Posted on by Dr. Francis Collins
It was nearly 10 months ago on January 15 that a traveler returned home to the Seattle area after visiting family in Wuhan, China. A few days later, he started feeling poorly and became the first laboratory-confirmed case of coronavirus disease 2019 (COVID-19) in the United States. The rest is history.
However, new evidence published in the journal Science suggests that this first COVID-19 case on the West Coast didn’t snowball into the current epidemic. Instead, while public health officials in Washington state worked tirelessly and ultimately succeeded in containing its sustained transmission, the novel coronavirus slipped in via another individual about two weeks later, around the beginning of February.
COVID-19 is caused by the novel coronavirus SARS-CoV-2. Last winter, researchers sequenced the genetic material from the SARS-CoV-2 that was isolated from the returned Seattle traveler. While contact tracing didn’t identify any spread of this particular virus, dubbed WA1, questions arose when a genetically similar virus known as WA2 turned up in Washington state. Not long after, WA2-like viruses then appeared in California; British Columbia, Canada; and eventually 3,000 miles away in Connecticut. By mid-March, this WA2 cluster accounted for the vast majority—85 percent—of the cases in Washington state.
But was it possible that the WA2 cluster is a direct descendent of WA1? Did WA1 cause an unnoticed chain of transmission over several weeks, making the Seattle the epicenter of the outbreak in North America?
To answer those questions and others from around the globe, Michael Worobey, University of Arizona, Tucson, and his colleagues drew on multiple sources of information. These included data peretaining to viral genomes, airline passenger flow, and disease incidence in China’s Hubei Province and other places that likely would have influenced the probability that infected travelers were moving the virus around the globe. Based on all the evidence, the researchers simulated the outbreak more than 1,000 times on a computer over a two-month period, beginning on January 15 and assuming the epidemic started with WA1. And, not once did any of their simulated outbreaks match up to the actual genome data.
Those findings suggest to the researchers that the idea WA1 is responsible for all that came later is exceedingly unlikely. The evidence and simulations also appear to rule out the notion that the earliest cases in Washington state entered the United States by way of Canada. A deep dive into the data suggests a more likely scenario is that the outbreak was set off by one or more introductions of genetically similar viruses from China to the West Coast. Though we still don’t know exactly where, the Seattle area is the most likely site given the large number of WA2-like viruses sampled there.
Worobey’s team conducted a second analysis of the outbreak in Europe, and those simulations paint a similar picture to the one in the United States. The researchers conclude that the first known case of COVID-19 in Europe, arriving in Germany on January 20, led to a relatively small number of cases before being stamped out by aggressive testing and contact tracing efforts. That small, early outbreak probably didn’t spark the later one in Northern Italy, which eventually spread to the United States.
Their findings also show that the chain of transmission from China to Italy to New York City sparked outbreaks on the East Coast slightly later in February than those that spread from China directly to Washington state. It confirms that the Seattle outbreak was indeed the first, predating others on the East Coast and in California.
The findings in this report are yet another reminder of the value of integrating genome surveillance together with other sources of data when it comes to understanding, tracking, and containing the spread of COVID-19. They also show that swift and decisive public health measures to contain the virus worked when SARS-CoV-2 first entered the United States and Europe, and can now serve as models of containment.
Since the suffering and death from this pandemic continues in the United States, this historical reconstruction from early in 2020 is one more reminder that all of us have the opportunity and the responsibility to try to limit further spread. Wear your mask when you are outside the home; maintain physical distancing; wash your hands frequently; and don’t congregate indoors, where the risks are greatest. These lessons will enable us to better anticipate, prevent, and respond to additional outbreaks of COVID-19 or any other novel viruses that may arise in the future.
 The emergence of SARS-CoV-2 in Europe and North America. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. Science. 2020 Sep 10:eabc8169 [Epub ahead of print]
Coronavirus (COVID-19) (NIH)
Michael Worobey (University of Arizona, Tucson)
NIH Support: National Institute of Allergy and Infectious Diseases; Fogarty International Center; National Library of Medicine
Posted on by Dr. Francis Collins
The pandemic has already claimed far too many lives in the United States and around the world. Fortunately, as doctors have gained more experience in treating coronavirus disease 2019 (COVID-19), more people who’ve been hospitalized eventually will recover. This raises an important question: what does recovery look like for them?
