The Added Role of Phylogenetics in the HIV Prevention Toolbox

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 11847

Special Issue Editor

Special Issue Information

Dear Colleagues,

Despite remarkable advances in antiviral treatment and prevention paradigms, HIV/AIDS remains a global health challenge with 1.7-2 million new infections annually over the last decade. Inferences from phylogenetics can delineate the structure of transmission networks at an unprecedented detail, providing novel insights into regional epidemic drivers. In 2019, the US Centers for Disease Control and Prevention advanced phylogenetics as an essential ingredient in the design of prevention strategies towards epidemic control by 2030.

With this Special Issue, we wish to explore precisely what phylogenetics adds to the HIV prevention toolbox. We welcome articles that describe phylogenetic insights into specific issues, including

  1. The influence of route transmission and disease stage in divergent patterns of spread.
  2. The influence of migration and globalization in patterns of viral spread.
  3. The mixing of epidemics in key vulnerable populations.
  4. The evolution of viral epidemics in the era of highly potent therapy (e.g., integrase inhibitors and preexposure prophylaxis).
  5. Variations in the calling of clusters based on selected methodologies and topological cutoffs.
  6. Scientific validity and the ethics of recent publications that predict partners and directionality of transmission.

Prof. Dr. Bluma G. Brenner
Guest Editor

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Published Papers (5 papers)

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Editorial

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4 pages, 555 KiB  
Editorial
Phylogenetic Insights on Patterns of HIV-1 Spread and the Design of Epidemic Control Measures
by Bluma G. Brenner
Viruses 2022, 14(2), 332; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020332 - 07 Feb 2022
Cited by 1 | Viewed by 1251
Abstract
Phylogenetics provides a unique structural framework to track the spread of viral diseases, such as HIV-1 (human immunodeficiency virus type 1), the causative agent of AIDS (acquired immunodeficiency syndrome) [...] Full article
(This article belongs to the Special Issue The Added Role of Phylogenetics in the HIV Prevention Toolbox)
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Research

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16 pages, 3778 KiB  
Article
The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)
by 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 and The Montreal Primary HIV Infection (PHI) Cohort Study Group
Viruses 2021, 13(8), 1643; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081643 - 19 Aug 2021
Cited by 8 | Viewed by 2423
Abstract
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 [...] Read more.
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, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 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. Full article
(This article belongs to the Special Issue The Added Role of Phylogenetics in the HIV Prevention Toolbox)
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15 pages, 2720 KiB  
Article
Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control
by Nicholas Bbosa, Deogratius Ssemwanga, Rebecca N. Nsubuga, Noah Kiwanuka, Bernard S. Bagaya, John M. Kitayimbwa, Alfred Ssekagiri, Gonzalo Yebra, Pontiano Kaleebu and Andrew Leigh-Brown
Viruses 2021, 13(6), 970; https://0-doi-org.brum.beds.ac.uk/10.3390/v13060970 - 24 May 2021
Cited by 4 | Viewed by 2648
Abstract
Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV [...] Read more.
Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV pol sequences (728 Lake Victoria fisherfolk communities (FFCs), 592 female sex workers (FSWs) and 697 general population (GP)) to identify transmission networks on Maximum Likelihood (ML) phylogenetic trees and refined them using time-resolved phylogenies. Network generative models were fitted to the observed degree distributions and network parameters, and corrected Akaike Information Criteria and Bayesian Information Criteria values were estimated. 347 (17.2%) HIV sequences were linked on ML trees (maximum genetic distance ≤4.5%, ≥95% bootstrap support) and, of these, 303 (86.7%) that consisted of pure A1 (n = 168) and D (n = 135) subtypes were analyzed in BEAST v1.8.4. The majority of networks (at least 40%) were found at a time depth of ≤5 years. The waring and yule models fitted best networks of FFCs and FSWs respectively while the negative binomial model fitted best networks in the GP. The network structure in the HIV-hyperendemic FFCs is likely to be scale-free and shaped by preferential attachment, in contrast to the GP. The findings support the targeting of interventions for FFCs in a timely manner for effective epidemic control. Interventions ought to be tailored according to the dynamics of the HIV epidemic in the target population and understanding the network structure is critical in ensuring the success of HIV prevention programs. Full article
(This article belongs to the Special Issue The Added Role of Phylogenetics in the HIV Prevention Toolbox)
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10 pages, 563 KiB  
Article
Phylogenetic Clustering among Asylum Seekers with New HIV-1 Diagnoses in Montreal, QC, Canada
by Hyejin Park, Bluma Brenner, Ruxandra-Ilinca Ibanescu, Joseph Cox, Karl Weiss, Marina B. Klein, Isabelle Hardy, Lavanya Narasiah, Michel Roger and Nadine Kronfli
Viruses 2021, 13(4), 601; https://0-doi-org.brum.beds.ac.uk/10.3390/v13040601 - 01 Apr 2021
Cited by 3 | Viewed by 2446
Abstract
Migrants are at an increased risk of HIV acquisition. We aimed to use phylogenetics to characterize transmission clusters among newly-diagnosed asylum seekers and to understand the role of networks in local HIV transmission. Retrospective chart reviews of asylum seekers linked to HIV care [...] Read more.
Migrants are at an increased risk of HIV acquisition. We aimed to use phylogenetics to characterize transmission clusters among newly-diagnosed asylum seekers and to understand the role of networks in local HIV transmission. Retrospective chart reviews of asylum seekers linked to HIV care between 1 June 2017 and 31 December 2018 at the McGill University Health Centre and the Jewish General Hospital in Montreal were performed. HIV-1 partial pol sequences were analyzed among study participants and individuals in the provincial genotyping database. Trees were reconstructed using MEGA10 neighbor-joining analysis. Clustering of linked viral sequences was based on a strong bootstrap support (>97%) and a short genetic distance (<0.01). Overall, 10,645 provincial sequences and 105 asylum seekers were included. A total of 13/105 participant sequences (12%; n = 7 males) formed part of eight clusters. Four clusters (two to three people) included only study participants (n = 9) and four clusters (two to three people) included four study participants clustered with six individuals from the provincial genotyping database. Six (75%) clusters were HIV subtype B. We identified the presence of HIV-1 phylogenetic clusters among asylum seekers and at a population-level. Our findings highlight the complementary role of cohort data and population-level genotypic surveillance to better characterize transmission clusters in Quebec. Full article
(This article belongs to the Special Issue The Added Role of Phylogenetics in the HIV Prevention Toolbox)
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Review

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21 pages, 1681 KiB  
Review
The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review
by George M. Nduva, Jamirah Nazziwa, Amin S. Hassan, Eduard J. Sanders and Joakim Esbjörnsson
Viruses 2021, 13(6), 1174; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061174 - 19 Jun 2021
Cited by 9 | Viewed by 2326
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 [...] Read more.
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995–2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges. Full article
(This article belongs to the Special Issue The Added Role of Phylogenetics in the HIV Prevention Toolbox)
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