A national study of the molecular epidemiology of HIV-1 in

Australian Molecular Epidemiology Network-HIV (AMEN-HIV), Alison Castley, Shailendra Sawleshwarkar, Rick Varma, Belinda Herring, Kiran Thapa, Dominic Dwyer, Doris Chibo, Nam Nguyen, Karen Hawke, Rodney Ratcliff, Roger Garsia, Anthony Kelleher, David Nolan

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005.2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap .98%, genetic distance .1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of .3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01-AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.

LanguageEnglish
Article numbere0170601
JournalPloS one
Volume12
Issue number5
DOIs
Publication statusPublished - 1 May 2017

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Australian Molecular Epidemiology Network-HIV (AMEN-HIV) (2017). A national study of the molecular epidemiology of HIV-1 in. PloS one, 12(5), [e0170601]. https://doi.org/10.1371/journal.pone.0170601
Australian Molecular Epidemiology Network-HIV (AMEN-HIV). / A national study of the molecular epidemiology of HIV-1 in. In: PloS one. 2017 ; Vol. 12, No. 5.
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abstract = "Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005.2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap .98{\%}, genetic distance .1.5{\%} from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5{\%} of the 4,873 sequences (WA 59{\%}, SA 68.4{\%}, w-Syd 73.8{\%}, Vic 75.6{\%}, Qld 82.1{\%}), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23{\%} vs 24.5{\%} of sequences, p = 0.3). Significantly more subtype B clusters were comprised of .3 sequences compared with non-B clusters (45.0{\%} vs 24.0{\%}, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88{\%} compared to 53{\%} CRF01-AE and 17{\%} subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.",
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Australian Molecular Epidemiology Network-HIV (AMEN-HIV) 2017, 'A national study of the molecular epidemiology of HIV-1 in', PloS one, vol. 12, no. 5, e0170601. https://doi.org/10.1371/journal.pone.0170601

A national study of the molecular epidemiology of HIV-1 in. / Australian Molecular Epidemiology Network-HIV (AMEN-HIV).

In: PloS one, Vol. 12, No. 5, e0170601, 01.05.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A national study of the molecular epidemiology of HIV-1 in

AU - Australian Molecular Epidemiology Network-HIV (AMEN-HIV)

AU - Castley, Alison

AU - Sawleshwarkar, Shailendra

AU - Varma, Rick

AU - Herring, Belinda

AU - Thapa, Kiran

AU - Dwyer, Dominic

AU - Chibo, Doris

AU - Nguyen, Nam

AU - Hawke, Karen

AU - Ratcliff, Rodney

AU - Garsia, Roger

AU - Kelleher, Anthony

AU - Nolan, David

PY - 2017/5/1

Y1 - 2017/5/1

N2 - Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005.2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap .98%, genetic distance .1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of .3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01-AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.

AB - Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005.2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap .98%, genetic distance .1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of .3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01-AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.

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Australian Molecular Epidemiology Network-HIV (AMEN-HIV). A national study of the molecular epidemiology of HIV-1 in. PloS one. 2017 May 1;12(5). e0170601. https://doi.org/10.1371/journal.pone.0170601