WASHINGTON — A coroner in Indiana wanted to know if the coronavirus had killed a man in early March but said that her health department denied a test. Paramedics in New York City say that many patients who died at home were never tested for the coronavirus, even if they showed telltale signs of infection.

In Virginia, a funeral director prepared the remains of three people after health workers cautioned her that they each had tested positive for the coronavirus. But only one of the three people had the virus noted on the death certificate.

Across the United States, even as coronavirus deaths are being recorded in terrifying numbers — many hundreds each day — the true death toll is likely much higher.

More than 9,100 people with the coronavirus have been reported to have died in this country as of this weekend, but hospital officials, doctors, public health experts and medical examiners say that official counts have failed to capture the true number of Americans dying in this pandemic, as a result of inconsistent protocols, limited resources and a patchwork of decision-making from one state or county to the next.

In many rural areas, coroners say they don’t have the tests they need to detect the disease. Doctors now believe that some deaths in February and early March, before the coronavirus reached epidemic levels in the United States, were likely misidentified as influenza or only described as pneumonia.

With no uniform system for reporting coronavirus-related deaths in the United States and a continued shortage of tests, some states and counties have improvised, obfuscated and at times backtracked in counting the dead.

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“We definitely think there are deaths that we have not accounted for,” said Jennifer Nuzzo, a senior scholar at the Johns Hopkins University Center for Health Security, which studies global health threats and is closely tracking the coronavirus pandemic.

Late last week, the Centers for Disease Control and Prevention issued new guidance for how to certify coronavirus deaths, underscoring the need for uniformity and reinforcing the sense by health care workers and others that deaths have not been consistently tracked. In its guidance, the CDC instructed officials to report deaths where the patient has tested positive or, in an absence of testing, “if the circumstances are compelling within a reasonable degree of certainty.”

In infectious outbreaks, public health experts say that under typical circumstances it takes months or years to compile data that is as accurate as possible on U.S. deaths. The reporting system during an epidemic of this scale is particularly strained. And while experts say they believe that virus-related deaths have been missed, the extent of the problem is not at all clear.

But as mayors and governors hold daily news conferences reporting the latest figures of infections and deaths related to COVID-19, Americans have paid close attention to the locations and numbers of the sick and dead — one of the few metrics available for understanding the new and mysterious disease threatening their communities.

Public health experts say that an accurate count of deaths is an essential tool to understand a disease outbreak as it unfolds: The more deadly a disease, the more aggressively authorities are willing to disrupt normal life. Precise death counts can also inform the federal government on how to target resources, like ventilators from the national stockpile, to the areas of the country with the most desperate need.

For families who have lost a loved one in the midst of this epidemic, there is an urge simply to know: Was it the coronavirus?

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Lingering Questions

As the coronavirus outbreak began sweeping across the country last month, Julio Ramirez, a 43-year-old salesman in San Gabriel, California, came home from a business trip and began feeling unwell, suffering from a fever, cough and body aches. By the next day, he had lost his sense of taste and smell.

His wife, Julie Murillo, took him to an urgent care clinic several days later, where he was so weak he had to be pushed in a wheelchair. Doctors prescribed antibiotics, a cough syrup and gave him a chest X-ray, but they did not test for the coronavirus, she said. Just over a week after he returned from his trip and not long after President Donald Trump declared a national emergency over the outbreak, Murillo found him dead in his bed.

“I kept trying to get him tested from the beginning,” Murillo said in an interview. “They told me no.”

Frustrated, Murillo enlisted friends to call the CDC on her behalf, asking for her husband to be tested for the coronavirus post-mortem. Then she hired a private company to conduct an autopsy; the owner pleaded for a coronavirus test from local and federal authorities.

On Saturday afternoon, Murillo received a call from the Los Angeles County Department of Public Health, she said. The health department had gone to the funeral home where her husband’s body was resting and taken a sample for a coronavirus test. He tested positive.

A spokesman for the health department did not respond to questions about Ramirez, and it was not clear whether any systematic post-mortem testing was being conducted beyond his case.

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The work of counting deaths related to the coronavirus falls to an assortment of health care providers, medical examiners, coroners, funeral homes and local health departments that fill out America’s death certificates. Those documents typically include information on the immediate cause of death, such as a heart attack or pneumonia, as well as information on any underlying disease. In coronavirus cases, that would be COVID-19.

The federal government does not expect to produce a final tally of coronavirus deaths until 2021, when it publishes an annual compilation of the country’s leading causes of death. The data could come as early as January or as late as November of next year, based on the release date of recent years’ reports.

A New York Times tally of known COVID-related deaths, based on reports from state and local officials and tracked around the clock since late January, showed 9,164 deaths as of Sunday. On Friday, the National Center for Health Statistics, part of the CDC, began publishing preliminary estimates of coronavirus deaths, although a spokesman said that information would have a “lag of 1-2 weeks.” Its first estimate recorded 1,150 deaths, which is based on the number of death certificates that list COVID-19 as the underlying disease.

“It is not a ‘real time’ count of COVID deaths, like what the states are currently reporting,” Jeff Lancashire, a spokesman for the National Center for Health Statistics, said in an email.

But those who regularly work with death certificates say they worry that relying only on those documents may leave out a significant number of cases in which the coronavirus was confirmed by testing but not written down in the section where doctors and coroners are asked to note relevant underlying diseases. Generally, certificates require an immediate cause and encourage — but do not require — officials to note an underlying disease.

