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.
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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.
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