We Can Solve the Coronavirus-Test Mess Now—If We Want To

Further complicating matters, insurers don’t pay for testing that they don’t consider medically necessary. Yet testing people who don’t have symptoms will be important to getting covid-19 under control. The Centers for Disease Control and Prevention estimates that around forty per cent of viral transmissions occur before an infected person has any symptoms. Yes, a combination of distancing, hygiene, and mask-wearing when people can’t stay six feet apart can markedly reduce such transmissions. But, in many situations, we can’t count on people being able to maintain those measures. Testing is the only way to know whether a person is potentially contagious and in need of isolation.

Such “assurance testing” has been required by countries such as Iceland, France, and Germany for travellers from abroad in order to avoid a mandatory two-week quarantine; by states from Maine and Massachusetts to Hawaii and Alaska for out-of-state travellers; by many U.S. hospitals for all patients admitted for non-emergent surgery; and by the film and television industry, which plans to do regular testing of cast and crew members in order to start production again. The federal government has recommended that nursing homes test all staff once a week. Numerous colleges and universities have included repeated testing in their protocols for bringing students back to campus. Individuals are seeking assurance tests before visiting older family members.

The economist Paul Romer has argued for going further, saying that regular testing for every person in the United States should be our lead strategy for getting society back to normal. Those with a recent negative test would have permission to go without a mask; those with a positive test would be required to isolate for two weeks. The small Italian town of Vò, outside Padua City, took a similar approach. It offered testing to all its thirty-three hundred inhabitants at two points over two weeks during lockdown. Eighty-six per cent of the population came forward in the first round. Almost three per cent were infected, half of whom had no symptoms. In the second round, seventy-two per cent of the population was tested, with a 0.3-per-cent new-infection rate. With these last few cases isolated, the town was able to reopen long before the rest of Italy could.

But is any of this remotely feasible when we can’t even make sure that sick people can get tested in a timely way? The lunacy of our testing system is the lunacy of our health system in microcosm. We are now paying the price of our long, uniquely American resistance to making sure that everyone has proper health-care coverage, and to building an adequate public-health infrastructure. We have not fully grappled with the difficulties we’re up against. But, if we do, we have a chance to fix the problem before the worst of flu season hits.

The need for speed

The course of infection with the sars-CoV-2 virus is relatively brief. It starts with perhaps as little as a few hundred viral particles getting into your respiratory passage; then, if they take hold, they multiply to a viral count so high that you are exhaling millions of viral particles per hour. You are typically at your most contagious around day five of infection. Symptoms usually begin about the same time. In more than eighty per cent of cases, adequate oxygen levels can be maintained without hospitalization, and the body’s immune system can reduce viral counts rapidly. In these mild to moderate cases, researchers have found almost no transmission a week after the onset of symptoms, although recovery takes upward of two to three weeks for a third of such patients. (In cases of serious illness, the reduction in viral counts can take a week or so longer.) The goal of testing is to detect the virus as early as possible during infection.

The standard diagnostic test involves, as tens of millions of people now intimately know, a swab of the cavity deep behind the nasal passage—or, as more recently authorized by the Food and Drug Administration, of just inside the nose. A few labs have been approved to test saliva. The sample from the patient is analyzed for evidence of viral genetic material. The method of analysis, real-time polymerase chain reaction, PCR, is a small wonder of science, and, if it detects the sars-CoV-2 virus, the diagnosis approaches a-hundred-per-cent accuracy: false positives are rare. But false negatives are another matter. The miss rate among people with a symptomatic infection is upward of twenty per cent, owing either to sampling problems (the swab didn’t pick up enough of a specimen) or a viral count too low to be detected. That miss rate is even higher during the four days or so before symptoms begin—going from a hundred per cent on the first day of an infection to sixty-seven per cent on the fourth day, according to a Johns Hopkins study. A negative test is not a guarantee that a person is infection-free.

