, Kimani F, Lubano K, Bulimo W.  2020.  Multidisciplinary approach towards training of the next generation of forensic DNA analysts in Africa; a Kenyan perspective. Forensic Science International: Synergy. 2:123-125. Abstract
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SK, L, FL E, IM B, A N, W B, S O, V O, S L, J L, R J, J D, RC S.  2020.  Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages., 01. Virus evolution. Abstract
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EM, N'au, WD B, V M, S O, E M.  2020.  Genetic Analysis of HA1 Domain of Influenza A/H3N2 Viruses Isolated in Kenya During the 2007 to 2013 Seasons Reveal Significant Divergence from WHO-Recommended Vaccine Strains., 04. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases. Abstract
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Fardolo, EK, Bulimo W, Aluora PO, Gachara G.  2020.  Seroprevalence of Hepatitis E Virus among Voluntary Blood Donors in Nairobi County, Kenya: A Pilot Study. Journal of Biosciences and Medicines. 8:78-85. Abstractjbm_2020121415213791.pdf

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Kedogo, JL, Eyase F, Bulimo W, Asudi G, Kimani F, Muhia DM, Aluvaala E.  2020.  Validation of a Biomeme Smartphone-Based DNA Real-Time PCR Assay for Diagnosis of Human Malaria at the Point of Care . African Journal of Health Sciences. 33(3):31-44.202032-article_text-506081-1-10-20201207.pdf
Githaiga, JI, Angeyo HK, Kaduki KA, Bulimo WD.  2020.  Chemometrics-Enabled Raman Spectrometric Qualitative Determination and Assessment of Biochemical Alterations during Early Prostate Cancer Proliferation in Model Tissue, 2020. Journal of Spectroscopy. 2020(Crupi, Vincenza, Ed.).:8879985.: Hindawi AbstractWebsite

The use of Raman spectroscopy combined with multivariate chemometrics for disease diagnosis has attracted great attention from researchers in recent years. This is because it is a noninvasive and nondestructive detection approach with enhanced sensitivity. However, a major challenge when analyzing spectra from biological samples has been the detection of subtle biochemical alterations buried in background and fluorescence noise. This work reports a qualitative chemometrics-assisted investigation of subtle biochemical alterations associated with prostate malignancy in model biological tissue (metastatic androgen insensitive (PC3) and immortalized normal (PNT1a) prostate cell lines). Raman spectra were acquired from PC3 and PNT1a cells at various stages of growth, and their biochemical alterations were determined from difference spectra between the two cell lines (for prominent alterations) and principal component analysis (PCA) (for subtle alterations). The Raman difference spectra were computed by subtracting the normalized mean spectral intensities of PNT1a cells from the normalized mean spectral intensities of PC3 cells. These difference spectra revealed prominent biochemical alterations associated with the malignant PC3 cells at 566 ± 0.70 cm−1, 630 cm−1, 1370 ± 0.86 cm−1, and 1618 ± 1.73 cm−1 bands. The band intensity ratios at 566 ± 0.70 cm−1 and 630 cm−1 suggested that prostate malignancy can be associated with an increase in relative amounts of nucleic acids and lipids, respectively, whereas those at 1370 ± 0.86 cm−1 and 1618 ± 1.73 cm−1 suggested that prostate malignancy can be associated with a decrease in relative amounts of saccharides and tryptophan, respectively. In the analysis using PCA, intermediate-order and high-order principal components (PCs) were used to extract the subtle biochemical fingerprints associated with the cell lines. This revealed subtle biochemical differences at 1076 cm−1, (1232, 1234 cm−1), (1276, 1278 cm−1), (1330, 1333 cm−1), (1434, 1442 cm−1), and (1471, 1479 cm−1). The band intensity ratios at 1076 cm−1 and 1232 cm−1 suggested that prostate malignancy can be associated with an increase in subtle amounts of nucleic acids and amide III components, respectively. The method reported here has demonstrated that subtle biochemical alterations can be extracted from Raman spectra of normal and malignant cell lines. The identified subtle bands could play an important role in quantitative monitoring of early biomarker alterations associated with prostate cancer proliferation.

