Molecular Epidemiological Approaches Could Support HIV Prevention

The national HIV prevention strategy in Australia could be helped through the use of community support and molecular epidemiological approaches, according to a study published in The Lancet Regional Health – Western Pacific.¹ HIV transmission may see a decrease through the use of these methods.

Prevention and management of HIV has been a focus for Australia through their high treatment coverage for people living with HIV (PLWH). This includes widespread uptake of pre-exposure prophylaxis (PrEP), ways to obtain antiretroviral therapy for free in Victoria,² and access to self-testing for HIV. However, there are still challenges with further decreasing the incidence and transmission of HIV, especially in the indigenous groups of Australia. Contact tracing is a key strategy in preventing further transmission of HIV and can be strengthened through molecular epidemiological analyses.

The study aimed to apply molecular epidemiology and related models to a collection of HIV-1 pol gene sequences to reveal HIV transmission patterns that could help inform public health responses.

Plasma samples from patients who have HIV are forwarded to public health laboratories for genotyping as part of routine care for all new HIV cases. This study included samples from Victoria between January 1, 2000, and December 31, 2020. Year of diagnosis, initial CD4+ T-cell count, and exposure risk group were also available in the Victorian Department of Health. Each sample had a contiguous HIV pol sequence generated, and sequences with more 5% or more ambiguous bases were excluded.

Samples from patients who were 18 years or older at diagnosis, had complete and available data, and who were diagnosed in Victoria were included in the analysis. Molecular transmission networks were constructed using HIV-TRACE. The effective reproductive number was estimated using a Birth Death Skyline Serial model and was presented as a median of the posterior distribution.

A total of 5303 new HIV notifications in Victoria. An available HIV-1 pol sequence was found in 3507 of the individuals and were therefore included in the study. A total of 92.0% of the included individuals were men and the exposure risk group was male-to-male sex, which made up 78.6% of cases. Most of the HIV-1 pol sequences (86.1%) came from patients from 2005 and after. The majority of the included patients were born in Australia (63.9%).

Common subtypes or circulating recombinant forms (CRF) were identified. A subtype or CRF was identifiable in 92.9% of the sequences (95% CI, 92.0%-93.7%). The majority of identifiable sequences were subtype B (71.4%; 95% CI, 69.8%-72.9%), followed by CRF01_AE (16.1%; 95% CI, 14.9%-17.4%), then subtype C (8.5%; 95% CI, 7.6%-9.5%).

There were 359 molecular transmission groups identified through HIV-TRACE, which spanned from 2 to 301 individuals. The exposure risk group for individuals was primarily male-to-male sex (84.8%), with injecting drug use an exposure risk in a specific group (53.1%). Another large group also found male-to-female sex as a risk factor (42.9%), though this group only had 21 members. These 2 last groups had a place of acquisition more frequently cited as overseas (31.7% and 41.2% respectively).

Subtype B was the HIV-1 subtype or CRF most commonly observed in 14 of the 18 transmission groups. Patients were more likely to be part of a transmission group if they were men (adjusted OR [aOR], 1.50; 95% CI, 1.05-2.15), were born in Australia (aOR, 2.13; 95% CI, 1.80-2.53), had injectable drug use as a listed exposure (aOR, 2.13; 95% CI, 1.18-4.02), or had a place of acquisition of Victoria rather than overseas (aOR, 6.73; 95% CI, 5.40-8.41). When limited to diagnoses that came after 2018, when PrEP became more widely available, these associations between individuals that were part of a molecular transmission group increased for those born in Australia (aOR, 3.09; 95% CI, 2.03-4.73), if the place of HIV acquisition was in Victoria (aOR, 11.93; 95% CI, 6.75-21.97), and if injectable drug use was a listed exposure (aOR, 3.87; 95% CI, 1.06-19.30).

There were some limitations to the study. It depended on linkage to care to include sequences, which could have underrepresented some groups of people in Australia. All sequences were assumed to be from patients who had not been treated or had recently started treatment for HIV, but it is possible that the positive test came after a previous positive test, and therefore a patient could have been receiving treatment. Small transmission groups could not be analyzed for phylodynamic trends. Additionally, whole genome sequencing was not used but could be the focus of future studies.

The researchers concluded that molecular epidemiological approaches could help to prevent HIV, as it can determine those most at risk of contracting HIV. This can potentially be implemented in the future as part of a national HIV prevention strategy.

References

1. Taiaroa G, Chibo D, Herman S, et al. Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study. Lancet Reg Health West Pac. 2024;47:101103. doi:10.1016/j.lanwpc.2024.101103
2. Access to HIV treatment for people without Medicare. ASHM. 2022. Accessed July 8, 2024. https://ashm.org.au/about/news/access-to-hiv-treatment-for-people-without-medicare/