Soler Muriel, Pellerin Muriel, Malnou Cécile E, Dhumeaux Daniel, Kean Katherine M, Pawlotsky Jean-Michel
Department of Virology (EA 3489), Université Paris XII, Créteil, France.
Virology. 2002 Jun 20;298(1):160-73. doi: 10.1006/viro.2002.1494.
Hepatitis C virus (HCV) polyprotein translation depends on direct internal entry of the 40S ribosomal subunit mediated by an internal ribosome entry segment (IRES) located in the 5' noncoding (5'NC) region of the viral genome. HCV is genetically heterogeneous and is characterized by the existence of a quasispecies distribution of the virus population within a single infected individual. Cloning and sequencing strategies were used to characterize 5'NC quasispecies genetically. Similar to coding regions, the HCV 5'NC region was distributed as a quasispecies, but it appeared to be subjected to stronger conservatory constraints than other regions of the HCV genome, probably due to the need for structural (and functional) conservation of the IRES. Indeed, most of the quasispecies substitutions were in unpaired regions of the IRES or clustered such that base-pairing was maintained, whereas only 21% were expected to result in a loss of base-pairing. Quasispecies-related structural changes could be predicted in the core cruciform of IRES domain III composed of the RNA helices which extend from the four-way junction JIIIabc, mostly in minor variants, but sometimes in major ones. The results presented here suggest the simultaneous presence in infected patients of a mixture of genetically distinct but closely related IRES sequences that may have different structures. No significant genetic changes of 5'NC quasispecies were observed after interferon-alpha treatment, except in patients with mixed genotype infection who cleared one of the infecting strains during therapy, suggesting that the quasispecies distribution of IRES sequences does not play a role in HCV resistance to interferon-alpha therapy. In contrast, the overall quasispecies distribution of HCV genomes (including IRES sequences) might participate in regulation of hepatic and extrahepatic HCV replication.
丙型肝炎病毒（HCV）多聚蛋白的翻译依赖于40S核糖体亚基通过位于病毒基因组5'非编码（5'NC）区域的内部核糖体进入片段（IRES）介导的直接内部进入。HCV在基因上具有异质性，其特征是在单个受感染个体内存在病毒群体的准种分布。采用克隆和测序策略对5'NC准种进行基因特征分析。与编码区相似，HCV 5'NC区域也以准种形式分布，但与HCV基因组的其他区域相比，它似乎受到更强的保守性限制，这可能是由于IRES需要结构（和功能）保守。实际上，大多数准种替换发生在IRES的非配对区域或成簇分布，从而维持碱基配对，而只有21%的替换预计会导致碱基配对的丧失。在由从四向连接点JIIIabc延伸的RNA螺旋组成的IRES结构域III的核心十字形结构中，可以预测到与准种相关的结构变化，大多发生在次要变体中，但有时也发生在主要变体中。此处给出的结果表明，受感染患者体内同时存在遗传上不同但密切相关的IRES序列混合物，这些序列可能具有不同的结构。除了混合基因型感染患者在治疗期间清除了其中一种感染毒株外，在干扰素-α治疗后未观察到5'NC准种的显著基因变化，这表明IRES序列的准种分布在HCV对干扰素-α治疗的抗性中不起作用。相反，HCV基因组（包括IRES序列）的整体准种分布可能参与肝脏和肝外HCV复制的调节。
