Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms
Mikiko Mori, Hirotaka Ode, Mai Kubota, Yoshihiro Nakata, Takaaki Kasahara, Urara Shigemi, Reiko Okazaki, Masakazu Matsuda, Kazuhiro Matsuoka, Atsuko Sugimoto, Atsuko Hachiya, Mayumi Imahashi, Yoshiyuki Yokomaku, Yasumasa Iwatani
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.