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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


The Latest on COVID-19 Boosters

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COVID-19 Vaccine vials labeled dose one, dose two, and booster

More than 180 million Americans, including more than 80 percent of people over age 65, are fully vaccinated against the SARS-CoV-2 virus responsible for COVID-19. There’s no question that full vaccination is the best way to protect yourself against this devastating virus and reduce your chances of developing severe or long-lasting illness if you do get sick. But, to stay ahead of this terrible virus, important questions do remain. A big one right now is: How soon will booster shots be needed and for whom?

The answers to this question will continue to evolve as more high-quality data become available. But here’s what we know right now for the Pfizer-BioNTech booster. Late last week, Dr. Rochelle Walensky, the Director of the Centers for Disease Control and Prevention (CDC), recommended that:

  • Those 65 years and older and residents in long-term care settings should receive a booster shot at least 6 months after being fully vaccinated with the Pfizer-BioNTech vaccine,
  • People aged 50–64 years with underlying medical conditions should receive a booster shot at least 6 months after being fully vaccinated with the Pfizer-BioNTech vaccine,
  • Individuals aged 18–49 years with underlying medical conditions may receive a booster shot at least 6 months after getting fully vaccinated with their Pfizer-BioNTech vaccine, based on their individual benefits and risks.
  • Frontline workers who received the Pfizer-BioNTech vaccine may receive a booster. This group includes anyone age 18 through 64 whose frequent institutional or occupational exposure to SARS-CoV-2 puts them at high risk of COVID-19. [1]

Taken together, these CDC recommendations are in line with those issued two days earlier by the Food and Drug Administration (FDA) [2].

Some of the most-compelling data that was under review came from an Israeli study, published recently in the New England Journal of Medicine, that explored the benefit of booster shots for older people [3]. Israel, with a population of around 9 million, has a national health system and one of the world’s highest COVID-19 vaccination rates. That country’s vaccination campaign, based solely on Pfizer-BioNTech, was organized early in 2021, and so its experience is about three months ahead of ours here in the U.S. These features, plus some of the world’s largest integrated health record databases, have made Israel an important source of early data on how the Pfizer-BioNTech mRNA vaccine can be expected to work in the real world over time.

Earlier this year, Israeli public health officials noted evidence for an increased number of breakthrough infections, some of which were severe. So, at the end of July 2021, Israel approved the administration of third doses, or “boosters,” of the Pfizer-BioNTech vaccine for people ages 60 and up who had received their second dose at least five months before.

To find out how well these booster shots worked to bolster immune protection against COVID-19, researchers looked to more than 1.1 million fully vaccinated people who were at least 60 years old. They compared the rate of confirmed COVID-19 infection and severe illness from the end of July to the end of August among people who’d received a booster at least 12 days earlier with those who hadn’t gotten boosters.

Nearly 13,500 older individuals who’d been fully vaccinated before March 2021, got a breakthrough infection during the two months of study. Importantly, the rate of confirmed infection in the group that got boosters was 10 times lower on average than in the group that didn’t get boosters. The data on severe illness looked even better. Of course, there could be other factors at play that weren’t accounted for in the study, but the findings certainly suggest that a third Pfizer shot is safe and effective for older people.

Though the Israeli studies on booster shots are a little ahead of the international pack, we are starting to see results from the research underway in the U.S. Last week, for example, Johnson & Johnson announced new data in support of boosters to improve and extend immune protection in those who received its single-dose COVID-19 vaccine [4]. For people who received the Moderna mRNA vaccine, the company has already submitted its data to the FDA for booster authorization. A decision is expected soon.

As the critical evidence on boosters continues to emerge, the most important way to avoid another winter surge of COVID-19 is to follow all public health recommendations. Most importantly, that includes getting fully vaccinated if you haven’t already, and encouraging others around you to do the same. If you’re currently eligible for a booster shot, they are available at 80,000 locations across the nation, and can help you stay healthy and well for the coming holiday season.

For others eager to do everything possible to protect themselves, their families, and their communities against this terrible virus—but who are not yet eligible for a booster—sit tight for now. The data on booster shots are still coming in for folks like me who were immunized with the Moderna or Johnson & Johnson vaccines. It’s likely that the FDA and CDC will widen their recommendations in the coming weeks.

In the meantime, the Delta variant is still out there and circulating. That makes it critical to maintain vigilance. Wear a mask in indoor spaces, keep a physical distance from others, and remember to wash your hands frequently. We are all really tired of COVID-19, but patience is still required as we learn more about how best to stay ahead of this virus.

