Title Assay for 5\' noncoding region analysis of all human rhinovirus prototype strains.
Author Kiang, David; Kalra, Ishmeet; Yagi, Shigeo; Louie, Janice K; Boushey, Homer; Boothby, John; Schnurr, David P
Journal J Clin Microbiol Publication Year/Month 2008-Nov
PMID 18753359 PMCID PMC2576622
Affiliation 1.Viral and Rickettsial Disease Laboratories, California State Department of Public Health, Richmond, California 94804, USA. david.kiang@cdph.ca.gov.

Increasing recognition of the association of rhinovirus with severe lower respiratory tract illnesses has clarified the need to understand the relationship between specific serotypes of rhinovirus and their clinical consequences. To accomplish this, a specific and sensitive assay to detect and serotype rhinovirus directly from clinical specimens is needed. Traditional methods of serotyping using culture and serum neutralization are time-consuming, limited to certain reference laboratories, and complicated by the existence of over 100 serotypes of human rhinoviruses (HRVs). Accordingly, we have developed a sequence-based assay that targets a 390-bp fragment accounting for approximately two-thirds of the 5\' noncoding region (NCR). Our goal was to develop an assay permitting amplification of target sequences directly from clinical specimens and distinction among all 101 prototype strains of rhinoviruses. We determined the sequences of all 101 prototype strains of HRV in this region to enable differentiation of virus genotypes in both viral isolates and clinical specimens. We evaluated this assay in a total of 101 clinical viral isolates and 24 clinical specimens and compared our findings to genotyping results using a different region of the HRV genome (the VP4-VP2 region). Five specimens associated with severe respiratory disease in children did not correlate with any known serotype of rhinovirus and were found to belong to a novel genogroup of rhinovirus, genogroup C. Isolates were also found that corresponded to the genogroup A2 variant identified in New York and Australia and two other novel group A clusters (GAC1 and GAC2).

StrainID RV Species Serotype Length(nt) Country Year Strain Name
ANC07999 A 24 308 USA None
ANC08004 A 18 306 USA None
ANC08009 A 10 305 USA None
ANM08000 A 23 308 USA None
ANM08005 A 15 304 USA None
ANM08010 A 9 308 USA None
ANP08002 A 20 311 USA None
ANP08007 A 12 311 USA None
ANS07998 A 25 300 USA None
ANS08003 A 19 311 USA None
ANS08008 A 11 311 USA None
ANZ08001 A 22 305 USA None
ANZ08006 A 13 311 USA None
ANZ08011 A 8 308 USA None
BNC01529 B 26 311 USA None
BNM01530 B 14 311 USA None
BNP01532 B 4 307 None None
BNS01528 B 27 303 USA None
BNS01533 B 3 311 None None
BNZ01531 B 5 311 USA None
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