Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity–associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

We assay the utility of the single-test IMX-BVN-3/IMX-SEV-3 classifiers that require just 2.5 mL of patient blood in concurrently detecting viral and bacterial infections as well as predicting the severity and 30-day outcome from the infection. A point-of-care device, in development, will circumvent the need for blood culturing and drastically reduce the time needed to detect an infection.

SARS-CoV-2 is a novel respiratory virus that has quickly spread across the globe. The virus uses a protein called Spike and its associated receptor binding domain (RBD) to interact with angiotensin converting enzyme-2 (ACE-2) on the surface of epithelial cells in the respiratory tract. Although a definite correlate of protection against COVID-19 has yet to emerge, many studies have quantified anti-Spike and anti-RBD IgG antibody (Ab) levels, as well as neutralizing Ab in the blood to ascertain immunity. This approach misses out on Ab that are produced in the upper respiratory tract (URT) mucosa – the site of viral encounter. Whether intramuscularly (i.m.) administered COVID-19 vaccines can promote immunity in the mucosa is not well understood. We recently completed a study where we showed that anti-Spike/RBD IgG could be detected in the saliva following i.m. vaccination with either two doses of mRNA vaccines (Pfizer or Moderna) or with a heterologous dosing of Astra Zeneca followed by an mRNA vaccine. Administration of a second dose of mRNA boosted the IgG but not IgA response, with only 30% of participants remaining positive for IgA at this timepoint. At 6 months post-dose 2, these participants had diminished anti-Spike/RBD IgG levels, although secretory component associated anti-Spike Ab were more stable. Examining two prospective cohorts we found that participants who experienced breakthrough infections with SARS-CoV-2 had lower levels of vaccine-induced serum anti-Spike/RBD IgA at 2–4 weeks post-dose 2 compared to participants who did not experience an infection, whereas IgG levels were comparable between groups. These data suggest that COVID-19 vaccines that elicit a durable IgA response may have utility in preventing infection. We received funding support from CIHR (Fund #15992), a COVID-19 Immunity Task force grant, an “Ontario Together” province of Ontario grant, a CIHR team grant to CoVARR-Net, a Donation from the Royal Bank of Canada (RBC) and a donation from the Krembil Foundation to the Sinai Health System Foundation.

Neutralizing activity found in the blood following intramuscular vaccination protects against systemic disease from SARS-CoV-2 infection. Mild breakthrough mucosal infections in vaccinated individuals can contribute to transmission chains of infection, and as such the contribution of intramuscular vaccination to mucosal immunity is important to understand. We assessed vesicular stomatitis virus (VSV) SARS-CoV-2 SPIKE protein neutralization activities as well as anti-viral spike and RBD IgG and IgA isotype antibody binding, in saliva from individuals who had recovered from SARS-CoV-2 infection and people who received immunization. The various vaccination strategies deployed globally showed key differences in the extent of neutralizing activity that could be measured. Even in subjects with significant peak activity 2–4 weeks following a second dose of mRNA vaccination, this neutralizing activity was transient and significantly reduced within 3–6 months. Among adenoviral vectors, ChAdOx1 elicited significantly more salivary neutralizing activity and antibody levels compared to Ad26.S. A large range of salivary neutralizing activity is induced following different intramuscular SARS-COV-2 vaccination strategies. All were orders of magnitude lower than neutralization levels observed in blood, and it remains to be determined if any of the observed neutralizing activity in the saliva can neutralize virus in the upper respiratory tract upon exposure. Based on studies where high levels of mucosal IgA antibodies were induced in response to stimulation with aerosol intranasal vaccines, such vaccines could be important in lowering transmission of SARS-COV-2. Supported by The Fairbairn Foundation and SPARK