8 research outputs found
Genotypic Characterization of Resistance to Neuraminidase Inhibitors amongst Influenza A viruses that circulated in Kenya from 2008 to 2011
No full textBackground: Vaccines and antivirals are the mainstay for mitigation and clinical management of influenza infections. However, due to the ever changing antigenic profile, vaccine formulations are revised every year to keep them efficacious. Neuraminidase (NA) inhibitors, mainly oseltamivir and zanamivir, function both as prophylactic and treatment agents. In neuraminidase inhibition, inhibitor molecules mimic NA’s natural substrate and bind to the active site, preventing NA from cleaving host cell receptors and releasing new virus. Currently there exists no data on antiviral susceptibility profile of influenza A isolates circulating within the Eastern African region. Here we characterized the antiviral susceptibility of the 2008-2011 influenza A viruses circulating in Kenya. Methodology: Nasopharyngeal swab specimen from consenting outpatients of ages greater than or equal to two months were obtained and transported under the cold chain to the National Influenza Center (NIC) and screened by real-time RT-PCR using primers targeted at the matrix, and hemagglutinin genes of influenza A subtypes. Positive specimens were inoculated onto MDCK monolayers to isolate virus. RNA was extracted from virus isolates followed by PCR amplification of NA gene segments using gene-specific primers. Nucleotide sequencing of the NA amplicons was carried out using the BigDye chemistry prior to analyses using a suite of bioinformatics tools. Results: 836 influenza A viruses were isolated. 108 (13%) isolates were analyzed for susceptibility to NA inhibitors. 64% (7/11) of the 2008 seasonal influenza A/H1N1 isolates depicted oseltamivir resistant marker H275Y while all 33 influenza A/H3N2 isolates had H at position 275 hence were sensitive to oseltamivir. Similarly, genetic analysis of the A(H1N1)pdm09 strains in 2009 showed that all had H275 hence sensitive to oseltamivir. The same pattern was duplicated in 2 of the pandemic influenza A/ H1N1 isolates analyzed in the year 2010. Thus all A(H1N1)pdm09 isolated were sensitive to oseltamivir. In 2011 we isolated 14 isolates belonging to influenza A/H3N2 subtype. All these had H 275 in the NA protein implying sensitivity to oseltamivir. Overall, our genotypic data demonstrate that there was oseltamivir resistance in seasonal influenza A (H1N1) viruses isolated in Kenya in 2008-2009. Conclusion: Our study shows that seasonal influenza A/H1N1 was displaced in 2010 and 2011 after introduction influenza A(H1N1)pdm09 which has since replaced the previous seasonal influenza A/H1N1
Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa
No full textManagement 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
Surveillance of Human Parainfluenza viruses in Kenya during the 2007-2011 Period
No full textBackground: Human parainfluenza viruses (HPIVs) belong to the paramyxoviridae family and are classified into four types. These viruses account for a large percentage of pediatric respiratory disease, including syndromes such as upper respiratory tract infections (URTIs), laryngotracheobronchitis (croup), bronchiolitis, and pneumonia. HPIV is the major cause of croup in which type 1 is most frequent cause, followed by type 3 and type 2 respectively. In January 2007, through an existing influenza surveillance network, the Kenyan National Influenza center started screening for parainfluenza and other non-influenza respiratory viruses within the designated Influenza surveillance network made up of eight sentinel sites spread throughout the country. Objective: The objective of this study was to monitor and document circulation of Human parainfluenza viruses in Kenya in the period 2007-2011. Methodology: Specimens were collected from the nasopharynx using a flocked swab from consenting patients meeting the WHO influenza-like-illness (ILI) case definition. Specimens were transported to the NIC while observing the cold chain and inoculated into LLCMK2 cell line. After incubation and observation for cytopathic effect, all samples were screened by direct immunofluorescence assay (IFA) using the Respiratory Panel I Viral Screening and Identification kit (Chemicon International, Inc). Results: 14,990 nasopharyngeal swab samples were collected between January 2007-October 2011. HPIV were detected in 801 (5.3%) cases. 