Khera Tanvi, Todt Daniel, Vercauteren Koen, McClure C Patrick, Verhoye Lieven, Farhoudi Ali, Bhuju Sabin, Geffers Robert, Baumert Thomas F, Steinmann Eike, Meuleman Philip, Pietschmann Thomas, Brown Richard J P
Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
Laboratory of Liver Infectious Diseases, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium.
Antiviral Res. 2017 Mar;139:129-137. doi: 10.1016/j.antiviral.2017.01.001. Epub 2017 Jan 3.
Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity. In all transmissions, a genetic bottleneck was observed, although diverse viral populations were transmitted in each case. A low frequency cloud of mutations (<1%) was detectable in the donor inoculum and recipient mice, with single nucleotide variants (SNVs) > 1% restricted to a subset of nucleotides. The population of SNVs >1% was reduced upon transmission while the low frequency SNV cloud remained stable. Fixation of multiple identical synonymous substitutions was apparent in independent transmissions, and no evidence for reversion of T-cell epitopes was observed. In addition, susceptibility of founder populations to antiviral therapy was assessed. Animals were treated with protease inhibitor (PI) monotherapy to track resistance associated substitution (RAS) emergence. Longitudinal analyses revealed a decline in population diversity under therapy, with no detectable RAS >1% prior to therapy commencement. Despite inoculation from a common source and identical therapeutic regimens, unique RAS emergence profiles were identified in different hosts prior to and during therapeutic failure, with complex mutational signatures at protease residues 155, 156 and 168 detected. Together these analyses track viral population complexity at high-resolution in the human-liver chimeric mouse model post-transmission and under therapeutic intervention, revealing novel insights into the evolutionary processes which shape viral protease population composition at various critical stages of the viral life-cycle.
由于丙型肝炎病毒（HCV）具有高度受限的物种嗜性，用于疫苗和抗病毒化合物临床前评估的动物模型数量有限。人肝嵌合小鼠模型允许用源自患者的临床相关毒株进行异种攻击。然而，迄今为止，尚未使用最先进的测序技术对该模型中起始病毒群体的传播和纵向进化进行深入表征。聚焦于病毒基因组的NS3蛋白酶编码区域，通过Illumina测序确定供体接种物和个体受体小鼠中的突变谱并进行比较，以确定传播对起始病毒群体复杂性的影响。在所有传播中，均观察到遗传瓶颈，尽管每种情况下传播的病毒群体各不相同。在供体接种物和受体小鼠中可检测到低频突变云（<1%），大于1%的单核苷酸变异（SNV）仅限于核苷酸的一个子集。传播后，大于1%的SNV群体减少，而低频SNV云保持稳定。在独立传播中，多个相同同义替换的固定很明显，并且未观察到T细胞表位回复的证据。此外，评估了起始群体对抗病毒治疗的敏感性。用蛋白酶抑制剂（PI）单一疗法治疗动物以追踪耐药相关替代（RAS）的出现。纵向分析显示治疗期间群体多样性下降，治疗开始前未检测到大于1%的RAS。尽管来自共同来源并采用相同的治疗方案，但在治疗失败之前和期间，在不同宿主中鉴定出独特的RAS出现谱，在蛋白酶残基155、156和168处检测到复杂的突变特征。这些分析共同在人肝嵌合小鼠模型中高分辨率追踪了传播后和治疗干预下的病毒群体复杂性，揭示了对在病毒生命周期各个关键阶段塑造病毒蛋白酶群体组成的进化过程的新见解。
