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Learning to Protect Communities with COVID-19 Home Testing Programs

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Credit: Say Yes! COVID Test

With most kids now back in school, parents face a new everyday concern: determining whether their child’s latest cough or sneeze might be a sign of COVID-19. If so, parents will want to keep their child at home to protect other students and staff, while also preventing the spread of the virus in their communities. And if it’s the parent who has a new cough, they also will want to know if the reason is COVID-19 before going to work or the store.

Home tests are now coming online to help concerned people make the right choice quickly. As more COVID-19 home tests enter the U.S. marketplace, research continues to help optimize their use. That’s why NIH and the Centers for Disease Control and Prevention (CDC) are teaming up in several parts of the country to provide residents age 2 and older with free home-testing kits for COVID-19. These reliable, nasal swab tests provide yes-or-no answers in about 15 minutes for parents and anyone else concerned about their possible exposure to the novel coronavirus.

The tests are part of an initiative called Say Yes! COVID Test (SYCT) that’s evaluating how best to implement home-testing programs within range of American communities, both urban and rural. The lessons learned are providing needed science-based data to help guide public health officials who are interested in implementing similar home-testing programs in communities throughout their states.

After successful eight-week pilot programs this past spring and summer in parts of North Carolina, Tennessee, and Michigan, SYCT is partnering this fall with four new communities. They are Fulton County, GA; Honolulu County, HI; Louisville Metro, KY; and Marion County, IN.

The Georgia and Hawaii partnerships, launched on September 20, are already off to a flying start. In Fulton County, home to Atlanta and several small cities, 21,673 direct-to-consumer orders (173,384 tests) have already been received. In Honolulu County, demand for the tests has exceeded all expectations, with 91,000 orders received in the first week (728,000 tests). The online ordering has now closed in Hawaii, and the remaining tests will be distributed on the ground through the local public health department.

SYCT offers the Quidel QuickVue® At-Home COVID-19 test, which is supplied through the NIH Rapid Acceleration of Diagnostics (RADx) initiative. The antigen test uses a self-collected nasal swab sample that is placed in a test tube containing solution, followed by a test strip. Colored lines that appear on the test strip indicate a positive or negative result—similar to a pregnancy test.

The program allows residents in participating counties to order free home tests online or for in-person pick up at designated sites in their community. Each resident can ask for eight rapid tests, which equals two weekly tests over four weeks. An easy-to-navigate website like this one and a digital app, developed by initiative partner CareEvolution, are available for residents to order their tests, sign-up for testing reminders, and allow voluntary test result reporting to the public health department.

SYCT will generate data to answer several important questions about self or home-testing. They include questions about consumer demand, ensuring full community access, testing behavior, willingness to report test results, and, above all, effectiveness in controlling the spread of SARS-CoV-2, the coronavirus that causes COVID-19

Researchers at the University of North Carolina-Chapel Hill; Duke University, Durham, NC; and the UMass Chan Medical School, Worcester, MA, will help crunch the data and look for guiding themes. They will also conduct a study pre- and post-intervention to evaluate levels of SARS-CoV-2 in the community, including using measures of virus in wastewater. In addition, researchers will compare their results to other counties similar in size and infection rates, but that are not participating in a free testing initiative.

The NIH and CDC are exploring ways to scale a SYCT-like program nationally to communities experiencing surges in COVID-19. The Biden Administration also recently invoked the Defense Production Act to purchase millions of COVID-19 home tests to help accelerate their availability and offer them at a lower cost to more Americans. That encompasses many different types of people, including concerned parents who need a quick-and-accurate answer on whether their children’s cough or sneeze is COVID-19.

Links:

COVID-19 Research (NIH)

Say Yes! COVID Test

Rapid Acceleration of Diagnostics (RADx) (NIH)

NIH Support: National Institute of Biomedical Imaging and Bioengineering; National Heart, Lung, and Blood Institute; National Institute on Minority Health and Health Disparities


COVID-19 Infected Many More Americans in 2020 than Official Tallies Show

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Map of U.S.. Counties showing varying levels of COVID-19 infection
Caption: Percentage of people in communities across the United States infected by the novel coronavirus that causes COVID-19 as of December 2020. Credit: Pei S, Nature, 2021.

