Flood of coronavirus data overwhelms Washington state’s disease reporting system, causing data lag



Even as the new coronavirus spread from cities in Washington to its small towns and rural communities, Department of Health (DOH) officials admitted on Tuesday that they were grappling with another thorny issue of the pandemic: a flood of case data overwhelms system disease reports.

As a result, public reporting of new cases of the coronavirus statewide has come to a halt. The last Washington data update posted on the DOH website on Tuesday was from lab results reported three days earlier – March 28 at midnight.

The lag, in turn, has partially blinded health officials and the public to the latest information on the spread of the disease statewide.

Washington State Health Secretary John Wiesman acknowledged that timely and accurate information is essential for formulating public health strategies, but tempered concerns about data issues and said they had not yet had a negative impact on the state’s response.

“Our team is on it. This is a top priority for us, and we understand the importance of having the data both for our use and for transparency to the public, ”Wiesman said in a telephone interview with the Seattle Times.

“But that doesn’t change our strategy or the public health actions we need to take at the moment,” he said. “Obviously we don’t want this to last very long – that wouldn’t be good. “

Wiesman and state health official Dr Kathy Lofy each said on Tuesday that the data obtained to date has given officials a solid understanding that the coronavirus outbreak has spread across the country. State, beyond the only population centers of King and Snohomish counties. Social distancing strategies, like those ordered by Gov. Jay Inslee, remain the best way to mitigate the spread, they said.

Managers usually only see meaningful trends by analyzing at least a week of data – not the roughly two days they are missing now, Lofy added. The longer data periods coincide with the incubation period of the virus, which is typically five to seven days, but can be up to two weeks.

“It’s only been Sunday, so the last two days we haven’t received [the data]”Lofy said.” Obviously that’s very important to us. But it’s the longer term trend that we’re really looking for “when making policy decisions.

“Overwhelmedd the system ”

For more than a week, late, incomplete and inaccurate data reports hampered the health department’s daily updates of coronavirus cases, leading to a constant stream of complaints in public forums, questions from journalists about numbers that do not add up and differences in the number of positive tests and confirmed cases.

Managers largely attribute the problems to a volume issue. As coronavirus testing in Washington has intensified dramatically over the past month – with 21 labs in Washington now testing patient samples – thousands of new data reports, with both positive and negative test results, have poured in. the Washington Disease Reporting System (WDRS).

The system, however, was not configured to take negative test results, Wiesman said. Before the coronavirus pandemic, the reporting system generally received “only positive results – say from someone who contracted E.coli in one county, or a case of measles in another,” he said. .

“With the coronavirus, we are now importing data from all negative tests,” Wiesman said. “At the start of the epidemic, when testing was limited, it was not a problem. But now we get as many as 6,000 to 7,000 test results – both positive and negative – every day. It sort of overwhelmed the system.

Negative results, which make up about 93% of the data, arrive without corresponding information on where those results came from, so they cannot be traced to any particular county, Wiesman said.

“Sometimes these are sent several times from the same laboratories on the same day,” he added.

Finding duplicate reports is a manual process that often requires validation of the data by local public health departments, he said. As the volume of data has grown, this manual process has significantly slowed the state’s ability to regularly update or provide complete and accurate data, Wiesman said.

“One day last week we alone had 2,000 duplicates that we had to go through by hand to make sure we had reliable numbers,” he said.

To fix the problem, the state hired Conduent, the system’s Maven software vendor, to essentially rewrite its proprietary code on the fly. The goal will be to separate positive and negative test data, possibly creating a new tool for negative cases, said Jennifer McNamara, DOH’s director of information.

Other states, notably New York, also use the same reporting system and have encountered similar challenges with complete and timely lab reports in the past, McNamara said. “We have been in contact with our colleagues in New York… (and) they have shared with us ways to minimize disruption.”

One of New York’s suggestions was to try to streamline reporting from individual labs by limiting the number and timing of their daily reports, she said.

“We hope that by tomorrow we will be able to report figures that we can be comfortable with in terms of the accuracy of the data,” McNamara said Tuesday.

Once the fixes are made, Wiesman said he expects the state to release updated data every day before 3 p.m., listing a full day of data reported the day before. The state’s latest data update reported 4,896 statewide positive cases and 195 deaths – numbers that have now been out of date for at least three days.

In addition to positive and negative test results, the state also intends to include the number of daily deaths, information on the sex and age of patients, and hospitalization data when available, a he declared.

Already, the DOH site has made several upgrades, including new visualizations showing confirmed cases, epidemiological curve, cumulative number of cases and deaths, numbers of tests and demographic information, he said. declared.

Flatten the curve

Even when the fixes are made, Wiesman noted that “every dataset has limits.”

Dr Jared Roach of the Seattle-based Institute for Systems Biology said state data is likely to have inconsistencies as it is reported daily.

For example, some confirmed cases may have been reported on the date of a positive result, while others on the day the test was taken. Some cases have been reported in the county where a patient has tested positive, while others have been reported in a county of residence.

Researchers who rely on state data incorporate that uncertainty into their models, Roach said. Scientists assessing ‘flattening the curve’, for example – evidence that social distancing and other measures slow infection rates – create an upper and lower bound that shows how many hospital beds might be needed as the pandemic progresses.

Modeling to estimate when Washington’s epidemic will peak, like that of the University of Washington’s Institute for Health Metrics and Evaluation (IHME), bases trajectories on death data, not positive or negative cases. , Lofy said. This means that the IHME model, which estimates Washington’s cases will peak around April 19, would likely not be affected by a lag in reported test scores, she said.

“Most of the people who die are probably tested for COVID-19,” she said, “so we think the tests [for deaths] is probably fairly comprehensive ‘to date, with less of a lag issue for positive and negative daily test results.

But Lofy acknowledged on Tuesday that gaps in available tests, which have haunted surveillance of the spread of the pandemic in Washington and across the United States, have hampered understanding – and continue to do so.

“We have seen a dramatic increase in the number of cases detected just recently” statewide, she said. “It’s hard to say if we are seeing an increase in COVID-19 activity or if we haven’t tested enough. So the testing capacity issues we have been grappling with certainly make it more difficult to interpret the data we have now that we have broader tests.

Reporter Mike Reicher contributed to this report.

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