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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 EP, Chen MY, Duchene S, Hocking JS, Lewin SR, Williamson DA. Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 47:101103. [PMID: 38953059 PMCID: PMC11215101 DOI: 10.1016/j.lanwpc.2024.101103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/15/2024] [Indexed: 07/03/2024]
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.
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Affiliation(s)
- George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sophie Herman
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mona L. Taouk
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Megan Gooey
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jodie D'Costa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Rizmina Sameer
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicole Richards
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Elaine Lee
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lydya Macksabo
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nasra Higgins
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Soo Jen Low
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Genevieve E. Martin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael A. Moso
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Leon Caly
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jacqueline Prestedge
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Christopher K. Fairley
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Victoria, Australia
- School of Translational Medicine, Monash University, Melbourne, Victoria
| | - Eric P.F. Chow
- Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Victoria, Australia
- School of Translational Medicine, Monash University, Melbourne, Victoria
| | - Marcus Y. Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Victoria, Australia
- School of Translational Medicine, Monash University, Melbourne, Victoria
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jane S. Hocking
- Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Obeng BM, Kelleher AD, Di Giallonardo F. Molecular epidemiology to aid virtual elimination of HIV transmission in Australia. Virus Res 2024; 341:199310. [PMID: 38185332 PMCID: PMC10825322 DOI: 10.1016/j.virusres.2024.199310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
The Global UNAIDS 95/95/95 targets aim to increase the percentage of persons who know their HIV status, receive antiretroviral therapy, and have achieved viral suppression. Achieving these targets requires efforts to improve the public health response to increase access to care for those living with HIV, identify those yet undiagnosed with HIV early, and increase access to prevention for those most at risk of HIV acquisition. HIV infections in Australia are among the lowest globally having recorded significant declines in new diagnoses in the last decade. However, the HIV epidemic has changed with an increasing proportion of newly diagnosed infections among those born outside Australia observed in the last five years. Thus, the current prevention efforts are not enough to achieve the UNAIDS targets and virtual elimination across all population groups. We believe both are possible by including molecular epidemiology in the public health response. Molecular epidemiology methods have been crucial in the field of HIV prevention, particularly in demonstrating the efficacy of treatment as prevention. Cluster detection using molecular epidemiology can provide opportunities for the real-time detection of new outbreaks before they grow, and cluster detection programs are now part of the public health response in the USA and Canada. Here, we review what molecular epidemiology has taught us about HIV evolution and spread. We summarize how we can use this knowledge to improve public health measures by presenting case studies from the USA and Canada. We discuss the successes and challenges of current public health programs in Australia, and how we could use cluster detection as an add-on to identify gaps in current prevention measures easier and respond quicker to growing clusters. Lastly, we raise important ethical and legal challenges that need to be addressed when HIV genotypic data is used in combination with personal data.
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Affiliation(s)
- Billal M Obeng
- The Kirby Institute, University of New South Wales, Sydney, Australia
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Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Selvey C, Nigro SJ, Fraser N, Price K, Holden J, Lee FJ, Dwyer DE, Bavinton BR, Geoghegan JL, Grulich AE, Kelleher AD. Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia. J Int AIDS Soc 2021; 24:e25655. [PMID: 33474833 PMCID: PMC7817915 DOI: 10.1002/jia2.25655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/27/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses. METHODS We used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01_AE (CRF01_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics. RESULTS We identified 104 subtype B and 11 CRF01_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01_AE respectively. We observed a > 2-fold increase in the number of NSW-specific CRF01_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above-average growth rate (>1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01_AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals. CONCLUSIONS The large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01_AE.
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Affiliation(s)
| | - Angie N Pinto
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
- Royal Prince Alfred HospitalSydneyNSWAustralia
| | - Phillip Keen
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
| | - Ansari Shaik
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
| | | | - Hanan Salem
- New South Wales Health Pathology‐RPARoyal Prince Alfred HospitalCamperdownNSWAustralia
| | | | | | - Neil Fraser
- Positive Life New South WalesSydneyNSWAustralia
| | | | | | - Frederick J Lee
- New South Wales Health Pathology‐RPARoyal Prince Alfred HospitalCamperdownNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Dominic E Dwyer
- New South Wales Health Pathology‐ICPMRWestmead HospitalWestmeadNSWAustralia
| | | | - Jemma L Geoghegan
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Andrew E Grulich
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
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Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Selvey C, Nigro SJ, Fraser N, Price K, Holden J, Lee FJ, Dwyer DE, Bavinton BR, Grulich AE, Kelleher AD, On Behalf Of The Nsw Hiv Prevention Partnership Project. Increased HIV Subtype Diversity Reflecting Demographic Changes in the HIV Epidemic in New South Wales, Australia. Viruses 2020; 12:E1402. [PMID: 33291330 PMCID: PMC7762219 DOI: 10.3390/v12121402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022] Open
Abstract
Changes over time in HIV-1 subtype diversity within a population reflect changes in factors influencing the development of local epidemics. Here we report on the genetic diversity of 2364 reverse transcriptase sequences from people living with HIV-1 in New South Wales (NSW) notified between 2004 and 2018. These data represent >70% of all new HIV-1 notifications in the state over this period. Phylogenetic analysis was performed to identify subtype-specific transmission clusters. Subtype B and non-B infections differed across all demographics analysed (p < 0.001). We found a strong positive association for infections among females, individuals not born in Australia or reporting heterosexual transmission being of non-B origin. Further, we found an overall increase in non-B infections among men who have sex with men from 50 to 79% in the last 10 years. However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. However, we found seven non-B clusters (≥5 sequences) indicative of local ongoing transmission. In conclusion, we present how the HIV-1 epidemic has changed over time in NSW, becoming more heterogeneous with distinct subtype-specific demographic associations.
