Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

• Published in: PLoS pathogens Vol. 8; no. 3; p. e1002529
• Main Authors: Henn, Matthew R., Boutwell, Christian L., Charlebois, Patrick, Lennon, Niall J., Power, Karen A., Macalalad, Alexander R., Berlin, Aaron M., Malboeuf, Christine M., Ryan, Elizabeth M., Gnerre, Sante, Zody, Michael C., Erlich, Rachel L., Green, Lisa M., Berical, Andrew, Wang, Yaoyu, Casali, Monica, Streeck, Hendrik, Bloom, Allyson K., Dudek, Tim, Tully, Damien, Newman, Ruchi, Axten, Karen L., Gladden, Adrianne D., Battis, Laura, Kemper, Michael, Zeng, Qiandong, Shea, Terrance P., Gujja, Sharvari, Zedlack, Carmen, Gasser, Olivier, Brander, Christian, Hess, Christoph, Günthard, Huldrych F., Brumme, Zabrina L., Brumme, Chanson J., Bazner, Suzane, Rychert, Jenna, Tinsley, Jake P., Mayer, Ken H., Rosenberg, Eric, Pereyra, Florencia, Levin, Joshua Z., Young, Sarah K., Jessen, Heiko, Altfeld, Marcus, Birren, Bruce W., Walker, Bruce D., Allen, Todd M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2012; Public Library of Science (PLoS)
• Subjects: Adaptations; Algorithms; Biology; CD8 antigen; CD8-Positive T-Lymphocytes - immunology; Data processing; DNA sequencing; Epitopes; Evolution; Genetic aspects; Genetic Variation; Genome, Viral - genetics; Genome-Wide Association Study; Genomes; Genomic Structural Variation; Genomics; Health aspects; Histocompatibility antigen HLA; HIV (Viruses); HIV Infections - immunology; HIV Infections - prevention & control; HIV Infections - virology; HIV-1 - genetics; HIV-1 - immunology; HIV-1 - pathogenicity; Human immunodeficiency virus 1; Humans; Immune Evasion - genetics; Immune Evasion - immunology; Immune response; Immune system; Immunity; Immunology; Infection; Infections; Lymphocytes T; Medicine; Mutation; Nucleotide sequencing; Oligonucleotide Array Sequence Analysis; Pathogens; Physiological aspects; Replication; Reversion; RNA, Viral - analysis; Sequence Analysis, RNA; Vaccines; Viral genetics; Viral Vaccines - immunology; Viremia; United States; HIV Infections; HIV-1; Genome, Viral; Genome-Wide Association Study; Oligonucleotide Array Sequence Analysis; Humans; CD8-Positive T-Lymphocytes; Genetic Variation; Genomic Structural Variation; Immune Evasion; Sequence Analysis, RNA; RNA, Viral; Viral Vaccines

Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform...