Teamwork Between Labs Helped NYC Flu Response

City’s public health laboratory worked closely with hospital labs to handle A/Novel H1N1 testing

CEO SUMMARY: Shaped by the experiences of 9/11 and the anthrax outbreak in 2001, the New York City Department of Health and Mental Hygiene revised and improved its preparedness plan. With the outbreak of influenza A/Novel H1N1 this spring, the Public Health Department benefited from effective collaboration with area hospitals and commercial laboratories. The public health laboratory, although testing as many flu specimens in a day as it typically tests during one year, kept pace with the incoming sample flow and provided timely results to health officials.

WHEN CLINICAL LABORATORIES WANT to assess the lessons learned from the recent outbreak of A/Novel H1N1 influenza, a good starting point is New York City, for two reasons.

One, it was among the first regions in the United States to confirm positive cases of A/Novel H1N1. Two, as a densely-populated urban environment and transportation hub, its experience in responding to these types of outbreaks offers many useful insights. In particular, the collaboration between the New York City Health Department and the city’s hospitals and commercial labs during the A/Novel H1N1 outbreak was quite effective.

“New York City certainly is a place in which congregate settings are a way of life,” explained Sara T. Beatrice, Ph.D., the Laboratory Director and Assistant Commissioner of the city’s Department of Health. “A large percentage of people commute on buses and subways and live in multi-dwelling housing units. Our citizens recreate in smaller areas with more people involved to higher degree than most other cities.

“We have a detailed pandemic influenza preparedness plan,” she added. “It calls for a highly organized system of outreach between the Department of Health and the medical community, the city’s hospitals, and commercial laboratories.

“Accordingly, while our public health laboratory experienced a much higher level of testing demand for A/Novel H1N1 during the outbreak, we also had a level of samples that we could manage,” said Beatrice. “We believe our preparedness plan played a role in containing the level of samples we tested.

Surveillance Testing

“Based on our experience with similar outbreaks, we have learned that when a new cluster is identified, the number of samples taken should be the minimal number to indicate that it is or is not a true cluster,” Beatrice noted. “In this way, our approach was unlike that of many parts of the country—where anyone who presented had a sample collected and tested. Our approach is to have much more focused testing.

“It is important that the response plan evolves over the course of an event, meaning the questions that we want to answer at the very beginning may be different than the questions that we want answered two weeks later,” continued Beatrice. “In New York City, the first question to answer was: Is the pathogen here? The next questions are: Is it in a congregate setting? Is it severe? Is there community transmission?

Lessons Learned from 9/11

“Our experience with anthrax in New York City in 2001 taught us the importance of reducing the wave of samples that can swamp the public health laboratory,” stated Beatrice. “The anthrax event generated a huge number of samples from individuals who had no probable cause. When that happened, the anthrax-tainted letters that had been sent to NBC News and ABC News were stuck in the middle of that massive deluge of inappropriate submissions that came into our lab.

“That experience taught us that it actually takes longer to answer the important questions and to get the testing done on the critical samples when you test every sample,” she said. “That’s why, despite the pressures from the emergence of A/Novel H1N1, the people involved in this event could stay focused and perform the testing at an appropriate and manageable level.

Cooperation Required

“In order to do as well as we did, we had to have good cooperation from hospital labs and we got that cooperation because we have an excellent network of sentinel labs here,” observed Beatrice. “This was a lesson we learned after 9/11 and the anthrax outbreak. There was a clear need to strengthen the relationship between the public health laboratories, hospitals, and commercial laboratories.

“Each year we offer different types of training and outreach to hospitals and laboratories,” added Beatrice. “We know all the lab directors and supervisors. During the A/Novel H1N1 outbreak, those established relationships made it easier for us to set up conference calls with various hospital labs to review how best to collect and transport flu samples to the health department.”

That communication was an important part of the success of the outreach between the city Health Department and the hospitals and commercial labs. The Bureau of Communicable Diseases had daily conference calls with the hospitals in all five boroughs.

