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Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia.

Timmermans A, Melendrez MC, Se Y, Chuang I, Samon N, Uthaimongkol N, Klungthong C, Manasatienkij W, Thaisomboonsuk B, Tyner SD, Rith S, Horm VS, Jarman RG, Bethell D, Chanarat N, Pavlin J, Wongstitwilairoong T, Saingam P, El BS, Fukuda MM, Touch S, Sovann L, Fernandez S, Buchy P, Chanthap L, Saunders D - PLoS ONE (2016)

Bottom Line: Most genes showed signatures of purifying selection.A single specimen of EV71 was found.Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.

ABSTRACT
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.

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Related in: MedlinePlus

H3N2 maximum likelihood phylogenetic trees (aLRT support >70 for all vaccine clades and major nodes) for the (A) HA and (B) NA segments for 10 samples from Cambodia and references in Genbank (grey) collected in 2011 and 2012. Vaccine strains are highlighted in red. Samples are colored coded by sampling site.
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pone.0152529.g006: H3N2 maximum likelihood phylogenetic trees (aLRT support >70 for all vaccine clades and major nodes) for the (A) HA and (B) NA segments for 10 samples from Cambodia and references in Genbank (grey) collected in 2011 and 2012. Vaccine strains are highlighted in red. Samples are colored coded by sampling site.

Mentions: All sequences were highly related with no more than 1.77% divergence between the samples and the furthest related respective vaccine (S9 Table, Fig 6) for any of the segment. The majority of segments were more closely related to the A/Victoria/361/2011 vaccine strain; therefore all subsequent analyses were compared to this strain. For the HA gene, when compared to the A/Victoria/361/2011 vaccine strain, all samples on average had 9 amino acid changes within the HA segment (S10 Table). There were several amino acid changes among the sequenced samples occurring in antigenic sites, polymorphic sites or which resulted in a change of glycosylation (Table 5). For the NA gene, several amino acid substitutions resulted in addition/loss of glycosylation sites, or were found in polymorphic or antigenic/catalytic sites (epitopes) (Table 5). For the MP gene, it was noted that all samples contained the S31N mutation that may confer adamantane resistance as determined by the Genbank Influenza Viral Resource Annotation tool [32]. No features or changes of interest were seen within the NS segment for any sample.


Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia.

Timmermans A, Melendrez MC, Se Y, Chuang I, Samon N, Uthaimongkol N, Klungthong C, Manasatienkij W, Thaisomboonsuk B, Tyner SD, Rith S, Horm VS, Jarman RG, Bethell D, Chanarat N, Pavlin J, Wongstitwilairoong T, Saingam P, El BS, Fukuda MM, Touch S, Sovann L, Fernandez S, Buchy P, Chanthap L, Saunders D - PLoS ONE (2016)

H3N2 maximum likelihood phylogenetic trees (aLRT support >70 for all vaccine clades and major nodes) for the (A) HA and (B) NA segments for 10 samples from Cambodia and references in Genbank (grey) collected in 2011 and 2012. Vaccine strains are highlighted in red. Samples are colored coded by sampling site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814059&req=5

pone.0152529.g006: H3N2 maximum likelihood phylogenetic trees (aLRT support >70 for all vaccine clades and major nodes) for the (A) HA and (B) NA segments for 10 samples from Cambodia and references in Genbank (grey) collected in 2011 and 2012. Vaccine strains are highlighted in red. Samples are colored coded by sampling site.
Mentions: All sequences were highly related with no more than 1.77% divergence between the samples and the furthest related respective vaccine (S9 Table, Fig 6) for any of the segment. The majority of segments were more closely related to the A/Victoria/361/2011 vaccine strain; therefore all subsequent analyses were compared to this strain. For the HA gene, when compared to the A/Victoria/361/2011 vaccine strain, all samples on average had 9 amino acid changes within the HA segment (S10 Table). There were several amino acid changes among the sequenced samples occurring in antigenic sites, polymorphic sites or which resulted in a change of glycosylation (Table 5). For the NA gene, several amino acid substitutions resulted in addition/loss of glycosylation sites, or were found in polymorphic or antigenic/catalytic sites (epitopes) (Table 5). For the MP gene, it was noted that all samples contained the S31N mutation that may confer adamantane resistance as determined by the Genbank Influenza Viral Resource Annotation tool [32]. No features or changes of interest were seen within the NS segment for any sample.

Bottom Line: Most genes showed signatures of purifying selection.A single specimen of EV71 was found.Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus