Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms
Year: 2022
Type: article
Abstract: HIV-1 is characterized by large genetic differences, including HIV-1 recombinant forms (RFs). Conventional genetic analyses require time-consuming pretreatments, i.e., cloning or single-genome amplification, to distinguish RFs from dual- or multiple-infection cases. In this study, we developed a new analytical system for HIV-1 sequence data obtained by nanopore sequencing. The error rate of this method was reduced to ~0.06%. We applied this system for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection, which were extracted from 373 cases of HIV patients based on our retrospective analysis of HIV-1 drug resistance genotyping test results. We found that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Our protocol will be useful for epidemiological surveillance to examine HIV-1 transmission as well as for genotypic tests of HIV-1 drug resistance in clinical settings.
Source: Microbiology Spectrum
Language: English
Topic: HIV Research and Treatment
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,500
Awards: G2775601475, Analysis of novel molecular mechanisms for APOBEC3A-mediated antiviral activity and mutagenesis, G5605476505, G6151955707, G7577909444, The mechanism of complex formation between HIV-1 Vif and host factor APOBEC3, Extensive studies on anti-retroviral mechanisms mediated by APOBEC3H
OpenAlex ID: W4288066909