Then there are the many suspected cases.

Susan Perry, a funeral director in Virginia, said that she was told by health workers and families that three recently deceased people who were handled by her funeral home had tested positive for the coronavirus so that she and her staff could take necessary precautions with the bodies. The virus was indicated on only one death certificate.

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“This probably happens all the time with different diseases, but this is the first time I’m paying attention to it,” Perry said. “If we don’t know the numbers, how are we going to be able to prepare ourselves and protect ourselves?”

‘Now We’re Having the ‘Aha!’ Moment’

Early on in the U.S. outbreak, deaths may have been overlooked, hospital officials said. A late start to coronavirus testing in this country hampered hospitals’ ability to detect the infection among patients with flulike symptoms in February and early March. And doctors at several hospitals reported treating pneumonia patients who eventually died before testing was available, and when providers didn’t yet know the disease was circulating in their area.

“When I was working before we had testing, we had a ton of patients with pneumonia,” said Geraldine Ménard, chief of general internal medicine at Tulane Medical Center in New Orleans, a city that is now battling one of the country’s most potent outbreaks. “I remember thinking it was weird. I’m sure some of those patients did have it. But no one knew back then.”

An emergency department physician in San Francisco recalled two specific deaths that were likely caused by the coronavirus but that were not identified as such at the time. One patient died at home; a family member who lived in the same home later tested positive for the virus. Another patient was an older man who came to the hospital with typical coronavirus symptoms and who had been in contact with someone recently traveling to China but arrived at the hospital before testing was available.

In New York City, where the health system is battling the country’s worst outbreak, emergency medical workers say that infection and death rates in the city are likely far higher than what is being reported. Given a record-high number of calls, many ambulance crews have encouraged anyone who is not critically ill to stay home. The result, medics say, is that many presumed coronavirus patients may not ever know if they actually had the virus, so anyone who later dies at home may never be formally categorized as having had it.

Across the country, coroners are going through their own process of reevaluation, questioning the official death count and reconsidering certain deaths that occurred before testing was widely available in the United States. Coroners and medical examiners in the United States generally investigate deaths that are considered unusual, result from accidents or suicides, or occur at home.

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Joani Shields, the coroner in Monroe County, Indiana, said she has wondered about a man who was diagnosed with pneumonia in her county and died in early March.

A coronavirus test was requested at the time, but the local health department denied it, saying the supply of the tests was too limited.

“I wish we could have tested him,” she said. “A month ago, should we have been testing all these people who had pneumonia and COVID symptoms? I think we should have. But the tests weren’t available.”

In Shelby County, Alabama, Lina Evans, the coroner, said she is now suspicious of a surge in deaths in her county earlier this year, many of which involved severe pneumonias.

“We had a lot of hospice deaths this year, and now it makes me go back and think, wow, did they have COVID? Did that accelerate their death? I question all of that,” she said.

It is too late now to find out whether those patients’ deaths were related to the coronavirus. But Evans, who is also a nurse, is frustrated that she will never know.

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“When we go back to those deaths that occurred earlier this year — people who were negative for flu — now we’re having the ‘aha!’ moment,” she said. “They should have been tested for the coronavirus. As far as underreporting, I would say definitely.”

Disparate Reporting, More Waiting

Even now, as coronavirus deaths are occurring each day by the hundreds and testing is more widely available, there is a patchwork of standards about information being reported by state and local health officials on deaths. Uncertainties and inconsistencies about the numbers have quickly emerged.

Health departments have had to backtrack on cases of previously reported deaths. In Florida, the state rescinded its announcement of a COVID death in Pasco County. In Hawaii, the state’s first announced coronavirus death was later recategorized as unrelated to the coronavirus after officials admitted misreading test results. And in Los Angeles, county officials announced that a child had died from the virus, then said they were unsure whether the virus caused the death, then declined to explain the confusion.

Adding to the complications, different jurisdictions are using distinct standards for attributing a death to the coronavirus and, in some cases, relying on techniques that would lower the overall count of fatalities.

In Blaine County, Idaho, the site of a growing outbreak, the local health authority requires a positive test in order to certify that a death is the result of coronavirus. But in Alabama, also the site of a significant cluster, the state health department requires a physician to review a person’s medical records to decide whether the virus was actually the root cause of death.

“This is in the interest of having the most accurate and most transparent data that we can provide,” said Karen Landers, a district medical officer with the Alabama Department of Public Health. “We recognize that different sites might do it differently.”

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So far, the state has received reports of 45 people with the coronavirus dying but has certified only 31 of those deaths as a result of the virus.

Experts who study mortality statistics caution that it may take months for scientists to calculate a fatality rate of the coronavirus in the United States that is as accurate as possible.

Yet some researchers say there may never be a truly accurate, complete count of deaths. It has happened before. Experts believe that widespread news coverage in 1976 of a potential swine flu epidemic — one that never materialized — led to a rash of deaths recorded as influenza that, in years prior, would have only been categorized as pneumonia.

“We’re still debating the death toll of the Spanish flu,” said Stéphane Helleringer, associate professor at the Johns Hopkins University Bloomberg School of Public Health. “It might take a long time. It’s not just that the data is messy, but because the effects of a pandemic disease are very complex.”