Protocol trumps practice. This principle seems clear enough, but complying with it is not always as straight-forward as it sounds. Years of practicing medicine has reinforced the way a physician responds to medical situations. But do these responses run counter to the investigational plan? Can a site’s commitment to standard of care affect its ability to meet enrollment targets?


There’s a lot to consider.



What’s Your Standard of Care?
When deciding whether or not to conduct a particular study, a PI needs to verify that the protocol is aligned with practice norms. For example, an early phase trial might exclude a medication that is part of a practice’s routine therapy. Is the study placebo-controlled? Does it feature a specific comparator drug? Will it include a washout period? Any of these elements could present enrollment challenges or preclude a site from accepting a study at all. Responsible sites want to make thoughtful decisions about study suitability; they want to provide realistic enrollment estimates. Sponsors want this too, and can help sites do both these things by providing them a sufficient level of detail about protocol procedures as early as possible.


The Road to Deviations is Often Paved with Good Intentions
Therapeutic misconception – a well-documented phenomenon in clinical research – occurs when a study participant “fails to appreciate the distinction between the imperatives of clinical research and of ordinary treatment.”* Study participants are not alone in this. Researchers blur the distinction themselves when they conduct procedures that are consistent with clinical care but deviate from the protocol. This may be particularly true for PIs who recruit participants from their own practices. An endocrinologist might ordinarily reduce dosage for a particularly diminutive patient. A pulmonologist would often skip a scheduled chest x-ray she felt wasn’t needed to avoid exposing her patient to unnecessary radiation. An orthopedic surgeon may decide his patient needs more recovery time than usual before attempting her first walk. In a clinical care setting, these decisions are sound, made in an individual patient’s best interest. In a clinical trial, if they differ from the investigational plan and haven’t been approved by the Sponsor, they’re protocol deviations.**

It May be Par for the Course, But It's Still an AE
Specialists who have experience treating particular conditions are also familiar with the complications that ordinarily accompany them. A nephrologist, for instance, knows that a patient with end-stage renal disease frequently experiences bloat from a buildup of fluid between dialysis sessions. Though useful for a doctor treating patients, this knowledge can actually work against a doctor running a trial. How? A PI may fail to report a stomach ache as an AE because it’s so typical, so expected. “Bloat is common for renal patients. If I recorded every GI incident, I’d be recording AEs all day.” At its surface, this PI’s argument sounds reasonable, but what if the study drug itself is contributing to the participant’s discomfort? In order to assess the drug’s gastrointestinal effect, the PI must document the frequency and severity of all GI events.

Lab values that are either above or below normal range are also prime candidates for AE underreporting. “Of course the participant’s liver enzyme is high – we’re testing a cholesterol drug.”

The Importance of Study Oversight
Any GCP course worth its registration fee will discuss the distinction between standard of care and the study protocol. In practice, the distinction is not always as obvious as training sessions might suggest. This is where well-trained CRAs come in. As site monitors, CRAs are in a position to catch deviations that result from lapses into standard of care. Reading through progress notes, a monitor can ensure that any untoward medical event has been reported as an Adverse Event. They can verify that procedures conducted by the PI and site staff are compliant with the protocol. Then, by reviewing which types of data must be collected and emphasizing the importance of following certain protocol procedures, monitors can take the opportunity to re-educate study personnel and help them avoid these common pitfalls.

_______________________________________________________________________
* Lidz CW, Appelbaum PS (2002) The therapeutic misconception: problems and solutions. Med Care 40: V55-V63.

**Andrew Snyder of the HealthEast Care System wrote a thoughtful piece describing the compatibilities that do exist between clinical care and clinical research. His arguments provide a useful counterpoint to the issues we’re raising here. https://firstclinical.com/journal/2017/1707_Research_vs_Care.pdf

A version of this article originally appeared in InSite, the Journal of the Society for Clinical Research Sites.

Over the years, attendees of MAGI Clinical Research Conferences have collected a set of practical, actionable suggestions for improving clinical trials. More than eighty such tips appear in the July 2019 edition of Journal of Clinical Research Best Practices*.  In this post, Polaris auditors weigh in on some of their favorite MAGI suggestions. Surprising no one, they also were eager to share some of their own.

Our Favorites Tips from MAGI

So how does a clinical trial tip earn a spot on our exalted Faves List?  First, it must be something we don’t see too often, or not as much as we’d like.(If most organizations already do a useful thing, it doesn’t really qualify as a helpful tip; it’s really just a common practice.) Second, the effort to implement the tip can’t be too onerous. If a practice requires too much interdepartmental coordination, change management, training, money, or resources, it’s not a tip. It’s a full-blown initiative.