Kivata, MW, Mbuchi M, Eyase F, Bulimo WD, Kyanya CK, Oundo V, Mbinda WM, Sang W, Andagalu B, Soge OO, McClelland RS, Distelhorst J.  2020.  Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya, 2020. 20(1):703. Abstractkivata_et_al-2020-bmc_infectious_diseases.pdfkivata_et_al-2020-bmc_infectious_diseases.pdfWebsite

Treatment of gonorrhea is complicated by the development of antimicrobial resistance in Neisseria gonorrhoeae (GC) to the antibiotics recommended for treatment. Knowledge on types of plasmids and the antibiotic resistance genes they harbor is useful in monitoring the emergence and spread of bacterial antibiotic resistance. In Kenya, studies on gonococcal antimicrobial resistance are few and data on plasmid mediated drug resistance is limited. The present study characterizes plasmid mediated resistance in N. gonorrhoeae isolates recovered from Kenya between 2013 and 2018.

Umuhoza, T, Bulimo WD, Oyugi J, Schnabel D, Mancuso JD.  2020.  Prevalence and factors influencing the distribution of influenza viruses in Kenya: Seven-year hospital-based surveillance of influenza-like illness (2007-2013). PLoS One. 15(8):e0237857. Abstractumuhoza_et_al_2020.pdfWebsite

BACKGROUND: Influenza viruses remain a global threat with the potential to trigger outbreaks and pandemics. Globally, seasonal influenza viruses' mortality range from 291 243-645 832 annually, of which 17% occurs in Sub-Saharan Africa. We sought to estimate the overall prevalence of influenza infections in Kenya, identifying factors influencing the distribution of these infections, and describe trends in occurrence from 2007 to 2013. METHODS: Surveillance was conducted at eight district hospital sites countrywide. Participants who met the case definition for influenza-like illness were enrolled in the surveillance program. The nasopharyngeal specimens were collected from all participants. We tested all specimens for influenza viruses with quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) assay. Bivariate and multivariate log-binomial regression was performed with a statistically significant level of p<0.005. An administrative map of Kenya was used to locate the geographical distribution of surveillance sites in counties. We visualized the monthly trend of influenza viruses with a graph and chart using exponential smoothing at a damping factor of 0.5 over the study period (2007-2013). RESULTS: A total of 17446 participants enrolled in the program. The overall prevalence of influenza viruses was 19% (n = 3230), of which 76% (n = 2449) were type A, 21% (n = 669) type B and 3% (n = 112) A/ B coinfection. Of those with type A, 59% (n = 1451) were not subtyped. Seasonal influenza A/H3N2 was found in 48% (n = 475), influenza A/H1N1/pdm 2009 in 43% (n = 434), and seasonal influenza A/ H1N1 in 9% (n = 88) participants. Both genders were represented, whereas a large proportion of participants 55% were

Opanda, S, Bulimo W, Gachara G, Ekuttan C, Amukoye E.  2020.  Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene. PLoS One. 15(2):e0228029. Abstractpone.0228029.pdf

