Reverse transcription genome exponential amplification reaction assay for rapid and universal detection of human rhinoviruses

Arch Virol. 2016 Jul;161(7):1891-8. doi: 10.1007/s00705-016-2858-z. Epub 2016 Apr 30.

Abstract

Human rhinoviruses (HRVs) have long been recognized as the cause of more than one-half of acute viral upper respiratory illnesses, and they are associated with more-serious diseases in children, such as asthma, acute otitis media and pneumonia. A rapid and universal test for of HRV infection is in high demand. In this study, a reverse transcription genome exponential amplification reaction (RT-GEAR) assay targeting the HRV 5' untranslated region (UTR) was developed for pan-HRV detection. The reaction was performed in a single tube in one step at 65 °C for 60 min using a real-time fluorometer (Genie(®)II; Optigene). The RT-GEAR assay showed no cross-reactivity with common human enteroviruses, including HEV71, CVA16, CVA6, CVA10, CVA24, CVB5, Echo30, and PV1-3 or with other common respiratory viruses including FluA H3, FluB, PIV1-4, ADV3, RSVA, RSVB and HMPV. With in vitro-transcribed RNA containing the amplified regions of HRV-A60, HRV-B06 and HRV-C07 as templates, the sensitivity of the RT-GEAR assay was 5, 50 and 5 copies/reaction, respectively. Experiments to evaluate the clinical performance of the RT-GEAR assay were also carried out with a panel of 143 previously verified samples, and the results were compared with those obtained using a published semi-nested PCR assay followed by sequencing. The tested panel comprised 91 HRV-negative samples and 52 HRV-positive samples (18 HRV-A-positive samples, 3 HRV-B-positive samples and 31 HRV-C-positive samples). The sensitivity and specificity of the pan-HRVs RT-GEAR assay was 98.08 % and 100 %, respectively. The kappa correlation between the two methods was 0.985. The RT-GEAR assay based on a portable Genie(®)II fluorometer is a sensitive, specific and rapid assay for the universal detection of HRV infection.

Publication types

  • Evaluation Study

MeSH terms

  • Genome, Viral
  • Humans
  • Picornaviridae Infections / diagnosis*
  • Picornaviridae Infections / virology
  • RNA, Viral / genetics*
  • Respiratory Tract Infections / diagnosis
  • Respiratory Tract Infections / virology
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Reverse Transcription
  • Rhinovirus / genetics*
  • Rhinovirus / isolation & purification
  • Sensitivity and Specificity

Substances

  • RNA, Viral