The Science of Testing

Some science and explanation behind same-day COVID testing before indoor singing

Version: 21-July-2023

See also: COVID Testing Before Indoor Singing

What About “False Negatives”?

Symptomatic: It has become more common for people to notice symptoms a day or two before their rapid antigen test turns positive. This is likely due to immune activation, and may be even more pronounced when someone is vaccinated. This doesn’t mean that the antigen test doesn’t work. It just means that the amount of virus in their body was still too low for the test, but high enough to stimulate the immune system. But for our purposes, if a person has symptoms they should not attend a singing at all, regardless of their antigen test result.

Asymptomatic: It is possible to test people in a small window of time (for a few days after exposure) where they have already been infected, but they haven’t grown enough virus to turn the antigen test positive, and they don’t even have symptoms yet. But those people who don’t have enough virus to turn the antigen test positive are also not contagious to others. The negative antigen test in that case is not a failure (“inaccurate”), since no one gets infected at the singing.

For purposes of screening people for participation in singing, the relevant question is not whether they are PCR-positive, but whether they are contagious to others. Think of the rapid antigen test as a test for contagiousness.

It’s initially hard to wrap one’s head around the idea that we are not testing for: who will eventually get COVID; who will eventually have symptoms; who already has a positive PCR test; who will develop a positive rapid antigen test in the future.

We are only testing for who is contagious (infectious) during that brief window of time when we sing together.

Mina, 2020

While the possibility of a false positive test could be substantial, particularly in a low-prevalence population, we are not trying to accurately diagnose a disease here. We are trying to make the singing safer. We exclude all persons with a positive antigen test in order to protect the entire group, and invite those persons to come sing another day, when their test is negative. In practice, very few people would face canceling their attendance at a singing because of a false-positive test. (Jang, 2023)

Science!

  • For this to work, the prevalence of COVID in the community should be fairly low:
    • Less than 2% of the population is contagious, or below about 40 new diagnosed cases / 100k population / day, just as a rough guide. [1]
    • Requiring that singers be asymptomatic and have no recent direct exposure also helps to lower this pre-test probability.
    • The antigen test is highly specific, and given the modest prevalence, almost everyone will test negative.
    • Under these conditions, the negative predictive value of the test is >95%, even when the sensitivity of the test is no greater than 50-60%. (Merck, 2022)
Woloshin et al., 2020
  • In fact, rapid antigen tests are >85% sensitive to detect COVID infection if the person’s viral load is high enough to be contagious to others (>106 copies/ml, or equivalently, a cycle-threshold Ct<25). (Gallichotte, 2020, Figure 2; Korenkov, 2021; Peeling, 2022; Pickering, 2021; Schuit, 2021; Wölfel, 2020) By comparison, PCR testing has a detection limit of about 103, and the time needed to transition between those two levels is on the order of one to two days.
  • For our purpose, comparison of the antigen test to the presence of culturable virus is more important than comparison to PCR-positivity. PCR tests remain positive for weeks after the patient ceases to be contagious. Antigen test sensitivity is much higher (>95%) when compared to same-day culturable virus, the situation where you expect people to be infectious. (Chu, 2002; Korenkov, 2021; LaScola, 2020; Lopera, 2022; Said, 4 Jan 2022; Cosimi, 2022; Van Kampen, 2021; Pekosz, 2021; Tariq, 2021)
Puhach, 2022: Fig. 1: Methods to measure infectious virus and RNA viral load.
Methods to measure infectious virus and RNA viral load. (Puhach, 2022: Fig. 1.)
Viral culture as contagiousness standard (Larremore, 2021)

  • In the pre-symptomatic screening situation, the frequency of testing and the quick availability of a result are more important than test sensitivity. (Larremore, 2021) In our application, the ability to quickly screen the entire class on the day of the singing greatly reduces the probability of viral transmission on that day. Conversely, social or geographic resistance to testing will compromise its effectiveness.
  • While it’s not that easy to translate these laboratory data to actual screening results for pre-symptomatic infection, we also don’t have to press very hard to see that rapid-antigen testing immediately before singing can create an extra layer of safety.
  • Nothing about testing precludes:
    • Screening singers for symptoms referable to Covid, or recent direct exposure. These are fundamental precautions.
    • Using environmental precautions such as room ventilation and air filtration.

Other questions about testing before indoor singing?

