As many viruses continue to make the rounds in our communities, it is paramount to monitor your symptoms and know when the right time is to seek medical care in person.
PEORIA - OSF HealthCare hospitals, clinics, and emergency departments across the state continue to see a big influx of people seeking care. The increase in patients in waiting rooms can lead to elevated exposure of germs and viruses, plus longer wait times.
As many viruses continue to make the rounds in our communities, it is paramount to monitor your symptoms and know when the right time is to seek medical care in person. Sarah Overton, the Chief Nursing Officer for OSF Medical Group, Home Care and Employee Health, stresses the importance of virtual care when your symptoms are mild.
“That way we’re not exposing you to anyone in the public and you’re not exposing the health care worker to illness,” Overton says. “Unfortunately, we are seeing an increase in health care worker illness where our nurses and doctors have to stay home because they are being exposed to illness.”
Photo: Andrea Piacquadio/Pexels
Hospitals across the state and in the OSF Ministry network have been seeing a spike in COVID-19 patients. If you suspect you have COVID-19 but your symptoms are mild, take an at-home COVID-19 test.
The federal government has another stockpile of at-home tests that are free to order on COVID.gov. Every household can receive four free rapid tests. Dr. Brian Curtis, Vice President of Clinical Specialty Services with OSF HealthCare, says taking tests at home will help free up space at medical facilities.
“Coming in just to get tested takes up spots for the people that are really sick or are high-risk,” Dr. Curtis says.
“The Emergency Room is reserved for those true emergencies,” Overton adds. “We have patients that have heart attacks and lung issues with their COPD. Additional patients overflowing the Emergency Room takes away precious time from assessing those patients who shouldn’t be exposed to those viruses while being in our waiting rooms.”
But COVID-19 isn’t the only virus making the rounds in our communities right now. Influenza, Respiratory Syncytial Virus (RSV) and others are being seen often as well. So how can we stop the spread of viruses?
· Stay home when you aren’t feeling well.
· Wash your hands and use hand sanitizer regularly.
· Cough or sneeze into your elbow.
· Wipe down high-touch surfaces with disinfectant wipes.
· Don’t share glasses or silverware with others.
· Receive the flu shot.
For treating mild symptoms at home, Dr. Curtis offers some guidance for using over-the-counter options.
“You can take Tylenol or Motrin for fevers and aches. Make sure to drink plenty of fluids and get plenty of rest,” Dr. Curtis says.
Overton says to make sure you read the labels on any over-the-counter medication you buy. If you have any questions, you can ask a retail pharmacist, or send a message through MyChart to your OSF care team.
When is the right time to be seen?
“If you have a super deep cough that’s hanging on for quite a while or have a fever that lasts for several days,” Overton says. “Or if you have high-risk factors and may benefit from some of our medications for COVID, like Paxlovid, which are readily available in our retail pharmacy locations. We also have COVID-19 boosters able to be administered in our primary care offices.”
“There is a medication for influenza, but if you have a mild case, you’ll have more side effects from the medication than you are having from influenza itself. As far as RSV goes, there’s really no treatment for it except for supportive care.”
If you are sick and plan to visit a medical facility, please cover your face with a mask to decrease exposure to the health care workers.
Colds and viruses tend to last one to two weeks. If your symptoms are more serious or linger on much longer than that, reach out to your primary care team and schedule an appointment. You can also consider an in-person or virtual visit to OSF OnCall Urgent Care. A virtual visit is available 24/7.
DALLAS -- As people with HIV age, their risk of heart attack increases far more if they also have untreated hepatitis C virus, even if their HIV is treated, according to new research published today in the Journal of the American Heart Association, an open access, peer-reviewed journal of the American Heart Association.
Since the introduction of antiretroviral therapies to treat HIV in the late 1990s, the lifespan of people with HIV has increased dramatically. However, even with treatment, studies have found the heart disease risk among people with HIV is at least 50% higher than people without HIV. This new study evaluated if people with HIV who also have hepatitis C – a viral liver infection – have a higher risk of heart attack.
"HIV and hepatitis C coinfection occurs because they share a transmission route - both viruses may be transmitted through blood-to-blood contact," said Keri N. Althoff, Ph.D., M.P.H., senior author of the study and an associate professor in the department of epidemiology at the Johns Hopkins Bloomberg School of Public Health in Baltimore. "Due in part to the inflammation from the chronic immune activation of two viral infections, we hypothesized that people with HIV and hepatitis C would have a higher risk of heart attack as they aged compared to those with HIV alone."
