key: cord-0746486-imz2s7sm
authors: Velavan, Thirumalaisamy P.; Meyer, Christian G.
title: COVID-19: A PCR-defined pandemic
date: 2020-12-01
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2020.11.189
sha: ac1d8cd457b45c5b7899fa3fe568e51b7d6ec33b
doc_id: 746486
cord_uid: imz2s7sm

nan

statement can be made with regard to the actual infectivity of an individual. Several studies now suggest that enduring positive RTPCRs do not necessarily indicate replication of competent viruses. As there is a strong correlation between PCR results and the feasibility of virus culture with respect to Ct values, a guideline could be implemented in order to provide sound recommendations, e.g., inclusion of antigen tests or determination of the RNA copy number, on the of selfisolation of health-care workers, quarantined individuals from high-risk areas and others. Such evidence-based guidelines might exert an enormous societal impact.

Keywords: COVID-19; SARS-CoV-2; pcr; Antigen; Ct value; Viral shedding; virus viability; RTPCR; Societal impact

The numbers of COVID-19 cases are steadily increasing in many parts of the world and the global and devastating impact of the current pandemic on all aspects of our life is evident.

The number of positive molecular diagnostic tests, which are largely based on real-time (RT) PCR assays which detect genetic material of the causing agent SARS-CoV-2, still form the basis for reporting both symptomatic and asymptomatic cases worldwide. These figures are also used to calculate the basic reproduction number, defined as R-zero (R0), a value relating to the average number of people an infected individual will infect. Asymptomatic carriers of the virus, including those superspreading the virus, are not routinely captured in common testing strategies which rather concentrate on symptomatic individuals, returnees from high risk areas and other high risk groups (Nikolai et al., 2020) . Clearly, any adscription of positive results to a COVID-19 diagnosis requires the occurrence of clinical symptoms and further evaluation and confirmation by physicians, including the appraisal of distinct laboratory parameters.

In diagnostic SARS-CoV-2 assays, RT-PCR is based on the detection of the amount of distinct genetic fragments of the virus in an individual. The amount of gene fragments is routinely determined semi-quantitatively by using the cycle threshold (Ct) value, which corresponds to the number of PCR amplification cycles in the diagnostic assays required to yield positive results. Ct values increase with decreasing viral loads and low Ct values J o u r n a l P r e -p r o o f indicate a high viral load . In ambiguous cases, true quantitative assays can be applied.

When assessing impending public health risks as in the current pandemic and when imposing Observations so far suggest a mean and median incubation period of 5 and 4-5 days, respectively (Lauer et al., 2020 , McAloon et al., 2020 from exposure to onset of symptoms. Viral RNA is detectable in the airways 2-3 days before onset of symptoms, peak at the onset of symptoms and decrease in the following 7-8 days in most patients (Rhee et al., 2020 , Team, 2020 , Wolfel et al., 2020 , Zou et al., 2020 . Viral load kinetics and duration of viral shedding are vital elements in determining the SARS-CoV-2 infectivity. A systematic review and metanalysis has confirmed that SARS-CoV-2 viral shedding may be longer and is proportional to severe illness. However, the viability of the virus is short and not beyond 9 days of illness (Cevik M, 2020) .

Studies evaluating the duration of SARS-CoV-2 infectivity based on cell culture and/or secondary infection rates clearly imply that the virus cannot be cultured from respiratory samples after day 8 of clinical disease (Bullard et al., 2020 , Cevik M, 2020 , La Scola et al., 2020 . A detailed virological analysis of COVID 19 cases confirms that the virus can only be cultured from respiratory samples during the first week of symptoms, but not after day 8 in spite of persisting high virus loads as determined by quantitative RT-PCR (Wolfel et al., 2020) . In addition, the CDC has collected data from adults of various age groups and varying disease severity, indicating that the virus could not be cultured more than 10 days after onset of symptoms (CDC, 2020); virus culture was always unfeasible when Ct values exceeded 33 (La Scola et al., 2020 , Rhee et al., 2020 . Notably, CDC reasonably recommends a symptombased decision for returning from isolation, specifically rejecting exclusively the test-based strategy, unless it would result in an earlier decision.

A prospective cohort study with the first 100 COVID-19 patients in Singapore also showed that attempts to culture the virus failed in all PCR-positive samples with Ct values >30 (Young et al., 2020) . A study of the Korean Centers for Disease Control and Prevention, including 285 patients who had recovered from COVID-19 clinically and were discharged from hospitals, showed that these individuals were tested positive again by PCR an average of 45 days after the onset of the first symptoms (CDC Korea, 2020) . Ct values are lowest shortly after symptom onset and correlate significantly with time elapsed since onset of symptoms (Salvatore et al., 2020) .

Defining the duration of infectivity of SARS-CoV-2 has major implications in determining incidences. Several studies now suggest that enduring positive RT-PCRs do not necessarily indicate the presence of replication-competent viruses (Alexandersen et al., 2020, Rhee et al., J o u r n a l P r e -p r o o f 2020). In fact, sustained RNA detection does not indicate sustained infectivity and SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active virus replication (Alexandersen et al., 2020) . It has also been shown that the contagiousness in patients with mild or moderate COVID-19 decreases rapidly to near zero approximately 10 days after symptom onset (Rhee et al., 2020) .

Early testing for SARS-CoV-2 of individuals with symptoms is important to determine infectivity based on low Ct values and early isolation practices to effectively interrupt SARS-CoV-2 transmission should be commenced when first symptoms appear. However, testing individuals 7 days after the onset of symptoms, which is more likely to be done in low-and middle-income countries, but also occurs in developed countries, only contributes to the assessment of the case numbers. Thus, the veracity of the testing strategy with regard to an estimation of infectivity is questionable. It has to be considered whether only laboratory diagnoses of SARS-CoV-2 by RT-PCR are sufficient to allow assessment of infectivity.

The availability of SARS-CoV-2 antigen testing offers advantages over the diagnosis of SARS-CoV-2 by RT-PCR in terms of reliability. Rapid antigen testing works best in cases of high viral load, in pre-symptomatic and early symptomatic cases up to five days after the onset of symptoms. Rapid antigen testing is sensitive enough for cases with high viral load or low RT-PCR cycle threshold (Ct <25) . The European Centre for Disease Prevention and Control (ECDC 2020) agrees on antigen testing with a WHO performance requirement of >80% sensitivity and >97% specificity . Compared to diagnoses of SARS-CoV-2 by RT-PCR, rapid antigen testing can help to reduce further transmission through early detection, allowing a rapid start of contact tracing (ECDC 2020) .

As there is a strong correlation between PCR results and the feasibility of virus culture with respect to Ct values, a guideline could be implemented in order to provide sound recommendations, e.g., inclusion of antigen tests or determination of the RNA copy number, on the of self-isolation of health-care workers, quarantined individuals from high-risk areas and others. Clinical parameters as well as prolonged infectivity in immunocompromised individuals need to be taken into account. Such evidence-based guidelines might exert an enormous societal impact.

All authors disclose no conflict of interest. 

☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

ECDC 2020: Options for the use of rapid antigen tests for COVID-19 in the EU/EEA and the UK.

European Center for Disease Prevention and Control. https://www.ecdc.europa.eu/sites/default/files/documents/Options-use-of-rapid-antigen-testsfor-COVID-19.pdf, (accessed on 24 November 2020)

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