Abstract
We report a whole‐genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248D in the neuraminidase proteins with consistent mutations in all gene segments distinguishing isolates from the 2009/2010 to 2010/2011 seasons. Phylogenetic analysis showed low genetic evolution, with genetic distances of 0%–1.3% and 0.1%–1.6% for HA and NA genes, respectively. The amino acid substitutions did not lead to antigenic differences from the reference strains.
Highlights
Despite increased capabilities for the detection and surveillance of influenza viruses in many parts of the world,[1] whole-genomic data on the viruses from sub-Saharan Africa remain limited
We report the whole-genome analysis of and genetic variations among the pandemic influenza A(H1N1)pdm[09] viruses isolated between July 2009 and May 2011 from four hospital sites in Uganda
While the influenza A(H1N1)pdm[09] strains isolated in this study had specific amino acids that defined them, they were generally similar to the reference strains, with no significant antigenic variation from the vaccine strain A/California/07/2009.8 Consistent with findings from previous reports,[9–12] the isolates from our study showed low genetic diversity
Summary
Despite increased capabilities for the detection and surveillance of influenza viruses in many parts of the world,[1] whole-genomic data on the viruses from sub-Saharan Africa remain limited. Whole- genome sequencing provides the needed evidence for scientifically sound public health interventions including vaccine development. Due to constant viral antigenic evolution, it is important to continually examine the evolutionary changes in the strains for appropriate vaccine selection each year.[2] The influenza A(H1N1)pdm[09] virus was first reported in Uganda in July 2009 and subsequently spread and established rapidly within the population where it was thereafter routinely detected. We report the whole-genome analysis of and genetic variations among the pandemic influenza A(H1N1)pdm[09] viruses isolated between July 2009 and May 2011 from four hospital sites in Uganda
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