12 research outputs found
Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia
<div><p>Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1–77) presenting with influenza-like-illness (ILI) at 4 sentinel sites in western Cambodia between May 2010 and December 2012. Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. ILI-specimens negative for influenza were cultured, followed by rRT-PCR for enterovirus and rhinovirus (EV/RV) and EV71. Influenza was found in 168 cases (29%) and occurred almost exclusively in the rainy season from June to November. Isolated influenza strains had close antigenic and phylogenetic relationships, matching vaccine and circulating strains found elsewhere in Cambodia. Influenza vaccination coverage was low (<20%). Western Cambodian H1N1(2009) isolate genomes were more closely related to 10 earlier Cambodia isolates (94.4% genome conservation) than to 13 Thai isolates (75.9% genome conservation), despite sharing the majority of the amino acid changes with the Thai references. Most genes showed signatures of purifying selection. Viral culture detected only adenovirus (5.7%) and parainfluenza virus (3.8%), while non-polio enteroviruses (10.3%) were detected among 164 culture-negative samples including coxsackievirus A4, A6, A8, A9, A12, B3, B4 and echovirus E6 and E9 using nested RT-PCR methods. A single specimen of EV71 was found. Despite proximity to Thailand, influenza epidemiology of these western Cambodian isolates followed patterns observed elsewhere in Cambodia, continuing to support current vaccine and treatment recommendations from the Cambodian National Influenza Center. Amino acid mutations at non-epitope sites, particularly hemagglutinin genes, require further investigation in light of an increasingly important role of permissive mutations in influenza virus evolution. Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed.</p></div
H3N2 maximum likelihood phylogenetic trees (aLRT support >70 for all vaccine clades and major nodes) for all segments analyzed in this study for 10 samples from Cambodia (colored in blue) and references in Genbank collected in 2011 and 2012.
<p>Vaccine strains are highlighted in red and clades defined by brackets. Unique sample that did not fall within vaccine clades highlighted in yellow with percent nucleotide identity indicated in bottom right table.</p
Changes in glycosylation, antigenic and polymorphic sites linked to amino acid (AA) substitutions and sub-antigenic/catalytic sites (epitopes) where AA substitutions were found for hemagglutinin (HA) and neuraminidase (NA) segments of H3N2.
<p>Changes in glycosylation, antigenic and polymorphic sites linked to amino acid (AA) substitutions and sub-antigenic/catalytic sites (epitopes) where AA substitutions were found for hemagglutinin (HA) and neuraminidase (NA) segments of H3N2.</p
Dataset descriptions and models used in maximum likelihood phylogenetic analysis.
<p>Dataset descriptions and models used in maximum likelihood phylogenetic analysis.</p
General characteristics of the study population.
<p>General characteristics of the study population.</p
IC<sub>50</sub>-values (nM) of influenza A and B isolates from 2011 to oseltamivir and zanamivir [Range(s) = Range for sensitive control isolates; Range(r) = Range for resistant control isolates).
<p>IC<sub>50</sub>-values (nM) of influenza A and B isolates from 2011 to oseltamivir and zanamivir [Range(s) = Range for sensitive control isolates; Range(r) = Range for resistant control isolates).</p
Influenza and other respiratory viruses detected between 2010–2012.
<p>(A) Number of ILI and influenza subtypes, May 2010-Dec 2012. (B) Number of other respiratory viruses among influenza-negative ILI specimens May 2010-Dec 2012.</p
Laboratory testing flowchart for influenza-like-illness (ILI).
<p>Laboratory testing flowchart for influenza-like-illness (ILI).</p
Enteroviruses and rhinoviruses detected by viral culture and sequencing between May 2010-April 2012.
<p>(A) Number of enteroviruses and rhinoviruses detected by EV/RV assay in 164 culture negative specimens, May 2010-April 2012. (B) Number and percentage of enterovirus and rhinovirus serotypes among a total of 50 (17 EV and 33 RV) positive samples.</p
pH1N1 and H3N2 amino acid changes <sup>a</sup> specific to sample sets for the HA and NA genes.
<p>pH1N1 and H3N2 amino acid changes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152529#t004fn002" target="_blank"><sup>a</sup></a> specific to sample sets for the HA and NA genes.</p