So here they are. Each tip from MAGI attendees is in bold font. Our accompanying commentary is in plain text:

• To help ensure quality study conduct, clinical sites should prepare protocol-specific quality checklists for each study. We’ve written about quality checklists from the auditing perspective before. They’re not a panacea, certainly, but that doesn’t mean they can’t be very useful.
  
  
• After study close-out, sponsors and CROs should consider holding conference calls with groups of sites to capture lessons learned. This in turn could be used to improve training, SOPs, SIVs, etc.
  
  
• As a recruitment aid, clinical sites should create pocket-sized, laminated study cards that list the inclusion/exclusion criteria for a study.  Site staff members can keep these cards in their lab coat pockets and quickly refer to them when treating a patient who could be a potential subject.
  
  
• CROs should share risk assessments and mitigation plans with Sponsors. We agree, but would also encourage CROs to keep the sites involved and aware of risks so they can anticipate them and proceed accordingly.
  
  
• Sponsors/CROs should ensure proper qualifications of vendors prior to executing contracts. It’s hard to argue with this logic, but we don’t see it as much as we should. Too often qualification audits come after the paperwork has been signed. Should the audit uncover noncompliance or quality risks at the vendor site, it’s much harder to get the vendor to make necessary changes after the contract is in place.
  
  
• CROs should align 3rd party contracts with the Sponsor/CRO contract and the Clinical Trial Agreement. Yep.

Additional Tips from Polaris QA/Compliance Auditors

The MAGI list of clinical trial tips brought others to mind that we wanted to share. We applied the same criteria to these suggestions as we did to the MAGI contributions: (1) not necessarily rare, but not as common as it could be, and (2) not overly complex or expensive to implement.

• When evaluating outsourcing partners and clinical sites, Sponsors and CROs should make sure to look at personnel turnover rates. Frequent turnovers may suggest underlying problems that could jeopardize study conduct and quality.
  
  
• Sponsors and CROs should make sure their Monitoring Report templates are consistent with the Clinical Monitoring Plan (CMP). For example:
  
  
• The CMP calls for a focus on a particular set of critical variables, but the report template only has a place for recording that 100% SDV was completed. This means that there’s no way to document that the monitor put special emphasis on anything.
• The CMP requires bi-direction review of study data – a confirmation that what is in the CRF can be verified in the source, and all pertinent data in the source can be found in the CRF – but the report template only allows for the former to be documented.
  
  
• Every member of the site team has valuable input. It’s important to include the study PI, CRC, pharmacist, and other key personnel in the discussions. In 2017, we wrote an article about the important, yet often overlooked, input that the pharmacist on site can provide.
  
  
• There are many reasons that trial participants leave a study, many of which can’t be remedied with improved site practices. But sites that demonstrate they value the participation of their study volunteers, and honor the time they’re spending and contribution they’re making, tend to have better retention results. To that end:
  
  
• To help participants schedule their time, sites can prepare calendars that include all study visit dates and indicate the activities and procedures they entail. (This, of course, needs to be approved by the IRB).
• When participants arrive, they shouldn’t have to sit in a waiting room or empty exam room; they should be seen immediately so they don’t feel their time is being wasted.
• Sites can provide beverages and light snacks to their study participants who especially appreciate them immediately after a fasting blood draw (protocol permitting, naturally). It’s a small courtesy, and not difficult to do. Whose day isn’t brightened by a proffered nosh?**

Uh oh. Now we got you all thinking about mini muffins and cheddar popcorn. Go ahead. Grab a treat. We'll talk later.

________________________________________________________________
 * Journal of Clinical Research Best Practices, July 2019

** Proffered Nosh™ would be a really great name for a restaurant. Or a fictional Scotland Yard Inspector -- legendary for his wit, brilliance, wine pairings, and fashion sense.

Objective responses seen in 29% of patients with locally advanced basal cell carcinoma (BCC)

April saw the company add new CEO, receive approval for lead ADC drug, and launch a public offering of stock.

Sanofiâs insulin aspart biosimilar receives positive opinion from the EMAâs CHMP.

Much attention has been paid to the impact of the COVID-19 pandemic on the supply chain for medicines we rely on, but there has been less focus on the impact of medicines yet to come. The advancements in cancer care … Continue reading →

by Abrahm Lustgarten

The scientists who study how diseases emerge in a changing environment knew this moment was coming. Climate change is making outbreaks of disease more common and more dangerous.