References:

[1] CDC statement on ACIP booster recommendations. Centers for Disease Control and Prevention news release. September 24, 2021

[2] FDA authorizes booster dose of Pfizer-BioNTech COVID-19 vaccine for certain populations. Food and Drug Administration news release. September 22, 2021

[3] Protection of BNT162b2 vaccine booster against Covid-19 in Israel. Bar-On YM, Goldberg Y, Mandel M, Bodenheimer O, Freedman L, Kalkstein N, Mizrahi B, Alroy-Preis S, Ash N, Milo R, Huppert A. N Engl J Med. 2021 Sep 15.

[4] Johnson & Johnson announces real-world evidence and Phase 3 data confirming strong and long-lasting protection of single-shot COVID-19 vaccine in the U.S. Johnson & Johnson. September 21, 2021.

Links:

COVID-19 Research (NIH)


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)


Following COVID-19 Vaccines Across the United States

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Vaccine Tracker

Recently, there is a new and very hopeful COVID-19 number for everyone to track: the total number of vaccine doses that have been administered in the United States. If 80 percent of Americans roll up their sleeves in the coming months and accept COVID-19 vaccinations, we can greatly slow the spread of the novel coronavirus in our communities and bring this horrible pandemic to an end in 2021.

So far, more than 20 million people in our country have received one or two doses of either the Pfizer or Moderna vaccine. While this number is lower than initially projected for a variety of logistical reasons, we’re already seeing improvements in the distribution system that has made it possible to get close to 1 million doses administered per day.

If you want to keep track of the vaccine progress in your state over the coming weeks, it’s now pretty easy to do online. A fine resource is the vaccine information on the Centers for Disease Control and Prevention (CDC) COVID Data Tracker. It offers an interactive state-by-state map, as well as data on vaccinations in long-term care facilities. Keep in mind that there’s a delay of three to five days in reporting actual vaccinations from the states.

There’s also a lot of useful information on the Johns Hopkins Coronavirus Resource Center’s Vaccine Tracker. Posting the daily updates is a team, led by William Moss, that draws on the expertise of data scientists, analysts, programmers, and researchers. The Hopkins team gathers its vaccination data from each state’s official dashboard, webpages, press releases, or wherever cumulative numbers are reported. Not all states publish the same vaccine information, and that’s what can make the Vaccine Tracker so challenging to compile.

The Hopkins team now presents on its homepage the top 10 U. S. states and territories to vaccinate fully the highest percentage of their residents. With another click, there’s also a full rundown of vaccine administration by state and territory, plus the District of Columbia. The site also links to lots of other information about COVID-19—including cases, testing, contact tracing, and an interactive tool about vaccine development.

In uncertain times, knowledge can be a source of comfort. That’s what makes these interactive COVID-19 resources so helpful and empowering. They show that, with time, safe and effective COVID-19 vaccines will indeed coming to everyone. I hope that you will accept your vaccine, like I did when given the opportunity. However, until we get to the point where most Americans are immunized, we must stay vigilant and keep up our tried-and-true public health measures such as wearing masks, limiting physical interactions (especially indoors), and washing our hands.

Links:

COVID-19 Research (NIH)

CDC COVID Data Tracker (Centers for Disease Control and Prevention, Atlanta)

Coronavirus Resource Center (Johns Hopkins University School of Medicine)

William Moss (Johns Hopkins University, Baltimore)

International Vaccine Access Center (Johns Hopkins Bloomberg School of Public Health, Baltimore)



Genome Data Help to Track COVID-19 Superspreading Event

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Boston skyline
Credit: iStock/Chaay_Tee

When it comes to COVID-19, anyone, even without symptoms, can be a “superspreader” capable of unknowingly infecting a large number of people and causing a community outbreak. That’s why it is so important right now to wear masks when out in public and avoid large gatherings, especially those held indoors, where a superspreader can readily infect others with SARS-CoV-2, the virus responsible for COVID-19.

Driving home this point is a new NIH-funded study on the effects of just one superspreader event in the Boston area: an international biotech conference held in February, before the public health risks of COVID-19 had been fully realized [1]. Almost a hundred people were infected. But it didn’t end there.

In the study, the researchers sequenced close to 800 viral genomes, including cases from across the first wave of the epidemic in the Boston area. Using the fact that the viral genome changes in very subtle ways over time, they found that SARS-CoV-2 was actually introduced independently to the region more than 80 times, primarily from Europe and other parts of the United States. But the data also suggest that a single superspreading event at the biotech conference led to the infection of almost 20,000 people in the area, not to mention additional COVID-19 cases in other states and around the world.

