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BACKGROUND: Trends in HIV diagnoses differ across Australia and are primarily driven by men who have sex with men (MSM). We use national population surveillance data to estimate the incidence of HIV infections among MSM by jurisdiction and infer the proportion of undiagnosed infections. METHODS: Annual surveillance data for AIDS diagnoses, HIV diagnoses and recently acquired HIV infections were obtained from 1980 to 2009. A modified statistical back-projection method was used to reconstruct HIV incidence by jurisdiction. RESULTS: HIV incidence among MSM peaked for all jurisdictions in the early 1980s and then declined into the early 1990s, after which incidence increased. Trends then differ between jurisdictions. In New South Wales (NSW) and South Australia, estimated HIV incidence peaked at 371 and 50 cases respectively in 2003, and has since decreased to 258 and 24 cases respectively in 2009. HIV infections in Queensland (Qld) have more than doubled over the past decade, from 84 cases in 2000 to 192 cases in 2009. Victoria and Western Australia have seen a rise in HIV incidence from 2000 to 2006 (to a peak of 250 and 38 incident cases respectively), followed by a plateau to 2009. HIV incidence in the Northern Territory, Tasmania and Australian Capital Territory have increased since 2000; however, case numbers remain small (<20 per year). The estimated proportion of HIV infections not yet diagnosed to 2009 ranges from 10% (NSW) to 18% (Qld), with an average of 12% across Australia. CONCLUSIONS: HIV diagnosis trends among MSM in Australia reflect changes in estimated incidence to 2009, and reveal the largest increase in the past 10 years in Qld.