Fusion machinery of coronavirus Spike

Coronaviruses (CoVs) are important pathogens in human medicine, as demonstrated by the dual phenomenon of zoonotic emergence of highly pathogenic respiratory viruses at the beginning of the century (SARS-CoV-1 in 2002 and MERS-CoV in 2012), preceding a third emergence that led to the Covid-19 pandemic caused by SARS-CoV-2. Before gaining the interest of the scientific community in human medicine, CoVs were already considered significant viruses in veterinary medicine. They can indeed cause severe diseases in domestic and farm animals, with a complex pathophysiology, exhibiting for instance a dual digestive and respiratory tropism. Some of these viruses, such as porcine CoVs, can jeopardize both the industry and the animal welfare. An emblematic example is the reemergence of PEDV (porcine epidemic diarrhea virus) in the United States in 2013, which decimated 10% of the national pig herd. PEDV now threatens multiple areas in the world similarly as other animal CoVs which have recently emerged, mainly in pigs. This includes PDCoV (porcine delta-CoV), discovered in 2009, and SADS-CoV (swine acute diarrhea syndrome CoV), isolated in 2016, both of which cause as PEDV an acute digestive illness in piglets with high lethality rates. No antiviral is available for these three viruses. Vaccines exist for PEDV but they face challenges due to the emergence of viral variants in the Spike gene that escape neutralizing antibodies. Importantly, both SADS-CoV and PDCoV have a documented zoonotic potential. Lastly, it is alarming that some of porcine CoVs such as PEDV are capable of multiplying in the upper respiratory tract and transmitting through airborne routes, making it difficult to control epidemics and highlighting the panzootic risk of these viruses.

 There are four phylogenetic groups within CoVs: α, β, γ, and δ. Human CoVs responsible for severe pulmonary diseases all belong to the phylogenetic group of β-CoVs, and these are now well characterized. However, viruses belonging to the other groups exhibit unique characteristics, particularly in viral entry mechanisms, which remain poorly understood. PEDV and SADS-CoV are α-CoVs, while PDCoV is a δ-CoV. Studying the mechanisms by which these important pathogens for animal health infect cells is essential to limit infections and to prevent the zoonotic risk posed by an α- or δ-CoV.

The Spike protein of CoVs is a key protein: 1) it is the main target of antibodies elicited after vaccination or natural infections, and viral escape associated with mutations in the Spike gene makes vaccines inefficient against porcine CoVs; 2) it is the protein mediating virus entry after binding to carbohydrates present at the cell surface and/or specific protein receptor(s). The Spike proteins of α- and δ-CoVs have been far less characterized than the Spikes of β-CoVs, and it is important to note that CoV Spikes exhibit an exceptional functional and structural diversity.

We are studying use emerging, potentially zoonotic and pathogenic porcine CoVs as models to study the functional diversity of the Spike proteins of α- and δ-CoVs, paving the way to the development of antivirals blocking the virus entry. We use cellular systems such as pseudoviruses and cell-cell fusion assays to functionnaly and structurally characterize different ligands targeting their Spike protein, and also wich to study the molecular and cellular determinants of the fusion machinery.