Contact David Brodeur

Sources

[1] My “back of the envelope” calculation is as follows:

  • 40 new reported cases per day per 100,000 population
  • each reported case represents 10 actual new cases (ascertainment bias)
  • each new case will be contagious to others for 5 days
  • 40/100,000 X 10 X 5 X 100% =2% prevalence of contagion
  • Boucau, J, et al. “Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection.” N Engl J Med, 29 Jun 2022, https://doi.org/10.1056/NEJMc2202092
    • 25% of omicron patients require 10 days or more to clear the virus.
  • Boum, Y, et al. Performance and operational feasibility of antigen and antibody rapid diagnostic tests for COVID-19 in symptomatic and asymptomatic patients in Cameroon: a clinical, prospective, diagnostic accuracy study. The Lancet Inf Dis, 1 Aug 2021, 21(8):P108901096. https://doi.org/10.1016/S1473-3099(21)00132-8
  • Bullard, J, et al. Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples. Clin Inf Dis 71(10):2663-2666 (15 Nov 2020). https://doi.org/10.1093/cid/ciaa638
  • “COVID-19 Testing Guidance.” American Academy of Pediatrics, 17 Nov 2021. https://www.aap.org/en/pages/2019-novel-coronavirus-covid-19-infections/clinical-guidance/covid-19-testing-guidance/
  • Cosimi LA, et al. Duration of Symptoms and Association With Positive Home Rapid Antigen Test Results After Infection With SARS-CoV-2. JAMA Netw Open. 2022;5(8):e2225331, 3 Aug 2022. https://doi.org/10.1001/jamanetworkopen.2022.25331
  • Chu, VT, et al. Comparison of Home Antigen Testing With RT-PCR and Viral Culture During the Course of SARS-CoV-2 Infection. JAMA Intern Med. Published online April 29, 2022. https://doi.org/10.1001/jamainternmed.2022.1827
  • Ditzler, Andy. “Our Mutual Burdens Bear: The Risky Business of Sacred Harp Singing.” Sacred Harp Atlanta, 4 Jul 2022.  https://www.facebook.com/groups/45458433401/posts/10159244673973402/
  • Gallichotte, EN, et al. Longitudinal surveillance for SARS-CoV-2 RNA among asymptomatic staff in five colorado skilled nursing facilities: Epidemiologic, virologic and sequence analysis. medRxiv 2020.06.08.20125989, (2020). doi.org/10.1101/2020.06.08.20125989. See Figure 2.
  • “Guidance for COVID-19 Prevention in K-12 Schools.” CDC, 5 Nov 2021. https://www.cdc.gov/coronavirus/2019-ncov/community/schools-childcare/k-12-guidance.html
  • Jang, EJ, et al. Positive Predictive Value of Rapid Antigen Tests in School During SARS-CoV-2 Omicron Variant Surge. Pediatr Infect Dis J. (2023) Jan; 42(1): e6–e8. https://doi.org/10.1097%2FINF.0000000000003751
    • Positive predictive values as low as 71% in asymptomatic school teachers; 86-94% for all those tested with weekly school screening.
  • Korenkov, M, et al. Evaluation of a Rapid Antigen Test To Detect SARS-CoV-2 Infection and Identify Potentially Infectious Individuals. J Clin Microbiol 59(9): e00896-21, Aug 2021. https://doi.org/10.1128/JCM.00896-21
  • Larremore, DB, et al. Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening. Sci. Adv. 7:eabd5393, 1 Jan 2021. https://doi.org/10.1126/sciadv.abd5393
  • LaScola, B, et al. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur. J. Clin. Microbiol. Infect. Dis. 39, 1059–1061 (2020). doi.org/10.1007/s10096-020-03913-9
  • Lopera, et al. The Usefulness of Antigen Testing in Predicting Contagiousness in COVID-19. Microbiol Spectr. 2022 Mar-Apr; 10(2): e01962-21. https://doi.org/10.1128/spectrum.01962-21
    • “SARS-CoV-2 contagiousness is highly unlikely with a negative antigen test since it exhibited a negative predictive value of 99.9% compared to viral culture. … Screening people with antigen testing is a good approach to prevent SARS-CoV-2 contagion and allow returning to daily activities.”
  • Merck Manual, “Clinical Calculator: Negative Predictive Value of a Test.” 2022. https://www.merckmanuals.com/professional/multimedia/clinical-calculator/negative-predictive-value-of-a-test
    • Assume a prevalence of 2%, and a specificity of 99%
    • Sensitivity of 50% in asymptomatic patients, relative to PCR
    • Sensitivity of 85 to 95% in contagious patients, relative to low cycle threshold, or positive viral culture.
    • The probability that the entire class is not contagious is the product of all their negative predictive values. With NPV of 99.9%, a class of 50 singers still has a 5% chance of an outbreak, (1-[0.999]50]).
  • Mina, MJ, et al. Rethinking Covid-19 Test Sensitivity — A Strategy for Containment. N Engl J Med 2020; 383:e120. https://doi.org/10.1056/NEJMp2025631