Researchers analyzed health information for 23,361 people with HIV (17% female, 49% non-Hispanic white) in the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) between 2000 and 2017 and who had initiated antiretroviral treatment for HIV. All were between 40 to 79 years of age when they enrolled in the NA-ACCORD study (median age of 45 years). One in 5 study participants (4,677) were also positive for hepatitis C. During a median follow-up of about 4 years, the researchers compared the occurrence of a heart attack between the HIV-only and the HIV-hepatitis C co-infected groups as a whole, and by each decade of age.
The analysis found:
With each decade of increasing age, heart attacks increased 30% in people with HIV alone and 85% in those who were also positive for hepatitis C.
The risk of heart attack increased in participants who also had traditional heart disease risk factors such as high blood pressure (more than 3 times), smoking (90%) and Type 2 diabetes (46%).
The risk of heart attack was also higher (40%) in participants with certain HIV-related factors such as low levels of CD4 immune cells (200cells/mm3, signaling greater immune dysfunction) and 45% in those who took protease inhibitors (one type of antiretroviral therapy linked to metabolic conditions).
"People who are living with HIV or hepatitis C should ask their doctor about treatment options for the viruses and other ways to reduce their cardiovascular disease risk," said lead study author Raynell Lang, M.D., M.Sc., an assistant professor in the department of medicine and community health sciences at the University of Calgary in Alberta, Canada.
"Several mechanisms may be involved in the increased heart attack risk among co-infected patients. One contributing factor may be the inflammation associated with having two chronic viral infections," Lang said. "There also may be differences in risk factors for cardiovascular disease and non-medical factors that influence health among people with HIV and hepatitis C that plays a role in the increased risk."
According to a June 2019 American Heart Association scientific statement, Characteristics, Prevention, and Management of Cardiovascular Disease in People Living With HIV, approximately 75% of people living with HIV are over the age of 45. "Even with effective HIV viral suppression, inflammation and immune dysregulation appear to increase the risk for heart attack, stroke and heart failure." The statement called for more research on cardiovascular disease prevention, causes and treatment in people with HIV.
"Our findings suggest that HIV and hepatitis C co-infections need more research, which may inform future treatment guidelines and standards of care," Althoff said.
The study is limited by not having information on additional factors associated with heart attack risk such as diet, exercise or family history of chronic health conditions. Results from this study of people with HIV receiving care in North America may not be generalizable to people with HIV elsewhere. In addition, the study period included time prior to the availability of more advanced hepatitis C treatments.
"Because effective and well-tolerated hepatitis C therapy was not available during several years of our study period, we were unable to evaluate the association of treated hepatitis C infection on cardiovascular risk among people with HIV. This will be an important question to answer in future studies," Lang said.
Meggan Ingram was fully vaccinated when she tested positive for COVID-19 early this month. The 37-year-old’s fever had spiked to 103 and her breath was coming in ragged bursts when an ambulance rushed her to an emergency room in Pasco, Washington, on Aug. 10. For three hours she was given oxygen and intravenous steroids, but she was ultimately sent home without being admitted.
Seven people in her house have now tested positive. Five were fully vaccinated and two of the children are too young to get a vaccine.
As the pandemic enters a critical new phase, public health authorities continue to lack data on crucial questions, just as they did when COVID-19 first tore through the United States in the spring of 2020. Today there remains no full understanding on how the aggressively contagious delta variant spreads among the nearly 200 million partially or fully vaccinated Americans like Ingram, or on how many are getting sick.
The nation is flying blind yet again, critics say, because on May 1 of this year — as the new variant found a foothold in the U.S. — the Centers for Disease Control and Prevention mostly stopped tracking COVID-19 in vaccinated people, also known as breakthrough cases, unless the illness was severe enough to cause hospitalization or death.
Individual states now set their own criteria for collecting data on breakthrough cases, resulting in a muddled grasp of COVID-19’s impact, leaving experts in the dark as to the true number of infections among the vaccinated, whether or not vaccinated people can develop long-haul illness, and the risks to unvaccinated children as they return to school.
