Deep sequencing for HIV-1 clinical management.

Area of Science:

• Virology and Infectious Diseases
• Genomics and Molecular Diagnostics
• Public Health and Epidemiology

Background:

• The global fight against human immunodeficiency virus type 1 (HIV-1) is challenged by a rising epidemic of drug resistance.
• Significant progress in HIV-1 treatment and prevention over the past decade is at risk.
• Next-generation sequencing (NGS) technologies are emerging as powerful tools for understanding and combating HIV-1 resistance.

Purpose of the Study:

• To review available Next-Generation Sequencing (NGS) platforms for HIV-1 diagnosis.
• To analyze factors influencing the clinical utility and implementation of NGS testing for HIV-1.
• To evaluate the evidence for ultrasensitive genotyping over Sanger sequencing in routine HIV-1 diagnostics.

Main Methods:

• Comprehensive literature review of Next-Generation Sequencing (NGS) platforms relevant to HIV-1.
• Analysis of factors impacting the clinical utility of NGS in HIV-1 diagnostics, including cost-effectiveness and accessibility.
• Evidence synthesis comparing ultrasensitive genotyping via NGS with traditional Sanger sequencing for HIV-1 diagnosis.

Main Results:

• Next-generation sequencing (NGS) platforms are becoming more cost-effective and accessible for HIV-1 resistance monitoring.
• Clinical utility of NGS testing is influenced by factors such as cost, workflow integration, and data analysis capabilities.
• The evidence supporting ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis requires further evaluation.

Conclusions:

• Making Next-Generation Sequencing (NGS) accessible, particularly in low- and middle-income countries (LMICs), is crucial for global HIV-1 eradication efforts.
• Reducing sequencing costs, especially library preparation, and improving automated bioinformatic analyses are essential.
• Addressing these challenges will be vital to ending the HIV-1 pandemic and sustaining global health gains.