A negative test is, however, an indicator that a person is unlikely to be contagious at the time the test was done. As a rule, infectiousness is directly related to viral load, and so are positive test results. Still, each day that passes after a negative test reduces its value. A one-time test is not an adequate solution, then, if you’re the Boston Symphony Orchestra and you want a hundred musicians to be able to practice every day as an ensemble again, with no masks or distancing, while some of them are blowing horns and woodwinds so hard that they have to shake the spit out of them. If a group is going to work or live together on an ongoing basis but can’t take the necessary restrictive measures, or wants to relax them, repeated assurance testing is necessary to avoid outbreaks.

How often the testing must be repeated varies from once a day to once a week, depending on the baseline prevalence of infections in the group, among other factors. It’s especially helpful for groups that can be isolated from the larger community. The National Women’s Soccer League did just that, confining participants in its month-long Challenge Cup to an athletic village it created outside Salt Lake City and testing participants on arrival and then before every game. Not a single athlete tested positive after initial screening and admission to the village.

A few critics have argued that PCR testing for people without symptoms is overly sensitive, catching many people when their viral counts are too low to be contagious. Some of them, it’s true, could be on the downswing of infection, but most will be on the upswing (when it’s important to catch them), particularly when they’ve had a previous negative test.

An oddity about sars-CoV-2 transmission is that many infected people, whether or not they have symptoms, won’t pass it along. (Contact-tracing studies find that, among people who live with someone diagnosed with covid-19, sixty to ninety per cent never become infected.) And yet a particular person can, in the right settings—like a crowded bar or workplace—infect scores of others. There is a measure in epidemiology called the dispersion factor, which indicates how much a disease clusters. sars-CoV-2 has an unusually low dispersion factor—an estimated eighty per cent of transmissions are caused by just ten per cent of cases. By contrast, the 1918 influenza had a very high dispersion factor: there was almost no clustering at all.

Perhaps just a subset of people are prone to spread sars-CoV-2. Or perhaps everyone with the infection sheds the virus, but only in occasional eruptions during a short period of infectivity. You stop the spread by avoiding large indoor crowds that could include a person in the midst of an eruption, by masking everyone to contain an eruption, and by testing people so you can identify and isolate positive cases during the period when they can erupt. But that is possible only if you get the results fast.

The Kansas State University football team is a cautionary example in this respect. It set out to create a bubble of its own when the N.C.A.A. allowed practices to begin on June 1st. All players were tested upon arrival and isolated as a group from the rest of the community—so far, so good. The first ninety-six players to arrive tested negative. A last group of twenty-four players, largely freshmen, arrived a few days later and were tested on a Friday. But they didn’t get the results until Monday—and that window was all the virus needed. As the Times reported, teammates spent the weekend hanging out. One player who would test positive played video games at an apartment with up to fifteen players; another infected player joined a group that drove out together to a lake. Although the protocol was to wear masks and maintain distancing off the field, the rules slipped. Within a week, two cases had become fourteen, and the team’s practices were shut down.

Unused capacity

To fix testing, we have to accelerate two lines of operation: test collection and test processing. The primary challenge of test collection—sticking a fifty-cent swab in someone’s nose—is last-mile logistics, which can be more intricate than most realize. You’ve got to manage people flow; it can be a challenge just to find locations where potentially infectious people can turn up without infecting others. Then there’s the flow of supplies, which involves having adequate quantities of the swabs and tubes that your particular lab requires, plus the personal protective equipment required for the staff. There’s the information flow—gathering and linking a patient’s information, the provider information, and the bar code on the specimen tube in a way that the laboratory can deal with. And there’s the financial flow—figuring out the billing system required to get reimbursed by the correct payer, which, for a particular person, could be Medicare or Medicaid, a private insurer, an employer, the state, the patient herself, or any number of other sources. Running a test-collection operation can be a nightmare for scores of reasons. You have to navigate supply shortages, neighborhoods that object to having lines of cars turn up at a pharmacy or clinic parking lot, business-insurance plans that may not cover you if you provide testing, and building owners with liability concerns. You may be unable to use your label printer and computer system if there’s no Wi-Fi in the parking-lot drive-up location you’ve picked.

