Browsing by Author "Bulimo, Wallace D."

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    Amino acid sequence analysis and identification of mutations in the NS gene of 2009 influenza A (H1N1) isolates from Kenya.
    (Virus Genes, 2011-05) Gachara, George; Symekher, Samuel; Mbithi, J. N.; Simwa, James; Ng'ayo, Musa; Magana, Japheth; Bulimo, Wallace D.
    Although the important role of the nonstructural (NS) gene of influenza A virus in virulence and replication is well-established, the knowledge about the extent of variation in the NS gene of 2009 influenza A (H1N1) viruses in Kenya and Africa is scanty. This study analysed the NS gene of 31 isolates from Kenya in order to obtain a more detailed knowledge about the genetic variation of NS gene of 2009 influenza A (H1N1) isolates from Kenya. A comparison with the vaccine strain and viruses isolated elsewhere in Africa was also made. The amino acid sequences of the non-structural protein, NS1 of the viruses from this study and the vaccine strain revealed 18 differences. Conversely, the nuclear export protein (NEP) of the isolates in this study had 11 differences from the vaccine strain. Analysis of the NS1 protein showed only one fixed amino acid change I123V which is one of the characteristics of clade 7 viruses. In the NEP, the amino acid at position 77 was the most mutable with 9 (39%) of all mutations seen in this protein. A mutation A115T which is a characteristic of clade 5 viruses was noted in the isolates from Lagos, Nigeria. The study shows a substantial number of mutations in the NS gene that has not been reported elsewhere and gives a glimpse of the evolution of this gene in the region.
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    Evidence in Kenya of Reassortment Between Seasonal Influenza A(H3N2) and Influenza A(H1N1)pdm09 to yield A(H3N2) Variants With the Matrix Gene Segment of A(H1N1)pdm09
    (Molecular Biology Reports, 2012-02) Gachara, George; Bulimo, Wallace D.; Opot, Benjamin H; Murage, Margaret W; Wurapa, Eyako K
    Background: Influenza viruses evolve rapidly and undergo frequent reassortment of different gene segments leading to emergence of novel strains with new traits possessing pandemic potential. Objectives: To determine evidence of reassortment amongst A(H1N1)pdm09 and H3N2 co-circulating influenza virus subtypes and relate these to adamantine antiviral resistance. Methodology: Nasopharyngeal swabs in virus transport medium were collected from patients with influenza-like illness. The presence of influenza was determined using real-time PCR followed by culture in MDCK cells. Haemagglutination inhibition was carried out to confirm the identity of the virus. Complete haemagglutinin (HA), matrix (M) and neuraminidase (NA) genes were sequenced and analyzed using a suite of bioinformatics tools. Results: Influenza A(H3N2) was detected in 32 out of 708 samples collected between October and December 2010. Analysis of the HA gene confirmed it to be of the H3 subtype. However, analysis of the matrix gene showed that 28 of the isolates had the M gene of influenza A(H3N2) viruses while 4 had the M gene of the A(H1N1)pdm09 viruses. Discussion: Our results show that four of the 32 influenza A(H3N2) viruses isolated had acquired the M gene segment of the A(H1N1)pdm09 virus by reassortment. This has implications in their transmissibility as the M gene is implicated in the increased transmissibility of the A(H1N1)pdm09 viruses.
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    Impact of Influenza A(H1N1)pdm09 Virus on Circulation Dynamics of Seasonal Influenza Strains in Kenya.
    (The American Journal of Tropical Medicine and Hygiene, 2013-03) Gachara, George; Majanja, Janet; Njoroge, Rose N; Achilla, Rachel; Wurapa, Eyako K; Wadegu, Meshack; Mukunzi, Silvanos; Mwangi, Josephat; Njiri, James; Bulimo, Wallace D.
