Lab Matters Winter 2018 - Page 8

feature Protection against influenza, circa 1918. Soldiers wearing gauze masks walk down a street in Seattle, WA. Photo: Science Photo Library H1N1 in the laboratory and in public health, generally. That’s concerning, because by most people’s measures, that was a pretty wimpy pandemic.” Since 2009, a lot has happened. Molecular, reverse-transcription polymerase chain reaction (PCR) testing for a panel of influenza viruses—with automated, real- time electronic reporting from laboratory information management systems to CDC—is now in place in all state and some local public health laboratories, plus a few US Department of Defense labs. “Still not where we should be” On a scale of 1 to 10, from unprepared to super prepared, Jernigan rates the current state of US influenza preparedness a 5. Shult rates it a “5 or 6.” But even a 5 is a vast improvement. WHO began its global influenza program in 1947. Today, the organization’s GISRS includes six major collaborating centers— including CDC and St. Jude Children’s Research Hospital in Tennessee (the only center focused exclusively on influenza ecology in animals) in the US—four regulatory laboratories responsible for verifying the potency and safety of vaccines and antivirals, and the 140 or so national influenza centers that collect virus specimens and submit them to their designated collaborating center for advanced antigenic and genetic analysis. In the United States, after a 2003 SARS scare and a 2003-2004 H5N1 “bird flu” scare, the federal government pumped new resources into infectious disease preparedness. President George H.W. Bush released the National Strategy for Pandemic Influenza in 2005 and signed the Pandemic & All-hazards Preparedness Act the next year. Also in 2005, the US Department of Health and Human Services drafted its own pandemic influenza plan, which was updated last year. 6 LAB MATTERS Winter 2018 Thanks to this focus and funding, said Jernigan, “a lot of stuff actually improved—surveillance, stockpiling of antiviral drugs, the beginning of making ‘pre-pandemic’ vaccines against viruses like H5N1, improvements in incident response management.” Among other things, CDC funded APHL to begin an ambitious project helping public health laboratories institute real-time, electronic influenza rep orting to CDC. And, in 2008, CDC awarded a contract to establish the Influenza Reagent Resource (now the International Reagent Resource), through which authorized users worldwide can access influenza test reagents at no cost via a web storefront. Many of these activities were still ramping up when—with all eyes looking to the East for threats like SARS and H5N1—the 2009 A(H1N1) virus made a surprise entry into the US via Mexico. It didn’t matter; the laboratory-based surveillance system worked. The Naval Health Research Center in San Diego identified the first two cases of the virus, and the San Diego County Public Health Laboratory identified the next three. But while the response to that pandemic is considered a success, it clearly taxed the public health system. Shult said, “We had four to six years planning before the 2009 pandemic and we had PCR [in about 18 state labs]. But for a two-to-three-month period, we were running to our very max to deal with In 2010, APHL and CDC established three National Influenza Reference Centers (NIRCs): the Wisconsin State Laboratory of Hygiene, New York’s Wadsworth Center and the California Public Health Laboratory. These centers fill three critical roles: • Centralization of costly and complex viral culture, as well as drug susceptibility testing and other specialized work on cultured isolates. “It made sense to centralize viral culture in reference labs and get the public health laboratories focused on state-of-the-art PCR methods, which are hands down the most sensitive and specific method for flu diagnostics and subtyping [and don’t require culture],” explained Shult. • Since 2015, centralization of next- generation sequencing on the original clinical specimens, with raw data feeds coming off laboratory instruments straight to a processing pipeline on the APHL Informatics Messaging Services platform for cloud-based analysis. Viral genomes are then made available to data submitters, as well as CDC bioinformatics staff in Atlanta. “That has transformed the amount of information we’re able to get on influenza viruses throughout the [flu] season,” said Jernigan. • Provision of viral isolates to CDC so the agency can perform further antigenic characterization and grow the candidate viruses for the next season’s flu vaccine. PublicHealthLabs @APHL