At the end of last year, you may recall hearing news reports that the number of COVID-19 cases in the United States had topped 20 million. While that number came as truly sobering news, it also likely was an underestimate. Many cases went undetected due to limited testing early in the year and a large number of infections that produced mild or no symptoms.

Now, a recent article published in Nature offers a more-comprehensive estimate that puts the true number of infections by the end of 2020 at more than 100 million [1]. That’s equal to just under a third of the U.S. population of 328 million. This revised number shows just how rapidly this novel coronavirus spread through the country last year. It also brings home just how timely the vaccines have been—and continue to be in 2021—to protect our nation’s health in this time of pandemic.

The work comes from NIH grantee Jeffrey Shaman, Sen Pei, and colleagues, Columbia University, New York. As shown above in the map, the researchers estimated the percentage of people who had been infected with SARS-CoV-2, the novel coronavirus that causes COVID-19, in communities across the country through December 2020.

To generate this map, they started with existing national data on the number of coronavirus cases (both detected and undetected) in 3,142 U.S. counties and major metropolitan areas. They then factored in data from the Centers for Disease Control and Prevention (CDC) on the number of people who tested positive for antibodies against SARS-CoV-2. These CDC data are useful for picking up on past infections, including those that went undetected.

From these data, the researchers calculated that only about 11 percent of all COVID-19 cases were confirmed by a positive test result in March 2020. By the end of the year, with testing improvements and heightened public awareness of COVID-19, the ascertainment rate (the number of infections that were known versus unknown) rose to about 25 percent on average. This measure also varied a lot across the country. For instance, the ascertainment rates in Miami and Phoenix were higher than the national average, while rates in New York City, Los Angeles, and Chicago were lower than average.

How many people were potentially walking around with a contagious SARS-CoV-2 infection? The model helps to answer this, too. On December 31, 2020, the researchers estimate that 0.77 percent of the U.S. population had a contagious infection. That’s about 1 in every 130 people on average. In some places, it was much higher. In Los Angeles, for example, nearly 1 in 40 (or 2.42 percent) had a SARS-CoV-2 infection as they rang in the New Year.

Over the course of the year, the fatality rate associated with COVID-19 dropped, at least in part due to earlier diagnosis and advances in treatment. The fatality rate went from 0.77 percent in April to 0.31 percent in December. While this is great news, it still shows that COVID-19 remains much more dangerous than seasonal influenza (which has a fatality rate of 0.08 percent).

Today, the landscape has changed considerably. Vaccines are now widely available, giving many more people immune protection without ever having to get infected. And yet, the rise of the Delta and other variants means that breakthrough infections and reinfections—which the researchers didn’t account for in their model—have become a much bigger concern.

Looking ahead to the end of 2021, Americans must continue to do everything they can to protect their communities from the spread of this terrible virus. That means getting vaccinated if you haven’t already, staying home and getting tested if you’ve got symptoms or know of an exposure, and taking other measures to keep yourself and your loved ones safe and well. These measures we take now will influence the infection rates and susceptibility to SARS-CoV-2 in our communities going forward. That will determine what the map of SARS-CoV-2 infections will look like in 2021 and beyond and, ultimately, how soon we can finally put this pandemic behind us.

Reference:

[1] Burden and characteristics of COVID-19 in the United States during 2020. Pei S, Yamana TK, Kandula S, Galanti M, Shaman J. Nature. 2021 Aug 26.

Links:

COVID-19 Research (NIH)

Sen Pei (Columbia University, New York)

Jeffrey Shaman (Columbia University, New York)


New Metric Identifies Coronavirus Hotspots in Real Time

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High viral load found from PCR helps to predict hotspots

During the pandemic, it’s been critical to track in real time where the coronavirus is spreading at home and abroad. But it’s often hard for public health officials to know whether changes in the reported number of COVID-19 cases over time truly reflect the spread of the virus or whether they are confounded by changes in testing levels or lags in the reporting of results.

