title: Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya.
abstract: Quantitative real-time polymerase chain reaction (qRT-PCR) assay of the upper respiratory tract is used increasingly to diagnose lower respiratory tract infections. The cycle threshold (CT ) values of qRT-PCR are continuous, semi-quantitative measurements of viral load, although interpretation of diagnostic qRT-PCR results are often categorized as positive, indeterminate, or negative, obscuring potentially useful clinical interpretation of CT values. From 2008 to 2010, naso/oropharyngeal swabs were collected from outpatients with influenza-like illness, inpatients with severe respiratory illness, and asymptomatic controls in rural Kenya. CT values of positive specimens (i.e., CT values < 40.0) were compared by clinical severity category for five viruses using Mann-Whitney U-test and logistic regression. Among children <5 years old we tested with respiratory syncytial virus (RSV), inpatients had lower median CT values (27.2) than controls (35.8, P = 0.008) and outpatients (34.7, P < 0.001). Among children and older patients infected with influenza virus, outpatients had the lowest median CT values (29.8 and 24.1, respectively) compared with controls (P = 0.193 for children, P < 0.001 for older participants) and inpatients (P = 0.009 for children, P < 0.001 for older participants). All differences remained significant in logistic regression when controlling for age, days since onset, and coinfection. CT values were similar for adenovirus, human metapneumovirus, and parainfluenza virus in all severity groups. In conclusion, the CT values from the qRT-PCR of upper respiratory tract specimens were associated with clinical severity for some respiratory viruses.
authors.affiliation: Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. jafuller@jhsph.edu
authors.forename: James A
authors.initials: JA
authors.lastname: Fuller
authors.forename: M Kariuki
authors.initials: MK
authors.lastname: Njenga
authors.forename: Godfrey
authors.initials: G
authors.lastname: Bigogo
authors.forename: Barrack
authors.initials: B
authors.lastname: Aura
authors.forename: Maurice O
authors.initials: MO
authors.lastname: Ope
authors.forename: Leonard
authors.initials: L
authors.lastname: Nderitu
authors.forename: Lilian
authors.initials: L
authors.lastname: Wakhule
authors.forename: Dean D
authors.initials: DD
authors.lastname: Erdman
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Feikin
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D005260:Female; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007297:Inpatients; D007630:Kenya; D008297:Male; D008875:Middle Aged; D009305:Nasopharynx / Q000821:virology; D009960:Oropharynx / Q000821:virology; D010045:Outpatients; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012141:Respiratory Tract Infections / Q000473:pathology* / Q000821:virology*; D012720:Severity of Illness Index; D019562:Viral Load; D014777:Virus Diseases / Q000473:pathology* / Q000821:virology*; D055815:Young Adult