Processing tests is a very different enterprise. It is exacting. Most diagnostic tests are performed by putting a sample into a device and getting a result. But large-scale molecular diagnostic testing—in which segments of genetic material are read—isn’t done with off-the-shelf kits; these are laboratory-developed tests, meaning that running them is less like operating an appliance than like doing a procedure, with multiple steps requiring precision and tight controls. The basic coronavirus PCR test starts with a reduction process—a series of steps to wash the specimen from the swab, inactivate any virus present, and separate out the genetic material (both human and viral). What arrives at the lab as a six-inch specimen tube of material is reduced, by means of chemical reagents and various machines, to a few extracted drops of nucleic acids. Then comes the viral-detection phase. Enzymes and probes—special stretches of DNA—are added that, under the right conditions, recognize and bind to sars-CoV-2 RNA. (The genome of coronaviruses is made of RNA, not DNA.) The binding of a probe triggers a reaction that creates a DNA transcription of the viral RNA template. That enables the final steps: the signalling process.

The mixture is now put into a PCR machine—in essence, a tiny oven that sequentially heats and cools the mixture to precise temperatures, triggering further reactions that generate new copies of the viral genetic material. Each cycle of heating and cooling doubles the number of copies. After thirty cycles, up to a billion copies of viral DNA are produced from each strand. A separate marker in the mix recognizes the DNA and releases a fluorescent dye that can be measured by an optical device in the machine; there’s a threshold above which the test is considered positive. The result is checked by a technician and released electronically back to the test site. Although labs are constantly making improvements to this chain of steps in order to increase efficiency and accuracy, the whole process, from receiving a sample at a lab to sending a result, typically takes between six and twelve hours.

Running a clinical laboratory in the United States requires making the entire collecting and processing operation run smoothly. That’s why testing here is dominated by such a small number of national laboratories. The big four commercial labs are really logistics and distribution companies wrapped around a network of regional laboratories. That’s also what makes them a chokepoint. As Quest and LabCorp have both warned, they do not have the ability to expand their systems quickly enough to meet current needs, let alone meet the demands that will come with flu season.

Yet we have other laboratories with large amounts of untapped processing capacity ready to provide next-day results. In July, for instance, I visited the Broad Institute, a large academic laboratory affiliated with M.I.T. and Harvard, in Cambridge, Massachusetts, which has provided coronavirus testing for area hospitals, clinics, and others. As Sheila Dodge, the senior director of Broad Genomics, explained as she walked me through its molecular-testing operation, they had the capacity to process up to thirty-five thousand tests per day. With a few weeks’ notice, they could expand that to a hundred thousand a day—more than fifteen per cent of the nation’s current capacity. But, when I visited, they were receiving just a few thousand test specimens per day. I saw an entire room of machines standing by, mostly idle.

It’s the same story elsewhere. I spoke to leaders at the University of Minnesota’s Genomics Center, who reported that they have unused capacity to deliver up to twenty-five thousand tests a day. And there are numerous other university-based and independent molecular-diagnostics laboratories with the ability to expand the country’s testing capacity. Several companies—including Guardant Health and Helix, in California; Kailos Genetics, in Alabama; and Ginkgo Bioworks, in Boston—are rolling out advanced molecular-testing techniques that could enable them to collectively process hundreds of thousands of tests a day. Whereas the usual charge for test processing is a hundred dollars or more, most of these labs are willing to charge much less—from fifty dollars to as little as twenty dollars. What’s missing is the logistics operation to connect their supply of tests to the people who need them and to the entities that pay for them.

These remarkable scientific enterprises aren’t sitting on their hands. Each is making a herculean effort to connect to places seeking tests, one by one. The Broad Institute has built support for more than a hundred area colleges. Nonetheless, the labs are connected to only a fraction of those they could serve.

