Evaluation and Limitations of Different Approaches Among COVID-19 Fatal Cases Using Whole-exome Sequencing Data (preprint)

Background: COVID-19 caused by SARS-CoV-2 infection may result in various disease symptoms and severity, ranging from asymptomatic, through mild, up to very severe and fatal cases. Although environmental, clinical, and social factors play important roles in both susceptibility to SARS-CoV-2 infection and COVID-19 disease progress, it is becoming evident that both pathogen and host genetic factors are important too. Here we report whole-exome sequencing (WES) findings of 27 individuals who died as a result of COVID-19 infection, especially focusing on frequencies of DNA variants in genes previously associated with SARS-CoV-2 infection and COVID-19 severity. Results: : We selected risk DNA variants/alleles or target genes using four different approaches: 1) aggregated GWAS results from the GWAS Catalog; 2) selected publications from PubMed; 3) the aggregated results of the Host Genetics Initiative database; and 4) a commercial DNA variant annotation/interpretation tool providing its own knowledgebase. We divided these variants/genes into those reported to influence the susceptibility to SARS-CoV-2 infection and those influencing COVID-19 severity. Based on these, we compared frequencies of alleles among the fatal COVID-19 cases to frequencies identified in two population control datasets (non-Finnish European population from the gnomAD database and genomic frequencies specific for the Slovak population from our own database). Our comparisons delineated a trend of higher frequencies of severe COVID-19 associated risk alleles among fatal COVID-19 cases, when compared to both control population datasets. This trend reached statistical significance specifically when using the HGI derived variant list. We also analyzed other approaches to WES data evaluation, where we showed their usage as well as limitations. Conclusions: : Although our results proved the likely involvement of host genetic factors pinned out by previous studies for COVID-19 disease severity, careful considerations about the molecular-testing strategies and the evaluated genomic positions may have a strong impact on the utility of genomic testing.

Mitoxantrone modulates a glycosaminoglycan-spike complex to inhibit SARS-CoV-2 infection (preprint)

Spike-mediated entry of SARS-CoV-2 into human airway epithelial cells is an attractive therapeutic target for COVID-19. In addition to protein receptors, the SARS-CoV-2 spike (S) protein also interacts with heparan sulfate, a negatively charged glycosaminoglycan (GAG) attached to certain membrane proteins on the cell surface. This interaction facilitates the engagement of spike with a downstream receptor to promote viral entry. Here, we show that Mitoxantrone, an FDA-approved topoisomerase inhibitor, targets a spike-GAG complex to compromise the fusogenic function of spike in viral entry. As a single agent, Mitoxantrone inhibits the infection of an authentic SARS-CoV-2 strain in a cell-based model and in human lung EpiAirway 3D tissues. Gene expression profiling supports the plasma membrane as a major target of Mitoxantrone but also underscores an undesired activity targeting nucleosome dynamics. We propose that Mitoxantrone analogs bearing similar GAG-binding activities but with reduced affinity for DNA topoisomerase may offer an alternative therapy to overcome breakthrough infections in the post-vaccine era.

B.1.1.7 and B.1.351 variants are highly virulent in K18-ACE2 transgenic mice and show different pathogenic patterns from early SARS-CoV-2 strains (preprint)

SARS-CoV-2 continues to circulate globally resulting in emergence of several variants of concern (VOC), including B.1.1.7 and B.1.351 that show increased transmissibility and enhanced resistance to antibody neutralization. In a K18-hACE2 transgenic mouse model, we demonstrate that Both B.1.1.7 and B.1.351 are 100 times more lethal than the original SARS-CoV-2 bearing 614D. Mice infected with B.1.1.7 and B.1.351 exhibited more severe lesions in internal organs than those infected with early SARS-CoV-2 strains bearing 614D or 614G. Infection of B.1.1.7 and B.1.351 also results in distinct tissue-specific cytokine signatures, significant D-dimer depositions in vital organs and less pulmonary hypoxia signaling before death as compared to the mice infected with early SARS-CoV-2 strains. However, K18-hACE2 mice with the pre-existing immunity from prior infection or immunization were resistant to the lethal reinfection of B.1.1.7 or B.1.351, despite having reduced neutralization titers against these VOC. Our study reveals distinguishing pathogenic patterns of B.1.1.7 and B.1.351 variants from those early SARS-CoV-2 strains in K18-hACE2 mice, which will help to inform potential medical interventions for combating COVID-19.