AUTHOR=Ode Hirotaka , Matsuda Masakazu , Matsuoka Kazuhiro , Hachiya Atsuko , Hattori Junko , Kito Yumiko , Yokomaku Yoshiyuki , Iwatani Yasumasa , Sugiura Wataru TITLE=Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq JOURNAL=Frontiers in Microbiology VOLUME=6 YEAR=2015 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.01258 DOI=10.3389/fmicb.2015.01258 ISSN=1664-302X ABSTRACT=
Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from