Deep sequencing for HIV-1 clinical management.
The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting -or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis. Now that global HIV-1 eradication might be within our reach, making NGS accessible also to LMICs has become a priority. Reductions in sequencing costs, particularly in library preparation, and accessibility to low-cost, robust but simplified automated bioinformatic analyses of NGS data will remain essential to end the HIV-1 pandemic.
IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain. Electronic address: mcasadella@irsicaixa.es.
Maria
M
Casadellà
IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain; Universitat de Vic - Central de Catalunya, Vic, Catalonia, Spain; HIV-1 Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain.
Roger
R
Paredes
D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use; D023241:Antiretroviral Therapy, Highly Active; D019295:Computational Biology; D003906:Developing Countries; D019468:Disease Management; D024882:Drug Resistance, Viral; D005838:Genotype; D015658:HIV Infections / Q000175:diagnosis / Q000188:drug therapy / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods / Q000592:standards; D006801:Humans; D008826:Microbial Sensitivity Tests; D009154:Mutation; D056189:Viral Tropism
D019380:Anti-HIV Agents
Antiretroviral therapy; HIV resistance; HIV-1; Low-frequency variants; Next-generation sequencing; Tropism