Diagnosis of coronavirus infections

Coronavirus disease 2019 (COVID-19)
The WHO has published several testing protocols for diagnosis of the disease. The standard method of testing is real time reverse transcription polymerase chain reaction (rRT-PCR). The test can be done on respiratory samples obtained by various methods, including nasopharyngeal swab or sputum sample. Results are generally available within a few hours to two days. Blood tests can be used, but these require two blood samples taken two weeks apart and the results have little immediate value. Scientists were able to isolate a strain of the coronavirus and publish the genetic sequence so that laboratories across the world could independently develop PCR tests to detect infection by the virus.

COVID-19 testing can also be done with antibody test kits. Antibody assays use a blood serum sample and can provide a positive result even if the person has recovered and the virus is no longer present.

Diagnostic guidelines released by Zhongnan Hospital of Wuhan University suggested methods for detecting infections based upon clinical features and epidemiological risk. These involved identifying patients who had at least two of the following symptoms in addition to a history of travel to Wuhan or contact with other infected patients: fever, imaging features of pneumonia, normal or reduced white blood cell count, or reduced lymphocyte count.

Middle East respiratory syndrome (MERS)
The interim case definition of the WHO is that a confirmed case is identified in a person with a positive lab test by molecular diagnostics including either a positive PCR on at least two specific genomic targets or a single positive target with sequencing on a second.
According to the WHO, a probable case is:

  • A person with a fever, respiratory infection, and evidence of pneumonia or acute respiratory distress syndrome, and testing for MERS-CoV is unavailable or negative on a single inadequate specimen, and the person has a direct link with a confirmed case.
  • A person with an acute febrile respiratory illness with clinical, radiological, or histopathological evidence of pulmonary parenchymal disease (e.g. pneumonia or acute respiratory distress Syndrome) and an inconclusive MERS-CoV laboratory test (that is, a positive screening test without confirmation) and a resident of or traveler to Middle Eastern countries where MERS-CoV virus is believed to be circulating in the 14 days before onset of illness.
  • A person with an acute febrile respiratory illness of any severity and an inconclusive MERS-CoV laboratory test (that is, a positive screening test without confirmation) and the person has a direct epidemiologic link with a confirmed MERS-CoV case.

MERS cases have been reported to have low white blood cell count, and in particular low lymphocytes. The WHO recommends obtaining samples fro PCR testing from the lower respiratory tract via bronchoalveolar lavage (BAL), sputum sample or tracheal aspirate as these have the highest viral loads. There have also been studies utilizing upper respiratory sampling via nasopharyngeal swab.

Several highly sensitive RT-PCR assays exist for rapid identification of MERS-CoV from patient-derived samples. These assays attempt to amplify upE (targets elements upstream of the E gene), open reading frame 1B (targets the ORF1b gene) and open reading frame 1A (targets the ORF1a gene). The WHO recommends the upE target for screening assays as it is highly sensitive. In addition, hemi-nested sequencing amplicons targeting RdRp (present in all coronaviruses) and nucleocapsid (N) gene fragments can be generated for confirmation via sequencing. Reports of potential polymorphisms in the N gene between isolates highlight the necessity for sequence-based characterization. The WHO recommended testing algorithm is to start with an upE RT-PCR and if positive confirm with ORF 1A assay or RdRp or N gene sequence assay for confirmation. If both an upE and secondary assay are positive it is considered a confirmed case.

Protocols for biologically safe immunofluorescence assays (IFA) have also been developed, but betacoronaviruses antibodies are known to cross-react within the genus. This effectively limits their use to confirmatory applications. A more specific protein-microarray based assay has also been developed that did not show any cross-reactivity against population samples and serum known to be positive for other betacoronaviruses. Due to the limited validation done so far with serological assays, WHO guidance is that cases where the testing laboratory has reported positive serological test results in the absence of PCR testing or sequencing, are considered probable cases of MERS-CoV infection, if they meet the other conditions of that case definition.

Severe acute respiratory syndrome (SARS)
Severe acute respiratory syndrome (SARS) may be suspected in a patient who has:

  • Any of the symptoms (fever, muscle pain, lethargy symptoms, cough, or sore throat), including a fever of 38 °C (100 °F) or higher, and

  • Either a history of:
      • Contact (sexual or casual) with someone with a diagnosis of SARS within the last 10 days or
      • Travel to any of the regions identified by the WHO as areas with recent local transmission of SARS.

For a case to be considered probable, a chest X-ray must be positive for atypical pneumonia or respiratory distress syndrome. The WHO has added the category of "laboratory confirmed SARS" for patients who would otherwise be considered "probable" but who have not yet had a positive chest X-ray changes, but have tested positive for SARS based on one of the approved tests (ELISA, immunofluorescence or PCR). The appearance of SARS in chest X-rays is not always uniform but generally appears as an abnormality with patchy infiltrates.