Virus infections and the host response.

The physiological response to virus infection is generally initiated at the cellular level following replication (tenOever, 2016). After virus entry, the infected cell detects the presence of virus replication through use of any one of a number of pattern recognition receptors (PRRs) (Janeway and Medzhitov, 2002). These receptors serve as sentinels for a variety of microbes both inside and outside of the cell by physically engaging distinct structures that are shared amongst different pathogens. In the case of virus infection, cellular detection of replication is largely mediated by a family of intracellular PRRs that sense aberrant RNA structures that often form during virus replication (Janeway and Medzhitov, 2002). Engagement of virus-specific RNA structures culminates in the oligomerization of these receptors and the activation of downstream transcription factors, most notably the interferon regulator factors (IRFs) and Nuclear Factor (NF) kB (Hur, 2019). Transcriptional activation of IRFs and NFkB results in the launching of two general antiviral programs. The first is the engagement of cellular antiviral defenses, which is mediated by the transcriptional induction of Type I and III interferons (IFN-I and IFN-III) and the subsequent upregulation of interferon stimulated genes (ISGs) (Lazear et al., 2019). The second arm of the antiviral response involves the recruitment and coordination of specific subsets of leukocytes, which is orchestrated primarily by chemokine secretion (Proudfoot, 2002; Sokol and Luster, 2015).

 

A recent study has provided important new insights into viral behavior and regulation of the host response following SARS-CoV-2 infection (Bianco-Melo et. al., 2020). This study examined the host transcriptional response to virus infection in a broad range of experimental systems. These systems included human airway epithelial cell lines, primary bronchial epithelial cells, animal model (ferret) and COVID-19 patients. Importantly, the gene expression response induced by SARS-CoV-2 infection was also compared to that induced by other highly pathogenic viruses and common respiratory viruses such as Influenza A virus (IAV), human parainfluenza virus type 3 (HPIV3), and respiratory syncytial virus (RSV). These studies revealed that SARS-CoV2 infection produced a unique and inappropriate inflammatory response that was characterized by reduced innate antiviral defenses coupled with exuberant inflammatory cytokine production are the defining and driving feature of COVID-19.

 

A highlight of these findings was the suppression of the antiviral response through inhibition of expression of Type-1 and Type-III interferons (IFN-I, IFN-III). As a result, the signaling response to both these classes of interferons was also diminished. Cellular antiviral defenses are primarily mediated through the transcriptional induction of Type-I and III interferons, which subsequently induce the upregulation of interferon-stimulated genes (ISGs). The importance of these two cytokine classes in driving the antiviral response was demonstrated by treating SARS-CoV2 infected cells with IFN-I. This led to a dramatic reduction of viral replication when detected at the level of both RNA and protein (Bianco-Melo et. al., 2020).

 

A surprising finding in these studies was that, despite a complete lack of IFN-I and III expression, the response to SARS-CoV2 infection still elicited a strong chemotactic and inflammatory response. This was indicated by increased expression of CCL20, CXCL1, IL-1B, IL-6, CXCL3, CXCL5, CXCL6, CXCL2, CXCL16, and TNF. These broad findings could be subsequently confirmed through longitudinal studies in ferrets, which were used as the animal model for infection. These studies revealed that the inflammatory cytokine response was initiated very early in the infection, which then continued to expand even as virus levels began to wane. Importantly, inflammatory cytokines persisted even after the clearance of the virus in these animals.

 

Finally, the COVID-19 infection-specific signature of low IFNI/II and high inflammatory cytokine/chemokine could also be confirmed in post mortem lung samples of COVID-19 patients. The gene expression profiles observed in the samples also correlated well with the pattern of circulating cytokines and chemokines seen in serum samples from a cohort of COVID-19 infected individuals. Based on these cumulative findings, it was suggested that while suppression of IFNI/III facilitated persistence and growth of infection, it was the concomitant induction of the inflammatory cytokines and chemokines that constituted the primary drivers of the signature pathology seen in COVID-19 patients.

 

How does the virus regulate host responses?

Viruses have evolved a spectrum of countermeasures to combat, and mitigate, the generation of antiviral responses by the host. Depending on the efficacy of these countermeasures, viruses inflict different degrees of morbidity and mortality. In general, modulation of the host response is achieved through the expression of viral proteins, which interact with their cellular counterparts within the intracellular milieu of the infected cell.  For example, in the closely

related SARS-CoV-1, IFN antagonism has been attributed to ORF3B, ORF6, and the nucleoprotein (N) gene products (Frieman et al., 2010; Kopecky-Bromberg et al., 2007). SARS-CoV-1 also encodes nsp1, a nuclease that has been implicated in cleaving host mRNA to prevent ribosomal loading and causing host shut-off (Kamitani et al., 2006). Similar to SARS-CoV-1, IAV also encodes the IFN-I/-III antagonist, nonstructural protein 1 (NS1), that blocks initial detection by the PRR through binding and masking aberrant RNA produced during infection (Garcia-Sastre et al., 1998).

