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Indication - Coronavirus disease (COVID-19)
SARS-CoV-2 nucleic acid test
Facility level:
2. Laboratory
Assay formats
NAT
Status history
First added in 2020
Purpose type
Diagnosis
Purpose
To diagnose infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic individuals suspected of having been exposed; For surveillance and confirmation of outbreaks
Specimen types
Upper respiratory specimens (e.g. nasopharyngeal and oropharyngeal) and lower respiratory specimens (e.g. BAL)
WHO prequalified or recommended products
WHO supporting documents
Diagnostic testing for SARS-CoV-2. Interim guidance (11 September 2020). https://www.who.int/publications/i/item/diagnostic-testing-for-sars-cov-2 Guidance on SARS CoV-2 testing is reviewed regularly based on available evidence. For up to date guidance see: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance-publications?publicationtypes=f85a3610-b102-4287-a6df-f3bc0b2e9f7c
Codes
ICD11 code: RA01.1

Summary of evidence evaluation

Many studies have shown that RT-PCR testing has high analytical sensitivity for detecting SARS-CoV-2 viral infection. Because the swabbing process and late swabbing may miss the virus, clinical sensitivity may be lower than the analytical sensitivity, as has been demonstrated in studies which used repeat swabs in those who were initially RT-PCR negative. Because the possibility of false negatives in those with symptoms or known exposure cannot be ruled out, repeated RT-PCR tests should be considered. Although clinical specificity has been shown to be exceptionally high, no data on specificity were presented in the submission. However, it may be possible to extract relevant data from large COVID-19 prevalence studies, such as the Real Time Assessment of Community Transmission (REACT) in the United Kingdom, as the false positive rate must be less than the total positive rate. These data suggest a specificity of 99.85%.

Summary of SAGE IVD deliberations

Given the seriousness of the global SARS CoV-2 pandemic the SAGE IVD recommended listing a NAT for the diagnosis of SARS CoV-2 infection. Although the evidence was preliminary at the time of submission, SAGE IVD recognized the need to make a SARS CoV-2 NAT available and its role as an essential tool in managing the pandemic. NAT remains the assay of choice for diagnosing infection according to international guidelines. Although most of the evidence provided was collected for RT-PCR tests, SAGE IVD decided to list the assay format as a NAT, thereby allowing countries to consider other types of amplification – such as transcription-mediated amplification – for selection and procurement based on local quality assessment. In considering the use of POC NATs, SAGE IVD raised some concerns about the lack of evidence available at the time of discussion. SAGE IVD highlighted the rapid advance in evidence generation for SARS CoV-2 testing and recommended this listing be reviewed as and when additional evidence is published.

SAGE IVD recommendation

SAGE IVD recommended including the SARS-CoV-2 NAT category in the third EDL: • as a disease-specific IVD for use in clinical laboratories (EDL 3, Section II.b); • using a nucleic acid test format; • to diagnose infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic individuals suspected of having been exposed to the virus and for surveillance and confirmation of outbreaks. The group requested the addition of a note to the test category entry in the EDL stating the listing was based on evidence for RT-PCR tests and other types of nucleic acid amplification require more evidence and should be subject to further review.

Details of submission from 2020

Background

Disease condition and impact on patients COVID-19 is a result of infection caused by the SARS-CoV-2 virus. COVID-19 infection presents a challenge for clinical diagnosis, as many infected (and infectious) patients may present as asymptomatic (1–4). COVID-19 typically presents with flu-like symptoms of respiratory disease from mild to moderate to severe. The common symptoms at early onset include fever, cough, headache, myalgia and fatigue. More severe cases present with symptoms of pneumonia and ARDS, including shortness of breath, confusion, low blood pressure, persistent pain or pressure in the chest, and lethargy. Diarrhoea and bloody sputum are indications of progressive severity, as are patchy shadows and ground-glass opacity observed in chest x-ray and tomography scans. Severe complications include sepsis, respiratory failure, heart failure and septic shock. The median time from exposure to onset of symptoms is 4 days for fever and cough. While asymptomatic cases do not appear to progress to severe cases, mild to moderate cases may deteriorate, depending on the timing and level of care received. Severe cases typically require hospitalization, with deterioration requiring intensive care and mechanical ventilation. The mortality rate for COVID-19 has been described as 9% of severe cases (3). SARS-CoV-2 appears to be more infectious than SARS or MERS (Middle East respiratory syndrome), with a longer period of infectivity (as measured by persistent viral shedding) before the onset of symptoms, with transmissions also noted in the days to weeks after symptoms have disappeared (4). Age appears to play a significant role in morbidity and mortality risk for COVID-19 (2, 5–7). As seen with SARS-CoV, very few SARS-CoV-2 deaths have been reported for the paediatric population, in stark contrast to the 14.8% mortality rate observed for patients > 80 years and 8% mortality rate for patients 70–79 years (7–9). Older patients are more likely to present as severe cases and are two to three times more likely to develop ARDS and require mechanical ventilation, with an observed 49% mortality rate for critical cases. The majority of younger and paediatric cases present asymptomatic or mild cases of respiratory infection, even with high levels of detected viraemia, though COVID-19 paediatric fatalities have been documented. COVID-19 also disproportionally impacts patients with co-morbidities such as hypertension, diabetes, cardiovascular disease, and chronic pulmonary or liver disease (4, 10, 11). Does the test meet a medical need? The clinical utility of SARS-CoV-2 infection testing lies in early identification and isolation of cases, but also in choosing the right therapeutic approach in a clinical picture that can mimic several other entities (12). Although the treatment options for less severe forms of COVID-19 are limited, there is increasing evidence of beneficial treatment of severe cases with dexamethasone (13, 14). Other therapeutic options are the right supportive care, such as optimized ventilation strategies and prevention of secondary infections, as well as anticipation and prevention of complications specific to COVID-19 (e.g. inflammation, renal failure, cardiovascular and neurological complications) (14, 15). The latter aspect is more relevant in HICs with advanced clinical and intensive care capacity. In low-income countries lacking capacity for advanced treatment options, greater emphasis is placed on preventing nosocomial infections and on public health measures such as isolation and quarantine. Identification of COVID-19 may also limit further diagnostic investigations for other etiologies and eventually limit antibiotic use for empiric treatment of assumed bacterial pneumonia (16). In a health care settings, early identification of infected individuals (both patients and health care workers) can prevent unrecognized spread of the virus within an institution. Early identification allows for proper isolation of infected patients, and appropriate use of PPE for health care workers. As the test is mostly based on conventional RT-PCR technology, it does not represent a new or specifically innovative technology. Nonetheless, it has the advantage of ample experience with the method, and standard reagents and laboratory equipment are sufficient to carry out testing. Because SARS-CoV-2 is a global pandemic pathogen, in most areas the positive predictive value (PPV) of a SARS-CoV-2 diagnostic test based on PCR is high, especially for patients in high-risk groups. How the test is used According to current WHO interim guidance, wherever possible, suspected active SARS-CoV-2 infections should be tested using a NAT, such as real-time RT-PCR. A positive NAT result is considered a confirmed case. A negative result does not rule out infection in cases where clinical suspicion is high. An additional sample and NAT test are recommended in these patients. For more information, see the WHO interim guidance on diagnostic testing for SARS-CoV-2 at: https://www.who.int/publications/i/item/diagnostic-testing-for-sars-cov-2.

