title: Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore.
abstract: To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Community-ARI and inpatient-ARI was also combined with mild and severe cases of influenza from a historical prospective study as mild-ARI and severe-ARI respectively to evaluate the performance of clinical case definitions. We analysed 130 community-ARI and 140 inpatient-ARI episodes (5 inpatient-ARI excluded because multiple pathogens were detected), involving 138 and 207 samples respectively. Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. No such patterns were observed for non-influenza respiratory virus infections. PathChip added substantially to viruses detected for community-ARI only. Clinical case definitions discriminated influenza from other mild-ARI but performed poorly for severe-ARI and for older participants. Rational strategies for diagnosis and surveillance of influenza and other respiratory virus must acknowledge the differences between ARIs presenting in community and hospital settings.
authors.affiliation: Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.
authors.forename: Lili
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.|Biodefence Centre, Singapore Armed Forces, Singapore.
authors.forename: Vernon Jian Ming
authors.initials: VJ
authors.lastname: Lee
authors.affiliation: National Public Health Laboratory, Ministry of Health, Singapore.
authors.forename: Lin
authors.initials: L
authors.lastname: Cui
authors.affiliation: National Public Health Laboratory, Ministry of Health, Singapore.|Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore.
authors.forename: Raymond
authors.initials: R
authors.lastname: Lin
authors.affiliation: Department of Infectious Diseases, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore.
authors.forename: Chyi Lin
authors.initials: CL
authors.lastname: Tan
authors.affiliation: Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.
authors.forename: Linda Wei Lin
authors.initials: LW
authors.lastname: Tan
authors.affiliation: Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.
authors.forename: Wei-Yen
authors.initials: WY
authors.lastname: Lim
authors.affiliation: Department of Infectious Diseases, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore.
authors.forename: Yee-Sin
authors.initials: YS
authors.lastname: Leo
authors.affiliation: Genome Institute Singapore, Singapore.
authors.forename: Louie
authors.initials: L
authors.lastname: Low
authors.affiliation: Genome Institute Singapore, Singapore.
authors.forename: Martin
authors.initials: M
authors.lastname: Hibberd
authors.affiliation: Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.|Department of Clinical Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore.
authors.forename: Mark I-Cheng
authors.initials: MI
authors.lastname: Chen
mesh_terms: D000328:Adult; D000368:Aged; D017934:Coronavirus / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D006801:Humans; D009980:Influenza A virus / Q000235:genetics / Q000302:isolation & purification*; D008297:Male; D008875:Middle Aged; D060885:Multiplex Polymerase Chain Reaction; D009305:Nasopharynx / Q000821:virology; D011446:Prospective Studies; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000473:pathology / Q000821:virology; D012229:Rhinovirus / Q000235:genetics / Q000302:isolation & purification*; D012720:Severity of Illness Index; D012846:Singapore
chemical_list: D012367:RNA, Viral