Because COVID-19 is still a new condition, there aren’t a lot of data out there yet to answer that question. But a recent study of 55 people recovering from COVID-19 in China offers some early insight into the recovery of lung function . The results make clear that—even in those with a mild-to-moderate infection—the effects of COVID-19 can persist in the lungs for months. In fact, three months after leaving the hospital about 70 percent of those in the study continued to have abnormal lung scans, an indication that the lungs are still damaged and trying to heal.
The findings in EClinicalMedicine come from a team in Henan Province, China, led by Aiguo Xu, The First Affiliated Hospital of Zhengzhou University; Yanfeng Gao, Zhengzhou University; and Hong Luo, Guangshan People’s Hospital. They’d heard about reports of lung abnormalities in patients discharged from the hospital. But it wasn’t clear how long those problems stuck around.
To find out, the researchers enrolled 55 men and women who’d been admitted to the hospital with COVID-19 three months earlier. Some of the participants, whose average age was 48, had other health conditions, such as diabetes or heart disease. But none had any pre-existing lung problems.
Most of the patients had mild or moderate respiratory illness while hospitalized. Only four of the 55 had been classified as severely ill. Fourteen patients required supplemental oxygen while in the hospital, but none needed mechanical ventilation.
Three months after discharge from the hospital, all of the patients were able to return to work. But they continued to have lingering symptoms of COVID-19, including shortness of breath, cough, gastrointestinal problems, headache, or fatigue.
Evidence of this continued trouble also showed up in their lungs. Thirty-nine of the study’s participants had an abnormal result in their computed tomography (CT) lung scan, which creates cross-sectional images of the lungs. Fourteen individuals (1 in 4) also showed reduced lung function in breathing tests.
Interestingly, the researchers found that those who went on to have more lasting lung problems also had elevated levels of D-dimer, a protein fragment that arises when a blood clot dissolves. They suggest that a D-dimer test might help to identify those with COVID-19 who would benefit from pulmonary rehabilitation to rebuild their lung function, even in the absence of severe respiratory symptoms.
This finding also points to the way in which the SARS-CoV-2 virus seems to enhance a tendency toward blood clotting—a problem addressed in our Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) public-private partnership. The partnership recently initiated a trial of blood thinners. That trial will start out by focusing on newly diagnosed outpatients and hospitalized patients, but will go on to include a component related to convalescence.
Moving forward, it will be important to conduct larger and longer-term studies of COVID-19 recovery in people of diverse backgrounds to continue to learn more about what it means to survive COVID-19. The new findings certainly indicate that for many people who’ve been hospitalized with COVID-19, regaining normal lung function may take a while. As we learn even more about the underlying causes and long-term consequences of this new infectious disease, let’s hope it will soon lead to insights that will help many more COVID-19 long-haulers and their concerned loved ones breathe easier.
 Follow-up study of the pulmonary function and related physiological characteristics of COVID-19 survivors three months after recovery. Zhao YM, Shang YM, Song WB, Li QQ, Xie H, Xu QF, Jia JL, Li LM, Mao HL, Zhou XM, Luo H, Gao YF, Xu AG. EClinicalMedicine.2020 Aug 25:100463
Coronavirus (COVID-19) (NIH)
How the Lungs Work (National Heart, Lung, and Blood Institute/NIH)
Computed Tomography (CT) (National Institute of Biomedical Imaging and Bioengineering/NIH)
Zhengzhou University (Zhengzhou City, Henan Province, China)
Posted on by Dr. Francis Collins
Coronaviruses are a frequent cause of the common cold. Most of us bounce back from colds without any lasting health effects. So, you might think that individuals who survive other infectious diseases caused by coronaviruses—including COVID-19—would also return to normal relatively quickly. While that can be the case for some people, others who’ve survived even relatively mild COVID-19 are experiencing health challenges that may last for weeks or even months. In fact, the situation is so common, that some of these folks have banded together and given their condition a name: the COVID “long-haulers.”
Among the many longer-term health problems that have been associated with COVID-19 are shortness of breath, fatigue, cognitive issues, erratic heartbeat, gastrointestinal issues, low-grade fever, intolerance to physical or mental activity, and muscle and joint pains. COVID-19 survivors report that these symptoms flair up unpredictably, often in different combinations, and can be debilitating for days and weeks at a time. Because COVID-19 is such a new disease, little is known about what causes the persistence of symptoms, what is impeding full recovery, or how to help the long-haulers.