Over the past few decades, the number of emerging infectious diseases that spread to people — especially coronaviruses and other respiratory illnesses believed to have come from bats and birds — has skyrocketed. A new emerging disease surfaces five times a year. One study estimates that more than 3,200 strains of coronaviruses already exist among bats, awaiting an opportunity to jump to people.

The diseases may have always been there, buried deep in wild and remote places out of reach of people. But until now, the planet’s natural defense systems were better at fighting them off.

Today, climate warming is demolishing those defense systems, driving a catastrophic loss in biodiversity that, when coupled with reckless deforestation and aggressive conversion of wildland for economic development, pushes farms and people closer to the wild and opens the gates for the spread of disease.

Aaron Bernstein, the interim director for the C-Change Center for Climate, Health and the Global Environment at Harvard University’s T.H. Chan School of Public Health, said that ignoring how climate and rapid land development were putting disease-carrying animals in a squeeze was akin to playing Russian roulette.

“Nature is trying to tell us something,” Bernstein said.

Scientists have not suggested that climate played any direct role in causing the current COVID-19 outbreak. Though the virus is believed to have originated with the horseshoe bat, part of a genus that’s been roaming the forests of the planet for 40 million years and thrives in the remote jungles of south China, even that remains uncertain.

Scientists have, however, been studying the coronaviruses of southern China for years and warning that swift climate and environmental change there — in both loss of biodiversity and encroachment by civilization — was going to help new viruses jump to people.

There are three ways climate influences emerging diseases. Roughly 60% of new pathogens come from animals — including those pressured by diversity loss — and roughly one-third of those can be directly attributed to changes in human land use, meaning deforestation, the introduction of farming, development or resource extraction in otherwise natural settings. Vector-borne diseases — those carried by insects like mosquitoes and ticks and transferred in the blood of infected people — are also on the rise as warming weather and erratic precipitation vastly expand the geographic regions vulnerable to contagion. Climate is even bringing old viruses back from the dead, thawing zombie contagions like the anthrax released from a frozen reindeer in 2016, which can come down from the arctic and haunt us from the past.

Thus the COVID-19 pandemic, even as it unfolds in the form of an urgent crisis, is offering a larger lesson. It is demonstrating in real time the enormous and undeniable power that nature has over civilization and even over its politics. That alone may make the pandemic prologue for more far-reaching and disruptive changes to come. But it also makes clear that climate policy today is indivisible from efforts to prevent new infectious outbreaks, or, as Bernstein put it, the notion that climate and health and environmental policy might not be related is “a ​dangerous delusion.”

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The warming of the climate is one of the principal drivers of the greatest — and fastest — loss of species diversity in the history of the planet, as shifting climate patterns force species to change habitats, push them into new regions or threaten their food and water supplies. What’s known as biodiversity is critical because the natural variety of plants and animals lends each species greater resiliency against threat and together offers a delicately balanced safety net for natural systems. As diversity wanes, the balance is upset, and remaining species are both more vulnerable to human influences and, according to a landmark 2010 study in the journal Nature, more likely to pass along powerful pathogens.

The casualties are amplified by civilization’s relentless push into forests and wild areas on the hunt for timber, cropland and other natural resources. Epidemiologists tracking the root of disease in South Asia have learned that even incremental and seemingly manageable injuries to local environments — say, the construction of a livestock farm adjacent to stressed natural forest — can add up to outsized consequences.

Around the world, according to the World Resources Institute, only 15% of the planet’s forests remain intact. The rest have been cut down, degraded or fragmented to the point that they disrupt the natural ecosystems that depend on them. As the forests die, and grasslands and wetlands are also destroyed, biodiversity sharply decreases further. The United Nations warns that the number of species on the planet has already dropped by 20% and that more than a million animal and plant species now face extinction.

Losing species has, in certain cases, translated directly to a rise in infectious disease.

Americans have been experiencing this phenomenon directly in recent years as migratory birds have become less diverse and the threat posed by West Nile encephalitis has spread. It turns out that the birds that host the disease happen to also be the tough ones that prevail amid a thinned population. Those survivors have supported higher infection rates in mosquitoes and more spread to people.

Similarly, a study published last month in the journal Proceedings of the Royal Society B found that as larger mammals suffer declines at the hands of hunters or loggers or shifting climate patterns, smaller species, including bats, rats and other rodents, are thriving, either because they are more resilient to the degraded environment or they are able to live better among people.

It is these small animals, the ones that manage to find food in garbage cans or build nests in the eaves of buildings, that are proving most adaptable to human interference and also happen to spread disease. Rodents alone accounted for more than 60% of all the diseases transmitted from animals to people, the researchers found.

