Seasonal Human Coronaviruses OC43, 229E, and NL63 Induce Cell Surface Modulation of Entry Receptors and Display Host Cell-Specific Viral Replication Kinetics (preprint)

The emergence of the COVID-19 pandemic prompted increased interest in seasonal human coronaviruses. 229E, OC43, NL63 and HKU1 are endemic seasonal coronaviruses that cause the common cold and are associated with generally mild respiratory symptoms. In this study, we identified cell lines that exhibited cytopathic effects (CPE) upon infection by three of these coronaviruses and characterized their viral replication kinetics and the effect of infection on host surface receptor expression. We found that NL63 produced CPE in LLC-MK2 cells, while OC43 produced CPE in MRC-5, HCT-8 and WI-38 cell lines, while 229E produced CPE in MRC-5 and WI-38 by day 3 post-infection. We observed a sharp increase in nucleocapsid and spike viral RNA (vRNA) from day 3 to day 5 post-infection for all viruses, however the abundance and the proportion of vRNAs copies measured in the supernatants and cell lysates of infected cells varied considerably depending on the virus-host cell pair. Importantly, we observed modulation of coronavirus entry and attachment receptors upon infection. Infection with 229E and OC43 led to a downregulation of CD13 and GD3, respectively. In contrast, infection with NL63, and also with OC43, lead to an increase in ACE2 expression. Attempts to block entry of NL63 using either soluble ACE2 or anti-ACE2 monoclonal antibodies demonstrated the potential of these strategies to greatly reduce infection. Overall, our results enable a better understanding of seasonal coronaviruses infection kinetics in permissive cell lines, and reveal entry receptor modulation that may have implications in facilitating co-infections with multiple coronaviruses in humans. IMPORTANCESeasonal human coronavirus are an important cause of the common cold associated with generally mild upper respiratory tract infections that can result in respiratory complications for some individuals. There are no vaccines available for these viruses, with only limited antiviral therapeutic options to treat the most severe cases. A better understanding of how these viruses interact with host cells is essential to identify new strategies to prevent infection-related complications. By analyzing viral replication kinetics in different permissive cell lines, we find that cell-dependent host factors influence how viral genes are expressed and virus particles released. We also analyzed entry receptor expression on infected cells and found that these can be up or down modulated depending on the infecting coronavirus. Our findings raise concerns over the possibility of infection enhancement upon co-infection by some coronaviruses, which may facilitate genetic recombination and the emergence of new variants and strains.

Relative Ratios of Human Seasonal Coronavirus Antibodies Predict the Efficiency of Cross-Neutralization of SARS-CoV-2 Spike Binding to ACE2 (preprint)

Antibodies raised against highly prevalent human seasonal coronaviruses (sCoVs), which are responsible for the common cold, are known to cross-react with SARS-CoV-2 antigens. This cross-reactivity prompts questions about their protective role against SARS-CoV-2 infections and COVID-19 disease severity. However, the relationship between sCoV exposure and SARS-CoV-2 correlates of protection have not been clearly identified. Here we performed a cross-sectional analysis of cross-reactivity and cross-neutralization to three SARS-CoV-2 antigens using pre-pandemic serum from four different groups: pediatrics and adolescents (<21 yrs of age), persons 21 to 70 yrs of age, persons older than 70 yrs of age, and persons living with HCV or HIV. We find that antibody cross-reactivity to SARS-CoV-2 antigens varied between 1.6% and 15.3% depending on the cohort and the isotype-antigen pair analyzed. We also demonstrate a broad range of neutralizing activity (0-45%) in pre-pandemic serum that interferes with SARS-CoV-2 spike attachment to ACE2. While the abundance of sCoV antibodies did not directly correlate with neutralization efficiency, by using machine learning methodologies, we show that neutralizing activity is rather dependent on the latent variables related to the pattern ratios of sCoVs antibodies presented by each person. These were independent of age or sex, and could be accurately predicted by comparing the relative ratios of IgGs in sera directed to NL63, 229E, HKU-1, and OC43 spike proteins. More specifically, we identified antibodies to NL63 and OC43 as being the two most important predictors of latent variables responsible for protection, and 229E as being the least weighted. Our data support that exposure to sCoVs triggers various cellular and immune responses that influence the efficiency of SARS-CoV-2 spike binding to ACE2, and may impact COVID-19 disease severity through various other latent variables.