  • Peeling, RW, et al. Diagnostics for COVID-19: moving from pandemic response to control. The Lancet 399(10326):757-768, 19 Feb 2022. https://doi.org/10.1016/S0140-6736(21)02346-1
    • “Although Ag-RDTs have a lower limit of detection of only 105–106 genome copies per mL compared with 102–103 copies per mL for molecular tests, studies have shown that individuals with a viral load less than 106 genome copies per mL are unlikely to transmit the virus, making Ag-RDTs a useful rapid triage tool to identify those most likely to transmit infection.”
    • “Self-testing can be used to help to ensure a safe environment in settings where patrons or clients are likely to be unmasked, such as gyms and fitness studios, food and beverage establishments, and beauty and wellness salons. Such tests could help to protect patients and residents from infection when there are visitors to public hospital wards or residential care homes.”
  • Pekosz, A, et al. Antigen-Based Testing but Not Real-Time Polymerase Chain Reaction Correlates With Severe Acute Respiratory Syndrome Coronavirus 2 Viral Culture. Clinical Infectious Diseases, Volume 73, Issue 9, 1 November 2021, Pages e2861–e2866, https://doi.org/10.1093/cid/ciaa1706
  • Pickering, S. et al. Comparative performance of SARS-CoV-2 lateral flow antigen tests and association with detection of infectious virus in clinical specimens: a single-centre laboratory evaluation study. Lancet Microbe 2, e461–e471 (2021). https://doi.org/10.1016/S2666-5247(21)00143-9
    • “… sensitivity of the LFDs increased to at least 94·7% when only including samples with detected viral growth.”
  • Pray, IW, et al. Performance of an Antigen-Based Test for Asymptomatic and Symptomatic SARS-CoV-2 Testing at Two University Campuses — Wisconsin, September–October 2020. MMWR Morb Mortal Wkly Rep 2021;69:1642–1647. https://dx.doi.org/10.15585/mmwr.mm695152a3
  • Prince-Guerra, JL, et al. Evaluation of Abbott BinaxNOW Rapid Antigen Test for SARS-CoV-2 Infection at Two Community-Based Testing Sites — Pima County, Arizona, November 3–17, 2020. MMWR 70(3);100–105 (22 Jan 2021) https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e3.htm
  • Puhach, O, et al. SARS-CoV-2 viral load and shedding kinetics. Nature Reviews Microbiology (2 Dec 2022). https://doi.org/10.1038/s41579-022-00822-w
  • “Rapid Testing.” Inf Dis Soc Amer, 25 Oct 2021. https://www.idsociety.org/covid-19-real-time-learning-network/diagnostics/rapid-testing/
  • Said, C. “Antigen tests as contagiousness tests.” RapidTests.org, 4 Jan 2022. https://www.rapidtests.org/blog/antigen-tests-as-contagiousness-tests
  • Said, C, and S Citrenbaum. “Rapid Tests.” rapidtests.org/faq
  • Schuit, E, et al. “Diagnostic accuracy of rapid antigen tests in asymptomatic and presymptomatic close contacts of individuals with confirmed SARS-CoV-2 infection: cross sectional study.” BMJ, 30 Jun 2021; 374:n1676 https://doi.org/10.1136/bmj.n1676
  • “Self-Testing” CDC, 4 Nov 2021. https://www.cdc.gov/coronavirus/2019-ncov/testing/self-testing.html
  • Sun, LH, and J Achenbach. “When you have covid, here’s how you know you are no longer contagious.” The Washington Post, 1 Aug 2022. https://wapo.st/3Sgr5hL
  • Tariq, M, et al. Viable Severe Acute Respiratory Syndrome Coronavirus 2 Isolates Exhibit Higher Correlation With Rapid Antigen Assays Than Subgenomic RNA or Genomic RNA. Front. Microbiol., 12 Nov 2021. https://doi.org/10.3389/fmicb.2021.718497
  • Van Kampen, J. J. A. et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19). Nat. Commun. 12, 267 (2021). https://doi.org/10.1038/s41467-020-20568-4
  • Vogels, C, et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 qRT-PCR assays. medRxiv (2020) https://doi.org/10.1101/2020.03.30.20048108
  • Volpe, A. “Yes, you should test for Covid before going to a gathering: Covid-19 isn’t over, so you should still test before group events.” Vox.com, 22 Jun 2022. https://www.vox.com/even-better/23169635/test-covid-party-concert-event-gathering
  • Wölfel, R, Et. al. “Virological assessment of hospitalized patients with COVID-2019.” Nature 581:465–469 (2020). https://doi.org/10.1038/s41586-020-2196-x
  • Woloshin, S, et al. “False Negative Tests for SARS-CoV-2 Infection — Challenges and Implications.” NEJM 383(6 Aug 2020):e38. https://doi.org/10.1056/NEJMp2015897

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