    We describe virus variations from patients with influenza-like illness before and after the appearance of influenza A(H1N1)pdm09 in Kenya during January 2008-July 2011. A total of 11,592 nasopharyngeal swabs were collected from consenting patients. Seasonal influenza B, A/H1N1, A/H3N2, A/H5N1, and influenza A(H1N1)pdm09 viruses were detected by real-time reverse transcription-polymerase chain reaction. Of patients enrolled, 2073 (17.9%) had influenza. A total of 1,524 (73.4%) of 2,073 samples were positive for influenza A virus and 549 (26.6%) were positive for influenza B virus. Influenza B virus predominated in 2008 and seasonal A(H1N1) virus predominated in the first half of 2009. Influenza A(H1N1)pdm09 virus predominated in the second half of 2009. Influenza A/H3N2 virus predominated in 2010, and co-circulation of influenza A(H1N1)pdm09 virus and influenza B virus predominated the first half of 2011. The reduction and displacement of seasonal A(H1N1) virus was the most obvious effect of the arrival of influenza A(H1N1)pdm09 virus. The decision of the World Health Organization to replace seasonal A(H1N1) virus with the pandemic virus strain for the southern hemisphere vaccine was appropriate for Kenya.
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    Molecular Epidemiology and Evolution of Influenza A(H1N1) pdm09 Virus in Kenya
    (2014-02-17) Maina, George Gachara; Bulimo, Wallace D.; Otieno, Micheal Frederick
    In April 2009, a novel influenza A virus was detected in Mexico and California. Thereafter, it spread globally to cause the first influenza pandemic of the 21st century. The virus was found to be antigenically unrelated to human seasonal influenza viruses but genetically related to viruses known to circulate in pigs. In view of its likely swine origin, it was initially referred to as ‘swine-origin influenza virus’ (S-OIV) A/H1N1, or pandemic influenza A (H1N1) 2009 virus but was later renamed by the World Health Organization as influenza A(H1N1)pdm09 virus. In its first year of circulation, the virus is estimated to have caused between 151,700 and 575,400 deaths globally. In Kenya, the virus was first detected in late June 2009 and in the next one year was the dominant virus in circulation. However, no laboratory confirmed deaths occurred in the country. The emergence and subsequent rapid global spread of this influenza virus provided a unique opportunity to observe the evolutionary dynamics of a pandemic influenza virus in Kenya, a tropical region where the virus circulates throughout the year. Understanding the evolution of influenza A(H1N1)pdm09 virus within the country is essential for studying global diversification, the emergence, spread and resistance of the viruses circulating in this region of the world, as well as determining the genetic relationships among the Kenyan strains and vaccine strains. The aim of this study therefore was to reconstruct the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Kenya during its first year of circulation. To accomplish this, the study undertook whole genome Sanger sequencing of 40 influenza A(H1N1)pdm09 virus isolates sampled nationwide during the pandemic period. To understand the evolutionary dynamics of the local A(H1N1)pdm09 viruses, the study employed the Bayesian evolutionary framework to analyze the resulting 320 individual gene sequences and the 40 complete genomes and compared them with sequences from two African countries, UK, USA and China isolated during the same period. The phylogenetic analyses showed that all of the Kenyan sequences sampled in the pandemic period grouped into at least four highly significant clusters and were interspersed with isolates from other countries. Two global clades (2 and 7) were identifiable within the first two weeks of the pandemic in Kenya, with clade 7 undergoing further diversification while clade 2 was not detected beyond the introductory foci. The time of the most recent common ancestor of the strains circulating in Kenya was estimated to be between April and June 2009, two months before the first laboratory confirmed case. High evolutionary rates and fast population growths was also observed. Progressive drift away from the vaccine strain was observed at both the nucleotide and amino acid level, with 2010 strains clustering separate from 2009 strains. A few unique clusters of amino acid changes were identified among all gene segments in the course of the pandemic, but no mutations previously associated with increased virulence were detected. The local strains were shown to be sensitive to neuraminidase inhibitors but resistant to adamantanes. Overall, results from this study indicate that two clades of influenza A(H1N1)pdm09 virus were introduced in Kenya and that the pandemic was sustained by multiple importations. They also indicate that clade 7 viruses dominated local transmission with an efficient community spread that was devoid of any spatial patterns but a progressive genetic drift was evident. In conclusion, adaptive evolution and viral migration seem to play a vital role in shaping the evolutionary dynamics of local A(H1N1)pdm09 viruses.