If you’re limiting yourself to a small subpopulation with only hospitalizations and deaths, you risk a biased viewpoint.
"It’s like saying we don’t count,” said Ingram after learning of the CDC’s policy change. COVID-19 roared through her household, yet it is unlikely any of those cases will show up in federal data because no one died or was admitted to a hospital.
The CDC told ProPublica in an email that it continues to study breakthrough cases, just in a different way. "This shift will help maximize the quality of the data collected on cases of greatest clinical and public health importance,” the email said.
In addition to the hospitalization and death information, the CDC is working with Emerging Infections Program sites in 10 states to study breakthrough cases, including some mild and asymptomatic ones, the agency’s email said.
Under pressure from some health experts, the CDC announced Wednesday that it will create a new outbreak analysis and forecast center, tapping experts in the private sector and public health to guide it to better predict how diseases spread and to act quickly during an outbreak.
Tracking only some data and not releasing it sooner or more fully, critics say, leaves a gaping hole in the nation’s understanding of the disease at a time when it most needs information.
"They are missing a large portion of the infected," said Dr. Randall Olsen, medical director of molecular diagnostics at Houston Methodist Hospital in Texas. "If you’re limiting yourself to a small subpopulation with only hospitalizations and deaths, you risk a biased viewpoint."
On Wednesday, the CDC released a trio of reports that found that while the vaccine remained effective at keeping vaccinated people out of the hospital, the overall protection appears to be waning over time, especially against the delta variant.
Among nursing home residents, one of the studies showed vaccine effectiveness dropped from 74.7% in the spring to just 53.1% by midsummer. Similarly, another report found that the overall effectiveness among vaccinated New York adults dropped from 91.7% to just under 80% between May and July.
The new findings prompted the Biden administration to announce on Wednesday that people who got a Moderna or Pfizer vaccine will be offered a booster shot eight months after their second dose. The program is scheduled to begin the week of Sept. 20 but needs approval from the Food and Drug Administration and a CDC advisory committee.
No vaccine is 100% percent effective against transmission, health officials warned.
This latest development is seen by some as another example of shifting public health messaging and backpedaling that has accompanied every phase of the pandemic for 19 months through two administrations. A little more than a month ago, the CDC and the FDA released a joint statement saying that those who have been fully vaccinated "do not need a booster shot at this time.”
The vaccine rollout late last year came with cautious optimism. No vaccine is 100% percent effective against transmission, health officials warned, but the three authorized vaccines proved exceedingly effective against the original COVID-19 strain. The CDC reported a breakthrough infection rate of 0.01% for the months between January and the end of April, although it acknowledged it could be an undercount.
As summer neared, the White House signaled it was time for the vaccinated to celebrate and resume their pre-pandemic lives.
Trouble, though, was looming. Outbreaks of a new, highly contagious variant swept India in the spring and soon began to appear in other nations. It was only a matter of time before it struck here, too.
"The world changed," said Dr. Eric Topol, director of the Scripps Research Translational Institute, "when delta invaded."
The current crush of U.S. cases — well over 100,000 per day — has hit the unvaccinated by far the hardest, leaving them at greater risk of serious illness or death. The delta variant is considered at least two or three times more infectious than the original strain of the coronavirus. For months much of the focus by health officials and the White House has been on convincing the resistant to get vaccinated, an effort that has so far produced mixed results.
Yet as spring turned to summer, scattered reports surfaced of clusters of vaccinated people testing positive for the coronavirus. In May, eight vaccinated members of the New York Yankees tested positive. In June, 11 employees of a Las Vegas hospital became infected, eight of whom were fully vaccinated. And then 469 people who visited the Provincetown, Massachusetts, area between July 3 and July 17 became infected even though 74% of them were fully vaccinated, according to the CDC’s Morbidity and Mortality Weekly Report.
While the vast majority of those cases were relatively mild, the Massachusetts outbreak contributed to the CDC reversing itself on July 27 and recommending that even vaccinated people wear masks indoors — 11 weeks after it had told them they could jettison the protection.
And as the new CDC data showed, vaccines continue to effectively shield vaccinated people against the worst outcomes. But those who get the virus are, in fact, often miserably sick and may chafe at the notion that their cases are not being fully counted.
"The vaccinated are not as protected as they think," said Topol, "They are still in jeopardy."
The CDC tracked all breakthrough cases until the end of April, then abruptly stopped without making a formal announcement. A reference to the policy switch appeared on the agency’s website in May about halfway down the homepage.
"I was shocked," said Dr. Leana Wen, a physician and visiting professor of health policy and management at George Washington University. "I have yet to hear a coherent explanation of why they stopped tracking this information.”
The CDC said in an emailed statement to ProPublica that it decided to focus on the most serious cases because officials believed more targeted data collection would better inform "response research, decisions, and policy."
Sen. Edward MMarkey, D-Mass., became alarmed after the Provincetown outbreak and wrote to CDC director Dr. Rochelle Walensky on July 22, questioning the decision to limit investigation of breakthrough cases. He asked what type of data was being compiled and how it would be shared publicly.
It is unclear how often breakthroughs occur or how widely cases are spreading among the vaccinated.
"The American public must be informed of the continued risk posed by COVID-19 and variants, and public health and medical officials, as well as health care providers, must have robust data and information to guide their decisions on public health measures," the letter said.
Markey asked the agency to respond by Aug. 12. So far the senator has received no reply, and the CDC did not answer ProPublica’s question about it.
When the CDC halted its tracking of all but the most severe cases, local and state health departments were left to make up their own rules.
There is now little consistency from state to state or even county to county on what information is gathered about breakthrough cases, how often it is publicly shared, or if it is shared at all.
"We’ve had a patchwork of information between states since the beginning of the pandemic,” said Jen Kates, senior vice president and director of global health and HIV policy at Kaiser Family Foundation.
She is co-author of a July 30 study that found breakthrough cases across the U.S. remained rare, especially those leading to hospitalization or death. However, the study acknowledged that information was limited because state reporting was spotty. Only half the states provide some data on COVID-19 illnesses in vaccinated people.
"There is no single, public repository for data by state or data on breakthrough infections, since the CDC stopped monitoring them,” the report said.
In Texas, where COVID-19 cases are skyrocketing, a state Health and Human Services Commission spokesperson told ProPublica in an email the state agency was "collecting COVID-19 vaccine breakthrough cases of heightened public health interest that result in hospitalization or fatality only."
Other breakthrough case information is not tracked by the state, so it is unclear how often breakthroughs occur or how widely cases are spreading among the vaccinated. And while Texas reports breakthrough deaths and hospitalizations to the CDC, the information is not included on the state’s public dashboard.
"We will be making some additions to what we are posting, and these data could be included in the future," the spokesperson said.
I thought, ‘COVID is over and I’m going to Disney World,’
South Carolina, on the other hand, makes public its breakthrough numbers on hospitalizations and deaths. Milder breakthrough cases may be included in the state’s overall COVID-19 numbers but they are not labeled as such, said Jane Kelly, an epidemiologist at the South Carolina Department of Health and Environmental Control.
"We agree with the CDC,” she said, "there’s no need to spend public health resources investigating every asymptomatic or mild infection.”
In Utah, state health officials take a different view. "From the beginning of the pandemic we have been committed to being transparent with our data reporting and … the decision to include breakthrough case data on our website is consistent with that approach," said Tom Hudachko, director of communications for the Utah Department of Health.
Some county-level officials said they track as many breakthrough cases as possible even if their state and the CDC does not.
For instance, in Clark County, Nevada, home of Las Vegas, the public health website reported that as of last week there were 225 hospitalized breakthrough cases but 4,377 vaccinated people overall who have tested positive for the coronavirus.
That means that less than 5% of reported breakthrough cases resulted in hospitalization. "The Southern Nevada Health District tracks the total number of fully vaccinated individuals who test positive for COVID-19 and it is a method to provide a fuller picture of what is occurring in our community,” said Stephanie Bethel, a spokesperson for the health district in an email.
Sara Schmidt, a 44-year-old elementary school teacher in Alton, Illinois, is another person who has likely fallen through the data hole.
"I thought, ‘COVID is over and I’m going to Disney World,’" she said. She planned a five-day trip for the end of July with her parents. Not only had she been fully vaccinated, receiving her second shot in March, she is also sure she had COVID-19 in the summer of 2020. Back then she had all the symptoms but had a hard time getting tested. When she finally did, the result came back negative, but her doctor told her to assume it was inaccurate.
