Title Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses.
Author Lu, Xiaoyan; Holloway, Brian; Dare, Ryan K; Kuypers, Jane; Yagi, Shigeo; Williams, John V; Hall, Caroline B; Erdman, Dean D
Journal J Clin Microbiol Publication Year/Month 2008-Feb
PMID 18057136 PMCID PMC2238069
Affiliation 1.Gastroenteritis and Respiratory Virus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

Human rhinoviruses (HRVs) are important contributors to respiratory disease, but their healthcare burden remains unclear, primarily because of the lack of sensitive, accurate, and convenient means of determining their causal role. To address this, we developed and clinically validated the sensitivity and specificity of a real-time reverse transcription-PCR (RT-PCR) assay targeting the viral 5\' noncoding region defined by sequences obtained from all 100 currently recognized HRV prototype strains and 85 recently circulating field isolates. The assay successfully amplified all HRVs tested and could reproducibly detect 50 HRV RNA transcript copies, with a dynamic range of over 7 logs. In contrast, a quantified RNA transcript of human enterovirus 68 (HEV68) that showed the greatest sequence homology to the HRV primers and probe set was not detected below a concentration of 5 x 10(5) copies per reaction. Nucleic acid extracts of 111 coded respiratory specimens that were culture positive for HRV or HEV were tested with the HRV real-time RT-PCR assay and by two independent laboratories that used different in-house HRV/HEV RT-PCR assays. Eighty-seven HRV-culture-positive specimens were correctly identified by the real-time RT-PCR assay, and 4 of the 24 HEV-positive samples were positive for HRV. HRV-specific sequences subsequently were identified in these four specimens, suggesting HRV/HEV coinfection in these patients. The assay was successfully applied in an investigation of a coincidental outbreak of HRV respiratory illness among laboratory staff.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
ANC08229 A 94 575 USA 1999 None
ANC08234 A 82 534 USA 1999 None
ANC08239 A 76 599 USA 1999 None
ANC08244 A 68 620 USA 1999 None
ANC08249 A 63 531 USA 1999 None
ANC08254 A 58 494 USA 1999 None
ANC08259 A 53 526 USA 1999 None
ANC08264 A 46 529 USA 1999 None
ANC08269 A 40 602 USA 1999 None
ANC08274 A 33 561 USA 1999 None
ANC08279 A 28 533 USA 1999 None
ANC08284 A 21 557 USA 1999 None
ANC08289 A 15 603 USA 1999 None
ANC08294 A 9 597 USA 1999 None
ANC08299 A 1 564 USA 1999 None
ANM08225 A 100 529 USA 1999 None
ANM08230 A 90 528 USA 1999 None
ANM08235 A 81 534 USA 1999 None
ANM08240 A 75 520 USA 1999 None
ANM08245 A 67 528 USA 1999 None
ANM08250 A 62 611 USA 1999 None
ANM08255 A 57 530 USA 1999 None
ANM08260 A 51 524 USA 1999 None
ANM08265 A 45 534 USA 1999 None
ANM08270 A 39 588 USA 1999 None
ANM08275 A 32 599 USA 1999 None
ANM08280 A 25 580 USA 1999 None
ANM08285 A 20 591 USA 1999 None
ANM08290 A 13 576 USA 1999 None
ANM08295 A 8 517 USA 1999 None
ANP08227 A 96 528 USA 1999 None
ANP08232 A 88 540 USA 1999 None
ANP08237 A 78 541 USA 1999 None
ANP08242 A 73 534 USA 1999 None
ANP08247 A 65 541 USA 1999 None
ANP08252 A 60 601 USA 1999 None
ANP08257 A 55 531 USA 1999 None
ANP08262 A 49 521 USA 1999 None
ANP08267 A 43 524 USA 1999 None
ANP08272 A 36 609 USA 1999 None
ANP08277 A 30 604 USA 1999 None
ANP08282 A 23 514 USA 1999 None
ANP08287 A 18 566 USA 1999 None
ANP08292 A 11 601 USA 1999 None
ANP08297 A 2 576 USA 1999 None
ANS08228 A 8 519 USA 1999 None
ANS08233 A 85 560 USA 1999 None
ANS08238 A 77 524 USA 1999 None
ANS08243 A 71 605 USA 1999 None
ANS08248 A 64 611 USA 1999 None
ANS08253 A 59 529 USA 1999 None
ANS08258 A 54 522 USA 1999 None
ANS08263 A 47 523 USA 1999 None
ANS08268 A 41 532 USA 1999 None
ANS08273 A 34 605 USA 1999 None
ANS08278 A 29 563 USA 1999 None
ANS08283 A 22 587 USA 1999 None
ANS08288 A 16 533 USA 1999 None
ANS08293 A 10 570 USA 1999 None
ANS08298 A 1 606 USA 1999 None
ANZ08226 A 54 531 USA 1999 None
ANZ08231 A 89 596 USA 1999 None
ANZ08236 A 80 532 USA 1999 None
ANZ08241 A 74 535 USA 1999 None
ANZ08246 A 66 573 USA 1999 None
ANZ08251 A 61 616 USA 1999 None
ANZ08256 A 56 523 USA 1999 None
ANZ08261 A 50 603 USA 1999 None
ANZ08266 A 29 523 USA 1999 None
ANZ08271 A 38 603 USA 1999 None
ANZ08276 A 31 606 USA 1999 None
ANZ08281 A 24 600 USA 1999 None
ANZ08286 A 19 538 USA 1999 None
ANZ08291 A 12 578 USA 1999 None
ANZ08296 A 7 589 USA 1999 None
BNC01604 B 91 533 USA 1999 None
BNC01609 B 72 571 USA 1999 None
BNC01614 B 42 541 USA 1999 None
BNC01619 B 17 522 USA 1999 None
BNC01624 B 3 541 USA 1999 None
BNM01600 B 99 543 USA 1999 None
BNM01605 B 86 551 USA 1999 None
BNM01610 B 70 539 USA 1999 None
BNM01615 B 37 549 USA 1999 None
BNM01620 B 14 551 USA 1999 None
BNP01602 B 93 535 USA 1999 None
BNP01607 B 83 540 USA 1999 None
BNP01612 B 52 538 USA 1999 None
BNP01617 B 27 549 USA 1999 None
BNP01622 B 5 547 USA 1999 None
BNS01603 B 92 548 USA 1999 None
BNS01608 B 79 531 USA 1999 None
BNS01613 B 48 567 USA 1999 None
BNS01618 B 26 544 USA 1999 None
BNS01623 B 4 546 USA 1999 None
BNZ01601 B 97 544 USA 1999 None
BNZ01606 B 84 532 USA 1999 None
BNZ01611 B 69 533 USA 1999 None
BNZ01616 B 35 535 USA 1999 None
BNZ01621 B 6 573 USA 1999 None
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