Now, NIH-funded researchers have discovered a clever workaround to detect more accurately where COVID-19 hotspots are emerging. As published in the journal Science, the new approach focuses on the actual amount of virus present in a positive COVID diagnostic test [1], not just whether the test is positive or negative. What’s even better is these data on a person’s “viral load” are readily available from polymerase chain reaction, or PCR, tests that are the “gold standard” for detecting SARS-CoV-2, the virus responsible for COVID-19. In fact, if you’ve been tested for COVID-19, there’s a good chance you’ve had a PCR-based test.

Here’s how a PCR test for COVID-19 works. After a person provides a nasal swab or saliva sample, any genetic material in the sample is extracted and prepared for the PCR machine. It uses special nucleic acid primers that, if any genetic material from SARS-CoV-2 is present, will make millions more copies of them and result in a positive test result. PCR is an enzymatic reaction that works by running many cycles of heating and cooling; each cycle results in doubling of the genetic material present in the original sample.

But it turns out that PCR can go beyond a simple “yes” or “no” test result. It’s also possible to get some sense of how much coronavirus is present in a positive sample based on the number of cycles required to make enough copies of its genetic material to get the “yes” result. This measure is known as the “cycle threshold,” or Ct, value.

When a sample is run with lots of virus in it, the PCR machine doesn’t need to make so many cycles to reach detectable levels—and the Ct value is considered low. But, when the virus is barely present in a sample, the machine needs to run more cycles before it will reach the threshold for detection. In this case, the Ct value is high. This makes the Ct metric a bit counterintuitive: low Ct means a high level of infection, and high Ct means a low level of infection.

In the new study, researchers in Michael Mina’s lab, Harvard T. H. Chan School of Public Health, Boston, including James Hay and Lee Kennedy-Shaffer, wanted to use Ct values to understand better the overall trajectory of the spread of SARS-CoV-2. Their idea was a little out of the box, since Ct values weren’t being factored into a diagnostic testing process that was set up to give people a yes-or-no answer about COVID-19 status. In fact, Ct values were often discarded.

The team members had a hunch that the amount of virus in patient samples would vary based on whether an outbreak is increasing or declining. Their reasoning was that during an outbreak, when SARS-CoV-2 is spreading rapidly through a community, a larger proportion of infected individuals will have recently contracted the virus than when it is spreading more slowly. The researchers also knew that the virus reaches its peak level in humans soon after infection (generally a couple of days before symptoms begin), and then falls to very low but still detectable levels over the course of weeks or sometimes even months. So, when viral load within samples is highest—and Ct values are lowest—it suggests an outbreak of SARS-CoV-2 is underway. As an outbreak slows and cases fall, viral loads should fall and Ct values rise.

The researchers found that just 30 positive PCR test results on a single day were enough to give an accurate real-time estimate of the growth rate of SARS-CoV-2 infections based on Ct values. With Ct values from multiple time points, it was possible to reconstruct the epidemic curve and estimate the true number of people infected. They found that even Ct values collected from a single location at a single point in time could provide extremely valuable information about the growth or decline of an outbreak.

The findings suggest that these data can now be captured and put to good use as a key metric for decision-making and gauging the success of the pandemic response going forward. It’s also important to note that the value of these data are not unique to COVID-19 and the ongoing pandemic. It appears this can be extremely useful new way to monitor the course of other viral outbreaks, now and in the future, in a way that’s less susceptible to the vagaries of testing. The hope is that this will mean even greater success in capturing viral outbreaks and mobilizing resources in real time to the places where they are most needed.

Reference:

[1] Estimating epidemiologic dynamics from cross-sectional viral load distributions. Hay JA, Kennedy-Shaffer L, Kanjilal S, Lennon NJ, Gabriel SB, Lipsitch M, Mina MJ. Science. 2021 Jun 3.

Links:

COVID-19 Research (NIH)

Michael Mina (Harvard T. H. Chan School of Public Health, Boston)

NIH Support: Common Fund, National Institute of General Medical Sciences; National Cancer Institute


New Initiative Puts At-Home Testing to Work in the Fight Against COVID-19

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COVID-19 Update: Community At-Home Testing
Credit: nito/Shutterstock

Thankfully COVID-19 testing is now more widely available than it was earlier in the pandemic. But getting tested often still involves going to a doctor’s office or community testing site and waiting as long as a couple of days for the results. Testing would be so much easier if people could do it themselves at home. If the result came up positive, a person could immediately self-isolate, helping to stop the coronavirus that causes COVID-19, SARS-CoV-2, from spreading any further in their communities.