Decades ago, electric companies were organized in the same way that laboratory testing is organized today. They were vertical monopolies that ran their own power plants, transmission lines, and customer operations. That arrangement got the job done, but it meant that many communities endured brownouts and blackouts from a shortage of capacity, while others had an oversupply. And the companies impeded innovation such as cleaner and cheaper energy. The creation of a national electric grid that physically connected the electricity supply, plus the Energy Policy Act of 1992, which required transmission-line owners to allow electric-generation companies access to their power lines, opened the door for load balancing, increased supply, lower costs, and alternative energy production.

We have no national grid for the generation, transmission, or distribution of our testing supply—or, for that matter, the supply of ventilators, masks, intensive-care beds, or almost any other health-care resources. Now we’re paying the price. In power generation, the worry is that our national grid is aging; in health care, the worry is that we have no grid at all.

A grid is the goal

To see what a functional national grid can deliver when it comes to public health, consider South Korea. It supported test collection, test processing, and the connections between them. On January 27th, when the country had seen just three confirmed covid-19 cases, officials from Korea’s equivalents to the C.D.C. and F.D.A. held an urgent meeting with clinical laboratories and medical manufacturers, telling them to develop PCR tests for the new coronavirus spreading out of control in China, and to coördinate manufacturing swabs, reagents, and other necessary supplies. The government created an accelerated authorization process. By February 4th, one lab had isolated viral specimens from the three cases and reproduced the genetic material from them. Government scientists had varying dilutions put into test plates and delivered to participating laboratories as a kind of final exam for their molecular tests. If a laboratory correctly identified all the positives and negatives, its test was approved. By February 6th, the South Korean government had validated and approved tests from forty-six laboratories. Afterward, it carried out periodic cross-checks to make sure that testing remained accurate.

At the same time, the government coördinated with hospitals, clinics, and public-health agencies to set up test sites, agreeing to cover the testing costs for patients (at a flat rate of sixty-seven dollars a test), and creating a common scheduling system. (Dial 1339 from anywhere in the country and you can schedule a test nearby that day.) That scheduling system also allowed them to balance the testing loads, connecting laboratories that had extra capacity to test sites where that capacity was needed. Today, South Korea, with as many people as Florida and Texas combined, has some six hundred test sites, served by a hundred and eighteen authorized laboratories, with, typically, a one-day turnaround time. That’s what a grid can get you. Other countries followed South Korea’s example.

We never did. In fact, the United States has stymied rather than accelerated the ability of laboratories to develop testing capacity. In the labs of my hospital system, the Mass General Brigham—as in other academic and commercial labs—scientists began developing a coronavirus test in January, concerned that the outbreak in Asia could become a danger here. But, through February, the F.D.A. authorized only the C.D.C.’s coronavirus test. On February 20th, the Department of Health and Human Services sent out an e-mail blast to labs nationwide summarizing the Administration’s policy.

It is a stunning document. It stated that the C.D.C. had the only authorized test protocol in the country, and that only it and select state and local public-health laboratories could use it. Other clinical laboratories were supposed to send their patients’ swabs to an already backlogged C.D.C. Not only did the notice provide no encouragement for laboratories to develop tests; it actually blocked one of the principal means for labs to do so, declaring that “clinical laboratories should NOT attempt viral isolation from specimens” collected from patients thought to be infected.

Neal Lindeman, the head of my hospital’s molecular-testing laboratory, could only shake his head as he read the notice. “I thought it was foolish and dangerous,” he said. “I decided to ignore the e-mail. I didn’t think this plan was going to work for the country. So we just continued working on our test in the background.”

And, as became widely known, the C.D.C.’s plan did not work; its test kit had contaminated probes, and its protocol was flawed. The virus spread undetected nationwide for a month while we delivered hardly any tests at all. On February 29th, the F.D.A. finally reversed course, announcing that laboratories could develop and deploy their own coronavirus testing programs, so long as they also applied for emergency authorization from the agency. But, unlike its Korean counterpart, it provided no plan to streamline the test-authorization process. On the contrary, the agency made clear that it was not enough for a laboratory to show that its test yielded accurate results on blinded specimens. A detailed review of protocols would be required as well. Even slight deviations from the C.D.C.’s protocol required the laboratory to submit a separate “bridging study”—a term that had not been defined. Nor did the F.D.A. have enough experts to do the detailed review the agency required.

