Respiratory Virus Detection by PCR

Respiratory viruses cause significant morbidity and mortality, particularly among the elderly, children, and immunocompromised individuals. There are an estimated 200,000 hospitalizations due to influenza and 125,000 RSV-related hospitalizations in the U.S. annually. Parainfluenzas, human metapneumovirus and adenoviruses can cause respiratory disease that is clinically indistinguishable from illness caused by influenza and RSV. Bacterial atypical pneumonia pathogens include Mycoplasma pneumoniae and Chlamydophila pneumoniae.  M. pneumoniae typically  infects younger age groups, while C. pneumoniae has a higher incidence in the elderly. Long-lasting immunity does not occur following infection with either organism.

Traditional methods for detection of respiratory pathogens include rapid antigen detection tests, direct fluorescent antibody (DFA) staining, culture, and serology. None of these methods is ideal for diagnostic purposes. Rapid antigen testing is widely available but limited to detection of influenza and RSV, with sensitivity ranging from 50-90%. DFA testing has excellent sensitivity for most viruses, but is technically cumbersome to perform. Virus isolation by culture requires 2-10 days, so results are generally not available within a timeframe that is helpful for patient management. Additionally,  sensitivity of culture for respiratory viruses can be as low as 60%, and varies considerably depending on specimen collection and handling. Serologic testing for respiratory pathogens usually requires acute and convalescent samples and is usually not effective for early diagnosis.

Testing for respiratory pathogens by nucleic acid amplification tests, including PCR, greatly improves detection. The rate of viral identification increases by as much as 50% compared to traditional methods. For most respiratory pathogens, PCR detects several orders of magnitude less organism than culture. The sensitivity of PCR for the eight most common respiratory viruses ranges from 95-100%, with specificity of 99-100%. Of note, mixed viral infections are detected in up to 30% of respiratory specimens tested by PCR.

GenMark's eSensor® XT-8 system supports a broad range of molecular diagnostic tests including a Respiratory Viral Panel (RVP) that is classified as RUO. The assay detects and differentiates the following viruses:

  • Influenza A including subtypes H1, H3, and H1N1
  • Influenza B
  • RSV types A & B
  • Parainfluenza 1-4
  • Human metapneumovirus types A & B
  • Rhinovirus
  • Coronavirus OC43, NL63, 229E, and HKU1
  • Adenovirus types B, C, and E

Biofire’s Filmarray combines PCR and gene array technology to detect 17 viral and 3 bacterial pathogens, including M. pneumoniae, C. pneumoniae, and B. pertussis. This test should be ordered as ‘Respiratory Panel by PCR’. Testing is performed on nasopharyngeal swabs, nasal washes, and bronchoscopy specimens

Respiratory PCR is much more sensitive than rapid influenza antigen tests. Several cases have been observed where the rapid influenza test was negative but the respiratory PCR panel detected either influenza A or B. Sensitivity of PCR for the eight most common respiratory viruses ranges from 95 to100%, with specificity of 99 to100%. Mixed viral infections are detected in up to 30% of respiratory specimens tested by PCR.

Testing can be performed on nasopharyngeal swabs, nasal washes and bronchoscopy specimens. For optimal results, specimens should be collected within 3 to 5 days of symptom onset.


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