Viral Recombination Section, HIV Dynamics and Replication Program, NCI, Frederick, Maryland, USA.
Viral Mutation Section, HIV Dynamics and Replication Program, NCI, Frederick, Maryland, USA.
mBio. 2022 Oct 26;13(5):e0222022. doi: 10.1128/mbio.02220-22. Epub 2022 Aug 29.
Frequent recombination is a hallmark of retrovirus replication. In rare cases, recombination occurs between distantly related retroviruses, generating novel viruses that may significantly impact viral evolution and public health. These recombinants may initially have substantial replication defects due to impaired interactions between proteins and/or nucleic acids from the two parental viruses. However, given the high mutation rates of retroviruses, these recombinants may be able to evolve improved compatibility of these viral elements. To test this hypothesis, we examined the adaptation of chimeras between two distantly related human pathogens: HIV-1 and HIV-2. We constructed HIV-1-based chimeras containing the HIV-2 nucleocapsid (NC) domain of Gag or the two zinc fingers of HIV-2 NC, which are critical for specific recognition of viral RNA. These chimeras exhibited significant defects in RNA genome packaging and replication kinetics in T cells. However, in some experiments, the chimeric viruses replicated with faster kinetics when repassaged, indicating that viral adaptation had occurred. Sequence analysis revealed the acquisition of a single amino acid substitution, S18L, in the first zinc finger of HIV-2 NC. This substitution, which represents a switch from a conserved HIV-2 residue to a conserved HIV-1 residue at this position, partially rescued RNA packaging and replication kinetics. Further analysis revealed that the combination of two substitutions in HIV-2 NC, W10F and S18L, almost completely restored RNA packaging and replication kinetics. Our study demonstrates that chimeras of distantly related retroviruses can adapt and significantly enhance their replication by acquiring a single substitution. Novel retroviruses can emerge from recombination between distantly related retroviruses. Most notably, HIV-1 originated from zoonotic transmission of a novel recombinant (SIV) into humans. Newly generated recombinants may initially have significant replication defects due to impaired interactions between viral proteins and/or nucleic acids, such as between and -acting elements from the two parental viruses. However, provided that the recombinants retain some ability to replicate, they may be able to adapt and repair the defective interactions. Here, we used HIV-1 and HIV-2 Gag chimeras as a model system for studying the adaptation of recombinant viruses. We found that only two substitutions in the HIV-2 NC domain, W10F and S18L, were required to almost fully restore RNA genome packaging and replication kinetics. These results illustrate the extremely flexible nature of retroviruses and highlight the possible emergence of novel recombinants in the future that could pose a significant threat to public health.
频繁重组是逆转录病毒复制的一个标志。在极少数情况下，重组会发生在远缘逆转录病毒之间，产生新的病毒，这些病毒可能会对病毒进化和公共卫生产生重大影响。这些重组体最初可能由于来自两个亲本病毒的蛋白质和/或核酸之间的相互作用受损而具有显著的复制缺陷。然而，鉴于逆转录病毒的高突变率，这些重组体可能能够进化出这些病毒元件更好的兼容性。为了检验这一假设，我们研究了两种远缘人类病原体之间的嵌合体的适应性：HIV-1 和 HIV-2。我们构建了基于 HIV-1 的嵌合体，其中包含 HIV-2 Gag 的核衣壳（NC）结构域或 HIV-2 NC 的两个锌指，这对于病毒 RNA 的特异性识别至关重要。这些嵌合体在 T 细胞中表现出 RNA 基因组包装和复制动力学的显著缺陷。然而，在一些实验中，当重新传代时，嵌合病毒的复制速度更快，表明病毒已经适应了环境。序列分析显示，HIV-2 NC 的第一个锌指中获得了一个单一的氨基酸取代，S18L。这种取代代表了从该位置上保守的 HIV-2 残基到保守的 HIV-1 残基的转变，部分挽救了 RNA 包装和复制动力学。进一步的分析表明，HIV-2 NC 中的两个取代，W10F 和 S18L 的组合，几乎完全恢复了 RNA 包装和复制动力学。我们的研究表明，远缘逆转录病毒的嵌合体可以通过获得单个取代来适应并显著增强其复制能力。新的逆转录病毒可以通过远缘逆转录病毒之间的重组而产生。值得注意的是，HIV-1 起源于一种新型重组体（SIV）从动物传播到人类。由于新生成的重组体在病毒蛋白和/或核酸之间的相互作用受损，例如在来自两个亲本病毒的顺式作用元件之间，它们最初可能具有显著的复制缺陷。然而，只要重组体保留一些复制能力，它们就有可能适应并修复有缺陷的相互作用。在这里，我们使用 HIV-1 和 HIV-2 Gag 嵌合体作为研究重组病毒适应的模型系统。我们发现，仅 HIV-2 NC 结构域中的两个取代，W10F 和 S18L，就几乎完全恢复了 RNA 基因组包装和复制动力学。这些结果说明了逆转录病毒具有极其灵活的性质，并强调了未来可能出现新的重组体，这可能对公共卫生构成重大威胁。
