key: cord-260225-bc1hr0fr
authors: Sirpilla, Olivia; Bauss, Jacob; Gupta, Ruchir; Underwood, Adam; Qutob, Dinah; Freeland, Tom; Bupp, Caleb; Carcillo, Joseph; Hartog, Nicholas; Rajasekaran, Surender; Prokop, Jeremy W.
title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes
date: 2020-07-20
journal: J Proteome Res
DOI: 10.1021/acs.jproteome.0c00421
sha: 
doc_id: 260225
cord_uid: bc1hr0fr

[Image: see text] SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.

The SARS-CoV-2 (COVID-19) pandemic has impacted every component of life, including research and medicine. In just a few months from the onset of infections to writing of this review, 10573 papers/objects have been published on SARS-CoV-2 ( Figure 1 ). This body of literature primarily focuses on infectious diseases, the respiratory system, public environmental occupational health, biochemistry molecular biology, virology, immunology, pharmacology, microbiology, and healthcare science services, to name a few fields ( Figure 1A ). Title extraction of these papers reveals mainly clinically connected terms ( Figure 1B) . The extensive infectious disease and clinical base of this literature has yielded knowledge of viral entry, replication, immune response, and transmission. However, in a short window of time, biochemical and molecular biology insights into SARS-CoV-2 have yielded a smaller body of literature that continues to grow (1267 out of the 10573 items), taking more time for data generation than clinical descriptions.

Of these 1267 biochemistry/molecular biology items, 934 are primary articles ( Figure 1C ). Title and abstract word extraction from these biochemistry/molecular biology items, followed by counting mentions of all human (20368) or SARS-CoV-2 proteins, shows a heavy focus on ACE2 and spike (S) proteins ( Figure 1D ). The virus primarily enters cells through the interaction of the SARS-CoV-2 surface glycoprotein, Spike (S), interacting with the human encoded ACE2, similar to that of the SARS virus. 1,2 From the abstract/title terms, we identified 51/346 usages of ACE2 and 76/295 of Spike. Other human proteins with repeated mentions include TMPRSS2 (13 titles/49 abstract), ACE (1/32), FURIN (2/ 14), DPP4 (2/11), and C3 (2/2). Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). Only nsp6 and nsp11 for SARS-CoV-2 have no mentions within any of these titles or abstracts for biochemical linked papers on SARS-CoV-2. Overall this suggests a few papers specifically related to SARS-CoV-2 proteins have been published; however, a large body of literature exists for the original SARS and other coronaviruses that can give interpretation of the diverse functions performed by the viral-coded proteins and how they interact with human biology.

The advancement of knowledge of the SARS-CoV-2 proteome has been slower than clinical insights due to the need for experimental work that is slow and that is being hampered by social isolation. The 29903 base-pair single-stranded RNA genome of SARS-CoV-2 (NCBI NC_045512.2) has a 265 base-pair 5′ UTR, multiple protein-coding segments, and a 228 base-pair 3′ UTR. SARS-CoV-2 has a 79% genomic similarity with SARS-CoV, a known human pathogen, with both known to enter cells through the binding of human ACE2. 3, 4 In addition to SARS-CoV and SARS-CoV-2, five other coronaviruses are capable of human-to-human transmission and infection (HKU1, NL63, OC43, 229E, and MERS-CoV). 5 Hundreds of Coronaviridae family member genomes have been sequenced in human and other vertebrate hosts, 6,7 and many structures have been solved for Coronaviridae species proteins, allowing for systematic assessments of the knowledge base.

Our group implemented a sequence-to-structure-to-function analysis 8, 9 to understand SARS-CoV-2 proteins, developing a robust understanding of protein conservation, structure, and molecular dynamics. 10 The data generated for each protein was then developed into the Viral Integrated Structural Evolution Dynamic Database (VIStEDD), a publicly released database of multiple tools for the virus. The database can be accessed at https://prokoplab.com/vistedd/. These tools consist of educational resources for the proteins coded by SARS-CoV-2 (molecular videos, 3D protein model prints, amino acid details of conservation, and dynamics), the mapping of critical sites to each protein, and the insights into how SARS-CoV-2 interacts with human proteins. Generating this database has given our team a diverse understanding of SARS-CoV-2, particularly for host protein interactions of each of the viral proteins.

