OIA25-0115
18 March 2025
Stephan Hokke
[FYI request #30166 email]
Dear Stephan Hokke
Thank you for your email of 21 February 2025, following up on your previous information
request (OIA24-0905) relating to testing for high pathogenicity avian influenza (HPAI). Your
request has been considered under the Official Information Act 1982 (OIA).
You requested the following:
I made a request earlier "Protocol and results for tests done to detect chicken flu
recently at Otago chicken farm" in which you reported that the cycle count was 45.
Yet the plateau is at about 32. So why go to 45?
My reference is:
https://assets.publishing.service.gov.uk/media/5f85c727d3bf7f633cfcbd1f/Understan
ding Cycle Threshold
Ct
in SARS-CoV-2 RT-PCR .pdf
Figure 1 on page 5 shows the plateau.
Therefore. In the recent testing for the Otago chicken farms, what would be the
result at 32 cycles?
Also, does your PCR equipment plateau the same as per figure 1 on page 5? Are
you able to run such a calibration test?
The Ct count of 45 caused me to take pause. Perhaps your machines plateau at a
higher count as per the UK govt the plateau is at about 32 so why go above that
level? I am sending a new request to ascertain that point.
I am not yet convinced that the standard you used is the actual cause of the Avian
Flu. Is there a paper that proves this by use of Koch's Postulate?
The Ministry for Primary Industries (MPI)'s Animal Health Laboratory diagnostic protocol for
Influenza A Polymerase Chain Reaction (PCR) employs a 45-cycle cut-off. This approach
has been validated to ensure high sensitivity, particularly for detecting low viral loads.
Although the Public Health England document you referenced shows a plateau around 32
cycles for SARS-CoV-2 reverse transcription (RT)-PCR assays, it is important to clarify that
the figure illustrates the stages of RT-PCR, but also includes the number of cycles, with the
cut-off in the figure being 40 cycles. This is consistent with the typical PCR cut-off range of
30-45 cycles. It is also important to note that assay characteristics, including amplification
kinetics, plateau phases, and cut-off points, are typically assay- and pathogen-specific.
Regarding your concern about establishing Influenza A virus as the cause of the disease, it is
important to note that Koch’s Postulates, while historical y significant, are not always fully
applicable to viral pathogens, particularly in the era of molecular diagnostics. Furthermore,
although these postulates have been foundational in microbiology, their application in
modern diagnostics can present both ethical and practical challenges, especially when
considering animal welfare.
Charles Fergusson Building, 38–42 Bowen Street
PO Box 2526
Wel ington 6140, New Zealand
biosecurity.govt.nz
Should you have any concerns with this response, I would encourage you to raise these with
the Ministry for Primary Industries at [email address]. Alternatively, you
are advised of your right to also raise any concerns with the Office of the Ombudsman.
Contact details are: Office of the Ombudsman, PO Box 10152, Wellington 6143 or at
[email address].
Yours sincerely
Fleur Francois
Director, Diagnostics, Readiness and Surveillance
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