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Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.
Ode, Hirotaka; Matsuda, Masakazu; Shigemi, Urara; Mori, Mikiko; Yamamura, Yoshimi; Nakata, Yoshihiro; Okazaki, Reiko; Kubota, Mai; Setoyama, Yuka; Imahashi, Mayumi; Yokomaku, Yoshiyuki; Iwatani, Yasumasa.
Afiliación
  • Ode H; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Matsuda M; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Shigemi U; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Mori M; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Yamamura Y; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Nakata Y; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Okazaki R; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Kubota M; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Setoyama Y; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Imahashi M; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Yokomaku Y; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
  • Iwatani Y; Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan. iwatani.yasumasa.cp@mail.hosp.go.jp.
Sci Rep ; 14(1): 12099, 2024 05 27.
Article en En | MEDLINE | ID: mdl-38802662
ABSTRACT
HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different drug target proteins. Since the number of targets has increased with the addition of a new class of antiretroviral drugs, a simple high-throughput system for assessing nucleotide sequences throughout the HIV-1 genome is required. Here, we developed a new solution using nanopore sequencing of viral pangenomes amplified by PCR. Benchmark tests using HIV-1 molecular clones demonstrated an accuracy of up to 99.9%. In addition, validation tests of our protocol in 106 clinical samples demonstrated high concordance of drug resistance and tropism genotypes (92.5% and 98.1%, respectively) between the nanopore sequencing-based results and archived clinical determinations made based on Sanger sequencing data. These results suggest that our new approach will be a powerful solution for the comprehensive survey of HIV-1 drug resistance mutations in clinical settings.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Infecciones por VIH / VIH-1 / Genoma Viral / Farmacorresistencia Viral / Secuenciación de Nanoporos / Mutación Límite: Humans Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Japón

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Infecciones por VIH / VIH-1 / Genoma Viral / Farmacorresistencia Viral / Secuenciación de Nanoporos / Mutación Límite: Humans Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Japón