Multiple studies have begun building systemic insights for SARS-CoV-2 infections. Multiple groups have performed systematic data assessment of ACE2 expression and protein staining, suggesting the physiological cell types that can be targeted by the virus. They have shown expression in many tissues throughout humans, with expression within the lung found on the apical surface of polarized bronchial secretory epithelia cells. 11−14 Once the virus enters the cells, it results in the alteration of broad biological pathways, including translation, splicing, protein homeostasis, and nucleic acid metabolism. 15 Epithelial organoid cultures exposed to the virus produce a robust change in RNA expression patterns for cytokine and interferon intracellular immune responses that give rise to tissue signals. 16 Single cell profiling within the lungs of patients shows the intracellular cytokine/interferon response results in the recruitment of macrophages in severe cases and T-cells in moderate cases, with a high potential for therapeutic intervention. 17, 18 Over activation of the cytokine/interferon response is connected to poor outcomes within patients, correlating with macrophage activation syndrome. 19 Additional adverse outcomes for the activation of apoptosis within lymphocytes have been observed and may contribute to the noted lymphopenia. 20 Proteomics and metabolomics of patient sera show the same macrophage dysfunction, while also elucidating platelet and complement dysregulation with the identification of severity classifiers. 21−23 In totality, the physiological response to the virus is likely mediated by a combination of immune system activation and the direct human interaction partners, altering cellular processes. An understanding of these detailed biological interactions can shed light on potential therapeutic opportunities while building a fundamental knowledge of viral biology.

To date, few studies have been performed that systematically look at mapping how the SARS or coronavirus proteins physically interact with human proteins. Structural level insights for coronavirus proteins are surprisingly deficient of human interaction partners. 10 A few of these proteins have been targeted for interaction assessments, such as the nucleocapsid protein 24,25 (shown below). It has been speculated that the understanding of virus−host interactions represents a major untapped potential of viral inhibitors. 26 A 2018 review highlights the literature of viral−host interactions for coronaviruses, focused on synergizing the knowledge of independent experiments for virus receptors, translation, membrane dynamics, immune regulation, cell cycle control, and replication. 27 The more recent work by Gordon et al. 28 covering the systematic affinity purification of 26 different SARS-CoV-2 proteins within human cells has elucidated many mechanisms and drug compounds for the regulation of viral processes. 28 Bringing this data together with our VIStEDD tools, we provide a current snapshot of SARS-CoV-2 viral proteins ( Figure 2 ).

ORF1ab is a large protein that is proteolytically cleaved to produce 16 different proteins, many involved in RNA replication.

The NMR structure of 2gdt has been solved, 29 and 250 sequences have been identified by Basic Local Alignment Search Tool (BLAST). Nsp1 interacts with proteins of the alpha DNA polymerase ( Figure 2 ) and is involved in regulating endonucleolytic RNA cleavage of mRNA, allowing the virus to enrich viral RNA within a cell. 30, 31 Nsp1 has been shown to interact with ribosomal subunits, resulting in the inhibition of translation, 5′ mRNA capping changes, and mRNA destabilization. 32−34 From a SARS-CoV yeast two hybrid screen, nsp1 was identified to interact with immunophilins, showing that it alters the intracellular immune response. 35 Expression of nsp1 drives changes in interferon signaling. 36 These processes make nsp1 a potential virulence factor. 36−38 See prokoplab.com/ nsp1 for additional information.

The protein has no solved protein structure, with ITASSERgenerated predictions 39 that are mostly (67%) coiled, and 246 sequences have been identified by BLAST. All of the protein interaction partners are acetylated ( Figure 2 ). The protein has been suggested to be dispensable to viral replication but does impact rates of replication. 40 See prokoplab.com/nsp2 for additional information.

The protein has hundreds of solved X-ray crystal structures with a C4 zinc finger, and 3180 sequences have been identified by BLAST. The papain-like proteinase cleaves the first four nsp proteins, 41 where inhibition can block viral replication. 42 The proteinase can cleave proteins and has been shown to have deubiquitinase activity. 43−45 This deubiquitinase function has been linked to the regulation of immune system cytokine response, 46,47 specifically the type-I interferon signaling pathway, 48 and has connection to virulence. 49 See prokoplab. com/papain_like_proteinase for additional information.

The protein has no solved protein structure, with ITASSERgenerated predictions 39 that are mostly (58%) coiled, and 3325 sequences have been identified by BLAST. Nsp4 interacts with several proteins involved in mitochondrial import for inner membrane insertion (Figure 2 ). Nsp4 and nsp3 interact and form within the membrane and are involved in transcription complex assembly anchoring. 50, 51 The complex is involved in the double membrane secretory vesicle formation 52, 53 in the endoplasmic reticulum, 54 conferring with human protein interaction partners. 28 See prokoplab.com/nsp4 for additional information.