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Affiliation(s)
| | - Angie N Pinto
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
- Royal Prince Alfred Hospital, Sydney 2050, Australia
| | - Phillip Keen
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Ansari Shaik
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Alex Carrera
- HIV Reference Laboratory, Sydney 2010, Australia
| | - Hanan Salem
- New South Wales Health Pathology-RPA, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | | | | | - Neil Fraser
- Positive Life New South Wales, Sydney 2010, Australia
| | - Karen Price
- AIDS Council of NSW (ACON), Sydney 2010, Australia
| | | | - Frederick J Lee
- New South Wales Health Pathology-RPA, Royal Prince Alfred Hospital, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, Sydney 2050, Australia
| | - Dominic E Dwyer
- New South Wales Health Pathology-ICPMR, Westmead Hospital, Westmead 2145, Australia
| | - Benjamin R Bavinton
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Andrew E Grulich
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Anthony D Kelleher
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
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Sacks-Davis R, Chibo D, Peach E, Aleksic E, Crowe SM, El Hayek C, Marukutira T, Higgins N, Stoove M, Hellard M. Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia. PLoS One 2020; 15:e0237469. [PMID: 32870911 PMCID: PMC7462279 DOI: 10.1371/journal.pone.0237469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023] Open
Abstract
Background It is estimated that approximately half of new HIV diagnoses among heterosexual migrants in Victoria, Australia, were acquired post-migration. We investigated the characteristics of phylogenetic clusters in notified cases of HIV among heterosexual migrants. Methods Partial HIV pol sequences obtained from routine clinical genotype tests were linked to Victorian HIV notifications with the following exposures listed on the notification form: heterosexual sexual contact, injecting drug use, bisexual sexual contact, male-to male sexual contact or heterosexual sexual contact in combination with injecting drug use, unknown exposure. Those with heterosexual sexual contact as the only exposure were the focus of this study, with the other exposures included to better understand transmission networks. Additional reference sequences were extracted from the Los Alamos database. Maximum likelihood methods were used to infer the phylogeny and the robustness of the resulting tree was assessed using bootstrap analysis. Phylogenetic clusters were defined on the basis of bootstrap and genetic distance. Results HIV pol sequences were available for 332 of 445 HIV notifications attributed to only heterosexual sexual contact in Victoria from 2005–2014. Forty-three phylogenetic clusters containing at least one heterosexual migrant were detected, 30 (70%) of which were pairs. The characteristics of these phylogenetic clusters varied considerably by cluster size. Pairs were more likely to be composed of people living with HIV from a single country of birth (p = 0.032). Larger clusters (n≥3) were more likely to contain people born in Australian/New Zealand (p = 0.002), migrants from more than one country of birth (p = 0.013) and viral subtype-B, the most common subtype in Australia (p = 0.006). Pairs were significantly more likely to contain females (p = 0.037) and less likely to include HIV diagnoses with male-to-male sexual contact reported as a possible exposure (p<0.001) compared to larger clusters (n≥3). Conclusion Migrants appear to be at elevated risk of HIV acquisition, in part due to intimate relationships between migrants from the same country of origin, and in part due to risks associated with the broader Australian HIV epidemic. However, there was no evidence of large transmission clusters driven by heterosexual transmission between migrants. A multipronged approach to prevention of HIV among migrants is warranted.
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Affiliation(s)
- Rachel Sacks-Davis
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Doris Chibo
- Victorian Infectious Disease Reference Laboratory, Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Eman Aleksic
- Burnet Institute, Melbourne, Victoria, Australia
| | - Suzanne M. Crowe
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Carol El Hayek
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Tafireyi Marukutira
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Nasra Higgins
- Department of Health and Human Services, Melbourne, Victoria, Australia
| | - Mark Stoove
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Hepatitis Services, Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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