361 (45%) of the detections were HPIV-3 followed by HPIV-1 in 296 (37%) and 144 (18%) for HPIV-2 respectively. This confirms what has been observed elsewhere that HPIV1 and HPIV3 are the most frequently detected types. Analyses of co-infections involving HPIVs showed that HPIV1/HPIV2 (16cases) were the most frequent followed by HPIV1/HPIV3 (15) cases and HPIV2/HPIV3 (15 cases). There were 30 cases of triple infections of HPIV1/HPIV2/HPIV3. Generally, parainfluenza viruses circulated throughout the period under study. Parainfluenza virus infections were observed throughout the year with no distinct seasonal patterns. Conclusion: This study shows that parainfluenza viruses contributed to a significant level to the respiratory disease burden in Kenya in 2007-2011. Furthermore, our study has shown that parainfluenza viruses circulated in the human population in Kenya throughout the study period and did not show any distinct seasonality
Impact of Influenza A(H1N1)pdm09 Virus on Circulation Dynamics of Seasonal Influenza Strains in Kenya
No full textMolecular Surveillance of Adamantane Resistance among Human Influenza A Viruses Isolated in Four Epidemic Seasons in Kenya
No full textBackground: Adamantanes impede influenza A virus replication and are important in the treatment and prophylaxis of disease caused by these viruses. Genotypic characterization of influenza A viruses for mutations associated with resistance to adamantanes has not been fully investigated in Kenya. Objective: To characterize susceptibility of influenza A virus subtypes that circulated in Kenya from 2008-2011 to adamantanes. Methods: Archived influenza A virus strains obtained from 2008 to 2011 were propagated in MDCK cells prior to sequencing of the matrix and hemagglutinin gene segments, followed by bioinformatics analyses. Results: Ninety two virus strains consisting of 21 A/H3N2, 18 A/H1N1 and 53 A/H1N1pdm09 were analyzed. All A/H3N2 and A/H1N1pdm09 viruses displayed resistance to adamantanes due to the S31N/S31D amino acid substitution. All A/H1N1pdm09 virus strains belonged to the N-lineage characterized by S203T amino acid substitution in the HA1. All A/H1N1 viruses were sensitive to adamantane and were characterized by K140E amino acid substitution in the HA1. Conclusion: All Kenyan influenza A/H3N2 and A/H1N1pdm09 virus strains were resistant to adamantanes while seasonal A/H1N1 strains were sensitive to these drugs. During the study period, Amantadine and Rimantadine were inappropriate for prophylaxis and treatment of influenza disease caused by A/H3N2 and A/H1N1pdm09 virus subtypes in Kenya. Key words: Kenya, influenza A/H3N2, A/H1N1pdm09, A/H1N1, adamantane
Analyses of selection pressure on the Hemagglutinin gene of influenza A/H3N2 Viruses circulating in Kenya 2007-2011
No full textBackground: The hemagglutinin (HA) gene of Influenza viruses, especially the HA1 portion, exhibits a rapid rate of change, largely in response to human immune surveillance in a partially immune human population. Mutations in influenza viral genes accumulate over time and are under selection pressure during epidemics or pandemics. Objective: To determine whether the Kenyan influenza A/H3N2 viruses are undergoing adaptive evolution to become epidemic threats. Methods: Nasopharyngeal samples from patients meeting the WHO ILI case definition were collected between 2007 and 2010 from across Kenya. The detection of H3N2 virus was carried out using real-time RT-PCR. Positive samples were then cultured in MDCK cells and confirmed using the HAI assay. 