Nsp5 has hundreds of solved X-ray crystal structures, with the protein found in a dimer form with a cysteine protease function, 55, 56 and 3397 sequences have been identified by BLAST. The enzyme cleaves most of the proteins of the larger Rep protein with a highly conserved specificity, where inhibition is one of the most studied interventions. 57−59 See prokoplab.com/3c-like_proteinase for additional information. 

The protein has no solved protein structure, with ITASSERgenerated predictions 39 that are mostly (63%) coiled, and 2558 sequences have been identified by BLAST. Nsp6 interacts with multiple proteins involved in ATP hydrolysis-coupled cation transmembrane transport ( Figure 2 ). The protein is likely transmembrane-localized, along with nsp3/nsp4, 60 and is involved in autophagosome formations. 61−63 The few papers discussing nsp6 suggest a major future area of understanding and pharmaceutical intervention potential. See prokoplab. com/nsp6 for additional information.

There are several solved structures for nsp7 that interact with nsp12/nsp8 (6NUR, 2AHM, and 3UB0), 64−66 and 3256 sequences have been identified by BLAST. The nsp7 protein interacts with multiple small GTPases of the Ras complex, many of which are prenylation-regulated ( Figure 2 ). The nsp7/nsp8/nsp12 complex is a viral RNA-directed RNA polymerase unit, where nsp12 is enhanced through the binding of nsp7/nsp8. 67 See prokoplab.com/nsp7 for additional information.

There are several solved structures for nsp8 that interact with nsp12/nsp7 (6NUR and 3UB0), 64−66 and 3339 sequences have been identified by BLAST. The nsp8 protein interacts with proteins involved in translation, snRNA 3′-end processing, 7S RNA binding, and ribonucleoproteins ( Figure 2 ). In addition to the information provided for nsp7, nsp8 has been suggested to also interact with the ORF6 protein. 68 See prokoplab.com/nsp8 for additional information.

Nsp9 has many known protein structures, with the protein requiring dimerization to function, 69 and 3386 sequences have been identified by BLAST. Nsp9 interacts with multiple proteins of structural constituents of the nuclear pore ( Figure  2 ). Nsp9 and nsp10 interact with the nuclear factor-κB repressing factor (NKRF) and may cause an interleukin (IL)-8/IL-6-mediated chemotaxis of neutrophils and an overexuberant host inflammatory response. 70 Nsp9 is involved in viral RNA synthesis and RNA binding, which likely evolved from a protease. 71, 72 See prokoplab.com/nsp9 for additional information.

Nsp10 has many known protein structures, including those interacting with nsp14 and nsp16, and contains two zinc binding motifs; 73 3344 sequences have been identified by BLAST. Nsp10 stimulates nsp14 3′−5′ exoribonuclease/ mismatch excision 74, 75 and nsp16 2′-O-methyltransferase activities. 76, 77 The interface of interaction with nsp14 and nsp16 overlaps, suggesting a dynamic regulation process 78 that may involve the linkage of functions through a spherical dodecameric structure. 79 A peptide-based inhibition of the nsp10 interaction has been proposed as a potential viral regulator. 80 See prokoplab.com/nsp10 for additional information.

Nsp11 is a little-known small 1.3 kDa peptide with few interaction partners. 28 

Nsp12 has multiple known protein structures with a zinc active site and a structure that interacts with nsp7/nsp8, 64−66 and 5086 sequences have been identified by BLAST. Nsp12 is involved in the replication of plus-strand RNA through complement strand synthesis and then viral RNA synthesis. 81 The enzyme is highly targeted for therapeutic inhibition of viruses. It is also known as RdRp and is the target of the drug remdesivir. See prokoplab.com/rna-directed_rna_polymerase for additional information.

Nsp13 has multiple known protein structures with a zinc active site, and 5598 sequences have been identified by BLAST. Nsp13 interacts with multiple proteins involved in the centrosome−Golgi apparatus and centrosome ( Figure 2 ) and has a RNA and a DNA duplex-unwinding ability to separate strands with 5′ to 3′ polarity. 82−84 See prokoplab.com/helicase for additional information.

Nsp14 has multiple known protein structures with a zinc active site, and 2794 sequences have been identified by BLAST. Nsp14 has an S-adenosyl-l-methionine (SAM)-binding pocket and an exoribonuclease function that is involved in RNA capping, 85−87 and it interacts with nsp10 and is known to interact with the human DDX1 RNA helicase to enhance the virus replication. 88 See prokoplab.com/guanine-n7_ methyltransferase for additional information.

