New Flu Strain Expected In Upcoming Flu Season

Nation’s public health laboratories continue influenza testing at relatively high volumes

CEO SUMMARY: Public health labs continue to monitor for new cases of the A/Novel H1N1 flu, while preparing for what may be a difficult flu season this fall. Having coped with a 10-fold increase in testing volume, public health labs are assessing the lessons learned from the April/May flu outbreak. At the Association of Public Health Laboratories, activities are underway to better coordinate the services of public health labs in different regions of the country, as well as to develop contingency plans to ensure ample supplies and reagents for any future outbreak.

PUBLIC ATTENTION TO INFLUENZA A/NOVEL H1N1 MAY BE RECEDING, but public health laboratories still see a relatively high volume of flu testing as efforts continue to identify and study this new influenza strain.

“People forget that in the United States, 36,000 people die every year of seasonal influenza,” stated Rosemary Hume, Senior Advisor, Scientific Affairs, at the Association of Public Health Laboratories (APHL) in Silver Spring, Maryland. “Influenza is a serious disease whether it’s seasonal or novel. Fortunately this novel virus has so far turned out to be probably no more serious than seasonal influenza—but this strain could change over the summer. That is why close surveillance of new flu cases continues.”

The relative high volume of flu samples that continues to arrive in public health laboratories indicates that A/Novel H1N1 has not disappeared during the summer in the United States. That is one reason why public health officials believe that A/Novel H1N1 is likely to be present during the upcoming flu season, In turn, that has public health laboratories assessing the lessons learned during the initial outbreak of A/Novel H1N1, first identified in late April.

“APHL serves as the primary point of contact for the federal Centers for Disease Control and Prevention (CDC) to reach public health labs in the United States,” noted Hume. “So we were among the first that the CDC alerted to the discovery of the new influenza strain. In turn, we distributed information to our members, conducted regular conference calls, and sent email alerts to communicate new findings from the CDC to the nation’s network of public health labs.

CDC Experts

“This allowed us to bring the public health lab community together with CDC subject matter experts to discuss testing issues and to learn which states were seeing increasing demand for A/Novel H1N1 testing,” Hume continued. “During that time, we also surveyed our members on how they were doing and what they needed.

“We learned, for example, that there were backlogs in testing and, in some locations, there were shortages of supplies and reagents,” she added. “It was also quickly recognized that, given the flood of flu specimens for testing, there was an inadequate number of trained laboratory staff to meet that high demand for testing.

Shortage of Lab Staff

“Of all the limiting factors faced by public health laboratories, it was probably the shortage of staff at many facilities that limted or restricted their ability to respond in the most effective way,” noted Hume.

“In fact, one important lesson learned from this outbreak is that surge capacity is limited across the laboratory sector—in large part because clinical labs and public health labs are struggling to find enough qualified people to work in labs,” she observed. “There are workforce shortages in every sector of laboratory medicine. But public health labs have an acute staffing problem because of budget cuts in many states in recent years.

“That makes it important to have good strategies for triaging specimens, even as clinicians get good clinical guidance so they know which patients should be tested and which patients should not be tested,” continued Hume. “There will always be a demand for testing by the worried well. So every lab needs to have adequate resources—such as a rapid tests and point of care tests—and know how to use them judiciously.

Ongoing Data Collection

“We continue collecting data about this outbreak and ongoing transmission of this flu strain,” she stated. “Hardest hit by A/Novel H1N1 have been California, Illinois, Texas, and Wisconsin. But even in states that were not hit hard, there was a high demand for testing. In this way, this novel strain pandemic was quite similar to what we have seen in other outbreaks. Fortunately, we were prepared because every state could do influenza typing using the CDC’s five-target assay. Any unsubtypable specimens were sent to the CDC for confirmatory testing.

“Following the identification of A/Novel H1N1 in late April, the response of public health labs was good, in part because we have been working with the CDC on pandemic planning since about 2003,” Hume said. “Since then, important steps were taken to prepare for a novel flu outbreak or pan- demic. The focus was largely on the avian flu. But we knew we could be surprised with any strain. Therefore, much of this extensive preparation paid off during this event.

