High-throughput, single-molecule sequence analysis of virus populations in vivo

感染人类并引起疾病的病毒在体内以相关但不相同的遗传变异的准种存在。这些准种可以由个体中少量创始变异的多样化产生，在病毒持续复制的过程中，通过非有害随机突变的逐步积累而产生。这些病毒变体编码的多样性为病毒提供了一种重要的持久性机制，因为宿主介导的抗病毒反应或治疗性给予的抗病毒干预可能无法对抗具有某些逃逸突变的变体。这可能产生重要的医学后果，如与艾滋病毒耐药性相关的不良临床结果。

Viruses that infect humans and cause disease exist in vivo as quasispecies of related but non-identical genetic variants. These quasispecies can arise by diversification of a small number of founder variants in an individual by the progressive accumulation of non-deleterious random mutations during ongoing rounds of virus replication. The diversity encoded by these virus variants provides the virus with an important mechanism of persistence, as host-mediated antiviral responses or therapeutically-administered antiviral interventions may fail to act against variants with certain escape mutations. This can have important medical consequences, as exemplified by poor clinical outcomes associated with drug-resistance in HIV. Accurately characterizing genetic diversity of virus quasispecies in samples from infected individuals requires high-throughput sequencing of single molecules, sometimes over regions thousands of base-pairs in length. Current technologies for high-throughput sequencing, though very powerful, are limited in their ability to address this challenge. We are thus developing novel wet-lab and bioinformatic methods for high-throughput, single-molecule sequence analysis of virus genomes, and applying them to samples from people with medically-important viruses, focused initially on HIV.