As expected, an increase was observed in the number of significantly regulated phosphorylation sites and proteins over the infection time course, with the majority of regulation occurring at the level of phosphorylation (Figures 1E and 1F) as opposed to protein abundance (Figures 1G and 1H). Of the few proteins that significantly increased in abundance upon infection, the vast majority were SARS-CoV-2 viral proteins (Figure 1H). In contrast, the majority of host proteins decreased in abundance. This finding is consistent with mechanisms of host mRNA nuclear export and/or host mRNA translation inhibition, which are common in viral infections (Kuss et al., 2013; Walsh and Mohr 2011). Gene Ontology enrichment analysis of significantly downregulated proteins revealed several terms related to platelet regulation (Figures 1I and S1F). Several downregulated host proteins are known to be involved in platelet regulation, thrombosis, and prevention of blood coagulation, including APOH, CD9, TSPAN14, AHSG, SERPINA1, and A2M (Mather et al., 2016; Mangin et al., 2009; Taggart et al., 2000). The downregulation of these proteins suggests that they may mechanistically contribute to symptoms of blood coagulation and stroke in COVID-19 patients (Han et al., 2020).