Determinants of host cell tropism, viral innate immune evasion and attenuation in SARS-CoV-2

SARS-CoV-2是导致COVID-19的β冠状病毒，可感染肺上皮和胃肠道。尽管大多数人的病情一般较轻，但该病毒可在老年人和慢性炎症患者中引起毁灭性疾病和死亡。严重的COVID-19通常与广泛的免疫失调有关，免疫失调可导致明显的炎症反应，病毒传播到呼吸道以外，以及危及生命的细胞因子风暴。自2020年初首次测序以来，SARS-CoV-2获得了许多突变，产生了新的谱系，称为关注变体（VOCs），如a、b、g和d。获得性SARS-CoV-2突变与与其受体ACE2的结合亲和力增强、更有效的细胞进入、更高的病毒滴度和逃避单克隆抗体（mAb）治疗有关。然而，突变也可以改变对宿主来源的抗病毒因子的敏感性(1)，如i型干扰素，这对免疫控制具有重要意义。总之，这不仅强调了有效的免疫控制在清除SARS-CoV-2感染中的重要性，而且还强调了了解病毒如何对抗宿主先天免疫防御的必要性，这对于了解病毒发病机制和寻找新的治疗方法至关重要。在细胞水平上，I型干扰素通过上调ifn刺激基因（ISGs）来控制抗病毒反应，ISGs通过干扰病毒生命周期的各个方面来限制病毒的生长。已知具有抗SARS-CoV-2活性的isg包括ifn诱导的跨膜蛋白（IFITMs），如Neil实验室(2)所示。这些ifitm定位于质膜或内体，已知对几种病毒具有广泛的抗病毒活性。在SARS-CoV-2的情况下，我们发现IFITM2主要受病毒进入途径的限制。病毒研究的一个有趣的新兴领域是免疫控制和代谢之间的相互作用。由于代谢途径在调节炎症、免疫细胞分化和IFN产生方面的作用，病毒感染期间的代谢重布线是一种被充分观察到的现象，在免疫介导的病毒控制中具有重要意义。就SARS-CoV-2发病机制而言，分析轻度、中度和重度COVID-19患者的研究已经确定了不同的代谢特征，可以对患者进行分层，经常检测到氨基酸和脂质代谢的扰动（3-8）。这与其他代谢组学研究一致，发现血清中TCA代谢物减少，表明从氧化磷酸化到糖酵解作为主要ATP来源的转变，也被称为“Warburg效应”，可能是SARS-CoV-2感染的标志。然而，目前尚不清楚SARS-CoV-2如何重新连接细胞代谢组来影响免疫力，有几个重要的问题需要解决。首先，代谢重布线的机制基础尚不清楚。确定SARS-CoV-2如何重新连接受感染细胞的代谢组，将使当前的代谢研究从相关性分析扩展到因果关系。此外，确定代谢重组所需的特定病毒因子将提供可药物靶点。迄今为止还没有研究调查是否存在谱系特异性代谢组改变。关于这一点，在第1轮中，作为与药物科学研究所合作的一部分，我们确定了三种感兴趣的化合物（雷帕霉素、罗格列酮和替沙替尼），它们对SARS-CoV-2的复制有不同的影响。SARS-CoV-2对罗格列酮和替沙替尼都非常敏感，而雷帕霉素则增强了传染性。有趣的是，罗格列酮和雷帕霉素在代谢和免疫中具有双重作用。

SARS-CoV-2, the beta coronavirus responsible for COVID-19, infects the epithelium of the lung and the gastrointestinal tract. Despite a generally mild disease in most, the virus can cause devastating illness and mortality in the elderly and those with chronic inflammatory conditions. Severe COVID-19 is normally associated with extensive immune dysregulation that can lead to overt inflammatory responses, viral spread beyond the respiratory tract, and a life-threatening cytokine storm. Since it was first sequenced in early 2020, SARS-CoV-2 has acquired numerous mutations giving rise to new lineages known as variants of concern (VOCs) such as a, b, g, and D. Acquired SARS-CoV-2 mutations have been linked to enhanced binding affinity to its receptor ACE2, more efficient cell entry, higher viral titres and escape from monoclonal antibody (mAb) therapy. However, mutations can also alter sensitivity to host-derived antiviral factors (1), such as type-I interferons, which has important implications for immune control. Together, this highlights not only the importance of effective immune control in clearing SARS-CoV-2 infection, but also the need to understand how the virus antagonizes host innate immune defences which is of paramount importance for the understanding of viral pathogenesis and the search for novel therapeutics. At the cellular level, type I interferons govern the antiviral response by upregulating IFN-stimulated genes (ISGs) that restrict viral growth by interfering with various aspects of the viral lifecycle. ISGs with known activity against SARS-CoV-2 include the IFN-induced transmembrane proteins (IFITMs) as shown by the Neil Lab (2). These IFITMs are localized to either the plasma membrane or endosome and are known to have broad antiviral activity against several viruses. In the case of SARS-CoV-2 we found that IFITM2 is predominantly restrictive in a manner governed by route of viral entry. An intriguing and emerging area of viral research is the interplay between immune control and metabolism. Metabolic rewiring during viral infection is a well-observed phenomenon with important consequences in immune-mediated viral control due to the role metabolic pathways have in regulating inflammation, immune cell differentiation, and IFN production. In the case of SARS-CoV-2 pathogenesis, studies analysing mild, moderate, and severe COVID-19 patients have identified distinct metabolic signatures that can stratify patients, with perturbations in amino acid and lipid metabolism frequently detected (3-8). This is in line with other metabolomic studies identifying serum reductions in TCA metabolites, indicating that the switch from oxidative phosphorylation to glycolysis as the main ATP source, also known as the 'Warburg effect', is a likely hallmark of SARS-CoV-2 infection. However, it's unclear how SARS-CoV-2 rewires the cellular metabolome to influence immunity and there are several important questions that need to be addressed. Firstly, the mechanistic basis of metabolic rewiring remains unknown. Determining how SARS-CoV-2 rewires the metabolome of infected cells would extend current metabolic research from correlational analyses and towards cause and effect. Furthermore, identifying specific viral factors required for metabolic rewiring will provide druggable targets. No study to date has investigated if there are lineage-specific metabolome alterations. On that note, during rotation 1, as part of a collaboration with the Institute of Pharmaceutical Science, we identified three compounds of interest (rapamycin, rosiglitazone, and tesevatinib) with differential effects on SARS-CoV-2 replication. SARS-CoV-2 was exquisitely sensitive to both rosiglitazone and tesevatinib, whereas rapamycin was found to enhance infectivity. Interestingly, rosiglitazone and rapamycin have dual roles within metabolism and immunity.