That’s why I’m happy to report that the Centers for Disease Control and Prevention (CDC), in close collaboration with state and local public health departments and with NIH, has begun an innovative community health initiative called “Say Yes! COVID Test.” The initiative, the first large-scale evaluation of community-wide, self-administered COVID-19 testing, was launched last week in Pitt County, NC, and will start soon in Chattanooga/Hamilton County, TN.

The initiative will provide as many as 160,000 residents in these two locales with free access to rapid COVID-19 home tests, supplied through NIH’s Rapid Acceleration of Diagnostics (RADx) initiative. Participants can administer these easy-to-use tests themselves up to three times a week for one month. The goal is to assess the benefits of self-administered COVID-19 testing and help guide other communities in implementing similar future programs to slow the spread of COVID-19.

The counties in North Carolina and Tennessee were selected based on several criteria. These included local infection rates; public availability of accurate COVID-19 tracking data, such as that gathered by wastewater surveillance; the presence of local infrastructure needed to support the project; and existing community relationships through RADx’s Underserved Populations (RADx-UP) program. Taken together, these criteria also help to ensure that vulnerable and underserved populations will benefit from the initiative.

The test is called the QuickVue At-Home COVID-19 Test. Developed with RADx support by San Diego-based diagnostic company Quidel, this test is easily performed with a nasal swab and offers results in just 10 minutes. Last week, the test was among several authorized by the Food and Drug Administration (FDA) for over-the-counter use to screen for COVID-19 at home.

Participants can order their QuickVue test kits online for home delivery or local pick up. A free online tool, which was developed with NIH support by CareEvolution, LLC, Ann Arbor, MI, will also be available to provide testing instructions, help in understanding test results, and text message reminders about testing. This innovative tool is also available as a smartphone app.

A recent study, supported by the RADx initiative, found that rapid antigen testing for COVID-19, when conducted at least three times per week, achieves a viral detection level on par with the gold standard of PCR-based COVID-19 testing processed in a lab [1]. That’s especially significant considering the other advantages of a low-cost, self-administered rapid test, including confidential results at home in minutes.

The Say Yes! COVID Test initiative is an important next step in informing the best testing strategies in communities all over the country to end this and future pandemics. The initiative will also help to determine how readily people accept such testing when it’s made available to them. If the foundational data looks promising, the hope is that rapid at-home tests will help to encourage people to protect themselves and others by following the three W’s (Wear a mask. Wash your hands. Watch your distance), getting vaccinated, and saying “Yes” to the COVID-19 test.

Reference:

[1] Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. Smith RL, Gibson LL, Martinez PP, Heetderks WJ, McManus DD, Brooke CB, et al. medRxiv, 2021 March 20.

Links:

CDC and NIH bring COVID-19 self-testing to residents in two locales, NIH News Release, March 31, 2021

Say Yes! COVID Test

Rapid Acceleration of Diagnostics (RADx) (NIH)

COVID-19 Testing (CDC)

Quidel Corporation (San Diego, CA)

Coronavirus (COVID-19) Update: FDA Continues to Advance Over-the Counter and Other Screening Test Development, FDA News Release, March 31, 2021

NIH Support: National Heart, Lung, and Blood Institute; National Institute of Biomedical Imaging and Bioengineering


First Anniversary of NIH’s COVID-19 Testing Car Line

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I joined approximately 80 volunteers to mark the one-year anniversary of NIH’s COVID-19 Testing Car Line. The event was held at NIH’s Gateway entrance on March 17. Pictured here with me are some of the awesome volunteers, from various NIH institutes, centers, and offices, who have helped out in many ways and at many times throughout the year to test staff who report symptoms of COVID-19. Here are some fun facts from the line: First tests performed: March 18, 2020; Coldest Day: 25 degrees on January 29, 2021; Hottest Day: 99 degrees on July 20, 2020; Distinct Staff Tested: 5,291; Total Samples Taken: 7,797; Total Carline Positives: 502. Credit: NIH


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