Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 115; no. 30; pp. E7139 - E7148
• Main Authors: Ke, Ruian, Li, Hui, Wang, Shuyi, Ding, Wenge, Ribeiro, Ruy M., Giorgi, Elena E., Bhattacharya, Tanmoy, Barnard, Richard J. O., Hahn, Beatrice H., Shaw, George M., Perelson, Alan S.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 24.07.2018; Proceedings of the National Academy of Sciences
• Series: PNAS Plus
• Subjects: 60 APPLIED LIFE SCIENCES; Adaptation; Adaptation, Physiological - drug effects; Adaptation, Physiological - genetics; Antiviral Agents - therapeutic use; BASIC BIOLOGICAL SCIENCES; Biological Sciences; Drug resistance; Drug Resistance, Viral - drug effects; Drug Resistance, Viral - genetics; Genomes; Hepacivirus - genetics; Hepacivirus - metabolism; Hepatitis; Hepatitis C; Hepatitis C - drug therapy; Hepatitis C - genetics; Hepatitis C - metabolism; Hepatitis C virus; Humans; Immune response; Mathematical modeling; Mathematical models; Models, Biological; Molecular biology; Molecular modelling; Nucleotide sequence; Phylodynamic modeling; PNAS Plus; Populations; Proteinase inhibitors; Resistant mutant; Ribonucleic acid; RNA; RNA viruses; Sequences; Superinfection; Viral infections; Virology; Virus evolution; Virus persistence; Viruses; hepatitis C virus; mathematical modeling; phylodynamic modeling; virus persistence; virus evolution
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1805267115

RNA viruses exist as a genetically diverse quasispecies with extraordinary ability to adapt to abrupt changes in the host environment. However, the molecular mechanisms that contribute to their rapid adaptation and persistence in vivo are not well studied. Here, we probe hepatitis C virus (HCV) persistence by analyzing clinical samples taken from subjects who were treated with a second-generation HCV protease inhibitor. Frequent longitudinal viral load determinations and large-scale single-genome sequence analyses revealed rapid antiviral resistance development, and surprisingly, dynamic turnover of dominant drug-resistant mutant populations long after treatment cessation. We fitted mathematical models to both the viral load and the viral sequencing data, and the results provided strong support for the critical roles that superinfection and cure of infected cells play in facilitating the rapid turnover and persistence of viral populations. More broadly, our results highlight the importance of considering viral dynamics and competition at the intracellular level in understanding rapid viral adaptation. Thus, we propose a theoretical framework integrating viral and molecular mechanisms to explain rapid viral evolution, resistance, and persistence despite antiviral treatment and host immune responses.