"My guard was down," she said. She was less vigilant about wearing a mask in the Florida summer heat, assuming she was protected by the vaccination and her presumed earlier infection.
On the July 29 plane trip home, she felt mildly sick. Within days she was "absolutely miserable." Her coughing continued to worsen, and each time she coughed her head pounded. On Aug. 1 she tested positive. Her parents were negative.
Now, three weeks later, she is far from fully recovered and classes are about to begin at her school. There’s a school mask mandate, but her students are too young to be vaccinated. "I’m worried I will give it to them, or I will get it for a third time," she said.
But it is doubtful her case will be tracked because she was never hospitalized. That infuriates her, she said, because it downplays what is happening.
"Everyone has a right to know how many breakthrough cases there are," she said, "I was under the impression that if I did get a breakthrough case, it would just be sniffles. They make it sound like everything is under control and it’s not."
by Caroline Chen, ProPublica
On Jan. 29, New York Gov. Andrew Cuomo was promoting "marital bliss" at a coronavirus news conference.
Announcing that indoor dining would reopen at 25% capacity in New York City on Valentine's Day, and wedding receptions could also resume with up to 150 people a month after, Cuomo suggested: "You propose on Valentine’s Day and then you can have the wedding ceremony March 15, up to 150 people. People will actually come to your wedding because you can tell them, with the testing, it will be safe. … No pressure, but it's just an idea."
Cuomo isn't alone in taking measures to loosen pandemic-related restrictions. Michigan Gov. Gretchen Whitmer allowed indoor dining to resume at 25% capacity starting Feb. 1. Idaho Gov. Brad Little increased limits on indoor gatherings from 10 to 50 people. Massachusetts Gov. Charlie Baker is raising business capacity from 25% to 40%, including at restaurants and gyms. California Gov. Gavin Newsom lifted stay-at-home orders on Jan. 25.
To justify their reopening decisions, governors point to falling case counts. "We make decisions based on facts," Cuomo said. "New York City numbers are down."
But epidemiologists and public health experts say a crucial factor is missing from these calculations: the threat of new viral variants. One coronavirus variant, which originated in the United Kingdom and is now spreading in the U.S., is believed to be 50% more transmissible. The more cases there are, the faster new variants can spread. Because the baseline of case counts in the U.S. is already so high — we’re still averaging about 130,000 new cases a day — and because the spread of the virus grows exponentially, cases could easily climb past the 300,000-per-day peak we reached in early January if we underestimate the variants, experts said.
Furthermore, study after study has identified indoor spaces — particularly restaurants, where consistent masking is not possible — as some of the highest-risk locations for transmission to occur. Even with distanced tables, case studies have shown that droplets can travel long distances within dining establishments, sometimes helped along by air conditioning.
Let’s pretend that politicians wake up and don’t reopen restaurants and we avoid a big wave in March. Then we’re running downhill on the vaccines because the pipeline gets better and better. Then we can get our lives back.
We’re just in the opening stage of the new variants’ arrival in the United States. Experts say we could speed viruses’ spread by providing them with superspreading playgrounds or slow them down by starving them of opportunities to replicate.
"We’re standing at an inflection point," said Sam Scarpino, assistant professor at Northeastern University and director of the school’s Emergent Epidemics Lab. Thanks to the arrival of vaccines, he said, "we finally have the chance right now to bring this back under control, but if we ease up now, we may end up wasting all the effort we put in."
Dr. Luciana Borio, an infectious disease physician who was a member of the Biden-Harris transition team’s COVID-19 advisory board, put it more bluntly at a
congressional hearing on Feb. 3. "Our worst days could be ahead of us," she said.
I interviewed 10 scientists for this story and was surprised by the vehemence of some of their language. "Are you sure it could be that bad?" I asked, over and over.
Once in a while, when a virus replicates, a mistake occurs, and a letter in the strand of RNA is copied inaccurately. That’s called a mutation.
They unanimously said they expected B.1.1.7, the variant first discovered in the U.K., to eventually become the dominant version of coronavirus in the U.S. The Centers for Disease Control and Prevention has estimated that B.1.1.7 will become dominant in March, using a model that presumes it’s 50% more transmissible than the original "wildtype" coronavirus. The model’s transmission rate was based on experience in the U.K., which first detected B.1.1.7 in September and saw an increase in cases that became apparent in December, straining hospitals despite stringent closures and stay-at-home orders. So while our country appears relatively B.1.1.7-free right now, the situation could look drastically different in a matter of months.
