As many people recognize, misconceptions about COVID-19 data and its interpretation can undermine our commitment to making data-informed decisions and taking data-driven actions while combating the pandemic. In this third post in my coronavirus terms series, I’ll revisit and expand upon some of the terms and concepts I’ve covered in previous posts related to dashboard metrics and coronavirus testing.
It’s about time (again)
There’s a lot of data and metrics about the pandemic. It can be challenging to know what essential indicators to focus on during our efforts to slow coronavirus community spread. I think it's best to measure our overall effectiveness by the following three time intervals:
- The time interval between when you’re exposed and when when your quarantine* starts.
- The time interval between when your symptoms start and when you receive your viral test results.
- The time interval between when your symptoms start and when your isolation* starts.
*Quarantine and isolation are sometimes used interchangeably. While both mean avoiding contact with other people, let’s clarify the semantics. You quarantine an exposure before a viral test determines infection – regardless of symptoms. You isolate an infection after a positive viral test result – regardless of symptoms.
Timely testing is essential to minimizing these time intervals. Simply put, we need to:
- Viral test people as soon as either an exposure occurs or symptoms start.
- Receive those viral test results as quickly as possible.
- Immediately isolate people who viral-test positive.
In order to accomplish these goals, which viral tests should we use?
Different types of viral tests
In my first post, I differentiated antibody tests (which tell you if you had a previous infection) and viral tests (which tell you if you have a current infection). In my second post, I discussed the need for widespread viral testing and some alternative approaches (pool, surveillance, rapid) for addressing its challenges. Now let’s examine three types of viral tests.
Polymerase chain reaction (PCR) test
This test detects the specific genetic sequence (viral RNA) unique to the coronavirus using a specific mix of chemicals (reagents) and a laboratory machine (thermal cycler). The test:
- Is highly accurate, correctly detecting coronavirus more than 95% of the time.
- Is expensive and complex, with an end-to-end process that requires extensive training and expertise.
- Uses a nasopharyngeal swab (the long one that goes way up in the nose, which I can personally attest is unpleasant). It requires trained professionals to properly collect a sample, often only at a hospital, doctor’s office or official testing site.
- Has a relatively slow turnaround on test results, easily exacerbated by supply chain problems and laboratory backlogs.
- Has essentially been the viral test since the beginning of the pandemic. The overwhelming majority of the millions of coronavirus tests performed worldwide have been PCR tests.
Antigen test
This test detects viral proteins on the surface of coronavirus particles. It:
- Is less accurate than PCR, correctly detecting coronavirus about 70-80% of the time (varies by specific test).
- Entails a cheaper and less complex end-to-end process.
- Typically uses a nasal swab (the shorter one that only goes in the nostril). This means more people at more locations can properly collect a sample, with limited training.
- Has a relatively fast turnaround on test results, less impacted by supply chain problems and laboratory backlogs.
- Essentially works better for screening than diagnosis (more on that below).
Saliva test
This is also an antigen test. But beyond sampling saliva – and not requiring any type of nasal swab – this test has other unique characteristics. It:
- Is less accurate than PCR and is generally the least accurate type of antigen test.
- Entails the cheapest and least complex end-to-end process.
- Provides very fast turnaround on test results, usually within minutes. Some tests pending approval may not require sending the sample to a laboratory or even using a machine.
- Includes one of the most popular tests so far – SalviaDirect, which was developed by Yale University and funded by the NBA.
- Is the most likely candidate for future home testing and other testing not conducted by healthcare professionals.
The contagious continuum
As I mentioned above, quarantining the exposed and isolating the infected shared a common goal: keeping potentially contagious people away from others. However, that’s not what we’re testing for. In the US especially, we’re testing for infection. However, stopping spread means stopping contagion.
On average, it can take 3 to 5 days after getting infected to develop symptoms (if you develop any at all). Although you might remain symptomatic for several days, weeks, or even months, recent studies suggest that by 10 to 14 days after your infection (7 to 9 days after your symptoms start) you are no longer contagious. I call this the contagious continuum. It’s the time period we need to specifically target with testing.
Once you are no longer contagious, you are no longer a public health risk (although you still face individual health risks). Quarantines, isolation, shutdowns and shelter-in-place orders are all blunt, broad and mostly blind containment protocols for the contagious continuum. This is because we currently lack the testing needed to identify its exact start and end. And this is why it’s so important to get tested early. It’s also why we need to test asymptomatic people. They pose both the greatest threat to pandemic control and the greatest opportunity to end the pandemic.
You get what you test for: Diagnosis versus screening
Much of the current testing is diagnostic. Diagnosis is an essential prelude to medical treatment, but it does little to stop chains of transmission. While diagnostic testing must continue, we need to supplement it with testing done for the purpose of screening. Screening is essential to identifying the contagious and curbing coronavirus transmission within our communities. This is why relying solely on PCR tests is not the best option.
Even after you’re no longer contagious, millions of dead virus particles with intact strands of viral RNA can still line your mouth and nasal cavity. Due to its sensitivity (i.e., accuracy), you can PCR-test positive for weeks, if not months, after your initial infection. But at this point you’re no longer contagious. So it doesn't make sense to trace any contacts you’ve recently had (because you couldn't have infected any of them). Nor does it make sense for you to isolate. Timely testing, therefore, reduces both the number of people who need to be isolated and the duration of isolation.
More screening – not just more testing
Although capable of offering some sense of how contagious an infected person is, PCR tests are not being used that way. And many antigen tests, like Abbott’s BinaxNOW, still essentially require a prescription and are only authorized to be used on patients within 7 days of the onset of coronavirus symptoms. This is targeting diagnosis of the sick as opposed to screening of the exposed or random testing of asymptomatic people.
Symptomatic people are much more likely to have the virus and therefore much less likely to generate a false positive on any viral test. However, the fear of false positives should not prevent us from using less accurate tests for screening, while continuing to use the more accurate tests for diagnosis. Most people rightfully argue that we need to do more testing. We definitely do. But more precisely, we need to do more screening.
Highly accurate PCR tests seemed like the best option at the start of the pandemic. But many public health experts are now recommending alternative viral tests. Even if these alternatives are less accurate and more likely to miss some infections, they might eventually enable testing everyone, everyday.
Containing the contagious
The success of the strategy proven effective in combating coronavirus relies on being able to catch people with an active infection before others catch what they have. That strategy involves widespread testing and contact tracing while quarantining the exposed, isolating the infected and – perhaps most essential – containing the contagious. To do this, we need to test early, easily, quickly and frequently.
View the COVID-19 dashboard from SASLearn more about fallacies in COVID-19 data in this article from PreventEpidemics.org
