Le Guillou-Guillemette Hélène, Pivert Adeline, Bouthry Elise, Henquell Cécile, Petsaris Odile, Ducancelle Alexandra, Veillon Pascal, Vallet Sophie, Alain Sophie, Thibault Vincent, Abravanel Florence, Rosenberg Arielle A, André-Garnier Elisabeth, Bour Jean-Baptiste, Baazia Yazid, Trimoulet Pascale, André Patrice, Gaudy-Graffin Catherine, Bettinger Dominique, Larrat Sylvie, Signori-Schmuck Anne, Saoudin Hénia, Pozzetto Bruno, Lagathu Gisèle, Minjolle-Cha Sophie, Stoll-Keller Françoise, Pawlotsky Jean-Michel, Izopet Jacques, Payan Christopher, Lunel-Fabiani Françoise, Lemaire Christophe
Laboratoire de Virologie, CHU Angers, France.
HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
PLoS One. 2017 Apr 10;12(4):e0174651. doi: 10.1371/journal.pone.0174651. eCollection 2017.
The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies.
Direct sequencing of the entire NS5A and E1 genes was performed on 27 mutant strains. Quasispecies analyses in consecutive samples were also performed by cloning and sequencing the NS5A gene for all mutant and wild strains. We analyzed the mutant and wild-type sequence polymorphisms using Bayesian methods to infer the evolutionary history of and the molecular mechanism leading to the duplication-like event.
Quasispecies were entirely composed of exclusively mutant or wild-type strains respectively. Mutant quasispecies were found to have been present since contamination and had persisted for at least 10 years. This V3 duplication-like event appears to have resulted from non-homologous recombination between HCV-1b wild-type strains around 100 years ago. The association between increased liver disease severity and these HCV-1b mutants may explain their persistence in chronically infected patients.
These results emphasize the possible consequences of non-homologous recombination in the emergence and severity of new viral diseases.
RNA病毒新毒株的出现主要归因于突变或基因型内及基因型间的同源重组。非同源重组可能是有害的，且很少被检测到。在先前的研究中，我们鉴定出在NS5A基因中带有两个串联重复V3区域且开放阅读框未受破坏的HCV-1b毒株。这种多态性可能与肝病的不良病程相关，并可能参与肝癌的发生。在此，我们旨在表征这些突变毒株的起源，并确定V3重复所依赖的进化机制。
对27个突变毒株的整个NS5A和E1基因进行直接测序。还通过对所有突变株和野生株的NS5A基因进行克隆和测序，对连续样本进行准种分析。我们使用贝叶斯方法分析突变株和野生型序列多态性，以推断导致类似重复事件的进化历史和分子机制。
准种分别完全由突变株或野生株组成。发现突变准种自感染以来就已存在，并持续了至少10年。这种V3类似重复事件似乎是大约100年前HCV-1b野生型毒株之间非同源重组的结果。肝病严重程度增加与这些HCV-1b突变体之间的关联可能解释了它们在慢性感染患者中的持续存在。
这些结果强调了非同源重组在新病毒性疾病出现和严重程度方面可能产生的后果。