Experts are particularly concerned because we don’t have a handle on exactly how far B.1.1.7 has spread. Our current surveillance system sequences less than 1% of cases to see whether they are a variant.
Throwing an even more troubling wrench into the mix is that B.1.1.7 is continuing to morph. Just this week, scientists discovered that some B.1.1.7 coronaviruses in Britain had picked up a key change, known as the E484K mutation. That mutation had previously been found in the B.1.351 variant, which was first discovered in South Africa. Scientists have hypothesized that it’s the E484K mutation that has reduced the efficacy of some vaccines in South African trials, so this is incredibly worrying news.
"It’s really hard to thread this needle without sounding like a prophet of doom," said Angela Rasmussen, a virologist at Georgetown University’s Center for Global Health Science and Security. While vaccines bring hope, she said, governors who are moving to expand indoor dining are "completely reckless"; if they don’t course correct, "I don’t think it’s hyperbolic to say the worst could be yet to come."
The choices that our federal and state leaders make right at this moment will determine if we can bend the curve once and for all and start ending the pandemic, or if we ride the rollercoaster into yet another surge, this one fueled by a viral enemy harder to fight than ever before.
All of us have agency in deciding this narrative, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, stressed. "Certainly you need to be prepared for the possibility that things might get worse in the light of the variants, but that is not inevitable because there are things that we can do to mitigate against it,” he said in an interview. “We're not helpless observers of our own fate."
Fauci urged states to "double down on your public health measures … to have virtually everybody wear masks, to have everyone maintain social distance, to have everybody avoid congregate settings, and to have everybody wash their hands very frequently."
And don’t wait until it’s too late, warned Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota.
"We are so good at pumping the brakes after we’ve wrapped the car around the tree," he said. The new variants aren’t being complacent. "There’s still a lot of human wood out there for this coronavirus to burn."
To understand the epidemiologists’ warnings, it helps to understand what variants are, how they have been behaving and our limitations in knowing exactly how far they have spread.
People have a bad habit of anthropomorphizing the coronavirus: ascribing human-like intentions to it, as if a microbe can discern that we finally have a vaccine and try to evade it. But viruses don’t really have any schemes; they just reproduce. "Coronaviruses are a single strand of RNA in a sac of fat," epidemiologist Larry Brilliant reminded me. "They’re preprogrammed to replicate and continue replicating. That’s their job."
Once in a while, when a virus replicates, a mistake occurs, and a letter in the strand of RNA is copied inaccurately. That’s called a mutation. Many times, those mutations are neutral. Sometimes they are detrimental to the virus, and that lineage will quickly die off. Other times, they’re beneficial to the virus in some way, such as by making it more transmissible. When a version of the virus becomes functionally different, that’s when scientists consider it a variant.
As of Feb. 4, according to the CDC, the U.S. has found 611 cases of B.1.1.7, the variant first discovered in the United Kingdom, five cases of B.1.351, first identified in South Africa, and two cases of P.1., first identified in Brazil. But that’s almost certainly an undercount.
Part of the reason why epidemiologists are advocating for us to stay hunkered down is because the U.S. doesn’t know exactly where all the variant cases are.
The term that public health uses is "surveillance." I like to think of it as having eyes on the virus. In order to have good eyes on where coronavirus infections are in general, all you need is the regular swab tests that we’re all familiar with. But in order to tell whether a positive case is the wildtype coronavirus or one of the more nasty variants, an additional step is needed: genomic sequencing. For that, the sample needs to be sent on to a lab that has specialized machinery capable of conducting sequencing.
Until recently, sequencing in the U.S. was a patchwork effort, conducted by a mix of academic and public health agency labs keen to track the evolution of the coronavirus. Though the CDC hosted a
weekly call where those scientists already conducting sequencing could compare notes, there was no dedicated federal funding or coordination to ensure that samples were routinely gathered from across the country.