Warmer temperatures and higher rainfall associated with climate change — coupled with the loss of predators — are bound to make the rodent problem worse, with calamitous implications. In 1999, for example, parts of Panama saw three times as much rainfall as usual. The rat population exploded, researchers found. And so did the viruses rats carry, along with the chances those viruses would jump to people. That same year, a fatal lung disease transmitted through the saliva, feces and urine of rats and mice called hantavirus pulmonary syndrome emerged in Panama for the first time, according to a report in the journal Emerging Infectious Diseases.

As much as weather changes can drive changes in species, so does altering the landscape for new farms and new cities. In fact, researchers attribute a full 30% of emerging contagion to what they call “land use change.” Nothing drives land use shifts more than conversion for farmland and feedstock — a result of the push to feed the planet’s 7.8 billion people. As the global population surges to 10 billion over the next 35 years, and the capacity to farm food is stressed further again by the warming climate, the demand for land will only get more intense. Already, more than one-third of the planet’s land surface, and three-quarters of all of its fresh water, go toward the cultivation of crops and raising of livestock. These are the places where infectious diseases spread most often.

Take, for example, the 1999 Nipah outbreak in Malaysia — the true-life subject matter adapted for the film “Contagion.” Rapid clearcutting of the forests there to make way for palm plantations drove fruit bats to the edge of the trees. (Separate research also suggests that climate changes are shifting fruit bats’ food supply.) They found places to roost, as it happens, alongside a hog farm. As the bats gorged themselves on fruit, they dropped pieces of food from the branches, along with their urine, into the pigsties, where at least one pig is believed to have eaten some. When the pig was slaughtered and brought to market, an outbreak is believed to have been spread by the man who handled the meat. More than 100 people died.

The U.S. Centers for Disease Control and Prevention says that fully three-quarters of all new viruses have emerged from animals. Even the 2014 Ebola outbreak in West Africa is believed to have begun when a boy dug into a tree stump that happened to be the roost of bats carrying the virus.

As Christine Johnson, the associate director of the One Health Institute, an interdisciplinary epidemiological program at the University of California, Davis, puts it, global health policymakers have a responsibility to understand how climate, habitat and land use changes lead to disease. Almost every major epidemic we know of over the past couple of decades — SARS, COVID-19, Ebola and Nipah virus — jumped to people from wildlife enduring extreme climate and habitat strain, and still, “we’re naive to them,” she said. “That puts us in a dangerous place.”

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Once new diseases are let loose in our environment, changing temperatures and precipitation are also changing how those diseases spread — and not for the better. Warming climates increase the range within which a disease can find a home, especially those transmitted by “vectors,” mosquitoes and ticks that carry a pathogen from its primary host to its new victim.

A 2008 study in the journal Nature found nearly one-third of emerging infectious diseases over the past 10 years were vector-borne, and that the jumps matched unusual changes in the climate. Especially in cases where insects like infection-bearing mosquitoes are chasing warmer temperatures, the study said, “climate change may drive the emergence of diseases.”

Ticks and mosquitoes now thrive in places they’d never ventured before. As tropical species move northward, they are bringing dangerous pathogens with them. The Zika virus or Chikungunya, a mosquito-spread virus that manifests in intense joint pain, were once unseen in the United States, but both were transmitted locally, not brought home by travelers, in southern Texas and Florida in recent years.

Soon, they’ll be spreading further northward. According to a 2019 study in the journal PLOS Neglected Tropical Diseases, by 2050, disease-carrying mosquitoes will ultimately reach 500 million more people than they do today, including some 55 million more Americans. In 2013, dengue fever — an affliction affecting nearly 400 million people a year, but normally associated with the poorest regions of Africa — was transmitted locally in New York for the first time.

“The long-term risk from dengue may be much higher than COVID,” said Scott Weaver, the director of the Institute for Human Infections and Immunity at the University of Texas Medical Branch in Galveston. “It’s a disease of poor countries, so it doesn’t get the attention it deserves.”

The chain of events that ultimately leads to a pandemic can be long and subtle, steered by shifts in the ecosystem. The 1999 West Nile outbreak in the U.S., for example, came after climate-driven droughts dried up streams and rivers, leaving pools of stagnant water where mosquitoes bred unhindered. It turns out the loss of water also killed off their predators — dragonflies and frogs that depend on large watering holes were gone.

Coronaviruses like COVID-19 aren’t likely to be carried by insects — they don’t leave enough infected virus cells in the blood. But one in five other viruses transmitted from animals to people are vector-borne, said U.C. Davis’ Johnson, meaning it’s only a matter of time before other exotic animal-driven pathogens are driven from the forests of the global tropics to the United States or Canada or Europe because of the warming climate. “Climate is going to shift vulnerability to that,” Johnson said, “and I think some of these regions are not prepared.”

