title: Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital.
abstract: Numerous pathogens cause respiratory infections with similar symptoms. Routine diagnostics detect only a limited number of pathogens, leaving a gap in respiratory illness etiology surveillance. This study evaluated next-generation sequencing for unbiased pathogen identification. Respiratory samples collected in Thailand, Philippines, Bhutan, and Nepal, that were negative by several molecular and immunofluorescence assays, underwent viral cultivation. Samples which demonstrated cytopathic effect in culture (N = 121) were extracted and tested by Luminex xTAG respiratory viral panel (RVP) assay and deep sequencing by Roche 454 FLX Titanium system. Using RVP assay, 52 (43%) samples were positive for enterovirus or rhinovirus and another three were positive for respiratory syncytial virus B, parainfluenza 4, and adenovirus. Deep sequencing confirmed the Luminex assay results and identified additional viral pathogens. Human enteroviruses, including Enterovirus A type 71 and 12 types of Enterovirus B (EV-B) were identified from a hospital in Bangkok. Phylogenetic and recombination analysis showed high correlation of VP1 gene-based phylogeny with genome-wide phylogeny and the frequent genetic exchange among EV-B viruses. The high number and diversity of enteroviruses in the hospital in Bangkok suggests prevalent existence. The metagenomic approach used in our study enabled comprehensive diagnoses of respiratory viruses.
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Yanfei
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors.forename: Stefan
authors.initials: S
authors.lastname: Fernandez
authors.affiliation: International Vaccine Institute, Seoul, Republic of Korea.|Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors.forename: In-Kyu
authors.initials: IK
authors.lastname: Yoon
authors.affiliation: Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand.
authors.forename: Sriluck
authors.initials: S
authors.lastname: Simasathien
authors.affiliation: Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand.
authors.forename: Veerachai
authors.initials: V
authors.lastname: Watanaveeradej
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Yu
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Omely A
authors.initials: OA
authors.lastname: Marte-Salcedo
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Deidra J
authors.initials: DJ
authors.lastname: Shuck-Lee
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Thomas
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Jun
authors.initials: J
authors.lastname: Hang
authors.affiliation: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Jarman
mesh_terms: D000256:Adenoviridae / Q000235:genetics; D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D004770:Enterovirus / Q000235:genetics*; D004769:Enterovirus Infections / Q000175:diagnosis / Q000821:virology*; D005260:Female; D006761:Hospitals / Q000706:statistics & numerical data; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D056186:Metagenomics / Q000379:methods*; D008875:Middle Aged; D029482:Parainfluenza Virus 4, Human / Q000235:genetics; D010802:Phylogeny; D012136:Respiratory Syncytial Viruses / Q000235:genetics; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000821:virology*; D012229:Rhinovirus / Q000235:genetics; D013785:Thailand / Q000453:epidemiology; D055815:Young Adult