SARS-CoV-2 Defective Interfering Particles

Coronaviruses show high rates of recombination which leads to the generation of defective viral genomes (DVGs). The vast majority of DVGs represent dead-end products as they lack essential cis-acting elements for replication or packaging. However, under appropriate propagation conditions (i.e., high multiplicity of infection [moi]), DVGs can emerge that have lost significant coding potential yet retain the ability to propagate in the presence of parental virus. These DVGs attenuate viral titers by competing with the parental virus for limiting resources and have been coined defective interfering (DI) particles. We isolated DIs arising from serially passaged SARS-CoV-2 and present their genetic and functional characterization. The SARS-CoV-2 DI genomes encoded a novel Nsp1-10 fusion protein and behave as DIs to attenuate viral replication. Synthetic variants of SARS-CoV-2 DI genomes can be engineered as conditional, gene delivery vehicles.

冠状病毒具有较高的重组率，可诱导缺陷型病毒基因组（defective viral genomes，DVGs）的产生。绝大多数DVGs为终末无效产物，因其缺失了病毒复制与包装所必需的顺式作用元件。然而，在适宜的增殖条件下（即高感染复数[multiplicity of infection，MOI]），会出现一类特殊的DVGs：它们虽丧失了大量编码潜能，却仍可在亲本病毒存在时完成增殖。这类DVGs通过与亲本病毒竞争有限的增殖资源，进而降低病毒滴度，因此被命名为缺陷干扰颗粒（defective interfering，DI颗粒）。本研究分离得到了源自连续传代新型冠状病毒（SARS-CoV-2）的DI颗粒，并对其遗传与功能特征进行了系统表征。该新型冠状病毒的DI基因组编码一种全新的Nsp1-10融合蛋白，可作为DI颗粒发挥作用，抑制病毒复制。可对新型冠状病毒DI基因组的合成变体进行工程化改造，将其开发为条件性基因递送载体。