This response was appropriate given that the worried well were streaming into hospital emergency departments in large numbers. Daily interaction with hospitals to review protocols helped the public health labs meet this demand. “This was also the channel we used to craft the public information message,” said Beatrice. “The worried well needed to know what to do and what not to do. With most mild cases of the flu, the appropriate thing is to stay home and not go to an emergency department and spread that virus further.

“Our heaviest test volumes for A/Novel H1N1 were between April 21 and June 19,” Beatrice recalled. “The level of testing for that period peaked at about 100 A/Novel H1N1 tests a day when normally we run about 100 flu tests a year.

“During this event, our flu laboratory was dedicated to looking at clusters in congregate settings, such as schools and in hospitalized cases that met the case definitions,” she noted. “The number of samples that we tested was small in part because of the frontline testing performed by hospital labs and commercial labs.

Lab Surveillance System

“Initial discussions about A/Novel H1N1 began when we saw what was happening in Mexico, California, and Texas during the week of April 20,” Beatrice stated. “We initiated an active lab surveillance system through our Bureau of Communicable Disease outreach with numerous hospital laboratories in the five boroughs. The outreach goal was to communicate that, when hospital labs had cases of individuals who were ill and had tested positive on the rapid assay for influenza A, we wanted to receive those specimens so that we could test them for potential subtyping.

“Those first samples came in the evening of Friday, April 24,” Beatrice continued. “At the same time our first cluster was occurring at a high school in Queens, where a large number of students presented with flu-like illness. A batch of those samples arrived that same evening. Lab staff, who had already worked their full week, stayed over to test these specimens. They didn’t finish and leave the lab until 2 a.m. on that Saturday, April 25.

“From that day forward, it was a very heavy schedule for about two months,” she added. “We worked seven days a week, starting as early as 6 a.m. and finishing at 2 a.m. the next morning. It is only now beginning to slow down.

Seeing Spikes in Demand

“Demand for influenza testing was heavy for the first two weeks and then after the first couple of weeks, there was a slow-down, which is what happens if you look at a transmission graph,” she said. “For one or two weeks, we had no weekend work. But then the samples started rolling in again and we worked weekends up until about the middle of June. Over the week- end of June 20 and 21 we did not work and the weekend of June 13 and 14, we worked on Saturday but not Sunday. That workload shows that A/Novel H1N1 was a more protracted event here than it might have been elsewhere.

“Our public health laboratory is staffed with about 200 people. A team of 40 people performed A/Novel H1N1 testing. They were rotated on a seven-day sched- ule,” Beatrice said. “Some did testing. Some triaged samples and some worked the databases. Others prepared summary reports to help us push out information to various parts of the city government, along with the hospitals and doctors.”

The speedy and effective response of public health officials to the outbreak of A/Novel H1N1 in New York City required effective collaboration with hospital laboratories and commercial labs in the region. Because of prior planning and education, the New York City public health laboratory was able to stay up with the incoming flow of influenza specimens that required testing.

New York City Experienced A/H1N1 Cases and Deaths

TO DETERMINE THE LEVEL OF flu illness in New York City, the Health Department conducted a household survey in the first three weeks of May. The survey results showed that some 6.9% of New Yorkers experienced flu-like illness between May 1 and May 20. “The findings don’t tell us exactly how many New Yorkers have had A/Novel H1N1 influenza,” said Health Commissioner Thomas Farley, M.D. “But they suggest it has been widespread, and mild in most affected people.”

Since late April, 804 New Yorkers have been hospitalized with A/Novel H1N1 flu, and 32 deaths have been linked to the virus. Even with the survey, it was not clear what proportion of residents with flu-like illness had the A/Novel H1N1 virus, but the evidence suggested that A/H1N1 has spread widely in the city, Farley said. In fact, the peak period of A/Novel H1N1 activity may have occurred after the survey was completed.

As reported by the Centers for Disease Control and Prevention (CDC), through Friday, June 26, there have been 27,717 confirmed cases of A/Novel H1N1 influenza and 127 deaths in the United States. Confirmed A/Novel H1N1 cases have been reported in all 50 states, plus Puerto Rico and the U.S. Virgin Islands.


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