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Oahpp daily laboratory surveillance report template

Ontario Agency for Health Protection and Promotion (OAHPP):
Laboratory Viruses Respiratory Surveillance Report
Information current as of: Monday June 21, 2010
This report summarizes patient specimens (1 specimen/patient) collected and received at the Ontario
Agency for Health Protection and Promotion (OAHPP) public health laboratories (PHL) in Ontario for
influenza virus testing since September 1, 2009. This information is current as of Monday June 21, 2010
and is updated weekly. Note that influenza A positivity rates are only reported for influenza A tests
performed at the OAHPP Public Health Laboratories.
This report uses the specimen collection date to classify the specimens submitted. The PHL performs the
majority of subtype testing; however, several hospital laboratories also perform subtyping. Therefore, the
numbers reported here may not reconcile precisely with those reported through the integrated Public
Health Information System (iPHIS) since results from hospital laboratories may be entered into iPHIS
without being entered into the PHL database.
Pandemic influenza (pH1N1) is virtually absent in Ontario with the most recent Flu A/(pH1N1) positive
sample collected on May 19, 2010 in York Region. A Flu A/ (H3) positive sample was also collected
on May 19, 2010 in Toronto. The most recent influenza B sample was collected on March 24, 2010.
Low levels of parainfluenza viruses (PIV), adenovirus and respiratory syncytial virus (RSV) are
circulating in Ontario.

Case statistics:
Between September1, 2009 and June 21, 2010, a total 28,162 patient specimens and isolates (1/patient)
have been submitted for influenza testing and subtyping at the PHL and entered into the PHL electronic
system. Of those, 27,506 specimens and isolates have been tested for influenza A at the PHL, of which
5,043 (18.3%) were positive for Influenza A; an additional 487 patient specimens that tested positive for
influenza A at hospital laboratories were forwarded to the PHL for subtyping.
Five cases of seasonal influenza (H3) have been detected in Weeks 36, 37, 52, 2009, and Week 2 and
20, 2010. No seasonal influenza A H1 has been detected. Eight cases of influenza B have been
detected: one each in Week 40 of 2009 and Weeks 2, 8, 9, 10 and 12 of 2010, and two in Week 43 of
Please refer to Appendix 1 for further information on lab testing algorithms and interpreting subtyping

Figure 1. Total number of influenza A tests conducted, the number of influenza A positive cases and the
percent positive (5 day rolling average), September 1, 2009 – June 14, 2010**.

T T V V V V V V C C C C C C N N N N N N B B B B B B R R R R R R R R R R R R Y Y Y Y Y Y N N N O O N N N N N N D D D D D D JA JA JA JA JA JA FE FE FE FE FE FE M M M M M M A A A A A A M M M M M M JU JU JU Specimen collection date (DD/MM/YYYY)
Source: The Ontario Agency for Health Protection and Promotion (OAHPP) public health laboratories.

Figure 2. The number of positive influenza A test results by subtype (pH1N1, seasonal
H1/H3,indeterminate pH1N1 Influenza A - not subtyped & influenza B), September 1, 2009 – June 14,

Specimen collection date (DD/MM/YYYY)
Source: The Ontario Agency for Health Protection and Promotion (OAHPP) public health laboratories. For 1,567 specimens, no
specimen collection date was available; the date the specimen was received at the lab has been used as a proxy. **Data
collected since June 15, 2010 has been excluded from Figures 1 and 2. Since not all specimens collected on those dates have test
results available, the data from those days may not reflect the current situation.  Modification to testing algorithm
Resistance testing
A proportion of isolates undergo oseltamivir susceptibility testing, specifically looking for a nucleotide
mutation at position 275 for tyrosine (H275Y) in the neuraminidase gene, which confers resistance.
Table 1: PHL oseltamivir susceptibility testing results since September 1, 2009.

Total number of
Collection date of first
Isolate tested
Total tested
Total Positive (%)
resistant isolate
Source: The Ontario Agency for Health Protection and Promotion (OAHPP) public health laboratories. Nationally oseltamivir, amantadine and zanamivir susceptibility testing is conducted at the National Microbiology Laboratory (NML). Table 2: NML susceptibility assay results for influenza isolates in Canada from September 1, 2009 – May 6,

Isolates tested
Isolates tested
resistant to
resistant to
tested for
resistant to
Isolates tested
for Oseltamivir
for Amantadine
Influenza A

Influenza A

Influenza B

Influenza A

Source: Influenza and Respiratory Viruses Section, National Microbial Laboratory, Public Health Agency of Canada. Table 3: NML strain characterization of isolates from Ontario and Canada from September 1, 2009 to May
5, 2010.

Seasonal Influenza A (H1N1)
Seasonal Influenza A (H3N2)
Seasonal Influenza B
Pandemic Influenza A (H1N1)
Source: Influenza and Respiratory Viruses Section, National Microbial Laboratory, Public Health Agency of Canada. Note: Pandemic (2009) H1N1 vaccine component: A/California/07/2009 Seasonal influenza vaccine for 2009/2010: A/Brisbane/59/07-like (H1N1 component), A/Brisbane/10/2007-like (H3N2 component), B/Brisbane/60/2008-like (influenza B component).For the season to date, the vast majority of circulating influenza was the pH1N1 strain. However, of the seasonal influenza strains that circulated in Canada, most of the H3N2 subtype has drifted from the 2009/10 H3N2 vaccine component. Table 4: Influenza and other circulating respiratory viruses among influenza Vaccine Effectiveness (VE)
study specimens May 30 to June 19, 2010.

Detected viruses
Number of specimen submitted
Public Health Unit

Total number of positive specimens

Total number of specimens tested

Additional information on the VE study can be found at
Ontario Public Health Units

At the PHL, a patient is sorted into a public health unit (PHU) based on their place of residence. If this
information is not available, the address of the physician who submitted the sample is used to classify
patients into PHUs. As a result, influenza A cases may not necessarily be residents of the PHU in which
they have been classified.
Appendix 1
Changes to Testing Algorithm:

Due to technical changes made to the data extraction process, results, may differ slightly from those presented in the previous reports. All limitations on ambulatory (community) viral culture requests and influenza A subtyping have been removed. Viral culture testing was increased to all ambulatory samples and a minimum of 20% of influenza A negative RT-PCR tests. Viral culture testing increases as resources allowed. Subtyping was increased as resources allow. Only 20% of ambulatory (community) viral culture requests were being processed. Subtyping was performed on all intensive care samples, outbreak samples and on 20% of all additional influenza A positive tests. For additional details on modifications to the testing algorithm, please view the November Labstract at
Interpretation of subtyping results:

Indeterminate: a RT-PCR test reflects a very low level of the target (e.g. influenza, or influenza
subtype). Due to the level of target being near the threshold of detection it is not known if this is
a true positive result, or nonspecific activity giving a false positive response.
Untypeable: occurs when an influenza A is detected, but the sample does not match any of the
subtypes that can be tested for (e.g. pH1N1, seasonal H3N2, H1N1).
Unable to subtype: occurs when influenza A positive sample has a very low amount of virus and
the subtype cannot be detected.

A reference calendar of epidemiological weeks can be found at

This report and past versions are available on our website and can be viewed at anytime at


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