Supporting data for ‘Identification and Characterization of Viral and Host Factors Determining Virus Replication Fitness’

The understanding of viral fitness, a critical factor in viral transmission and evolution, remains incomplete, particularly regarding its dynamic flexibility in response to environmental pressure and within-host evolutionary mechanisms. The ongoing evolutionary trajectory of SARS-CoV-2 presents an opportunity for in-depth analysis of viral adaptability, especially to understand how variants of concern (VOC) impact viral fitness landscape.In my study, an investigation into the fitness of the Omicron BA.1 variant was conducted in comparison to the previously dominant Delta variant using a Syrian hamster model of COVID-19. The data revealed that the Delta variant initially demonstrated a higher fitness advantage than the Omicron variant in both in vitro and in vivo competition models without selection pressure. However, when immune selection pressure was introduced, the Omicron variant significantly outcompeted the Delta variant. Further investigations on the replication efficiency of Omicron BA.1 and BA.2 sub-lineages in cell cultures and a Syrian hamster model demonstrated a notable compromise in the fitness of the BA.1 variant due to the BA.1-specific spike mutation G496S. This discovery potentially explains the observed rising prevalence of BA.2 over BA.1.In parallel, when examining the host factors that control viral replication fitness, I discovered a close correlation between the heterogeneity of host glucose metabolism and the pathogenic damage induced by viral infection. The research revealed that the modulation of D-mannose flux rewires the virus-triggered immunometabolic response cascade, thereby reducing tissue damage. From a mechanistic perspective, D-mannose slows down glycolysis, which in turn limits the production of mitochondrial reactive oxygen species and succinate-mediated hypoxia-inducible factor-1α signal pathway, consequently leads to a decrease in proinflammatory cytokine production incited by the virus. Interestingly, the combined application of D-mannose and antiviral monotherapy demonstrates synergistic effects in vivo, even with delayed antiviral treatment in a mouse model of viral infections. Moreover, this research found that phosphomannose isomerase (PMI) activity governs the beneficial effects of D-mannose. Nevertheless, D-mannose does not inhibit PMI activity or viral fitness. To sum up, a PMI-focused therapeutic strategy can eliminate viral infection, while D-mannose treatment can reprogram glycolysis to manage collateral damage.Overall, this study shed light on the fitness capability and immune response characteristics of the Omicron and Delta variants and the evolutionary dynamics between BA.1 and BA.2 sub-lineages. It is beneficial to develop innovative vaccines and antiviral therapeutics to combat the emergent Omicron variant and its sub-lineages. The novel antiviral strategy revealed an exciting opportunity to inhibit PMI activity or to use D-mannose administration to reconfigure glycolysis metabolic pathways and mitigate collateral damage caused by virus infection.

对于病毒适应性而言，病毒复制力是一个至关重要的因素，它在病毒传播和进化过程中所展现出的动态灵活性，尤其是在应对环境压力和宿主内进化机制方面，其理解仍不完整。SARS-CoV-2的持续进化轨迹为深入分析病毒的适应性提供了契机，尤其是为了理解关切变异体（VOC）如何影响病毒复制力景观。在我的研究中，通过叙利亚仓鼠的COVID-19模型，对Omicron BA.1变异体的复制力进行了调查，并将其与之前占主导地位的Delta变异体进行了比较。数据表明，在体外和体内竞争模型中，未受到选择压力的影响时，Delta变异体最初在复制力上比Omicron变异体具有更高的优势。然而，当引入免疫选择压力时，Omicron变异体显著超越了Delta变异体。进一步对Omicron BA.1和BA.2亚系在细胞培养和叙利亚仓鼠模型中的复制效率的研究表明，由于BA.1特异性刺突突变G496S，BA.1变异体的复制力有所下降。这一发现可能解释了BA.2在BA.1之上流行率上升的现象。与此同时，在审视控制病毒复制力的宿主因素时，我发现宿主葡萄糖代谢的异质性与病毒感染引起的病理性损伤之间存在密切关联。研究揭示了通过调节D-甘露糖通量，病毒触发的免疫代谢反应级联重连，从而减轻组织损伤。从机制角度来看，D-甘露糖减缓了糖酵解，进而限制了线粒体活性氧和琥珀酸介导的缺氧诱导因子-1α信号通路的产生，最终导致由病毒引发的促炎细胞因子产生的减少。有趣的是，D-甘露糖与抗病毒单疗法的联合应用在体内表现出协同效应，即使在病毒感染小鼠模型中延迟抗病毒治疗的情况下也是如此。此外，这项研究还发现，磷酸甘露糖异构酶（PMI）活性调控了D-甘露糖的益处。尽管如此，D-甘露糖并不抑制PMI活性或病毒复制力。总之，以PMI为焦点的治疗策略可以消除病毒感染，而D-甘露糖治疗可以重新编程糖酵解来管理附带损伤。总体而言，本研究揭示了Omicron和Delta变异体的复制力能力和免疫反应特征，以及BA.1和BA.2亚系之间的进化动态。开发创新的疫苗和抗病毒疗法以应对新兴的Omicron变异体及其亚系是有益的。揭示的新型抗病毒策略为抑制PMI活性或利用D-甘露糖给药重新配置糖酵解代谢途径，以减轻病毒感染引起的附带损伤提供了令人兴奋的机会。