The changing climate won’t just affect how the diseases move about the planet, it will also shape how easily we get sick. According to a 2013 study in the journal PLOS Currents Influenza, warm winters were predictors of the most severe flu seasons in the following year. The brief respite in year one, it turns out, relaxed people’s natural defenses and reduced “herd immunity,” setting conditions for the virus to rage back with a vengeance.

Even harsh swings from hot to cold, or sudden storms — exactly the kinds of climate-induced patterns we’re already seeing — make people more likely to get sick. A study in the journal Environmental Research Letters linked the brutal 2017-18 flu season — which killed 79,000 people — to erratic temperature swings and extreme weather that winter, the same period in which a spate of floods and hurricanes devastated much of the country. If the climate crisis continues on its current trajectory, the authors wrote, respiratory infections like the flu will sharply increase. The chance of a flu epidemic in America’s most populated cities will increase by as much as 50% this century, and flu-related deaths in Europe could also jump by 50%.

“We’re on a very dangerous path right now,” said the University of Texas’ Weaver. Slow action on climate has made dramatic warming and large-scale environmental changes inevitable, he said, “and I think that increases in disease are going to come along with it.”

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Twelve months before the first COVID-19 case was diagnosed, a group of epidemiologists working with a U.S. Agency for International Development project called PREDICT, or Pandemic Influenza and other Emerging Threats, was deep in the remote leafy jungle of southern China’s Yunnan province hunting for what it believed to be one of the greatest dangers to civilization: a wellspring of emerging viruses.

A decade of study there had identified a pattern of obscure illnesses affecting remote villagers who used bat guano as fertilizer and sometimes for medicine. Scientists traced dozens of unnamed, emerging viruses to caves inhabited by horseshoe bats. Any one of them might have triggered a global pandemic killing a million people. But luck — and mostly luck alone — had so far kept the viruses from leaping out of those remote communities and into the mainstream population.

The luck is likely to run out, as Yunnan is undergoing enormous change. Quaint subsistence farm plots were overtaken by hastily erected apartment towers and high-speed rail lines, as the province endured dizzying development fueled by decades of Chinese economic expansion. Cities’ footprints swelled, pushing back the forests. More people moved into rural places and the wildlife trade, common to such frontier regions, thrived. With every new person and every felled tree, the bats’ habitat shrank, putting the viruses they carried on a collision course with humanity. By late 2018, epidemiologists there were bracing for what they call “spillover,” or the failure to keep a virus locally contained as it jumped from the bats and villages of Yunnan into the wider world.

In late 2018, the Trump administration, as part of a sweeping effort to bring U.S. programs in China to a halt, abruptly shut down the research — and its efforts to intercept the spread of a new novel coronavirus along with it. “We got a cease and desist,” said Dennis Carroll, who founded the PREDICT program and has been instrumental in global work to address the risks from emerging viruses. By late 2019, USAID had cut the program’s global funding.

USAID did not respond to a detailed list of questions from ProPublica.

The loss is immense. The researchers believed they were on the cusp of a breakthrough, racing to sequence the genes of the coronaviruses they’d extracted from the horseshoe bat and to begin work on vaccines. They’d campaigned for years for policymakers to fully consider what they’d learned about how land development and climate changes were driving the spread of disease, and they thought their research could literally provide governments a map to the hot spots most likely to spawn the next pandemic. They also hoped the genetic material they’d collected could lead to a vaccine not just for one lethal variation of COVID, but perhaps — like a missile defense shield for the biosphere — to address a whole family of viruses at once. (In fact, the gene work they were able to complete was used to test the efficacy of remdesivir, an experimental drug that early clinical trial data shows can help COVID-19 patients.)

Carroll said knowledge of the virus genomes had the potential “to totally transform how we think about future biomedical interventions before there’s an emergence.” His goal was to not just react to a pandemic, but to change the very definition of preparedness.

If PREDICT’s efforts in China had the remote potential to fend off the current COVID pandemic, though, it also offered an opportunity to study how climate and land development were driving disease.

But there has been little appetite for that inquiry among policymakers. PREDICT’s staff and advisers have pushed the U.S. government to consider how welding public health policy with environmental and climate science could help stem the spread of contagions. Climate change was featured in presentations that PREDICT staff made to Congress, according to U.C. Davis’ Johnson, who is now also the director of PREDICT, which received a temporary funding extension this spring. And until 2016, leadership of New York-based EcoHealth Alliance, the research group working under PREDICT funding in Yunnan, was invited several times to the White House to advise on global health policy.

