Information on data analysis for GB quarterly livestock and wildlife disease surveillance and emerging threat reports
Updated 2 December 2019
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GB quarterly disease surveillance and emerging threat reports for livestock and wildlife are published on GOV.UK.
Information in the Veterinary Investigation Diagnosis Analysis (VIDA) database is sourced from the APHA FarmFile and SRUC Veterinary Services Laboratory Information Management System (LIMS) databases. Diagnoses in these comply with agreed diagnostic criteria against which regular validations and audits are undertaken. Data recording by APHA and SRUC Veterinary Services was harmonised from 2007.
The expertise in disease investigation and comprehensive diagnostic laboratory facilities of APHA, SRUC Veterinary Services and partner post-mortem providers are widely acknowledged, and unusual, severe or unresponsive disease issues tend to be referred to the GB scanning surveillance network.
However recognised conditions where there is either no diagnostic test, or for which a clinical diagnosis offers sufficient specificity to negate the need for laboratory investigation, are unlikely to be represented. The report may therefore be biased in favour of unusual incidents or those diseases that require laboratory investigation for confirmation. APHA and SRUC have UKAS accreditation which complies with ISO 17025.
From September 2014, APHA contracted the additional services of partner post-mortem providers. From April 2015, these services were provided by the Royal Veterinary College, the University of Bristol, University of Surrey, Wales Veterinary Science Centre and SRUC Veterinary Services. These providers form part of the GB scanning surveillance network and contribute to the data recorded on the APHA FarmFile database. To achieve a VIDA diagnosis, all testing must be carried out by a laboratory with ISO 17025 accreditation.
The quarterly GB surveillance reports include analysis of disease data from the GB scanning surveillance network in relation to samples submitted in the relevant quarter of the year compared to the previous quarters and years. It aims to identify emerging or re-emerging disease related threats, including changes in endemic disease trends. The report includes a horizon scanning component describing potential threats identified outside GB. Further information can be found on the APHA Vet Gateway.
New and re-emerging diseases and threats
Detection of new and re-emerging diseases and threats (NRT) is a primary aim of government-funded scanning surveillance. NRT are diverse in nature; the most obvious being novel or notifiable diseases, or exotic diseases not detected currently in GB. However, NRT could also be a new strain of a pathogen already in GB; a new, rare or unusual antimicrobial resistance; a disease in animals with a public health concern (for example, zoonoses, toxicities) or a change in trend in an endemic disease. Submissions are particularly encouraged from disease outbreaks which are unusual, severe or unresponsive to treatment/control. As part of surveillance for NRT, submissions for which no diagnosis is reached (DNR) despite reasonable testing are regularly analysed in VIDA to detect increases in undiagnosed submissions which could indicate the presence of a new or emerging disease. Undiagnosed disease submissions are grouped broadly by the clinical presentation of disease and the body system affected. Quarterly trends in DNR are compared over time for both groups and significant increases in DNR are investigated by the Species Expert Group, alongside investigation of cases causing concern.
Statistical analysis of APHA DNR data is undertaken using an early detection system (EDS). This uses a statistical algorithm to estimate an expected number of DNR reports and a threshold value. If the current number of DNR reports exceeds the threshold (i.e. exceedance score>1), this indicates that the number of reports is statistically higher than expected. When this EDS identifies categories of submissions where the threshold DNR has been exceeded, the Species Expert Group reviews the data to investigate further. This review may involve assessment of individual DNR submissions. Where this DNR analysis finds no evidence of a new and emerging threat or other issue, the detail of these reviews in response to thresholds being exceeded is not likely to be reported.
Changes in disease patterns and risk factors
This section of the reports gives information on occurrence of selected diagnoses, or groups of diagnoses, recorded in VIDA. Disease trend charts, where shown, indicate the number of diagnoses (numerator) as a proportion of the number of submissions in which that diagnosis was possible (denominator) expressed as % diagnosable submissions and data is analysed for all of GB, England & Wales and for Scotland. Bars on charts indicate the 95% confidence limits. Note that the y-axis of the charts varies and therefore care must be taken when comparing individual charts.
Last updated: November 2019