Today, the U.S. sequences less than 1% of its total cases. This is a pittance compared to the U.K., which sequences around 8-10% of its positive test results. But volume alone isn’t the only thing that matters. Representation, meaning where the samples come from, is another crucial factor. Since most of the sequencing so far has come from voluntary efforts, the U.S. has suffered from uneven visibility, with a whole bunch of eyeballs in parts of the country that are biotechnology and academic hubs, like Boston, San Francisco and San Diego, and less in “surveillance deserts” like North and South Dakota. There, barely any samples have been sequenced at all, even when those states had explosions of COVID-19 cases.
Dr. Phil Febbo is chief medical officer at Illumina, one of the world’s biggest sequencing technology companies. Like so many parts of the coronavirus response, keeping a lookout for variants has suffered from a lack of federal leadership, Febbo said. As early as March of last year, Illumina representatives began meeting with federal agencies, advocating for a national genomic surveillance system.
"We talked to any three-lettered agency we could," Febbo said. "Those conversations were cordial: They said they heard what we were saying, but then they’d say, ‘But we need more tests, but can you do it in five minutes, can it be point-of-care?’" It wasn’t until Dec. 18, when B.1.1.7 was taking off in the United Kingdom, that Illumina finally got a call from the CDC offering to sign a contract with the company. (Since December, CDC has engaged Illumina to do surveillance work by signing twocontracts potentially worth up to $4.6 million.)
Today, Illumina sequences positive samples that are passed on from a diagnostic testing company, Helix. Each RNA strand of the SARS-CoV-2 virus has about 30,000 nucleotides, each represented by one of four letters. Illumina’s sequencers read through each sample’s code and compare each letter to a reference sequence, looking for significant changes. The data gets passed back to the CDC, which uses location data stripped of personal identifiers to map the spread of any variants that Illumina has picked up.
The CDC said it has contracted with several large commercial companies with the goal of sequencing up to 6,000 samples a week by mid-February. Through another program, called the National SARS-CoV-2 Strain Surveillance System, state public health labs are supposed to send a total of 1,500 samples to the agency every other week. This program went into effect on Jan. 25 and is still ramping up, according to a CDC spokesperson.
Febbo says more can be done to increase surveillance. He notes that the Biden administration, while clearly more invested in variant surveillance than the Trump administration, hasn’t set a public target in the same way it has for vaccinations with its "100 million shots" campaign. Illumina estimates that sequencing 5% of all samples would allow us to be confident that we are catching all variants of concern, and he would like the Biden administration to make that a public goal. It can be done, Febbo says: "It hasn’t been the lack of capacity, it’s been the lack of will."
Having clearer information about where variants are would give governors and local officials actual information with which to make decisions. Then they could say with confidence, "We can open indoor dining because we know that the variants aren’t circulating in our community." Absent that information, the only thing we can do is act like the variants are here.
The good news is that so far, the vaccines that have been made available to the public appear to be reasonably effective against the coronavirus variants. They may be slightly less effective against B.1.351, the variant discovered in South Africa, but none of the variants are total "escapes," so a vaccine should offer you at least partial protection against any form of the coronavirus you encounter.
All of the available shots give your immune system some familiarity with the virus, allowing it to be more prepared to meet the bug in the wild, whether it’s the original strain or a variant. Having a savvier immune system, in turn, means that even if you do get infected, you’re less likely to need to be hospitalized, and less likely to die.
"Regardless of what’s happening with this variant, we’re much better with [people’s immune systems] seeing SARS-CoV-2 after seeing the vaccine than not," said Derek Cummings, a biology professor at the University of Florida’s Emerging Pathogens Institute.
However, we’re not very far along with vaccinations yet. As of Feb. 4, only 2.1% of the U.S. population had been reported to have received both doses of the vaccine; 8.5% had received one dose. That means we’re in a precarious moment right now where the vast majority of the U.S. hasn’t had a chance to get protected, and the variants have a window to multiply. (Of course, those who have already gotten sick with COVID-19 have natural immunity, but some scientists are concerned that those who develop only mild symptoms may not gain as much innate immunity as those who receive a vaccine.)
Of the scientists I talked to, Caitlin Rivers, a computational epidemiologist at Johns Hopkins Center for Health Security, was the most optimistic about a potential variant-fueled surge. "I do think that B.1.1.7 has the possibility to precipitate a wave, but it probably won’t be as bad as the last wave, because we have a lot of preexisting immunity and we are rolling out the vaccines," she said. Thanks to the vaccines, the U.S. will have more population immunity by March, when the CDC predicts B.1.1.7 will become dominant, than the U.K. did when the variant hit there late last year. "It’s a low likelihood that we will have a gigantic fourth wave, but not impossible," she said.