Since Donald Trump was elected, the group hasn’t been invited back.

“It’s falling on deaf ears,” said Peter Daszak, EcoHealth Alliance’s president.

A White House spokesperson did not respond to an emailed request for comment.

What Daszak really wants — in addition to restored funding to continue his work — is the public and leaders to understand that it’s human behavior driving the rise in disease, just as it drives the climate crisis. In China’s forests, he looks past the destruction of trees and asks why they are being cut in the first place, and who is paying the cost. Metals for iPhones and palm oil for processed foods are among the products that come straight out of South Asian and African emerging disease hot spots.

“We turn a blind eye to the fact that our behavior is driving this,” he said. “We get cheap goods through Walmart, and then we pay for it forever through the rise in pandemics. It’s upside down.”

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by Michael Grabell

On Tuesday, March 31, an emergency room doctor at the main hospital in Grand Island, Nebraska, sent an urgent email to the regional health department: “Numerous patients” from the JBS beef packing plant had tested positive for COVID-19. The plant, he feared, was becoming a coronavirus “hot spot.”

The town’s medical clinics were also reporting a rapid increase in cases among JBS workers. The next day, Dr. Rebecca Steinke, a family medicine doctor at one of the clinics, wrote to the department’s director: “Our message is really that JBS should shut down for 2 weeks and have a solid screening plan before re-opening.”

Teresa Anderson, the regional health director, immediately drafted a letter to the governor.

But during a conference call that Sunday, Gov. Pete Ricketts made it clear that the plant, which produces nearly 1 billion pounds of beef a year and is the town’s largest employer, would not be shut down.

Since then, Nebraska has become one of the fastest-growing hot spots for the novel coronavirus in the United States, and Grand Island has led the way. Cases in the city of 50,000 people have skyrocketed from a few dozen when local health officials first reported their concerns to more than 1,200 this week as the virus spread to workers, their families and the community.

The dismissed warnings in Grand Island, documented in emails that ProPublica obtained under the state’s public records law, show how quickly the virus can spread when politicians overrule local health officials. But on a broader scale, the events unfolding in Nebraska provide an alarming case study of what may come now that President Donald Trump has used the Defense Production Act to try to ensure meat processing plants remain open, severely weakening public health officials’ leverage to stop the spread of the virus in their communities.

Ricketts spokesman Taylor Gage said the governor explained on the call with local officials that the plant would stay open because it was declared an essential industry by the federal government. Two and a half weeks later, as cases were rising among the state’s meatpacking workers, Ricketts, a Republican businessman whose father founded the brokerage TD Ameritrade, held a news conference and said he couldn’t foresee a scenario where he would tell the meatpacking plants to close because of their importance to the nation’s food supply.

“Can you imagine what would happen if people could not go to the store and get food?” he asked. “Think about how mad people were when they couldn’t get paper products.”

“Trust me,” he added, “this would cause civil unrest.”

In the last two weeks, small meatpacking towns across Nebraska have experienced outbreaks, including at a Tyson Foods beef plant in Dakota City, a Costco chicken plant in Fremont and a Smithfield Foods pork plant in Crete. With the governor vowing to keep plants open, the companies have only in recent days decided to close for deep cleanings as cases have grown to staggering levels.

In Grand Island, two hours west of Omaha, the consequences of the governor’s decision came quickly. The CHI Health St. Francis hospital, which has 16 intensive care beds, was soon overwhelmed. At one point in April, it had so many critical patients that it had to call in three different helicopter companies to airlift patients to larger hospitals in Lincoln and Omaha, said Beth Bartlett, the hospital’s vice president for patient care.

JBS workers felt the strain, too. Under pressure to keep the food supply chain flowing, some of the plant’s 3,500 workers, many hailing from Latin America, Somalia and Sudan, said they were told to report for work regardless. In a letter to the governor last week, Nebraska Appleseed, a nonprofit advocacy group, said a JBS worker had been told by his supervisor that if he tested positive, he should come to work anyway and “keep it on the DL” or he’d be fired. Some workers who’d been told to quarantine after being exposed told ProPublica this week that they were called back to work before the 14-day window recommended by the Centers for Disease Control and Prevention — even if they felt sick. One worker in the offal, or entrails, section recently fainted in the plant, they said, but was told he couldn’t go home.

Cameron Bruett, head of corporate affairs for JBS, said the company has worked in partnership with local officials to prevent the spread of the coronavirus and did not influence the governor’s decision to keep the plant open. He pointed to comments made recently by University of Nebraska Medical Center officials who toured the plant, who said JBS has put in place some “best practices,” including installing barriers on the meat cutting line, communicating new precautions in multiple languages and ensuring the proper use of masks.