The result: F.D.A. reviews took far too long. Furthermore, when a lab made improvements in its process—or adjustments to circumvent shortages in supplies—it had to return to petition for authorization all over again. The uncertainty about whether applications would succeed naturally made labs hesitate to make the investment necessary to scale up their operations. We’ve needed a speedier process, but we still also need the government to set and insure consistent standards. The F.D.A’s validation protocol needed reforming, not eliminating. So even some F.D.A. critics were shocked when, this August, in a barely reported move, the Trump Administration announced that lab-developed tests would no longer require F.D.A. review. This could open the door to tests with insufficient scientific oversight and yet more confusion for patients.

Even with the substantial capacity of F.D.A.-authorized coronavirus tests that we’ve already accumulated, the government launched no major effort to balance testing loads among them. There is still unmet demand and untapped capacity. At the same time, we are undersupplied with test centers. And we have no defined approach at all for some hundred million essential workers, students, and others who need access to assurance testing that health-care plans won’t pay for.

Conservatives have long opposed the government’s playing a direct role in addressing major gaps in the supply of health-care services. A third of U.S. counties have no childbirth facilities, and shortages of psychiatric beds are even worse. So maybe we should not be surprised that we have no such system for testing. It’s not just that we lack a national grid; we haven’t even agreed that we need one.

Innovation’s impasse

Will improvements in techniques and technologies get us out of our testing debacle? They can help a lot—but only if we fix the underlying problem we have with delivery.

Consider, for instance, pooled testing, in which you combine samples from a group of people in a single tube for a test run. A negative result will clear the entire group. If a tube comes up positive, you go back to the original samples and run them individually. During the Second World War, draftees were screened for syphilis through pooled testing. The Red Cross has used the technique to screen donated blood since 1999. In May, the Chinese government used the technique to screen the entire city of Wuhan, testing more than nine million people in ten days. (Just three hundred tests came back positive.)

Pooled testing is useful when you’re screening lots of healthy people for an uncommon disease and you don’t have enough testing machines or reagents. But we’ve made no commitment to setting up the systems required to physically screen large numbers of healthy people at scale—and pooling doesn’t work if you can’t collect the specimens to pool. In communities where disease rates are high, meanwhile, pooling isn’t so valuable: too many tests will come back positive, which slows the whole production line down to a crawl. Plus, the approach doesn’t do anything about bringing online unused lab capacity, which would be needed to deploy any testing strategy efficiently.

Sewage testing, one type of pooled testing, has real potential as a means of cost-efficient, large-scale screening. People infected with sars-CoV-2 shed the virus in their stool, and PCR testing of wastewater can detect the virus upward of four days before people typically obtain clinical testing. Several hundred communities have partnered with companies such as Biobot, a Boston-area startup, to monitor viral prevalence in their populations, and the C.D.C. has announced a National Wastewater Surveillance System to track the information. The technique could be especially useful when deployed in an institutional setting: for instance, to clear a nursing home or dormitory with a single daily PCR test. The University of Arizona prevented an outbreak when regular testing of sewage samples from twenty campus buildings turned up traces of the virus from a dormitory; swab-testing the three hundred and eleven residents the next day identified two with infections. The lower limit of detection still needs to be confirmed, but Biobot claims its system can pick up a single case in up to sixty-five-hundred people. And it’s comparatively cheap: the primary cost is installing a twenty-four-hour sampling system into a building’s wastewater outflow. But, again, the mere existence of the capability is not enough. Coördinated efforts and investment are required to deploy it. The supply of compositors, the sampling devices required, must be secured. And then you need a system to provide swift follow-up testing of individuals when a sewage test comes back positive.