Still, Rivers said, "now is not the time to relax." She, too, was critical of state policies to loosen restrictions. "When you create the same conditions that allowed the last surge, you should expect the same results," she said. “Our main move should be to reduce transmission as much as possible while we vaccinate as much as possible."
Time is not on our side, as the morphing B.1.1.7 variant showed us when it picked up the E484K mutation. While we are lucky that our vaccines still work against the current variants, we have to keep in mind that in this race between vaccines and variants, the variants aren’t staying static.
The big fear is that eventually, a variant will come along that provides the virus with a complete immune escape, preventing our vaccines from working against it. Even though we can update our vaccines, that would take time. The only way to guarantee that the virus won’t mutate into a variant that our current vaccines don’t cover is to lower transmission significantly, said genomic epidemiologist Alli Black: “The virus will continue to mutate as it continues to spread. We’re not going to stop that biological fact unless transmission stops.” And vaccinating everyone quickly is one key way to make it harder for the coronavirus to get from person to person in the first place.
“We need to start responding like the variants are going to take over and they are one of the biggest threats,” said Cummings, “or we won’t have vaccinated enough people when this rolls through.”
Throughout this pandemic, the U.S. has often been in the fortunate position of not being first when it comes to novel viral encounters. We weren’t the country where SARS-CoV-2 originated. We weren’t the place where B.1.1.7 was spawned. We’ve had the opportunity to look to other countries and learn from them, if only we’d choose to.
Epidemiologist after epidemiologist pointed out that the U.K., Denmark and Portugal required drastic measures — the dreaded L word, “lockdown” — to get B.1.1.7 under control. "We’ve seen that multiple different countries in Europe have had to close schools after making it a policy that schools would be the last to close," Rivers, from Johns Hopkins, noted.
If we don’t want the same fate to befall the U.S., now is the time to act, the scientists urged.
Improving surveillance can help. Utah Public Health Laboratory has a robust state sequencing program, analyzing a random sample of cases sent by the state’s two largest hospital groups. Kelly Oakeson, its chief scientist for next generation sequencing and bioinformatics, has set a goal of sequencing 10% of all cases in the state; his lab is currently doing about 3%. They could do more, he said. The only problem is that they don’t have enough pipette tips due to a national shortage. Oakeson said he’s hoping that the Biden administration will leverage the Defense Production Act to produce more pipette tips so he can increase his state’s surveillance capabilities.
“We can’t get transmission down through vaccination alone,” said Rasmussen, the Georgetown virologist. “We need to be encouraging leadership, both at the state and federal levels, to protect people, to have paid sick leave for people if they become symptomatic.”
A restaurant server in New York City, who was laid off early in the pandemic from a high-end steakhouse, told me he understood what the epidemiologists were saying from a scientific point of view. But, he asked, “if you want to shut everything down, who’s going to pay the bills?”
He continued, "In order to do what the epidemiologists want to get done, you can only do that with policies to support the people and make it worth their while to do it." He’s job hunting, and he said that if he was offered a position that put him indoors on Valentine’s Day, “I would have to take it.” He’d put on a double mask and go to work.
Whenever we have options, though, individual decisions can make a difference. Black, the genomic epidemiologist, encouraged everyone to limit travel as much as possible: "It just really facilitates introductions of these circulating variants."
Hang in there, urged Scarpino, the Northeastern professor, painting a hopeful picture: "Cases are coming down, vaccines are going up. Let’s pretend that politicians wake up and don’t reopen restaurants and we avoid a big wave in March. Then we’re running downhill on the vaccines because the pipeline gets better and better. Then we can get our lives back."
That sounded so tantalizing. Dream-worthy. Just a matter of good science-based public policy and collective compliance driving down the case counts until those little mindless RNA-filled fat sacs have nowhere to go, no one to infect, no way to replicate, no chances to mutate. I imagine them bumping around, lost without crowded indoor spaces to breed in, thwarted by vaccine-boosted immune cells, unable to find a host, dwindling, going, gone.
by Matt Sheehan