Bruett said no one is forced to come to work or punished for calling in sick. “Such actions, if true, would be grotesque and a clear violation of our culture,” he said.

The emails obtained by ProPublica show that local health officials have traced 260 cases to the JBS plant. But that was nearly two weeks ago and almost certainly underestimates the total. Anderson, who directs the Central District Health Department, said she hasn’t had enough tests to do targeted testing of JBS employees and is only testing people when they’re symptomatic. In Grand Island and its surrounding county, 32 people have died from the virus. According to workers, at least one of those was a JBS employee.

Across the country, more than 10,000 COVID-19 cases have been linked to meatpacking plants, and at least three dozen workers are known to have died, a ProPublica review of news reports and government health data shows.

While cases in the worst hit urban areas like New York appear to have plateaued, the nation’s meatpacking towns have continued to see spikes. A few large outbreaks have dominated public attention, but COVID-19 cases have popped up in well over 100 plants in mostly rural communities. There the virus’s impact is magnified by the workers’ sometimes cramped living conditions, with multiple generations of immigrant and refugee families often residing together in apartments, houses and trailers.

Before Trump’s order, more than 30 plants had shut down at least briefly to increase cleaning and control the spread among their workforces. The various closures have cut beef and pork production by more than a third compared with last year, causing supply chain disruptions for some supermarkets and fast-food chains.

Some of those closures show the role public health officials have had in the actions of large meatpacking companies like JBS, which has beef, pork and poultry plants in 27 states.

In Colorado, Dr. Mark Wallace of the Weld County Department of Public Health and Environment and state health director Jill Hunsaker Ryan grew worried that that if the coronavirus spread at JBS’ Greeley plant, it would have a “devastating” effect on the community that “would quickly overwhelm the medical resources available in the hospitals.”

Unlike Nebraska, Colorado’s health officials eventually ordered the JBS plant to close. But documents obtained by ProPublica show the protracted debate that came before that decision, with JBS invoking the governor to question the formal closure order. By the time the order was issued, some public officials felt the virus had been given too big a head start.

Like Grand Island, Greeley officials were already hearing by the end of March that hospital emergency rooms were seeing a “high number of JBS employees,” according to an email Wallace sent April 1 to the plant’s occupational health director.

“Their concern, and mine, is far too many employees must be working when sick and spreading infection to others,” Wallace wrote, urging the plant to take additional safety measures.

Three days later, Wallace wrote a more detailed letter to JBS’ human resources director, Chris Gaddis, documenting the virus’s spread and threatening to shut the plant down if it didn’t screen employees and ensure they could work 6 feet apart.

But as days passed, the situation in Greeley didn’t improve.

“Want you to know my colleagues are not reassured by what I’m sharing about measures being implemented,” Wallace wrote to Gaddis. “‘The cat’s out of the bag’ is what all health care providers are saying — too many sick people already, too much spread already, etc.”

After nine days of back-and-forth, JBS agreed to close the plant and Hunsaker Ryan and Wallace issued a formal shutdown order. But negotiations seemed to stretch until the last minute, emails show.

After Hunsaker Ryan sent JBS the order on the afternoon of April 10, Gaddis appeared confused. “It is our understanding from the telephone conversation that the governor did not want this letter sent,” Gaddis wrote. “Please confirm it was properly sent.”

Bruett said the company’s impression was that the governor didn’t feel a formal order “was necessary given our voluntary decision to shut down.” But Conor Cahill, a spokesman for Gov. Jared Polis, said: “Of course the governor wanted the health order sent. The governor has been clear that JBS needs to be more transparent with their staff and the public about the situation at their plant.”

Notified of the shutdown by his staff, Greeley Mayor John Gates wrote in an email, “In my opinion, that should have happened a week ago for the health and safety of their employees.”

On Wednesday, the state announced the latest numbers on the JBS outbreak: 280 employees had tested positive for COVID-19, and seven of them had died.

The Grand Island beef plant opened in 1965 in a sugar beet farming area. In recent decades, the plant has drawn immigrants from Mexico and Central America, and more recently refugees from Somalia and Sudan. In a sign of the area’s shifting workforce, Somali residents have opened a mosque in the old El Diamante nightclub and a community center in the former Lucky 7 Saloon next to a Salvadoran restaurant named El Tazumal.

