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IntroductionThe Laboratory Virology and Serology (LabVISE) Reporting Scheme is a passive surveillance scheme based on voluntary reports of infectious agents contributed by virology and serology laboratories around Australia. LabVISE provides information on a number of viruses and other infectious agents and basic demographic information of persons they infect.
In 1959 a group of virologists met to exchange information on viruses circulating in Victoria. Between 1962 and 1968 the group, which expanded to include virologists from other states, reported their findings quarterly in the Medical Journal of Australia. In 1975, the Commonwealth Department of Health in collaboration with virology laboratories, established the 'Virus Reporting Scheme', which was replaced in 1977 by the 'National Pathogen Reporting Scheme'. This scheme, consisting of 6 laboratories, sent data to the Commonwealth, which published the data in a fortnightly bulletin called the National Microbiological Laboratory Reporting Scheme. This scheme was replaced in 1992 by two parallel reporting schemes: Laboratory Database of Organisms from Sterile Sites (LabDOSS) and LabVISE. While LabDOSS collected data on bacterial and fungal infections, LabVISE collected data on pathogens diagnosed by virology and serology laboratories.
Meanwhile, a national database of communicable diseases was established in 1991 in the form of National Notifiable Diseases Surveillance System (NNDSS). The NNDSS, operating under the auspices of the Communicable Diseases Network Australia, reported on 49 diseases in the period 1991 to 2000. Several of these diseases were also reported by sentinel laboratories in LabVISE in the same period. In 1995, the laboratory schemes were reviewed and LabDOSS was discontinued, while LabVISE was simplified. There was a reduction in the number of pathogens under surveillance by LabVISE, primarily by removal of reports of hepatitis B and C isolations, which were being reported through the NNDSS. In addition, there was a reduction in the details collected on each isolate to a minimal dataset.
The National Communicable Diseases Surveillance Strategy (1996) recommended the strengthening of laboratory networks and collaborations between laboratories and epidemiologists. LabVISE was evaluated in 1999 and three options were presented to the Public Health Laboratory Network (PHLN). Of the three options, PHLN endorsed the retention and development of LabVISE as a broad based surveillance scheme with clear objectives and a feasibility study to assess additional uses of laboratory generated data and the possibility of real-time data transfer to state public health units and the commonwealth.
This report is the first assessment of data collected by LabVISE since 1996. LabVISE data for 1999 and 2000 were reported as part of the Australia's Notifiable Diseases Status reports for those years.1 In this report, we review data collected since 1991 using the current list of organisms and data fields and compare LabVISE data with other data sources such as NNDSS (where applicable).
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Materials and methods
Data collection and reporting laboratoriesThe LabVISE database contains over 645,000 records of infectious disease collected since 1982. Records include those previously collected by the 'National Pathogens Reporting Scheme' (1982-1992).
Data are reported to LabVISE as paper reports or electronic format. Electronic reporting by diskettes has been replaced more recently by e-mail. Over time, almost all laboratories have changed to report by e-mail although a few still rely on paper reports.
In 1999, the database was changed from a 'Focus mainframe' database to a 'MS Access' format to comply with year 2000 requirements. The Department of Health and Ageing had previously developed an Epi Info based data entry system to allow laboratories to enter and send data to LabVISE. This data extraction package was provided free of charge to contributing laboratories on request. In 1999, this system was replaced by the MS Access based system, 'LabData'.
In 1997, the LabVISE database was simplified by the removal of 12 fields (containing information on risk factors, clinical outcome, sources of clinical sample, methodology details and serogroup results). The data fields collected in LabVISE throughout the study period are shown in Table 1. Four fields are designated as mandatory and must be completed for a record to be accepted into the database.
Table 1. Data field names and descriptions used in LabVISE, 1991 to 2000
|Lab code||Unique 3-digit identification code for the sending laboratory||Mandatory|
|Lab ID||Unique patient identifier||Mandatory|
|Collection date||Date specimen was collected||Mandatory|
|2x2 identifier||Identifier composed of first 2 letters of first and first two letters of family name||Not mandatory|
|Sex||Gender of patient - Male (M), Female (F) or Unknown (U)||Not mandatory|
|Date of birth||Patient's date of birth||Not mandatory|
|Age||Patient's age at date of specimen collection||Not mandatory|
|Postcode||Postcode of patients residence||Not mandatory|
|Diagnosis||Primary diagnosis, coded according to Table (Appendix 1)||Not mandatory|
|Organism||Primary organism isolated or identified in specimen (codes, Appendix 2)||Mandatory|
* Mandatory fields must be complete for acceptance of a record into the LabVISE database
In 1997 the number of organisms under surveillance in LabVISE was reduced by the exclusion of organisms such as hepatitis B and C, Neisseria gonorrhoea and herpesvirus. The organisms currently under surveillance and the totals reported between 1991 and 2000 are shown in Appendix 2. Only reports of viral pathogens, Chlamydia, Mycoplasma, and Rickettsia are analysed in this report.
The Surveillance and Epidemiology Section of the Commonwealth Department of Health and Ageing publishes reports of data from LabVISE in Communicable Diseases Intelligence (CDI). This bulletin was produced fortnightly between 1978 and September 1997, four weekly between October 1997 and March 2000, monthly between April and December 2000, and quarterly from 2001. LabVISE annual reports were published in CDI for the years 1992 to 1995,2,3,4,5 the last two of these reports are also available on the Communicable Diseases Australia Website at http://www1.health.gov.au/internet/main/publishing.nsf/Content/cda-pubs-annlrpt-labannrep.htm.
Notes on interpretationLabVISE data are difficult to interpret for a number of reasons. The representativeness of the data is uncertain, since there are no denominator data available and the reporting by pathogen has not been consistent. Although some major reference laboratories have been reporting to LabVISE, not all are represented. Laboratories from the Northern Territory have not been contributing regularly, although data from the Northern Territory are available in LabVISE via reference laboratories in other states. While public laboratories are well represented in LabVISE, larger private laboratories are not. As more pathology testing is being done in the latter in recent years, the representativeness of LabVISE becomes more uncertain. Although LabVISE data are reported by state and territory of the patient, disease rates have not been calculated. Alternative measurements such as rates of positive tests in each laboratory may be possible in the future, however, total test figures have not been available to date.
Since the number of reporting laboratories and total reports have varied over the 10-year period, we have not been able to draw conclusions about rates or outbreaks, except where independently confirmed. The quality of LabVISE data has declined over time with details of viral serotypes for example, being less complete in more recent years. This limits the ability to comment on changes in viral serotypes circulating in Australia.
Further limitations on the interpretation of LabVISE data are the lack of agreed reporting protocols for contributing laboratories and the absence of diagnostic definitions, which would standardise reporting between laboratories. Although duplicate reports are removed from LabVISE, repeat testing of the same individual for the same pathogen on different occasions are not excluded, nor are the testing of one patient for the same condition by more than one laboratory. The mix of laboratories reporting to LabVISE is heavily biased toward the reference laboratories or laboratories of major hospitals, which may bias toward the reporting of rare infections. Finally, the decision to remove data on diagnostic method data from LabVISE reporting in 1996 was regrettable as the impact of new rapid screening technologies on infections reported can not be measured. The analysis of diagnostic methods used in LabVISE reported here are representative only of the period 1991 to 1996.
This article was published in Communicable Diseases Intelligence Volume 26, No 3, September 2002
CDI Vol 26, No 3, September 2002
LabVISE, 1991 to 2000
- Contents and Abbreviations
- Abstract and Authors
- Introduction and Methods
- Part A: General results
- Part A: General results cont
- Part B: Analysis of data by pathogen