Identification and characterization of viral and host factors determining virus replication fitness

Abstract

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.