Public health relevance

Prevalence and socioeconomic impact It is estimated that most transmissions occur in the pre-syndromic phase, and that viral loads peak before or around symptom onset (17, 18). Thus, early identification of infected individuals is essential to prevent further spread. Widely available testing for SARS-CoV-2 with high sensitivity and specificity makes it possible to identify infected individuals early, isolate them and limit transmission. In addition to individual diagnostics, identifying infected health care workers can prevent nosocomial spread and protect populations at high risk, such as those in institutions (e.g. nursing homes). The extent of circulating virus can also inform policy-makers for efficient planning of health care resources. Data on SARS-CoV-2 virus circulation obtained by direct virus detection can further help to adapt public health measures, such as social distancing, mask use and school closures. Due to the high infectivity of the virus, increased case numbers may indicate the necessity to shut down parts of official social interactions (e.g. gatherings and public transport) to prevent overwhelming health systems with high numbers of severe cases. Testing also helps to identify superspreading events. Although most participants may present asymptomatically, they may then serve as a reservoir for a new local outbreak (as has been observed in meat processing plants, clubs and fitness studios).

WHO or other clinical guidelines relevant to the test

WHO has published specific guidance on diagnostic testing for SARS-CoV-2 at: https://www.who.int/publications/i/item/diagnostic-testing-for-sars-cov-2 (19). These guidelines are updated based on the availability of evidence and are rapidly evolving. Other guidance documents have been published by the CDC. For example, a SARS-CoV-2 testing strategy for non-health-care workplaces (20) describes the five populations for which SARS-CoV-2 testing with viral tests (i.e. nucleic acid or antigen tests) is appropriate: • individuals with signs or symptoms consistent with COVID-19; • asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 to control transmission; • asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings; • individuals being tested to determine resolution of infection (i.e. test-based strategy for discontinuation of transmission-based precautions, health care personnel returning to work and discontinuation of home isolation); and • individuals being tested for purposes of SARS-CoV-2 public health surveillance. Other documents advise on strategies where testing resources are limited. For example, IDSA (21) advocates focusing on hospitalized patients and patients with respiratory disease, health care workers, outpatients and community surveillance. Similar documents are available from the ECDC on testing strategies for SARS-CoV-2 (22) as well as on surveillance by testing (23).

Evidence for diagnostic accuracy

Several clinical studies have reported on NAT sensitivity and specificity (24–30). As NATs are highly specific by design, false positive results rarely occur. Nonetheless, they have been described with the use of some automated systems, and occurred in the beginning of the pandemic due to contamination in manufacturing units for primers and probes (31, 32). False-negative results are mostly related to pre-analytical quality, but initially negative results have also been observed in hospitalized patients in two early studies from China and Singapore. Note that most hospitalizations occur after the first week of illness, when viral load is highest; lower RNA levels are observed when patients present with pneumonia. Many fewer false negatives have been reported in a larger cohort (26). In particular, improved assays and use of multiple targets have resulted in optimized detection.

Evidence for clinical usefulness and impact

Not available.

Evidence for economic impact and/or cost–effectiveness

No peer-reviewed literature on the economic impact of testing was available at the time of submission. However, a few preprint publications on the subject, such as a report on the clinical and economic impact of five SARS-CoV-2 testing strategies in Massachusetts by Neilan et al. (33), did find testing to be cost-effective. It appears highly likely that in the light of substantial economic losses due to COVID-19, testing will pay off as part of a containment strategy.

Ethical issues, equity and human rights issues

COVID-19 has disproportionally affected racial and ethnical minorities. Consequently, accessible testing and control of the pandemic will at least to some extent alleviate the disease burden on these populations (34).
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