What about at-home test collection? The F.D.A. has authorized a small number of companies—for example, LabCorp and the startup Everlywell—to give people home collection kits with specific, preapproved instructions for swabbing themselves or providing a saliva sample. Unsupervised self-collection can result in higher rates of missed infections, to be sure. And delivering and returning the tests by mail can add a couple of days to the testing process—although, as more labs gain approval for unsupervised collection kits, one can imagine pharmacies, workplaces, and schools facilitating pickup and drop-off sites that could speed it up. If we haven’t addressed the demand-capacity mismatch, however, the approach could still be slowed by lab-processing backups.

You could circumvent the lab bottleneck by means of tabletop “point of care” machines that can run sars-CoV-2 tests in clinics and other authorized settings without specialized personnel. They’re a marvel of miniaturization—akin to having your own electric generator. The White House uses these devices to test staff and visitors. There are versions that can run a PCR test in less than forty-five minutes. For those who have the money, such machines provide a means to buy your way around our broken system. But demand for the devices and the cartridges they require has far outpaced manufacturing capacity. Because each tabletop device can typically run only one sample at a time, the technology is at best a partial solution for getting to the millions of low-cost tests we need per day—there’s a difference between a Xerox machine and a printing plant. To deploy these devices, the country would still need a focussed national effort to boost the supply and get it to the populations that most need them.

A cheaper type of point-of-care test has emerged that takes just fifteen minutes. Unlike PCR tests, which detect the virus’s nucleic acids, this is an “antigen” test, which detects the virus’s proteins. Most involve machines. But the Abbott antigen test card, which has just come on the market, uses the same technology as home pregnancy tests and costs labs just five dollars. It embeds a filter-paper-like strip with antibodies that trigger the release of a dye and make a line appear when they recognize and bind to sars-CoV-2 proteins. The test is said to be almost as sensitive as PCR tests, but it has only been formally tested with (and authorized for) symptomatic patients. For people without symptoms, antigen tests are significantly less sensitive. The Abbott test card is still complex enough that it requires laboratory certification and a trained health-care worker to use it. But, with no machine needed, it’s easier to manufacture these tests at scale. The federal government has committed to buying a hundred and fifty million of these tests. How they’ll be distributed is unknown, however. With no grid to monitor need and link it with supply, distribution in this Administration has been left to the vagaries of political favor.

Simpler paper-strip antigen tests are in development that people can administer at home. They’d likely have yet lower sensitivity. But false negatives can be reduced by repeat testing—and that’s possible, because they’re cheap and fast. Advocates imagine people having a pack of strips at home and testing themselves every day or two in order to provide assurance for their school or workplace.

The weakness of antigen testing is not just its miss rate but also its rate of false positives. Two to three per cent of people without covid-19 nonetheless turn up positive with these tests, unlike with PCR testing. The antibodies that these tests use to recognize and attach to sars-CoV-2 proteins can also bind to unrelated proteins and cellular material. A quick, cheap test at the airport before you board a flight with a hundred other people sounds great. At present rates, one passenger might actually be unknowingly infected with the virus—current assurance-testing programs commonly find infection rates at or below one per cent. But two to three other uninfected passengers are likely to have a false positive result, be prohibited from boarding, and have to quarantine in whatever city they are in until they’re cleared by PCR testing. Today, most positive antigen tests will be false—an outcome that could prove untenable in many situations and inspire mistrust in the tests.

There are paper-strip molecular assays in development that, promising both precision and speed, could have the greatest transformative potential of any test. They recognize viral genetic material, typically using crispr-based technology, and are expected to avoid the false-positive problem of antigen tests. James Collins, an M.I.T. professor of biomedical engineering, is leading a team that, going a step yet further, is developing a face mask with a crispr-based sensor that signals if you develop a sars-CoV-2 infection.

