Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity.
BACKGROUND
Between 50% and 80% of asthma exacerbations are associated with viral respiratory tract infections (RTIs), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood because of the limited scope and throughput of conventional viral detection methods.


METHODS
We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize viral diversity in RTIs in adults with and without asthma.


RESULTS
The Virochip detected viruses in a higher proportion of samples (65%) than did culture isolation (17%) while exhibiting high concordance (98%) with and comparable sensitivity (97%) and specificity (98%) to pathogen-specific polymerase chain reaction. A similar spectrum of viruses was identified in the RTIs of each patient subgroup; however, unexpected diversity among human coronaviruses (HCoVs) and human rhinoviruses (HRVs) was revealed. All but one of the HCoVs corresponded to the newly recognized HCoV-NL63 and HCoV-HKU1 viruses, and >20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that formed a distinct genetic subgroup.


CONCLUSIONS
The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger-scale studies will be necessary to determine whether particular substrains of viruses confer an elevated risk of asthma exacerbation.
Kistler
Amy
A
Howard Hughes Medical Institute, Department of Medicine, University of California, San Francisco, CA 94158, USA. amy@derisilab.ucsf.edu
Avila
Pedro C
PC
Rouskin
Silvi
S
Wang
David
D
Ward
Theresa
T
Yagi
Shigeo
S
Schnurr
David
D
Ganem
Don
D
DeRisi
Joseph L
JL
Boushey
Homer A
HA
D000328:Adult; D001249:Asthma / Q000821:virology; D044822:Biodiversity; D017934:Coronavirus / Q000235:genetics / Q000302:isolation & purification*; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D017817:Nasal Lavage Fluid / Q000821:virology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000150:complications / Q000821:virology*; D012229:Rhinovirus / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D014773:Virology / Q000379:methods*; D014776:Virus Cultivation
D004279:DNA, Viral
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