More information is now emerging from the first detailed patient survey of post-COVID syndrome, also known as Long COVID . What’s unique about the survey is that it has been issued by a group of individuals who are struggling with the syndrome themselves. These citizen scientists, who belong to the online Body Politic COVID-19 Support Group, decided to take matters into their own hands. They already had a pretty good grip on what sort of questions to ask, as well as online access to hundreds of long-haulers to whom they could pose the questions.
The citizen scientists’ group, known as the Patient-led Research for COVID-19, brought a lot of talent and creativity to the table. Members reside in the United States, Canada, and England, and none have ever met face to face. But, between their day jobs, managing time differences, and health challenges, each team member spends about 20 hours per week working on their patient-led research, and are now putting the final touches on a follow-up survey that will get underway in the next few weeks.
For their first survey, the group members faced the difficult decision of whom to contact. First, they needed to define long hauler. For that, they decided to target people whose symptoms persisted for more than 2 weeks after their initial recovery from COVID-19. The 640 individuals who responded to the survey were predominately white females between the ages of 30 to 49 who lived in the United States. The members said that the gender bias may stem from women being more likely to join support groups and complete surveys, though there may be a gender component to Long COVID as well. About 10 percent of respondents reported that they had ultimately recovered from this post-COVID syndrome.
Another important issue revolved around COVID-19 testing. Most long-haulers in the online group had gotten sick in March and April, but weren’t so sick that they needed to be hospitalized. Because COVID-19 testing during those months was often limited to people hospitalized with severe respiratory problems, many long-haulers with mild or moderate COVID-like symptoms weren’t tested. Others were tested relatively late in the course of their illness, which can increase the likelihood of false negatives.
The team opted to cast a wide investigative net, concluding that limiting its data to only people who tested positive for COVID-19 might lead to the loss of essential information on long-haulers. It turns out that half of the respondents hadn’t been tested for SARS-CoV-2, the virus that causes COVID-19. The other half was divided almost equally between those who tested positive and those who tested negative. Here are some highlights of the survey’s findings:
Top 10 Symptoms: Respondents were asked to rank their most common symptoms and their relative severity. From highest to lowest, they were: mild shortness of breath, mild tightness of chest, moderate fatigue, mild fatigue, chills or sweats, mild body aches, dry cough, elevated temperature (98.8-100), mild headache, and brain fog/concentration challenges. Highlighting the value of patient-led research, the team was able to assemble an initial list of 62 symptoms that long-haulers often discuss in support groups. The survey revealed common symptoms that have been greatly underreported in the media, such as neurological symptoms. These include brain fog, concentration challenges, and dizziness.
Making a Recovery: Of the 60 respondents who had recovered, the average time to recovery was 27 days. The respondents who had not recovered had managed their symptoms for 40 days on average, with most dealing with health problems for 5 to 7 weeks. The report shows that the chance of full recovery by day 50 is less than 20 percent.
Exercise Capacity: About 65 percent of respondents now consider themselves mostly sedentary. Most had been highly physically active before developing COVID-19. Many long-haulers expressed concern that overexertion causes relapses
Testing. Respondents who reported testing positive for SARS-CoV-2 were tested on average earlier in their illness (by day 10) than those who reported testing negative (by day 16). The team noted that their findings parallel those in a recent published scientific study, which found false-negative rates for current PCR-based assays rose as the time between SARS-CoV-2 infection and testing increased . In that published study, by day 21, the false-negative rate reached 66 percent. Only two symptoms (loss of smell and loss of taste) occurred more frequently in respondents who tested positive; the other 60 symptoms were statistically the same between groups. The citizen scientists speculate that testing is not capturing a subset of COVID patients, and more investigation is required.
Since issuing their survey results on May 11, the team has met with staff from the Centers for Disease Control and Prevention and the World Health Organization. Their work also been mentioned in magazine articles and even cited in some papers published in scientific journals.
In their next survey, these citizen scientists hope to fill in gaps in their first report, including examining antibody testing results, neurological symptoms, and the role of mental health. To increase geographic and demographic diversity, they will also translate the survey into 10 languages. If you’re a COVID-19 long-hauler and would like to find out how to get involved, there’s still time to take part in the next survey.
 “What Does COVID-19 Recovery Actually Look Like?” Patient-led Research for COVID-19. May 11, 2020.
 Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction-Based SARS-CoV-2 Tests by Time Since Exposure. Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Ann Intern Med. 2020 Aug 18;173(4):262-267.
Coronavirus (COVID-19) (NIH)