The Added Role of Phylogenetics in the Prevention of HIV-1 and Related Viral Diseases

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (10 August 2023) | Viewed by 1778

Special Issue Editor

Special Issue Information

Dear Colleagues,

Despite remarkable advances in the Fast-Track "90-90-90"  treatment-as-prevention initiative, global HIV epidemic remain elusive with 1.5 million new infections annually over the last decade. Molecular phylogenetics is an exciting new direction to delineate the structure of transmission networks at an unprecedented detail, providing novel insights into regional epidemic drivers. In 2019, the US End the Epidemic by 2030 advanced phylogenetic surveillance as a fourth pillar to predict and respond to cluster outbreaks in key risk groups in different regional settings. 

With this Special Issue, we wish to explore precisely what phylogenetics adds to the prevention of HIV-1 and related viral diseases. We welcome articles that describe phylogenetic insights into specific issues, including:

  • Challenges in the identification of cluster types based on selected methodologies and genetic cut-offs.
  • Epidemiological and virological predictors of the genesis and
    expansion of clustered outbreaks.
  • The influence of migration and globalization in emerging patterns of viral spread.
  • The mixing of epidemics among key vulnerable populations.
  • The evolution of viral epidemics in the era of highly potent therapy (e.g., integrase inhibitors and preexposure prophylaxis), 90-90-90 Fast Track targets and COVID-19.
  • Addressing ethical challenges in the implementation of phylogenetic strategies. 

Prof. Dr. Bluma G. Brenner
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:

Research

12 pages, 1124 KiB  
Article
An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic
by Mark Howison, Fizza S. Gillani, Vlad Novitsky, Jon A. Steingrimsson, John Fulton, Thomas Bertrand, Katharine Howe, Anna Civitarese, Lila Bhattarai, Meghan MacAskill, Guillermo Ronquillo, Joel Hague, Casey W. Dunn, Utpala Bandy, Joseph W. Hogan and Rami Kantor
Viruses 2023, 15(3), 737; https://doi.org/10.3390/v15030737 - 13 Mar 2023
Viewed by 1512
Abstract
Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, [...] Read more.
Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission. Full article
Show Figures

Figure 1

Back to TopTop