Members of those communities became among the first to hit the area’s medical clinics as the virus began to spread. By the last week in March, the Family Practice of Grand Island, where Steinke works, had opened a special respiratory clinic to handle COVID-19 patients. That week, six of the patients had come from JBS. But over three days from March 30 to April 1, the clinic saw 25 patients that carried JBS insurance, indicating they were either employees or their dependents.

Danny Lemos’ father was one of the first JBS workers to get sick from the virus in late March. The 62-year-old, who’d worked at the plant for a year, had developed a fever and a cough.

“One day, he was laying in the living room on a chair, wrapped up in a blanket, shivering,” Lemos said. “My mom takes his temperature, and he had a temperature of 105 and he was really having trouble breathing.”

His father was rushed to the hospital and put on a ventilator.

Within days, Lemos said he also started having trouble breathing and joined his father in the ICU. Lemos, 39, was put in a medically induced coma and given a 20% chance of living, he said.

Surprisingly, he said, he eventually recovered and was released from the hospital in late April. His father, Danny Lemos Sr., has been in the hospital for more than a month, most of the time on a ventilator, and is only now starting to recover.

Lemos said JBS should have taken better precautions.

“Shutting down right away, I think, probably would have helped a ton,” he said. “Do I think it would have kept everybody from getting sick? No, because those same people are still going to be out and about in the community. But just being so many people in one building, it was like a ticking time bomb.”

In an interview this week, Steinke said that it was hard to get the message across to JBS that more needed to be done.

“Even if they did not stop or shut down, if they would have put in better protections right from the start,” she said, “we would not have seen such a rapid rise in cases.”

At one point before the governor’s decision, the emails ProPublica obtained show, officials found language on the U.S. Department of Agriculture’s website that said local authorities could close a plant and the USDA would follow those decisions, potentially giving the health district some leverage.

“I guess I will send it to … HR there and maybe he will take us more seriously,” Anderson, the local health director, wrote in an email to the city administrator.

Under Trump’s executive order, that guidance has been reversed: The USDA could try to overrule local decisions if federal officials disagree.

That could pose a risk to the USDA’s own workforce of federal food inspectors, who work inside the plants to ensure the meat is safe to eat. According to the emails, some inspectors at the JBS plant also tested positive. Because inspectors sometimes monitor multiple sites, one inspector noted that she had recently worked in two other plants that have also had outbreaks, potentially spreading the virus within other plants.

“From my perspective,” temporarily closing the JBS plant “would have reduced the transmission,” Anderson said in an interview this week. “But if you shut down a plant and your 3,700 employees have nowhere to go, where are they going to go and how far is the spread going to be outside the plant vs. inside the plant? And if you end up going a month, what happens to their ability to feed their families?”

Anderson said that the “general feeling” she got from the call with the governor was that they needed to do more testing. So after the governor blocked the effort to close the plant, she continued to try to work collaboratively with JBS to encourage more testing of their employees.

In the emails, JBS officials said they were open to testing but repeatedly expressed concern about public disclosure of the results. “We want to make sure that testing is conducted in a way that does not foment fear or panic among our employees or the community,” JBS chief ethics and compliance officer Nicholas White wrote in an email to Anderson on April 15.

A week later, after the number of JBS cases was released by Anderson, Tim Schellpeper, president of the company’s U.S. beef processing operations, emailed her that he was worried about the amount of national attention it was attracting. “Have you given more thought to adding clarity/correction around this in your comments today?” he asked.

As JBS officials fretted about the optics of testing their employees, tensions within the families of the workers mounted. As the number of sick workers grew, the daughter of one worker, Miriam, said she was panicking about what would happen to her mother, who worked on the plant’s kill floor. At the end of every shift, she said, she called her mother to make sure she was okay.

“It was dreadful,” said Miriam, who asked that her last name not be used to protect her mother from retaliation. “It was just kind of living in fear waiting for the day she would have a fever. We knew it was going to happen because she’s a JBS employee. We didn’t think it was preventable anymore.”

Then, one day, she got a call from her mother, telling her that she had developed a fever and was being sent home.

“As she was changing in the locker room, she calls me and you can just hear the fear in her voice,” Miriam said.

Shortly after, her father tested positive for the virus too. Thankfully, she said, both her parents had only mild symptoms and have since recovered. But JBS and the governor should have done more, Miriam said.

“It just seemed like they were kind of careless,” she said. “I think it would have been a smart idea if not to close down the plant, to take more action to help the employees. They’re essential, but they need protection. They need to be kept safe.”

In the meantime, Ricketts has said that his approach of keeping the state “open for business” worked. And at a news conference Friday, he underscored the importance of the meatpacking industry to the state’s economy, proclaiming May as “Beef Month” in Nebraska.

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