The findings, posted on medRxiv as a pre-print, come from Bronwyn MacInnis and Pardis Sabeti at the Broad Institute of MIT and Harvard in Cambridge, MA, and their many close colleagues at Massachusetts General Hospital, the Massachusetts Department of Public Health, and the Boston Health Care for the Homeless Program. The initial focus of MacInnis, Sabeti, and their Broad colleagues has been on developing genome data and tools for surveillance of viruses and other infectious diseases in and viral outbreaks in West Africa, including Lassa fever and Ebola virus disease.

Closer to home, they’d expected to focus their attention on West Nile virus and tick-borne diseases. But, when the COVID-19 outbreak erupted, they were ready to pivot quickly to assist several Centers for Disease Control and Prevention (CDC) and state labs in the northeastern United States to use genomic tools to investigate local outbreaks.

It’s been clear from the beginning of the pandemic that COVID-19 cases often arise in clusters, linked to gatherings in places such as cruise ships, nursing homes, and homeless shelters. But the Broad Institute team and their colleagues realized, it’s difficult to see how extensively a virus spreads from such places into the wider community based on case counts alone.

Contact tracing certainly helps to track community spread of the virus. This surveillance strategy depends on quick, efficient identification of an infected individual. It follows up with the identification of all who’ve recently been in close contact with that person, allowing the contacts to self-quarantine and break the chain of transmission.

But contact tracing has its limitations. It’s not always possible to identify all the people that an infected person has been in recent contact with. Genome data, however, is particularly useful after the fact for connecting those dots to get a big picture view of viral transmission.

Here’s how it works: as SARS-CoV-2 spreads, the virus sometimes picks up a new mutation. Those tiny spelling changes in the viral genome usually have no effect on how the virus causes disease, but they do serve as distinct genomic fingerprints. Using those fingerprints to guide the way, researchers can trace the path the virus took through a community and beyond, identifying connections among cases that would be untrackable otherwise.

With this in mind, MacInnis and Sabeti’s team set out to help Boston’s public health officials understand just how the epidemic escalated so quickly in the Boston area, and just how much the February conference had contributed to community transmission of the virus. They also investigated other case clusters in the area, including within a skilled nursing facility, homeless shelters, and at Massachusetts General Hospital itself, to understand the spread of COVID-19 in these settings.

Based on contact tracing, officials had already connected approximately 90 cases of COVID-19 to the biotech conference, 28 of which were included in the original 772 viral genomes in this dataset. Based on the distinct genomic fingerprint carried by the 28 genomes, the researchers went on to discover that more than one-third of Boston area cases without any known link to the conference could indeed be traced back to the event.

When the researchers considered this proportion to the number of cases recorded in the region during the study, they extrapolated that the superspreader event led to nearly 20,000 cases in the Boston area. In contrast, the genome data show cases linked to another superspreader event that took place within a skilled nursing facility, while devastating to the residents, had much less of an impact on the surrounding community.

The analysis also uncovered some unexpected connections. The dataset showed that SARS-CoV-2 was brought to clients and staff at the Boston Health Care for the Homeless Program at least seven times. Remarkably, two of those introductions also traced back to the biotech conference. Researchers also found infections in Chelsea, Revere, and Everett, which were some of the hardest hit communities in the Boston area, that were connected to the original superspreading event.

There was some reassuring news about how precautions in hospitals are working. The researchers examined cases that were diagnosed among patients at Massachusetts General Hospital, raising concerns that the virus might have spread from one patient to another within the hospital. But the genome data show that those cases, in fact, weren’t part of the same transmission chain. They may have contracted the virus before they were hospitalized. Or it’s possible that staff may have inadvertently brought the virus into the hospital. But there was no patient-to-patient transmission.

Massachusetts is one of the states in which the COVID-19 pandemic had a particularly severe early impact. As such, these results present broadly applicable lessons for other states and urban areas about how the virus spreads. The findings highlight the value of genomic surveillance, along with standard contact tracing, for better understanding of viral transmission in our communities and improved prevention of future outbreaks.

Reference:

[1] Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. Lemieux J. et al. medRxiv. August 25, 2020.

Links:

Coronavirus (COVID-19) (NIH)

Bronwyn MacInnis (Broad Institute of Harvard and MIT, Cambridge, MA)

Sabeti Lab (Broad Institute of Harvard and MIT)

NIH Support: National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institute of General Medical Sciences


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