The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002–2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/8/1643 |
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| author | Bluma G. Brenner Ruxandra-Ilinca Ibanescu Nathan Osman Ernesto Cuadra-Foy Maureen Oliveira Antoine Chaillon David Stephens Isabelle Hardy Jean-Pierre Routy Réjean Thomas Jean-Guy Baril Roger Leblanc Cecile Tremblay Michel Roger The Montreal Primary HIV Infection (PHI) Cohort Study Group |
| author_facet | Bluma G. Brenner Ruxandra-Ilinca Ibanescu Nathan Osman Ernesto Cuadra-Foy Maureen Oliveira Antoine Chaillon David Stephens Isabelle Hardy Jean-Pierre Routy Réjean Thomas Jean-Guy Baril Roger Leblanc Cecile Tremblay Michel Roger The Montreal Primary HIV Infection (PHI) Cohort Study Group |
| author_sort | Bluma G. Brenner |
| collection | DOAJ |
| description | Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002–2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, <i>n</i> = 5024) and heterosexuals (HET, <i>n</i> = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (<i>n</i> = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2–5 members) declined by 70% from 2006–2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration. |
| first_indexed | 2024-03-10T08:17:49Z |
| format | Article |
| id | doaj.art-ab4c0bb006b043ad801e294b6ba4e7c7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T08:17:49Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-ab4c0bb006b043ad801e294b6ba4e7c72023-11-22T10:12:37ZengMDPI AGViruses1999-49152021-08-01138164310.3390/v13081643The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)Bluma G. Brenner0Ruxandra-Ilinca Ibanescu1Nathan Osman2Ernesto Cuadra-Foy3Maureen Oliveira4Antoine Chaillon5David Stephens6Isabelle Hardy7Jean-Pierre Routy8Réjean Thomas9Jean-Guy Baril10Roger Leblanc11Cecile Tremblay12Michel Roger13The Montreal Primary HIV Infection (PHI) Cohort Study Group14McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, CanadaMcGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, CanadaMcGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, CanadaMcGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, CanadaMcGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, CanadaDepartment of Medicine, University of California, San Diego, CA 93903, USADepartment of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, CanadaDépartement de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, CanadaChronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, CanadaClinique Médicale l’Actuel, Montréal, QC H2L 4P9, CanadaClinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, CanadaClinique Médicale OPUS, Montréal, QC H3A 1T1, CanadaDépartement de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, CanadaDépartement de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, CanadaMontreal PHI Cohort of the Réseau Sida et Maladies Infectieuses, Centre de Recherche du CHUM, Montréal, QC H2X 0A9, CanadaPhylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002–2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, <i>n</i> = 5024) and heterosexuals (HET, <i>n</i> = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (<i>n</i> = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2–5 members) declined by 70% from 2006–2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.https://www.mdpi.com/1999-4915/13/8/1643HIV-1 transmissionmen having sex with mennon-B subtypesphylogeneticsHIV-TRACEtreatment-as-prevention |
| spellingShingle | Bluma G. Brenner Ruxandra-Ilinca Ibanescu Nathan Osman Ernesto Cuadra-Foy Maureen Oliveira Antoine Chaillon David Stephens Isabelle Hardy Jean-Pierre Routy Réjean Thomas Jean-Guy Baril Roger Leblanc Cecile Tremblay Michel Roger The Montreal Primary HIV Infection (PHI) Cohort Study Group The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) Viruses HIV-1 transmission men having sex with men non-B subtypes phylogenetics HIV-TRACE treatment-as-prevention |
| title | The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) |
| title_full | The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) |
| title_fullStr | The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) |
| title_full_unstemmed | The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) |
| title_short | The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020) |
| title_sort | role of phylogenetics in unravelling patterns of hiv transmission towards epidemic control the quebec experience 2002 2020 |
| topic | HIV-1 transmission men having sex with men non-B subtypes phylogenetics HIV-TRACE treatment-as-prevention |
| url | https://www.mdpi.com/1999-4915/13/8/1643 |
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