HIV Molecular Epidemiology for Prevention 2023

Dear Colleagues,

The molecular epidemiology of infectious diseases is being transformed by the increasing availability of pathogen nucleotide sequence data from advances in sequencing technologies and their global availability. Molecular sequences combined with epidemiologic data are critical for understanding pathogen emergence, transmission histories, identifying reservoirs and new infections, preventing onward transmission, monitoring disease progression, and linking infected persons to treatment and care. In 2017, the WHO estimated that about 36.9 million people were living with HIV globally. Of those, almost 940,000 died from AIDS-related illnesses and approximately 75% were unaware of their HIV status. For HIV, drug resistance monitoring is the standard of care for new diagnoses, and testing is routinely performed at commercial laboratories or frequently carried out for research studies. More recently, these HIV polymerase sequences are being used to identify persons with genetically similar strains, characterize transmission clusters and dynamics, and recognize clusters with rapid and active transmission, all of which permit focused public health interventions of limited resources to those persons and places with the highest risk of new infections. In the US, rapidly detecting and responding to clusters and outbreaks is a key pillar of the President’s 2019 initiative “Ending the HIV Epidemic” in the next decade. This goal is consistent with the WHO target of ending the HIV/AIDS epidemic by 2030. Transmission clusters can be identified using network and phylogenetic analyses of molecular sequences, or combinations of both, and bioinformatics methods are used or being developed to determine timing of infection, time–space clusters, the prediction of cluster growth and spread, and the modeling of transmission dynamics and targeted prevention strategies.

This Special Issue aims to provide new insights and advances in the molecular epidemiology of HIV infection, including how molecular epidemiology is being used for surveillance, understanding transmission dynamics (patterns, order, and probability), the spread of HIV locally and globally, phylodynamics, outbreak and cluster detection, transmission networks, the use of partial and whole genomes, ultradeep sequencing for molecular epidemiology, transmitted drug resistance, and the modeling of transmission clusters and targeted prevention strategies. We invite you to contribute original papers and review articles on these topics and other related topics to highlight recent advances in molecular epidemiologic methods used to study HIV transmission and prevention.

Dr. Dimitrios Paraskevis
Dr. Maja Stanojevic
Guest Editors

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.

• human immunodeficiency virus (HIV)
• molecular epidemiology
• transmission dynamics
• transmission networks and clusters
• cluster detection
• phylogenetic analysis
• phylodynamics
• drug resistance testing
• sequence analysis
• subtypes
• quasispecies
• public health response
• risk factors
• persons who inject drugs
• interventions
• pre- and post-exposure prophylaxis
• modeling
• prevention and care
• partner services
• contact tracing
• disease surveillance
• co-infections
• data integration and visualization
• bioinformatics

• HIV Molecular Epidemiology for Prevention in Viruses (11 articles)
• HIV Molecular Epidemiology for Prevention 2020 in Viruses (16 articles)