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2. Diagnostic testing of COVID-19
2.1.1 Severe acute respiratory syndrome (SARS)
This disease arose in South China in late 2002. Caused by the SARS caronavirus (SARS-CoV) and believed to have originated from horseshoe bats[1], SARS eventually was contained in the summer of 2003. The last known infection was in April 2004, due to a laboratory accident.[2] During that time, the following sample collection and test procedures evolved from the related outbreaks (note that this is only a summary; consult the cited literature directly for full details)[3][4][5][6][7]:
- Determine that the patient is indicating clinical and/or epidemiological evidence of SARS. As Knobler et al. put it: "SARS-CoV testing should be considered if no alternative diagnosis is identified 72 hours after initiation of the clinical evaluation and the patient is thought to be at high risk for SARS-CoV disease (e.g., is part of a cluster of unexplained pneumonia cases)."[5]
- Collect multiple specimen types at different time points of the patient's illness. Respiratory and plasma or serum specimens should be collected early into the first week of illness. Respiratory samples should be from nasopharyngeal aspirates and swabs in the upper respiratory tract, or in some cases fluids from the lower respiratory tract using bronchoalveolar lavage, tracheal aspiration, or a pleural tap. Whole blood (5 to 10 ml) is collected into either a serum separator tube for blood serum or EDTA tube for blood plasma. Stool samples are also of import early on for virus isolation or detection and are useful in at least the first and second weeks of the illness. Blood serum is usefull in weeks two and three for detecting a rising titre. Additionally, the literature also makes reference to methods of collecting specimens post-mortum.
- Conduct testing. At the time, the two primary test types used were enzyme immunoassay (EIA; today more commonly known as ELISA[8]) for detection of serum antibody and reverse transcription polymerase chain reaction (RT-PCR) for detection of the virus' RNA. The U.S. Centers for Disease Control and Preventions had this to say about these tests in May 2004[4]:
Both the EIA and the RT-PCR tests are sensitive and highly specific for SARS-CoV. The ability to diagnose SARS-CoV infection in a patient is often limited, however, by either the low concentration of virus in most clinical specimens (RT-PCR assays) or the time it takes a person to mount a measurable antibody response to SARS-CoV (serologic assays). The likelihood of detecting infection is increased if multiple specimens (e.g., stool, serum, respiratory tract specimens) are collected at several times during the course of illness.
The literature also makes reference to an immunofluorescence assay (IFA) for detecting antibody, with the CDC calling its results "essentially identical to those for the EIA for SARS antibody."[4] Tangentially, isolation of SARS-CoV in cell culture from a clinical specimen is also referenced, though such activity is reserved for Biosafety Level 3 (BSL-3) laboratories.
- Confirm the results. Laboratory confirmation is based on one of 1. initial local lab detection and subsequent national reference lab confirmation of a validated serology-based test detection; 2. isolation of SARS-CoV in cell culture with subsequent confirmation from a validated test; or 3. initial local lab detection and subsequent national reference lab confirmation of SARS-CoV RNA from a validated RT-PCR test which used either two clinical specimens from different sources or two same-source clinical specimens from two different days.
- Additionally, in the case of serology, one of the following must be true:
- SARS-CoV serum antibodies are detected in a single serum specimen; or,
- a "four-fold or greater increase in SARS-CoV antibody titer between acute- and convalescent-phase serum specimens tested in parallel"[4] is detected; or,
- a "negative SARS-CoV antibody test result on acute-phase serum and positive SARS-CoV antibody test result on convalescent-phase serum tested in parallel"[4] is detected.
- Of note is the WHO's January 2004 cautionary message about serological diagnostics in not only SARS-CoV but other types of coronaviruses. At that time, they showed a level of unsureness in regards to how coronaviruses elicited serological cross-reactions and generated antigenic recall. They also preached caution in interpreting serological results in non-epidemic periods and when no viral sequence data are available. Finally, they also mentioned the added difficulties of rate cases when coinfection with a related human coronavirus occurs, "although the use of expressed proteins in Western blots may help to sort this out."[6]
- Arrange for confirmatory testing to be performed by an appropriate test site in the case of a positive RT-PCR test.
- Report to state or local health departments details of patients radiographically confirmed with pneumonia with at least one SARS-CoV risk factor for exposure, clusters of healthcare workers with unexplained pneumonia, and any positive SARS-CoV test results. Additional international reporting of SARS by WHO Member States in regards to probable and laboratory-confirmed cases is also requested.
- Send off for an additional verification by an external member of the WHO's SARS Reference and Verification Laboratory Network before internationally announcing results as a laboratory-confirmed case.
2.2 Organizational and agency guidance on COVID-19 testing
2.3 Current test kits and their differences
2.4 Regulatory and recommended requirements for reporting test results
References
- ↑ McKie, R. (9 December 2017). "Scientists trace 2002 Sars virus to colony of cave-dwelling bats in China". The Guardian. https://www.theguardian.com/world/2017/dec/10/sars-virus-bats-china-severe-acute-respiratory-syndrome. Retrieved 03 April 2020.
- ↑ Normile, D. (2004). "Mounting Lab Accidents Raise SARS Fears". Science (5671): 659–61. doi:10.1126/science.304.5671.659. PMID 15118129.
- ↑ New York State Department of Health (February 2004). "Laboratory Testing for SARS". State of New York. https://www.health.ny.gov/diseases/communicable/sars/sars_reporting/attachment_6_dear_doctor_lab.htm. Retrieved 03 April 2020.
- ↑ 4.0 4.1 4.2 4.3 4.4 Centers for Disease Control and Prevention (21 May 2004). "Public Health Guidance for Community-Level Preparedness and Response to Severe Acute Respiratory Syndrome (SARS), Version 2 - Supplement F: Laboratory Guidance" (PDF). Centers for Disease Control and Prevention. https://www.cdc.gov/sars/guidance/f-lab/downloads/F-lab-full.pdf. Retrieved 03 April 2020.
- ↑ 5.0 5.1 Knobler, S.; Mahmoud, A.; Lemon, S. et al., ed. (2004). "Appendix C: In the absence of SARS-CoV transmission worldwide: Guidance for surveillance, clinical and laboratory evaluation, and reporting". Learning from SARS: Preparing for the Next Disease Outbreak. National Academies Press. pp. 292–302. doi:10.17226/10915. ISBN 9780309182157.
- ↑ 6.0 6.1 World Health Organization (23 January 2004). "WHO SARS International Reference and Verification Laboratory Network: Policy and Procedures in the Inter-Epidemic Period". World Health Organization. http://www.who.int/csr/resources/publications/en/SARSReferenceLab.pdf. Retrieved 03 April 2020.
- ↑ Liang, G.; Chen, Q.; Xu, J. et al. (2004). "Laboratory Diagnosis of Four Recent Sporadic Cases of Community-acquired SARS, Guangdong Province, China". Emerging Infectious Diseases 10 (10): 1774–81. doi:10.3201/eid1010.040445. PMC PMC3323270. PMID 15504263. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323270.
- ↑ Lequin, R.M. (2005). "Enzyme Immunoassay (EIA)/Enzyme-Linked Immunosorbent Assay (ELISA)". Clinical Chemistry 51 (12): 2415–18. doi:10.1373/clinchem.2005.051532. PMID 16179424.