Influenza A (H1N1) pdm09 virus emerged in North America in 2009 and has been established as a seasonal strain in humans. After an antigenic stasis of about six years, new antigenically distinct variants of the virus emerged globally in 2016 necessitating a change in the vaccine formulation for the first time in 2017. Herein, we analyzed thirty-eight HA sequences of influenza A (H1N1) pdm09 strains isolated in Kenya during 2015-2018 seasons, to evaluate their antigenic and molecular properties based on the HA1 sub-unit. Our analyses revealed that the A (H1N1) pdm09 strains that circulated in Kenya during this period belonged to genetic clade 6B, subclade 6B.1 and 6B.2. The Kenyan 2015 and 2016 isolates differed from the vaccine strain A/California/07/2009 at nine and fourteen antigenic sites in the HA1 respectively. Further, those isolated in 2017 and 2018 correspondingly varied from A/Michigan/45/2015 vaccine strain at three and fifteen antigenic sites. The predicted vaccine efficacy of A/California/07/2009 against Kenyan 2015/2016 was estimated to be 32.4% while A/Michigan/45/2015 showed estimated vaccine efficacies of 39.6% - 41.8% and 32.4% - 42.1% against Kenyan 2017 and 2018 strains, respectively. Hemagglutination-inhibition (HAI) assay using ferret post-infection reference antiserum showed that the titers for the Kenyan 2015/2016 isolates were 2-8-fold lower compared to the vaccine strain. Overall, our results suggest the A (H1N1) pdm09 viruses that circulated in Kenya during 2015/2016 influenza seasons were antigenic variants of the recommended vaccine strains, denoting sub-optimal vaccine efficacy. Additionally, data generated point to a swiftly evolving influenza A (H1N1) pdm09 virus in recent post pandemic era, underscoring the need for sustained surveillance coupled with molecular and antigenic analyses, to inform appropriate and timely influenza vaccine update.

Nyang'au, EM, Bulimo WD, Mobegi V, Opanda S, Magiri E.  2020.  Genetic Analysis of HA1 Domain of Influenza A/H3N2 Viruses Isolated in Kenya During the 2007 to 2013 Seasons Reveal Significant Divergence from WHO-Recommended Vaccine Strains. Int J Infect Dis. Abstractnyagau_et_al_2020.pdf

BACKGROUND: Influenza viruses evolve rapidly and cause regular seasonal epidemics in humans challenging effective vaccination. The virus surface HA glycoprotein is the primary target for the host immune response. Here, we investigated the vaccine efficacy and evolution patterns of human influenza A/H3N2 viruses that circulated in Kenyan in the period before and after the 2009 A/H1N1 pandemic, targeting the HA1 domain. MATERIALS AND METHODS: A hundred and fifteen HA sequences of Kenyan virus viruses were analyzed relative to the corresponding WHO vaccine reference strains using bioinformatics approaches. RESULTS: Our analyses revealed varied amino acid substitutions at all the five antigenic sites (A-E) of the HA1 domain, with a majority the changes occurring at sites A and B. The Kenyan A/H3N2 viruses isolated during 2007/2008 seasons belonged to A/Brisbane/10/2007- like viruses lineage, while those circulating in 2009 to 2012 belonged to the lineage of A/Victoria/361/2011-like viruses. The 2013 viruses clustered in clade 3C.3 of the A/Samara/73/2013-like viruses. The mean evolutionary rate of the A/H3N2 viruses analyzed in the study was at 4.17×10(-3) (95% HPD=3.09×10(-3) to 5.31×10(-3)) nucleotide substitutions per site per year, whereas the TMRCA was estimated at 11.18 (95% HPD=9.00-14.12) years ago from 2013. The Prediction of vaccine efficacy revealed modest vaccine efficaciousness during 2008, and 2010 influenza seasons, whilst sub-optimal effectiveness was registered in 2007,2009, 2012 and 2013. Further, the overall selective pressure acting on the HA1 domain was estimated at 0.56 (ω<1), suggesting that a majority of codon sites in the HA1 epitopes were evolving under purifying selection. CONCLUSIONS: Generally, our results highlight the genetic plasticity of A/H3N2 viruses and reveal considerable disparity in vaccine efficaciousness against the A/H3N2 viruses that circulated in Kenya, specifically during 2007,2009, 2012, and 2013 influenza seasons. Our findings underscore the importance and need for consistent surveillance and molecular characterization of influenza viruses, to inform decision making and enhance early of detection of strains with epidemic/pandemic potential as well as benefit in guiding decisions regarding the appropriate annual influenza vaccine formulations.

