Additional file 1: Figure S1. of The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya

Schematic diagram of the two versions of Taqman array cards (TAC) used in the study. Table S1. Viral and bacterial pathogens detected using Taqman array cards (TAC) among non-fatal and fatal cases and asymptomatic controls, by age group, western Kenya, 2009-11. Table S2. Distribution of respiratory pathogens among cases (non-fatal and fatal) and corresponding asymptomatic controls in rural western Kenya, 2009-11. (DOCX 614 kb

Identification and characterization of influenza A viruses in selected domestic animals in Kenya, 2010-2012

<div><p>Background</p><p>Influenza A virus subtypes in non-human hosts have not been characterized in Kenya. We carried out influenza surveillance in selected domestic animals and compared the virus isolates with isolates obtained in humans during the same period.</p><p>Methods</p><p>We collected nasal swabs from pigs, dogs and cats; oropharyngeal and cloacal swabs from poultry; and blood samples from all animals between 2010 and 2012. A standardized questionnaire was administered to farmers and traders. Swabs were tested for influenza A by rtRT-PCR, virus isolation and subtyping was done on all positive swabs. All sera were screened for influenza A antibodies by ELISA, and positives were evaluated by hemagglutination inhibition (HI). Full genome sequencing was done on four selected pig virus isolates.</p><p>Results</p><p>Among 3,798 sera tested by ELISA, influenza A seroprevalence was highest in pigs (15.9%; 172/1084), 1.2% (3/258) in ducks, 1.4% (1/72) in cats 0.6% (3/467) in dogs, 0.1% (2/1894) in chicken and 0% in geese and turkeys. HI testing of ELISA-positive pig sera showed that 71.5% had positive titers to A/California/04/2009(H1N1). Among 6,289 swabs tested by rRT-PCR, influenza A prevalence was highest in ducks [1.2%; 5/423] and 0% in cats and turkeys. Eight virus isolates were obtained from pig nasal swabs collected in 2011 and were determined to be A(H1N1)pdm09 on subtyping. On phylogenetic analysis, four hemagglutinin segments from pig isolates clustered together and were closely associated with human influenza viruses that circulated in Kenya in 2011.</p><p>Conclusion</p><p>Influenza A(H1N1)pdm09 isolated in pigs was genetically similar to contemporary human pandemic influenza virus isolates. This suggest that the virus was likely transmitted from humans to pigs, became established and circulated in Kenyan pig populations during the study period. Minimal influenza A prevalence was observed in the other animals studied.</p></div

Prevalence of PCR positivity for influenza A in nasal, oropharyngeal and cloacal swabs, by species and site, Kenya, May 2010-August 2012.

<p>Prevalence of PCR positivity for influenza A in nasal, oropharyngeal and cloacal swabs, by species and site, Kenya, May 2010-August 2012.</p

Analysis of HA segment of Kenya swine isolates alongside other contemporary isolates.

<p>Branches highlighted in red referto Kenya swine isolates while those in blue are Kenya human isolates. A/California/04/2009 is used to root the phylogenetic tree.</p

Distribution of hemagglutination-inhibition (HI) titers and proportion positive of enzyme-linked immunosorbent assay (ELISA)-positive pig sera against three reference antigens for household and slaughterhouse sites, May 2010 –August 2012 (n = 172)^*.

<p>Distribution of hemagglutination-inhibition (HI) titers and proportion positive of enzyme-linked immunosorbent assay (ELISA)-positive pig sera against three reference antigens for household and slaughterhouse sites, May 2010 –August 2012 (n = 172)^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192721#t003fn001" target="_blank">*</a>}.</p

Influenza A seroprevalence by ELISA among pigs sampled at the slaughter house, 2010–2012.

<p>Influenza A seroprevalence by ELISA among pigs sampled at the slaughter house, 2010–2012.</p

Proportion of enrolled households (HH) owning different animal types by study site, Kenya, May 2010-August 2012.

<p>Proportion of enrolled households (HH) owning different animal types by study site, Kenya, May 2010-August 2012.</p

Map of Kenya counties showing the location of the study sites, Kibera in Nairobi, Ndumbui-ini slaughterhouse in Kiambu County and Asembo in Siaya County.

<p>Map of Kenya counties showing the location of the study sites, Kibera in Nairobi, Ndumbui-ini slaughterhouse in Kiambu County and Asembo in Siaya County.</p

Adjusted odds ratios by demographic and environmental variables.

<p>Adjusted odds ratios by demographic and environmental variables.</p

Monthly distribution of 110 incident typhoid cases between 2010–2011 in Kibera with monthly precipitation overlaid.

<p>Monthly distribution of 110 incident typhoid cases between 2010–2011 in Kibera with monthly precipitation overlaid.</p