Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Uganda

Abstract

The increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/Brisbane/10/07), instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09) in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.

Genetic analysis of influenza B viruses isolated in Uganda during the 2009–2010 seasons

“…Within the period under this study (May 2009 through December 2010), 2,089 samples from patients showing influenza-like illnesses were collected. Although it is still unclear whether the tropics have influenza peak seasons or whether the virus circulates year-round [11], we have previously observed more ILI and corresponding influenza cases around August [12]. This is still true with influenza B and the present study: during this period, the peak of influenza activity in Uganda was observed in July and August (with 16/25 isolated viruses sampled in July or August).…”

Observations of Immuno-Gold Conjugates on Influenza Viruses Using Waveguide-Mode Sensors

“…In addition, a gene encoding hemagglutinin (HA) of (H3N2)v is related to the strain found circulating among individuals with chronic health issues in the 1990s [8]. Currently, among several types of influenza viruses classified based on 16 HA and 9 Neuraminidase, subtypes H3N2 and H1N1 are circulating in humans [9]. In addition, a new HA was found to occur in a distinct lineage of influenza A virus in little yellow-shouldered bats and was designated as H17 [10].…”

Epidemiology and Surveillance of Influenza Viruses in Uganda between 2008 and 2014

“…Samples were screened and subtyped using real-time reverse transcription polymerase chain reaction (RT-PCR) as previously described by Byarugaba et al (2011) [ 19 ]. Aliquots of PCR positive samples were inoculated in Madin-Darby canine kidney (MDCK) cell lines for virus isolation and culture and further confirmed using immuno-fluorescence assay and PCR and also Hemagglutination (HA) and Hemagglutination inhibition (HAI) assays ( Fig 1 ).…”

“…The goals of surveillance were two-fold: 1) to set up infrastructure for detection and characterization of influenza viruses in order to provide a rapid response to potential pandemics; and 2) to use long-term surveillance data to elucidate the epidemiology of seasonal influenza and inform vaccination strategies. In 2011, MUWRP reported on the molecular diagnostic methods and whole genome analysis of influenza A/H3N2 [ 19 ]. In this paper, we describe the epidemiology of circulating strains of influenza A, including A/H3N2, A/H1N1 pdm09, and the co-infection of H3N2 and H1N1 pdm09, and B from 2008 to 2014.…”