Nambati, EA, Njoka M, Eyase F, Majanja J, Njuguna N, Gitonga SM, Mwikwabe N, Lelo E, Mwangi M, kingoro A, Kimani F, Lubano K, Bulimo W.  2020.  Multidisciplinary approach towards training of the next generation of forensic DNA analysts in Africa; a Kenyan perspective. Forensic Science International: Synergy. 2:123-125. Abstract1-s2.0-s2589871x20300267-main.pdfWebsite

The uptake of forensic DNA testing technologies in Africa has been slow despite the revolutionary technology being discovered and adopted 3 decades ago. African governments and partners have invested in construction and equipping of forensic laboratories in Africa but the benefits are yet to be realised as the laboratories are still faced with the challenge of shortage of adequately trained personnel. This paper describes an innovative multidisciplinary training approach that was developed and used to train officers from the Directorate of Criminal Investigations Kenya. We report on the structure, implementation and effectiveness of the training. It is expected that with the increased number of trained forensic DNA analysts, there will be an improvement in quality of forensic DNA evidence presented in courts and a reduction in backlog in the forensic biology laboratories in Kenya.

Langat, SK, Eyase FL, Berry IM, Nyunja A, Bulimo W, Owaka S, Ofula V, Limbaso S, Lutomiah J, Jarman R, Distelhorst J, Sang RC.  2020.  Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype . Virus Evol. 6(1):veaa026. Abstractveaa026.pdfWebsite

Dengue fever (DF) is an arboviral disease caused by dengue virus serotypes 1-4 (DENV 1-4). Globally, DF incidence and disease burden have increased in the recent past. Initially implicated in a 1982 outbreak, DENV-2 recently reemerged in Kenya causing outbreaks between 2011 and 2014 and more recently 2017-8. The origin and the evolutionary patterns that may explain the epidemiological expansion and increasing impact of DENV-2 in Kenya remain poorly understood. Using whole-genome sequencing, samples collected during the 2011-4 and 2017-8 dengue outbreaks were analyzed. Additional DENV-2 genomes were downloaded and pooled together with the fourteen genomes generated in this study. Bioinformatic methods were used to analyze phylogenetic relationships and evolutionary patterns of DENV-2 causing outbreaks in Kenya. The findings from this study have shown the first evidence of circulation of two different Cosmopolitan genotype lineages of DENV-2; Cosmopolitan-I (C-I) and Cosmopolitan-II (C-II), in Kenya. Our results put the origin location of C-I lineage in India in 2011, and C-II lineage in Burkina Faso between 1979 and 2013. C-I lineage was the most isolated during recent outbreaks, thus showing the contribution of this newly emerged strain to the increased DENV epidemics in the region. Our findings, backed by evidence of recent local epidemics that have been associated with C-I in Kenya and C-II in Burkina Faso, add to the growing evidence of expanding circulation and the impact of multiple strains of DENV in the region as well as globally. Thus, continued surveillance efforts on DENV activity and its evolutionary trends in the region, would contribute toward effective control and the current vaccine development efforts.

Elusah, J, Bulimo WD, Opanda SM, Symekher SL, Wamunyokoli F.  2020.  Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene. PLOS ONE. 15(3):e0229355. Abstractelusa_et_al_2020.pdfWebsite

Human respirovirus type 3 (HRV3) is a leading etiology of lower respiratory tract infections in young children and ranks only second to the human respiratory syncytial virus (HRSV). Despite the public health importance of HRV3, there is limited information about the genetic characteristics and diversity of these viruses in Kenya. To begin to address this gap, we analyzed 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013. Viral RNA was extracted from the isolates, and the entire HN gene amplified by RT-PCR followed by nucleotide sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates grouped into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of isolates belonged to sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence analysis revealed high identities between the Kenyan isolates and the HRV3 prototype strain both at the amino acid (96.5–97.9%) and nucleotide (94.3–95.6%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection pressure analyses showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses revealed that the mean TMRCA for the HN sequence dataset was 1942 (95% HPD: 1928–1957), while the mean evolutionary rate was 4.65x10-4 nucleotide substitutions/site/year (95% HPD: 2.99x10-4 to 6.35x10-4). Overall, our results demonstrate the co-circulation of strains of cluster C HRV3 variants in Kenya during the study period. This is the first study to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene.

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