“In 2003, the CDC developed the five- target assay, which is a PCR protocol for the detection and subtyping of seasonal influenza and the H5 avian flu,” explained Hume. “It was just a test protocol; it wasn’t a kit. That test was rolled out to all the public health labs. These labs were provided training on that assay, which, for several years, served as the foundation for enhanced surveillance of the potential introduction of the novel strain. Public health labs have had ongoing training in how this assay would be used.”

Progress Since 2001

THE DARK REPORT points out that one important dimension to the public health laboratory response to the A/Novel H1N1 outbreak this spring has gone unreported by the major media. The effective response to this flu outbreak is a direct consequence of additional funding and resources that were made available to the CDC and public health agencies since 2001.

Increased funding over this decade was triggered by three events: in 2001, it was 9/11 and the anthrax attacks. In 2003, it was global concern about SARS and Avian flu. In 2009, public health laboratories were much better prepared to respond to influenza A/Novel H1N1 compared to 2003, when SARS first was detected. Also, in this latest flu pandemic, faster and more sensitive molecular testing technology made an important contribution to disease detection and epidemic control efforts.

New Molecular Testing Technology Plays Essential Role in Outbreak of A/Novel H1N1 Flu

MOLECULAR DIAGNOSTIC TESTING TECHNOLOGY proved an effective tool for rapid testing and subtyping during the recent outbreak of A/Novel H1N1 influenza.

“It only took about 12 days for the Centers for Disease Prevention and Control (CDC) to develop a test specifically for this novel strain of A/H1N1,” stated Rosemary Hume, Senior Advisor, Scientific Affairs, at the Association of Public Health Laboratories (APHL). “The CDC had it manufactured, packaged, quality-controlled, and out the door.

Flu Kits Shipped On May 1

“Those diagnostic test kits were shipped to public health laboratories on May 1,” she continued. “Our public health laboratory members were using these new test kits and reporting results during the week of May 5. To accomplish that within two weeks of the outbreak is an outstanding achievement.

“At that time, when A/Novel H1N1 was first identified, in the United States there were 36 public health labs that had both the FDA-cleared flu tests and the training to use these tests,” Hume said. “In fact, 43 states were completely ready—meaning their public health labs had been trained to use the diagnostic instruments before the outbreak. Thus was the result of a training program instituted last year on how to run the five-target assay on the Applied BioSystems 7500 Fast Dx. (See TDR, June 8, 2009.)

“Most public health laboratories in the United States had already installed the 7500 Fast Dx for use in research,” she continued. “But these instruments hadn’t yet been upgraded with the diagnostic capability. Thus, the right instrument was already in place, most lab staff had undergone previous training, and most were knowledgeable in using the FDA-cleared test. So the swine flu assay only needed to be added to the FDA-cleared five-target influenza assay.

Changed Out The Primers

“That shows the level of preparedness across the public health laboratories in this country,” observed Hume. “CDC-developed flu kits shipped out on May 1 were based on the FDA-cleared seasonal influenza test, developed primarily to detect swine flu. These updated kits used the same procedure and ran on the same equipment. CDC changed out the primers and the probes for the novel new A/H1N1strain of swine flu.

“In recent years, we’ve seen about 20 cases of swine flu annually in the United States. But it’s a different strain than A/Novel H1N1,” she said. “The strain we normally see results from human contact with hogs. It is usually a self-limiting strain and does not transmit from human to human. That is why, in the early days of this outbreak, the first question was: Is this strain a novel strain?

Ongoing Data Collection

“Back in 2007, as the CDC rolled out its five-assay influenza test, it recognized the need to provide standardized reagents. To do that, it was necessary to develop an FDA-cleared influenza test,” added Hume. “So the Association of Public Health Laboratories worked with CDC to do all of the validation studies. By October 2008, the CDC obtained clearance for the new five-target assay, which needs to be run on a PCR platform. The CDC used the 7500 Fast Dx.

“All this planning in recent years positioned public health laboratories to respond quite quickly to the emergence of the novel A/H1N1 influenza,” concluded Hume.


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