title: Yield of sputum for viral detection by reverse transcriptase PCR in adults hospitalized with respiratory illness.
abstract: Diagnostic tests for respiratory viral infections have traditionally been performed on nasopharyngeal swabs or washings. Reverse transcriptase PCR (RT-PCR) is rapid, sensitive, and specific for viral infection diagnosis but is rarely applied to sputum samples. Thus, we evaluated the diagnostic yield of RT-PCR for detection of nine virus types by the use of nose and throat swabs (NTS) and sputum samples from patients admitted to the hospital with acute respiratory tract illnesses. Adults hospitalized with acute respiratory tract illnesses were recruited during the winters of 2008 and 2009. At enrollment, combined nose and throat swabs and sputum samples were collected for RT-PCR for detection of nine common respiratory virus types. A total of 532 subjects admitted for 556 respiratory illnesses were enrolled. A total of 189 virus strains were identified. The diagnostic yields for detection of any virus were 23% (126/556) for NTS RT-PCR and 36% (146/404) for sputum RT-PCR. A total of 83 (44%) of 189 viral detections were positive by both methods, 43 (23%) were positive by NTS alone, and 63 (33%) were positive only with sputum samples. The inclusion of RT-PCR performed with sputum samples significantly increased the diagnostic yield for respiratory viral infections in adults. Further studies designed to adapt the use of sputum samples for commercial RT-PCR respiratory virus assays are needed.
authors.affiliation: University of Rochestera and Rochester General Hospital,b Rochester, New York, USA. ann.falsey@rochestergeneral.org
authors.forename: Ann R
authors.initials: AR
authors.lastname: Falsey
authors.forename: Maria A
authors.initials: MA
authors.lastname: Formica
authors.forename: Edward E
authors.initials: EE
authors.lastname: Walsh
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D005260:Female; D006760:Hospitalization; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009666:Nose / Q000821:virology; D010614:Pharynx / Q000821:virology; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D013183:Sputum / Q000821:virology*; D014773:Virology / Q000379:methods*; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology; D014780:Viruses / Q000302:isolation & purification*
references.citation: J Clin Microbiol. 2010 Apr;48(4):1501-3
references.pmid: 20164266
references.citation: J Infect. 2005 May;50(4):322-30
references.pmid: 15845430
references.citation: J Clin Virol. 2003 Apr;26(3):339-46
references.pmid: 12637083
references.citation: N Engl J Med. 2009 Aug 13;361(7):680-9
references.pmid: 19564631
references.citation: J Clin Microbiol. 2009 Nov;47(11):3439-43
references.pmid: 19726607
references.citation: J Am Geriatr Soc. 1996 Jan;44(1):71-3
references.pmid: 8537595
references.citation: Praxis (Bern 1994). 2010 Feb 17;99(4):235-40
references.pmid: 20166049
references.citation: Clin Infect Dis. 2010 Mar 1;50(5):747-51
references.pmid: 20121411
references.citation: N Engl J Med. 2009 Dec 24;361(26):2507-17
references.pmid: 20007555
references.citation: Eur Respir J. 2003 Jun;21(6):944-51
references.pmid: 12797486
references.citation: Arch Dis Child. 1979 Aug;54(8):587-92
references.pmid: 507912
references.citation: J Infect Dis. 2004 Feb 15;189(4):706-10
references.pmid: 14767825
references.citation: Clin Infect Dis. 2000 Sep;31(3):739-51
references.pmid: 11017824
references.citation: Clin Infect Dis. 2011 May;52 Suppl 4:S312-25
references.pmid: 21460290
references.citation: J Clin Microbiol. 2002 Jun;40(6):2051-6
references.pmid: 12037063
references.citation: J Clin Virol. 2003 Oct;28(2):169-74
references.pmid: 12957187
references.citation: J Clin Microbiol. 1996 Jul;34(7):1649-53
references.pmid: 8784563
references.citation: J Clin Virol. 2008 Jan;41(1):7-12
references.pmid: 18065263
references.citation: Thorax. 2003 Jan;58(1):37-42
references.pmid: 12511718
references.citation: Thorax. 2006 Jul;61(7):579-84
references.pmid: 16517571
references.citation: N Engl J Med. 2009 Dec 17;361(25):2493
references.pmid: 19923563
references.citation: J Infect Dis. 1983 Feb;147(2):181-4
references.pmid: 6827134
references.citation: Clin Infect Dis. 2005 Aug 1;41(3):345-51
references.pmid: 16007532
references.citation: Semin Respir Crit Care Med. 2007 Apr;28(2):222-42
references.pmid: 17458776
references.citation: J Virol Methods. 2002 Mar;101(1-2):127-33
references.pmid: 11849691
references.citation: J Clin Virol. 2009 Oct;46(2):129-33
references.pmid: 19665425
references.citation: N Engl J Med. 2003 Dec 18;349(25):2431-41
references.pmid: 14681510
references.citation: J Virol Methods. 2008 Nov;153(2):84-9
references.pmid: 18761378
references.citation: J Am Geriatr Soc. 2009 Mar;57(3):482-5
references.pmid: 19187415
references.citation: PLoS One. 2010 Sep 21;5(9):e12849
references.pmid: 20877727