We are on our way to an emporium of testing technologies. The trouble is that none of them will allow us to get around the necessity to upgrade and simplify our system for securing public health. Home-use paper-strip technologies have not yet received F.D.A. authorization. It will be months more before they can be produced in mass quantities. And, again, technologies do not implement themselves: we have to make sure that people actually have the tests in hand, that they won’t run out of them in hot-spot communities, that public-health authorities are notified when tests are positive, that positive cases get confirmatory tests and self-isolate, and that their contacts are traced and tested, too. If the development of essential technologies requires effort, skill, and investment, so does the delivery of them.

The San Francisco model

There are places in the country that have recognized that reality. San Francisco, one of the first American cities to be hit by the pandemic, has also been one of the best at curbing it. A big reason was Mayor London Breed’s decision, starting on March 6th, less than twenty-four hours after seeing the city’s first two confirmed cases, to back the aggressive recommendations of her city’s public-health director, Grant Colfax, to halt large gatherings, suspend nonessential travel, explore work-from-home options, and rapidly deploy a citywide testing program that remains one of the country’s most effective.

San Francisco’s leaders recognized the importance of universally available testing; residents needed to have an easy way to get tested regardless of what insurance they had or didn’t have, regardless of what relationship they had or didn’t have with a clinic, and regardless of whether or not they had a doctor’s order. The city’s hospitals, labs, and clinics were not going to meet that need, because that isn’t their job. In America, health-care systems are responsible for the care of individuals, not communities. So the city’s public-health department decided to step in.

It took an approach that resembles South Korea’s. Officials worked with local providers and laboratories to establish a network of free drive-through and walk-in sites, open to anyone who lives or works in the city. The city established a scheduling system, which people could access online or by phone, and outreach testing for nursing homes and other vulnerable communities. Public-health officers signed standing orders for each site, eliminating the need for a doctor’s referral. The city negotiated and paid most test costs. And officials made sure that they could enlist a network of labs to provide adequate capacity and keep turnaround time low. They established, in effect, a public option for testing. Although there are scores of other test sites provided by hospitals, clinics, and pharmacies across the city, the CityTest SF network has accounted for two-thirds of the city’s daily volume of tests. The program has literally been a lifesaver. Elsewhere in California, places like Los Angeles have exploded with covid-19 cases. San Francisco has kept the coronavirus contained.

All this, alas, makes San Francisco an anomaly. Historically, the work of public health has been separate from the work of health-care delivery, using measures outside the medical system to address controllable diseases like cholera, tuberculosis, and food poisoning. But even before the coronavirus crisis hit, the separation was making less and less sense. A wide range of diseases are now controllable with the modern tools of diagnostic testing, treatment, and prevention. As the coronavirus pandemic has demonstrated, the population-level distribution of medical tests, ventilators, and drugs matters as much to disease control as nonmedical measures such as masks and social distancing. Success requires integrating the systems focussed on individual care and those focussed on community needs.

We’ve long resisted that integration, though. The clearest indication is how we’ve spent our money. Spending per person on medical care was seventy-nine hundred dollars per American in 2008; it climbed to an estimated eleven thousand six hundred dollars in 2019. By contrast, the average spending per person allocated to state and local health departments was a measly eighty dollars per person in 2008, and fell to fifty-six dollars in 2019. Public-health agencies that are supposed to look after communities’ health have been forced to expand tattoo-parlor inspections while shrinking their programs to assure adequate maternal- and child-health services or screen for chronic illnesses like high blood pressure and diabetes.

Talk to city and state officials about what San Francisco accomplished, and you typically hear: “Just can’t do it.” So how has San Francisco been able to pull it off? In part, it’s because the last deadly pandemic it experienced—the H.I.V./aids crisis—taught the city that public health and medical care must work together. San Francisco has been a pioneer in guaranteeing that H.I.V. testing and treatment is readily available and affordable to all residents in need. Those reflexes, and the associated budgeting commitment, served the city well when the coronavirus arrived.

