RP-Deparment of Medical Laboratory Sciences
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Browsing RP-Deparment of Medical Laboratory Sciences by Author "Bulimo, W."
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Item Burden of Human Rhinovirus Infections in Influenza like Illnesses in Kenya(Elsevier, 2014) Kaburu, S. M.; Bulimo, W.; Maina, G. G.; Ongus, J.Background: There have been several recent reports of respiratory outbreaks with associated mortality due to human rhinovirus (HRV) infection. Studies on viral etiologies of Influenza-like illness have shown that many patients are infected with more than one viral agent with frequencies of co-infection being as high as 20%. From these studies, human rhinovirus has been shown as one of the most prominent respiratory viruses that co-infect patients with influenza. In Kenya, the ongoing Influenza surveillance has provided data that now allows for exploration of other respiratory viruses that cause influenza-like illnesses. Currently, there is scanty information on the patterns of HRV circulation throughout the country. Methods & Materials: This study utilized a retrospective cross-sectional descriptive design. It involved the use of 517 archived samples from the ongoing country-wide influenza Surveillance protocol. The archived nasopharyngeal specimens were collected from a study population comprising persons from two months of age onwards who attended outpatient clinics in the year 2008, in hospitals located in 8 different regions in Kenya presenting with influenza like illnesses. Viral RNA was extracted from the samples followed by real-time RT-PCR assays with HRV-specific primers for screening for HRV. Results: A total of 131 (25%) of the samples were positive for HRV. The highest prevalence (33%) was recorded from samples obtained from the Coast region of the country, followed by Western region (32.7%) while Eastern region had the lowest prevalence (11%). Children aged between 2 months -7 years were mostly infected while the age group ≥60 years was least affected. There was no significant difference in HRV infection in relation to gender. Conclusion: The study notes that HRV infection is a significant viral etiology of morbidity throughout the country. However, disparities were observed between different regions. The more humid regions in the country (Western and Coast) had the highest HRV prevalence. At the same time, children below 7 years were at a greater risk of HRV infection. Determination of the molecular characteristics of the rhinovirus strains to enable specific identification of the species and the evolutionary relationships is ongoing.Item Evolutionary Pattern of the Hemagglutinin Gene of Influenza B Viruses Isolated in Kenya 2005-2009(African Journal of Health Sciences, 2011-06-17) Gachara, George; Bulimo, W.; Magana, J.; Simwa, J.; Symekher, S.Background: In humans, the inability to provide lasting protection against influenza B virus infection is due, in part, to the rapid evolution of the viral surface glycoprotein, haemagglutinin (HA), which leads to a change in its antigenic nature. Therefore, the evolution of the haemagglutinin (HA) an important influenza antigen has and continues to be a subject of intensive research. In this study, we analyzed the evolution occurring in the haemagglutinin of influenza B viruses from Kenya since virological surveillance began in 2005. Methods: Thirty (30) influenza B haemagglutinin sequences of viruses isolated from different parts of the country between 2005-2009 at the NIC were analyzed. Nucleotide sequences, prediction of amino acid sequences, alignments, and phylogenetic tree construction were completed using BioEdit and MEGA® software Results: During the five year study period, the two influenza B lineages B/Yamagata and B/Victoria have co-circulated in two years (2005 and 2007) while B/Yamagata viruses exclusively circulated in 2008 and B/Victoria viruses in 2006 and 2009. The nucleotide sequence identity ranged from 92.9% – 97.0% among the B/Yamagata lineage viruses and 90.6% – 98.5% among the B/Victoria lineage viruses. There was generally noted more amino acid substitutions among the B/Yamagata lineage than the B/Victoria lineage. Substitutions were observed in all the epitope regions among B/Yamagata viruses compared to three epitopes in the B/Victoria viruses. Both lineages showed substitutions at position HA1 165. Conclusions: These results demonstrate that distinct viruses within the two lineages have been co-circulating in the country every year and that there has been a greater evolution of the B/Yamagata viruses. At the same time it is noted that like elsewhere, influenza B viruses in the country have continually been evolving by antigenic drift. In-order to understand whether reassortments have occurred, the study suggests periodic complete genomic sequencing of select.Item Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic(Elsevier, 2016) Gachara, George; Symekher, S.; Otieno, M.; Magana, J.; Opot, B.; Bulimo, W.An influenza pandemic caused by a novel influenza virus A(H1N1)pdm09 spread worldwide in 2009 and is estimated to have caused between 151,700 and 575,400 deaths globally.Whilewhole genome data on newvirus enables a deeper insight in the pathogenesis, epidemiology, and drug sensitivities of the circulating viruses, there are relatively limited complete genetic sequences available for this virus from African countries. We describe herein the full genome analysis of influenza A(H1N1)pdm09 viruses isolated in Kenya between June 2009 and August 2010. A total of 40 influenza A(H1N1)pdm09 viruses isolated during the pandemic were selected. The segments from each isolate were amplified and directly sequenced. The resulting sequences of individual gene segments were concatenated and used for subsequent analysis. These were used to infer phylogenetic relationships and also to reconstruct the time of most recent ancestor, time of introduction into the country, rates of substitution and to estimate a time-resolved phylogeny. The Kenyan complete genome sequences clustered with globally distributed clade 2 and clade 7 sequences but local clade 2 viruses did not circulate beyond the introductory foci while clade 7 viruses disseminated country wide. The time of the most recent common ancestor was estimated between April and June 2009, and distinct clusters circulated during the pandemic. The complete genome had an estimated rate of nucleotide substitution of 4.9 × 10−3 substitutions/site/year and greater diversity in surface expressed proteins was observed. We show that two clades of influenza A(H1N1)pdm09 virus were introduced into Kenya from the UK and the pandemic was sustained as a result of importations. Several closely related but distinct clusters co-circulated locally during the peak pandemic phase but only one cluster dominated in the late phase of the pandemic suggesting that it possessed greater adaptability