Host genome analysis of structural variations by Optical Genome Mapping provides clinically valuable insights into genes implicated in critical immune, viral infection, and viral replication pathways in patients with severe COVID-19

Abstract

BackgroundThe varied clinical manifestations and outcomes in patients with SARS-CoV-2 infections implicate a role of host-genetics in the predisposition to disease severity. This is supported by evidence that is now emerging, where initial reports identify common risk factors and rare genetic variants associated with high risk for severe/ life-threatening COVID-19. Impressive global efforts have focused on either identifying common genetic factors utilizing short-read sequencing data in Genome-Wide Association Studies (GWAS) or whole-exome and genome studies to interrogate the human genome at the level of detecting single nucleotide variants (SNVs) and short indels. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs) including copy number variants (CNVs), which account for a substantial proportion of variation among individuals. Thus, we investigated the host genomes of individuals with severe/life-threatening COVID-19 at the level of large SVs (500bp-Mb level) to identify events that might provide insight into the inter-individual clinical variability in clinical course and outcomes of COVID-19 patients.MethodsOptical genome mapping using Bionano’s Saphyr® system was performed on thirty-seven severely ill COVID-19 patients admitted to intensive care units (ICU). To extract candidate SVs, three distinct analyses were undertaken. First, an unbiased whole-genome analysis of SVs was performed to identify rare/unique genic SVs in these patients that did not appear in population datasets to determine candidate loci as decisive predisposing factors associated with severe COVID-19. Second, common SVs with a population frequency filter was interrogated for possible association with severe COVID-19 based on literature surveys. Third, genome-wide SV enrichment in severely ill patients versus the general population was investigated by calculating odds ratios to identify top-ranked genes/loci. Candidate SVs were confirmed using qPCR and an independent bioinformatics tool (FaNDOM).ResultsOur patient-centric investigation identified 11 SVs involving 38 genes implicated in three key host-viral interaction pathways: (1) innate immunity and inflammatory response, (2) airway resistance to pathogens, and (3) viral replication, spread, and RNA editing. These included seven rare/unique SVs (not present in the control dataset), identified in 24.3% (9/37) of patients, impacting up to 31 genes, of which STK26 and DPP4 are the most promising candidates. A duplication partially overlapping STK26 was corroborated with data showing upregulation of this gene in severely ill patients. Further, using a population frequency filter of less than 20% in the Bionano control dataset, four SVs involving seven genes were identified in 56.7% (21/37) of patients.ConclusionThis study is the first to systematically assess and highlight SVs’ potential role in the pathogenesis of COVID-19 severity. The genes implicated here identify novel SVs, especially STK26, and extend previous reports involving innate immunity and type I interferon response in the pathogenesis of COVID-19. Our study also shows that optical genome mapping can be a powerful tool to identify large SVs impacting disease outcomes with split survival and add valuable genomic information to the existing sequencing-based technology databases to understand the inter-individual variability associated with SARS-CoV-2 infections and COVID-19 mortality.

Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection

“…Given our findings of a protective role for membrane-anchored mucins against SARS-CoV-2, the development of therapeutics broadly antagonizing mucin expression should be pursued with caution. Structural variant studies of COVID-19 cases identified MUC4 loss-of-function to be associated with increased disease severity (Reay et al, 2021;Sahajpal et al, 2021). A more selective strategy promoting membrane-tethered mucins or reducing the secretion of gel-forming mucins may be more beneficial.…”

Covid-19 And Cancer: Insights Into Their Association And Influence On Genetic And Epigenetic Landscape

“…The identified structural variants were compared with the normal population by calculating the ratios to top-ranked genes. This study determined and confirmed the direct impact of some genes on the severity of disease in infected patients, and concluded that optical genome mapping is an efficient method to determine SARS-CoV-2 structural variants that help in the determination of disease outcome and mortality [ 96 , 97 ]. Recently, a patient-center-based investigation has identified 38 genes which are directly linked to different host–viral association pathways: innate/inflammatory immune responses, passage resistance, viral propagation, RNA editing and viral spread.…”

“…However, to resolve this issue, several advanced technologies have been utilized, such as optical genome mapping using BioNano’s Saphyr ® system (BioNano Genomics, CA, USA). By this technology, SARS-CoV-2-associated structural variants were identified in 37 hospitalized infected individuals [ 96 ]. Furthermore, the variants’ specific small or rare structural changes were analyzed in a similar group of patients by whole-genome sequencing analysis.…”