156 isolates from this period were selected for amplification of the HA1 portion of the HA gene and the resulting amplicons sequenced. Global estimates, ω, of dN and dS, averaged over the entire alignment, were compared to calculate the overall strength of selection using the HyPhy 2.0 software package implemented in datamonkey. Results: Analysis of neutrality using, Kumar’s method showed that ω varied from 0.50 in 2007, 0.36 in 2008, 0.32 in 2009, 0.61 in 2010 and 0.41 in 2011. Further site by site analysis identified amino acid positions 46, 158 and 173 to be under positive selection. Analysis of differential selection showed 7 sites that harbored two or more amino acid substitutions. Amino acid positions 158, 160 and 189 had the highest number of amino acid polymorphisms. Conclusions: Overall, this study shows that local Influenza A(H3N2) viruses have been evolving via a series of ‘adaptive bursts’ characterized by positive selection occurring largely in immunological epitopes B and D. In between these bursts there is little evidence for positive selection and newly-emergent strains slowly replace the existent strains. Based on this study alone, we propose that these bursts occur after every two years. Since in a single population, dN/dS <1does not follow monotonic function, it is difficult to infer selection pressure in these results. However, by focusing on the antigenic sites we were able to observe an evolutionary pattern in the Kenyan samples. Thus evolution of Kenyan Influenza A(H3N2) is characterized by non synonymous changes followed by a period of stasis that is then followed by another period of non synonymous changes which is followed by purification selection
Epidemiology of 2009 Pandemic Influenza A Virus Subtype H1N1 Among Kenyans Aged 2 Months to 18 Years, 2009–2010
No full textBackground.The US Army Medical Research Unit–Kenya (USAMRU-K) conducts surveillance for influenza-like illness (ILI) in Kenya. We describe the temporal and geographic progression of A(H1N1)pdm09 as it emerged in Kenya and characterize the outpatient population with A(H1N1)pdm09 infection.Methods.We included patients with ILI aged 2 months to 18 years enrolled during June 2009–August 2010. Respiratory specimens were tested by real-time reverse-transcription polymerase chain reaction for influenza virus. Patients with A(H1N1)pdm09 infection were compared to those with seasonal influenza A virus infection and those with ILI who had no virus or a virus other than influenza virus identified (hereafter, “noninfluenza ILI”).Results.Of 4251 patients with ILI, 193 had laboratory-confirmed A(H1N1)pdm09 infection. The first pandemic influenza case detected by USAMRU-K surveillance was in August 2009; peak activity nationwide occurred during October–November 2009. Patients with A(H1N1)pdm09 infection were more likely to be school-aged, compared with patients with seasonal influenza A virus infection (prevalence ratio [PR], 2.0; 95% confidence interval [CI], 1.3–3.1) or noninfluenza ILI (PR, 3.2; 95% CI, 2.4–4.3).Conclusions.USAMRU-K ILI surveillance detected the geographic and temporal distribution of pandemic influenza in Kenya. The age distribution of A(H1N1)pdm09 infections included more school-aged children, compared with seasonal influenza A virus infection and noninfluenza ILI
Were the WHO-recommended Human Influenza Vaccine Formulations Appropriate for Kenya During the 2010-2011 Season? Inferences from the HA1 Gene Analysis
No full textBackground: The knowledge of evolutionary patterns of the HA gene of the influenza virus is important in vaccine strain selection. Objective: Genetic analysis of HA1 of influenza viruses isolated in Kenya during the 2010-2011 season with reference to WHO vaccine strains. Methods: A total of twenty seven (27) influenza A (H1N1) pdm09, Nineteen (19) influenza A (H3N2) and Sixteen (16) influenza B virus isolates were analyzed. A partial HA1 gene was amplified by RT-PCR and sequenced. Results: Phylogenetic analyses revealed that influenza B viruses were closely related to B/Brisbane/60/2008 vaccine strain while A (H1N1) pdm09 viruses were genetic variants of A/California/07/2009. The Kenyan A (H1N1) pdm09 isolates had P83S, D97N, S185T, I321V and E374K amino acid substitutions. Influenza A/H3N2 isolates showed K62E, T212A and S214I simultaneous amino acid substitutions when compared to A/Perth/10/2009. The K62E change occurred at antigenic site E. Majority of the Kenyan H3N2 isolates further had S45N and K144N amino acid substitutions at sites C and A respectively, which introduced N-glycosylation motifs absent in the vaccine strain. Conclusion: The study showed that although the WHO 2010 vaccine strains recommendations for the southern hemisphere matched with influenza viruses which circulated in Kenya during the 2010-2011 season, the viruses had evolved genetically from the vaccine strains. Key words: Influenza vaccine formulations; HA1 gene; Kenya