 

A recent study has revealed that SARS-CoV-2 interacts extensively with the host cellular proteome, which presumably confers the virus with the potent capacity to modulate the host response. Thus, an interaction mapping of 26 of the 29 SARS-CoV-2 proteins, in infected cells, identified as many as 332 high-confidence SARS-CoV-2 and human protein-protein interactions (Gordon et. al., 2020). It is the tight regulatory capacity that such an interaction network potentially provides, which likely accounts for the robustness and pathogenicity of COVID-19 infections.

 

Refining drug repurposing strategies for the treatment of COVID-19 infections.

SARS- CoV-2 is transmitted primarily via respiratory droplets, with a possible, but unproven, fecal-oral transmission route. On infection, the median incubation period is approximately 4–5 days before symptom onset, with 97.5% of symptomatic patients developing symptoms within 11.5 days. At the point of hospital admission, patients with COVID-19 typically exhibit a fever and dry cough; less commonly, patients also experience difficulty in breathing, muscle and/or joint pain, headache/dizziness, diarrhea, nausea and the coughing up of blood. Within 5–6 days of symptom onset, SARS- CoV-2 viral load reaches its peak — significantly earlier than that of the related SARS- CoV, where viral load peaks at about 10 days after symptom onset. Severe COVID-19 cases progress to acute respiratory distress syndrome, on average around 8–9 days after symptom onset (reviewed in Tay et. al., 2020).

 

It is now clear that the pathophysiology of COVID-19 derives from an aggressive host inflammatory response (cytokine storm) that causes damage to the airways and, in more severe cases, also to multiple organs. That is, disease severity in infections is due to not only the virus infection but also the host response (Tay et. al., 2020). This implies that any treatment regimen for COVID-19 must not only target the virus but also attenuate the host inflammatory response. This latter component is especially important given recent findings that the inflammatory response persists even after the clearance of the virus (Bianco-Melo et. al., 2020).

 

These recent results – therefore – call for more informed approaches, when devising a drug repurposing strategy for the treatment of COVID-19 infections.

 

 

References

Bianco-Melo, D. Nissant-Payan, B.E., Liu, W-C., Uhl, S. et. al. (2020). Imbalanced host response to SARS-CoV-2 drives development of COVID-19. doi:10.1016/j.cell.2020.04.026

 

Frieman, M.B., Chen, J., Morrison, T.E., Whitmore, A., Funkhouser, W., Ward, J.M., Lamirande, E.W., Roberts, A., Heise, M., Subbarao, K., et al. (2010). SARS-CoV pathogenesis is regulated by a STAT1 dependent but a type I, II and III interferon receptor independent mechanism. PLoS Pathog 6, e1000849.

 

Garcia-Sastre, A., Egorov, A., Matassov, D., Brandt, S., Levy, D.E., Durbin, J.E., Palese, P., and Muster, T. (1998). Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. Virology 252, 324-330.

 

Gordon, D.E., Jang, G.M., Bouhaddou, M., Xu, J., Obernier, K. et. al. (2020) A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature https://doi.org/10.1038/ s41586-020-2286-9

 

Hawkis, P.T. and Stephens, L.R. (2014) PI3K signaling in inflammation. Biochem Biophys Acta http://dx.doi.org/10.1016/j.bbalip.2014.12.006

 

Hoffmann, M., Kliene-Weber, H., Schroeder, S., Kruger, N., Herrier, T. et. al. (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell https://doi.org/10.1016/j.cell.2020.02.052

 

Hur, S. (2019). Double-Stranded RNA Sensors and Modulators in Innate Immunity. Annu Rev Immunol 37, 349-375.

 

Janeway, C.A., Jr., and Medzhitov, R. (2002). Innate immune recognition. Annu Rev Immunol 20, 197-216.

 

Kamitani, W., Narayanan, K., Huang, C., Lokugamage, K., Ikegami, T., Ito, N., Kubo, H., and Makino, S. (2006). Severe acute respiratory syndrome coronavirus nsp1 protein suppresses host gene expression by promoting host mRNA degradation. Proc Natl Acad Sci U S A 103, 12885-12890.

 

Kopecky-Bromberg, S.A., Martinez-Sobrido, L., Frieman, M., Baric, R.A., and Palese, P. (2007). Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol 81, 548-557.

 

Lazear, H.M., Schoggins, J.W., and Diamond, M.S. (2019). Shared and Distinct Functions of Type I and Type III Interferons. Immunity 50, 907-923.

 

Proudfoot, A.E. (2002). Chemokine receptors: multifaceted therapeutic targets. Nat Rev Immunol 2, 106-115.

 

Sokol, C.L., and Luster, A.D. (2015). The chemokine system in innate immunity. Cold Spring Harb Perspect Biol 7.

 

 

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