Sindbis virus (SINV) is a mosquito borne virus maintained in nature in a mosquito-bird cycle, with human outbreaks known to occur in Northern Europe and parts of Africa. We analyzed five SINV strains isolated in Kenya from five different mosquito species and geographic locations between 2007 and 2013. Phylogenetic relationships and evolutionary inferences were performed using maximum likelihood and Bayesian phylogenetic inference approaches. Selection analyses were carried out based on the virus envelope glycoproteins (E1, E2) and non-structural protein (nsP4) genes. Phylogenetic analysis revealed that all the Kenyan SINV isolates belonged to genotype 1 with selection analyses suggesting that SINV E1, E2 and nsP4 protein encoding genes were predominantly evolving under negative selection.

Overall, the major genetic variations that occurred in seasonal A(H1) viruses either affected receptor binding or altered epitopes at the immunodominant sites. These genetic variations in seasonal A(H1N1) isolated in Kenya during 2007-2008 highlight the importance of continuing surveillance and characterization of emerging drift variants of influenza virus in Africa.

Abstract. We describe virus variations

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.

Background: RSV is the most common cause of severe lower respiratory disease in young infants. RSV infection causes both mild and serious respiratory diseases in older children and adults. Primary RSV infection predominantly arises in the first two years of life. In Kenya RSV is one of the leading cause of non influenza respiratory pathogen that affect children Kenya National Influenza Centre (NIC) began screening for RSV in Oct 2006 as part of the ongoing surveillance of Human Influenza and other respiratory viruses.The objective of this study was to determine the occurrences of RSV in Kenya Methods: Nasopharyngeal swab specimens were collected from consenting patient's ≥ 2 months old presenting with fever (≥ 38 • C) accompanied by cough and/or sore throat reported within 72 hours of onset of symptoms. Specimens were transported to the NIC where they were inoculated into Hep-2 cell line. RSV produces a characteristic CPE consisting of syncytia formation. After observing cells for Cytopathic effect, samples were analyzed by direct immunofluorescence assay (IFA).Results: A total of 12769 samples of nasopharyngeal aspirates were collected between October 2006 and October 2010. Respiratory viruses were isolated in 2609 representing 20% of these samples. Notably, 317 (12%) of these were RSV. Out of the 317 isolates, 198 (63%) were from children <2years, 105 (33%) were from 2-5years and 14 (4%) were from > 5years of age. Our results indicate that in Kenya, 96% of RSV cases occur in children < 5years of age with children < 2years being the most affected. Conclusion:This study emphasizes the importance of RSV surveillance and reinforces the need to diagnose these infections to provide epidemiological data that may be used to monitor the disease in Kenya. These findings also highlight the need to continue to improve respiratory virus detection assays in addition to RSV testing for the clinical diagnosis and community surveillance of respiratory viral infections in the country.