Some cities and even states—including Los Angeles, Illinois, Maine, and Tennessee—have created versions of San Francisco’s free coronavirus-testing model; the federal government set up test sites, too. Those sites received large numbers of people. But most programs don’t have sufficient funding to open enough sites—Illinois has only eleven, for instance—and the federal government opened just forty-one locations nationwide, most of which it shut down by the end of June, despite the accelerating spread of the disease. Some cities and states have run testing “blitzes,” providing public-sponsored, pop-up testing sites for a few days, with no scheduling required. But, again, because there isn’t the funding to open enough sites, lines are typically long. As cases spiked in July, almost a thousand people waited up to thirteen hours at such a site in Phoenix. Nor have these states created a system to shift testing loads to labs with capacity the way San Francisco did.

A serious national strategy for coronavirus testing—including universally available assurance testing for essential workers, travellers, students, and others—is clearly needed. Such a strategy would entail a major injection of funding, which would pay for itself many times over by getting the pandemic response, and therefore the economy, back on track. It would have the F.D.A. supervise the validation process for laboratory tests, but with a simplified and speeded-up process. And it would build our national grid for monitoring, distributing, and accelerating testing capacity, whatever technologies emerge.

President Trump, backed by the Republican politicians who have protected him, is clearly uninterested in pursuing such goals. But even the most committed Administration would have struggled to overcome the effects of the long, collective neglect of our public-health systems. Hospitals and clinics have had the resources to spend tens of billions of dollars installing electronic medical-record systems. A whole industry has developed to deliver such capabilities. Yet our thinly staffed public-health departments, which are expected to compile thousands of diagnostic-test results per day and follow up on outbreaks, have nothing of the kind. Some still receive test results by fax and must manually enter them into databases. They lack the means to readily measure, let alone manage, a community’s availability of coronavirus tests, ventilators, hospital beds, or personal protective equipment. Not a single state in the country reports coronavirus-test turnaround time and rates of mask wearing—two of our most critical indicators for shutting the virus down. They’d like to; they just don’t have the ability to collect the information.

The pandemic has given us all a master class on infectious disease, diagnostics, and the reality that individual health is inseparable from community health. Polling shows that an overwhelming majority of Americans want the government to cover the costs of not only testing but also treatment for the coronavirus. In turn, support has grown for expanding Medicare to cover all Americans for their medical needs, and for investment in public health.

Epidemiologists expect us to encounter one of the worst falls and winters in American history. We will have more American dead in a single year from the pandemic than we saw during any year of war we’ve faced. On Election Day, we’ll have a chance to turn out a President who has sacrificed tens of thousands of American lives—and undermined essential government institutions—to serve his own desires. And yet, amid the carnage, there’s a lot we can still do to advance the essential work of collaboration. In New England, for example, the Assurance Testing Alliance (of which I am a founder) has been assembling a logistics grid that links schools, nursing homes, and other institutions that need regular testing to those who have the capacity to deliver it. Already, the alliance has pushed the total cost of a PCR test to fifty dollars, with a next-day turnaround time. And, beginning in August, and catalyzed by a Rockefeller Foundation effort, ten governors (so far) have formed an interstate compact to purchase and distribute enough rapid-testing devices and supplies for the delivery of five million tests. This compact enables what you’d think the United States government was created to provide: a confederation of states working to meet their common needs. Participating states share and coördinate their testing capacity, rather than bidding against one another, as they did in order to procure scarce ventilators and P.P.E. earlier in the pandemic. Alternative infrastructures like this will prove all the more important if Trump continues to control the federal government.

Such efforts aren’t a replacement for national leadership, but they start the work that must be done to make ordinary physical interaction safe again, and to begin creating the public-health system we deserve. As the former Surgeon General C. Everett Koop once said, “Health care is vital to all of us some of the time, but public health is vital to all of us all of the time.” The pandemic has brought Americans a further lesson: our best chance for long, flourishing lives in the future requires that we build the foundations of our public health now.

Atul Gawande, a surgeon and public-health researcher, became a staff writer at The New Yorker in 1998.