HIV-DRIVES: HIV drug resistance identification, variant evaluation, and surveillance pipeline
Year: 2024
Type: article
Abstract: The global prevalence of resistance to the Human Immunodeficiency Virus (HIV) combined antiretroviral therapy (cART) emphasizes the need to continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently, integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring, with key challenges in the bioinformatic analysis and interpretation of the complex data generated while ensuring data security and privacy of patient information. To address these challenges, here, we present HIV-DRIVES (HIV Drug Resistance Identification, Variant Evaluation, and Surveillance), an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short-reads, FASTA, and sanger ab1.seq files. Availability and implementation HIV-DRIVES source codes and operation manual freely available at https://github.com/MicroBioGenoHub/HIV-DRIVES .
Source: Access Microbiology
Institutions: Ministry of Health, Infectious Diseases Institute, National Health Laboratory and Diagnostics Services, Makerere University, Amsterdam UMC Location University of Amsterdam, Amsterdam Institute for Global Health and Development, University of Manitoba, African Union Commission, Africa Centres for Disease Control and Prevention
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $858
OpenAlex ID: W4400733587