Pandemic Influenza Plan - Questar III

Section 2: Surveillance and Laboratory Testing
submissions were received from physicians in 39 counties.
o Outbreak investigations. The Wadsworth Center laboratory works closely with
epidemiologists in the NYSDOH and NYCDOHMH to detect and type respiratory
viruses in reported outbreaks, especially in nursing homes.
o Suspect cases of avian influenza or other novel influenza virus. The
Wadsworth Center will conduct appropriate testing and send samples to the CDC,
as necessary, for additional or confirmatory testing on patients suspected of
infection with avian influenza.
o Reference function. Wadsworth Center regularly receives influenza isolates from
commercial and hospital laboratories that do not have sub-typing capability.
• Diagnostic assays that will be used on samples received from NYS patients
Two procedures will be performed in parallel on incoming original diagnostic
samples.
1. A real-time RT-PCR assay for detection of influenza A and influenza B
viruses will be performed on the original sample. The assay will detect
influenza A, H1 and H3 sub-types. Based on an analysis of sequences
currently stored in public databases, other influenza A sub-types, such as
A/H5N1, should also be detected, but identification of these viruses has not
yet been validated in this assay. The result will be available in 24 to 72 hours
depending on the sample load that the laboratory is experiencing.
2. Again, depending on the sample load and on the history obtained with the
sample, the original specimen will be inoculated into three cell types that
support replication of respiratory viruses and appropriate reflex testing will be
performed. The result will be available in 4 to 14 days depending on how
readily the virus grows in cell culture.
o If the sample is from a patient who has a history of travel to an area where the
avian influenza virus is endemic, the sample will not be inoculated into cell
culture. The real-time RT-PCR detection assay will be performed and if the
presence of an influenza A virus is confirmed, sub-typing will be attempted on the
original sample using H1-, H3- and H5- and H7-specific assays. Additionally, a
portion of the original sample will be sent to CDC for confirmatory testing. If an
H5 influenza virus is shown not to be present, the sample will be inoculated into
cell culture.
o Once the isolate has been amplified in cell culture and has been confirmed as
influenza virus, sub-typing of the hemagglutinin (HA) and neuraminidase (NA)
genes will be performed using conventional RT-PCR if subtyping has not already
been achieved on the original sample. The sub-typing result will be available in
10 to 21 days depending on how well the isolate grows in cell culture and on the
February 7, 2006 2-14