Sims Anna, Weir Daniel J, Cole Sarah J, Hutchinson Edward
MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom.
J Virol. 2025 Apr 15;99(4):e0207724. doi: 10.1128/jvi.02077-24. Epub 2025 Mar 21.
The coinfection of individual cells is a requirement for exchange between two or more virus genomes, which is a major mechanism driving virus evolution. Coinfection is restricted by a mechanism known as superinfection exclusion (SIE), which prohibits the infection of a previously infected cell by a related virus after a period of time. SIE regulates coinfection for many different viruses, but its relevance to the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was unknown. In this study, we investigated this using a pair of SARS-CoV-2 variant viruses encoding distinct fluorescent reporter proteins. We show for the first time that SARS-CoV-2 coinfection of individual cells is limited temporally by SIE. We defined the kinetics of the onset of SIE for SARS-CoV-2 in this system, showing that the potential for coinfection starts to diminish within the first hour of primary infection and then falls exponentially as the time between the two infection events is increased. We then asked how these kinetics would affect the potential for coinfection with viruses during a spreading infection. We used plaque assays to model the localized spread of SARS-CoV-2 observed in infected tissue and showed that the kinetics of SIE restrict coinfection-and therefore sites of possible genetic exchange-to a small interface of infected cells between spreading viral infections. This indicates that SIE, by reducing the likelihood of coinfection of cells, likely reduces the opportunities for genetic exchange between different strains of SARS-CoV-2 and therefore is an underappreciated factor in shaping SARS-CoV-2 evolution.
Since SARS-CoV-2 first emerged in 2019, it has continued to evolve, occasionally generating variants of concern. One of the ways that SARS-CoV-2 can evolve is through recombination, where genetic information is swapped between different genomes. Recombination requires the coinfection of cells; therefore, factors impacting coinfection are likely to influence SARS-CoV-2 evolution. Coinfection is restricted by SIE, a phenomenon whereby a previously infected cell becomes increasingly resistant to subsequent infection. Here we report that SIE is activated following SARS-CoV-2 infection and reduces the likelihood of coinfection exponentially following primary infection. Furthermore, we show that SIE prevents coinfection of cells at the boundary between two expanding areas of infection, the scenario most likely to lead to recombination between different SARS-CoV-2 lineages. Our work suggests that SIE reduces the likelihood of recombination between SARS-CoV-2 genomes and therefore likely shapes SARS-CoV-2 evolution.
单个细胞的共感染是两个或多个病毒基因组之间进行交换的必要条件，这是推动病毒进化的主要机制。共感染受到一种称为超感染排除（SIE）的机制的限制，该机制在一段时间后禁止相关病毒感染先前已感染的细胞。SIE对许多不同病毒的共感染进行调节，但其与严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染的相关性尚不清楚。在本研究中，我们使用一对编码不同荧光报告蛋白的SARS-CoV-2变异病毒对此进行了研究。我们首次表明，SIE在时间上限制了单个细胞的SARS-CoV-2共感染。我们确定了该系统中SARS-CoV-2的SIE起始动力学，表明共感染的可能性在初次感染的第一小时内开始降低，然后随着两次感染事件之间时间的增加呈指数下降。然后，我们研究了这些动力学将如何影响在传播感染期间与病毒共感染的可能性。我们使用噬斑测定法对在受感染组织中观察到的SARS-CoV-2局部传播进行建模，并表明SIE动力学将共感染（以及因此可能发生基因交换的位点）限制在传播病毒感染之间受感染细胞的一个小界面处。这表明，SIE通过降低细胞共感染的可能性，可能减少了不同SARS-CoV-2毒株之间基因交换的机会，因此是塑造SARS-CoV-2进化中一个未被充分认识的因素。
自2019年SARS-CoV-2首次出现以来，它一直在持续进化，偶尔会产生令人担忧的变异株。SARS-CoV-2进化的方式之一是通过重组，即不同基因组之间交换遗传信息。重组需要细胞的共感染；因此，影响共感染的因素可能会影响SARS-CoV-2的进化。共感染受到SIE的限制，这是一种先前感染的细胞对后续感染越来越有抵抗力的现象。在此我们报告，SIE在SARS-CoV-2感染后被激活，并在初次感染后呈指数级降低共感染的可能性。此外，我们表明，SIE可防止在两个扩展感染区域之间的边界处细胞共感染，这种情况最有可能导致不同SARS-CoV-2谱系之间的重组。我们的工作表明，SIE降低了SARS-CoV-2基因组之间重组的可能性，因此可能塑造了SARS-CoV-2的进化。
