Unité de Génomique Virale et Vaccination, CNRS UMR-3569, Institut Pasteur, Paris, France.
J Virol. 2014 Apr;88(8):4161-72. doi: 10.1128/JVI.03223-13. Epub 2014 Jan 29.
Lentiviral RNA genomes present a strong bias in their nucleotide composition with extremely high frequencies of A nucleotide in human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV). Based on the observation that human optimization of RNA virus gene fragments may abolish their ability to stimulate the type I interferon (IFN-I) response, we identified the most biased sequences along the SIV genome and showed that they are the most potent IFN-I stimulators. With the aim of designing an attenuated SIV genome based on a reduced capacity to activate the IFN-I response, we synthesized artificial SIV genomes whose biased sequences were optimized toward macaque average nucleotide composition without altering their regulatory elements or amino acid sequences. A synthetic SIV optimized with 169 synonymous mutations in gag and pol genes showed a 100-fold decrease in replicative capacity. Interestingly, a synthetic SIV optimized with 70 synonymous mutations in pol had a normal replicative capacity. Its ability to stimulate IFN-I was reduced when infected cells were cocultured with reporter cells. IFN regulatory factor 3 (IRF3) transcription factor was required for IFN-I stimulation, implicating cytosolic sensors in the detection of SIV-biased RNA in infected cells. No reversion of introduced mutations was observed for either of the optimized viruses after 10 serial passages. In conclusion, we have designed large-scale nucleotide-modified SIVs that may display attenuated pathogenic potential.
In this study, we synthesized artificial SIV genomes in which the most hyperbiased sequences were optimized to bring them closer to the nucleotide composition of the macaque SIV host. Interestingly, we generated a stable synthetic SIV optimized with 70 synonymous mutations in pol gene, which had a normal replicative capacity but a reduced ability to stimulate type I IFN. This demonstrates the possibility to rationally change viral nucleotide composition to design replicative and genetically stable lentiviruses with attenuated pathogenic potentials.
慢病毒 RNA 基因组在其核苷酸组成上存在强烈的偏向性，人类免疫缺陷病毒 1 型 (HIV-1) 和猿猴免疫缺陷病毒 (SIV) 中的 A 核苷酸频率极高。基于人类对 RNA 病毒基因片段的优化可能会消除其刺激 I 型干扰素 (IFN-I) 反应的能力的观察结果，我们确定了 SIV 基因组中最偏向的序列，并表明它们是最有效的 IFN-I 刺激物。为了设计一种基于降低激活 IFN-I 反应能力的减毒 SIV 基因组，我们合成了人工 SIV 基因组，其偏向序列针对猕猴平均核苷酸组成进行了优化，而不改变其调节元件或氨基酸序列。在 gag 和 pol 基因中优化了 169 个同义突变的合成 SIV 显示出复制能力降低了 100 倍。有趣的是，在 pol 中优化了 70 个同义突变的合成 SIV 具有正常的复制能力。当感染细胞与报告细胞共培养时，其刺激 IFN-I 的能力降低。IFN 调节因子 3 (IRF3) 转录因子是 IFN-I 刺激所必需的，这表明细胞溶质传感器在检测感染细胞中的 SIV 偏向性 RNA 中起作用。在优化后的病毒中，无论是哪种病毒，在经过 10 次连续传代后都没有观察到引入的突变发生回复。总之，我们设计了大规模核苷酸修饰的 SIV，它们可能表现出减毒的致病潜力。
在这项研究中，我们合成了人工 SIV 基因组，其中最偏向的序列被优化以使其更接近猕猴 SIV 宿主的核苷酸组成。有趣的是，我们生成了一种稳定的合成 SIV，在 pol 基因中优化了 70 个同义突变，其复制能力正常，但刺激 I 型 IFN 的能力降低。这表明有可能合理改变病毒核苷酸组成，设计具有减毒致病潜力的复制和遗传稳定的慢病毒。
