Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study

George Taiaroa; Doris Chibo; Sophie Herman; Mona L Taouk; Megan Gooey; Jodie D'Costa; Rizmina Sameer; Nicole Richards; Elaine Lee; Lydya Macksabo; Nasra Higgins; David J Price; Soo Jen Low; Eike Steinig; Genevieve E Martin; Michael A Moso; Leon Caly; Jacqueline Prestedge; Christopher K Fairley; Eric P F Chow; Marcus Y Chen; Sebastian Duchene; Jane S Hocking; Sharon R Lewin; Deborah A Williamson

doi:10.1016/j.lanwpc.2024.101103

Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study

Lancet Reg Health West Pac. 2024 Jun 7:47:101103. doi: 10.1016/j.lanwpc.2024.101103. eCollection 2024 Jun.

Authors

George Taiaroa^{1

2}, Doris Chibo², Sophie Herman³, Mona L Taouk¹, Megan Gooey², Jodie D'Costa², Rizmina Sameer², Nicole Richards², Elaine Lee², Lydya Macksabo², Nasra Higgins⁴, David J Price^{1

5}, Soo Jen Low¹, Eike Steinig¹, Genevieve E Martin^{1

2}, Michael A Moso^{1

2}, Leon Caly^{1

2}, Jacqueline Prestedge^{1

2}, Christopher K Fairley^{6

7}, Eric P F Chow^{5

6

7}, Marcus Y Chen^{6

7}, Sebastian Duchene³, Jane S Hocking⁵, Sharon R Lewin^{1

8

9}, Deborah A Williamson^{1

2}

Affiliations

¹ Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
² Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
³ Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
⁴ Victorian Department of Health, Melbourne, Victoria, Australia.
⁵ Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia.
⁶ Melbourne Sexual Health Centre, Alfred Health, Melbourne, Victoria, Australia.
⁷ School of Translational Medicine, Monash University, Melbourne, Victoria.
⁸ Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia.
⁹ Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.

Abstract

Background: In Australia the incidence of HIV has declined steadily, yet sustained reduction of HIV transmission in this setting requires improved public health responses. As enhanced public health responses and prioritisation of resources may be guided by molecular epidemiological data, here we aimed to assess the applicability of these approaches in Victoria, Australia.

Methods: A comprehensive collection of HIV-1 pol sequences from individuals diagnosed with HIV in Victoria, Australia, between January 1st 2000 and December 31st 2020 were deidentified and used as the basis of our assessment. These sequences were subtyped and surveillance drug resistance mutations (SDRMs) identified, before definition of transmission groups was performed using HIV-TRACE (0.4.4). Phylodynamic methods were applied using BEAST (2.6.6), assessing effective reproductive numbers for large groups, and additional demographic data were integrated to provide a high resolution view of HIV transmission in Victoria on a decadal time scale.

Findings: Based on standard settings for HIV-TRACE, 70% (2438/3507) of analysed HIV-1 pol sequences were readily assigned to a transmission group. Individuals in transmission groups were more commonly males (aOR 1.50), those born in Australia (aOR 2.13), those with probable place of acquisition as Victoria (aOR 6.73), and/or those reporting injectable drug use (aOR 2.13). SDRMs were identified in 375 patients (10.7%), with sustained transmission of these limited to a subset of smaller groups. Informative patterns of epidemic growth, stabilisation, and decline were observed; many transmission groups showed effective reproductive numbers (R _e ) values reaching greater than 4.0, representing considerable epidemic growth, while others maintained low R _e values.

Interpretation: This study provides a high resolution view of HIV transmission in Victoria, Australia, and highlights the potential of molecular epidemiology to guide and enhance public health responses in this setting. This informs ongoing discussions with community groups on the acceptability and place of molecular epidemiological approaches in Australia.

Funding: National Health and Medical Research Council, Australian Research Council.

Keywords: HIV; Molecular epidemiology; Transmission.