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

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 ChowMarcus Y Chen, Sebastian Duchene, Jane S Hocking, Sharon R Lewin, Deborah A Williamson^*

^*Corresponding author for this work

School of Medicine

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	101103
Pages (from-to)	1-10
Number of pages	10
Journal	The Lancet Regional Health. Western Pacific
Volume	47
Early online date	7 Jun 2024
DOIs	https://doi.org/10.1016/j.lanwpc.2024.101103
Publication status	Published - Jun 2024

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Taiaroa, G., Chibo, D., Herman, S., Taouk, M. L., Gooey, M., D'Costa, J., Sameer, R., Richards, N., Lee, E., Macksabo, L., Higgins, N., Price, D. J., Jen Low, S., Steinig, E., Martin, G. E., Moso, M. A., Caly, L., Prestedge, J., Fairley, C. K., ... Williamson, D. A. (2024). Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study. The Lancet Regional Health. Western Pacific, 47, 1-10. Article 101103. https://doi.org/10.1016/j.lanwpc.2024.101103

@article{3a522df9d79241a3a061b494a45feb4c,

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

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.",

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

note = "Funding: National Health and Medical Research Council, Australian Research Council.",

year = "2024",

month = jun,

doi = "10.1016/j.lanwpc.2024.101103",

language = "English",

volume = "47",

pages = "1--10",

journal = "The Lancet Regional Health. Western Pacific",

issn = "2666-6065",

publisher = "Elsevier",

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Taiaroa, G, Chibo, D, Herman, S, Taouk, ML, Gooey, M, D'Costa, J, Sameer, R, Richards, N, Lee, E, Macksabo, L, Higgins, N, Price, DJ, Jen Low, S, Steinig, E, Martin, GE, Moso, MA, Caly, L, Prestedge, J, Fairley, CK, Chow, EPF, Chen, MY, Duchene, S, Hocking, JS, Lewin, SR & Williamson, DA 2024, 'Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study', The Lancet Regional Health. Western Pacific, vol. 47, 101103, pp. 1-10. https://doi.org/10.1016/j.lanwpc.2024.101103

TY - JOUR

T1 - Characterising HIV-1 transmission in Victoria, Australia

T2 - a molecular epidemiological study

AU - Taiaroa, George

AU - Chibo, Doris

AU - Herman, Sophie

AU - Taouk, Mona L

AU - Gooey, Megan

AU - D'Costa, Jodie

AU - Sameer, Rizmina

AU - Richards, Nicole

AU - Lee, Elaine

AU - Macksabo, Lydya

AU - Higgins, Nasra

AU - Price, David J

AU - Jen Low, Soo

AU - Steinig, Eike

AU - Martin, Genevieve E

AU - Moso, Michael A

AU - Caly, Leon

AU - Prestedge, Jacqueline

AU - Fairley, Christopher K

AU - Chow, Eric P F

AU - Chen, Marcus Y

AU - Duchene, Sebastian

AU - Hocking, Jane S

AU - Lewin, Sharon R

AU - Williamson, Deborah A

N1 - Funding: National Health and Medical Research Council, Australian Research Council.

PY - 2024/6

Y1 - 2024/6

N2 - 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.

AB - 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.

U2 - 10.1016/j.lanwpc.2024.101103

DO - 10.1016/j.lanwpc.2024.101103

M3 - Article

C2 - 38953059

SN - 2666-6065

VL - 47

SP - 1

EP - 10

JO - The Lancet Regional Health. Western Pacific

JF - The Lancet Regional Health. Western Pacific

M1 - 101103

ER -

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

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