Nsp15 has multiple known protein structures, and 2489 sequences have been identified by BLAST. Nsp15 is a Mn 2+dependent toric monomer to the hexamer enzyme involved in uridylate-specific cleavage 89,90 that may be regulated by nsp7/ nsp8, 91 and it interacts with the retinoblastoma protein to impact the cell cycle 92 and is also known as NendoU. See prokoplab.com/uridylate-specific_endoribonuclease for additional information.

Nsp16 has multiple known protein structures with Na, Mg, and S-adenosyl-l-methionine (SAM), and 2495 sequences have been identified by BLAST. Nsp16 is an SAM-based enzyme for the methylation of ribose 2′-OH in viral RNA capping 93, 94 and interacts with nsp10. 77 The protein is a critical component in the inhibition of the host type-I interferon response 95 and is also known as 2′-O-MTase. See prokoplab.com/2-omethyltransferase for additional information.

The spike surface glycoprotein has multiple known protein structures that are heavily glycosylated and form a trimer complex 96, 97 and is a known structure of the interaction with the dimer of heterodimers ACE2/SLC6A19 (6M17); 3 6612 sequences have been identified by BLAST. S is a class-I viral fusion protein 98 and drives the specificity of cell targets through the interaction with ACE2 to enter human cells. 99, 100 Following binding to the receptor, S undergoes a conformational change to allow viral entry. 101 For the protein to function correctly, it must be proteolytically cleaved by trypsin and, upon cell-binding proteases such as TMPRSS2, elevate entry through the mediating tropism. 102 S is of interest to the development of immunizations and rapid detection of coronaviruses, as its surface is exposed. 103, 104 See prokoplab. com/spike for additional information.

ORF3a has no solved protein structure, with ITASSERgenerated predictions, 39 and 65 sequences have been identified by BLAST. ORF3a is a three transmembrane helix protein where the extracellular component localizes the protein to the Golgi apparatus with a caveolin-1 binding potential 105 and is involved in the formation of viral particles. 106, 107 ORF3a has been shown to impact the cell cycle. 108 See prokoplab.com/3a for additional information.

The envelope protein (E) has no solved protein structure, with ITASSER-generated predictions, 39 and 94 sequences have been identified by BLAST. E is required for viral particle formation 109 with transmembrane helix-forming pentameric αhelical bundles with channel activity 110 that can contribute to the membrane permeability. 111 See prokoplab.com/e for additional information.

The membrane protein (M) has no solved protein structure, with ITASSER-generated predictions, 39 and 1507 sequences have been identified by BLAST. M has human interaction partners that are involved in the mitochondrial matrix ( Figure  2 ) and is a critical component of viral membranes that are involved in viral budding. 112 See prokoplab.com/m for additional information.

ORF6 has no solved protein structure, with ITASSERgenerated predictions, 39 and 31 sequences have been identified by BLAST. Two of the interaction partners are involved in the transcription-dependent tethering of RNA polymerase ( Figure  2 ). ORF6 can function toward the inhibition of beta interferons 113 through the regulation of the signal transducer and activator of transcription 1 (STAT1) 114 and endoplasmic reticulum (ER) stress 115 and can interact with nsp8. 68 See prokoplab.com/orf6 for additional information.

ORF7a has multiple known protein structures, and 42 sequences have been identified by BLAST. ORF7a has protein interaction partners involved in ribosomal large subunit biogenesis ( Figure 2 ) and localizes to the ER and Golgi network. 116 It can regulate the cell cycle in G0/G1 progression. 117 See prokoplab.com/7a for additional information.

ORF8 has no solved protein structure, with ITASSERgenerated predictions, 39 and 35 sequences have been identified by BLAST. ORF8 has multiple interaction partners involved in the ER lumen (Figure 2) and is a protein shared with SARSr-BatCoV, with a high positive selection. 118 See prokoplab.com/ orf8 for additional information.

The nucleocapsid protein (N) has multiple known protein structures, and 2261 sequences have been identified by BLAST. N has protein interaction partners involved in mRNA binding, the ribonucleoprotein complex, and the mRNA surveillance pathway (Figure 2 ) and is critical for the viral replication 119 in multiple processes, including viral RNA stability, replication, and packaging. 120 The protein is modified within the cell, including phosphorylation and ADPribosylation. 121, 122 The protein consists of three domains, with the N-terminal domain involved in RNA binding, the internal dynamic multimer structured unit, and the C-terminal domain, an acidic dimerization region. 123−125 The protein can interact with RNA by serving as a RNA chaperone 126 while also interacting with the M protein and human hnRNPA1 through the internal multimerization domain. 127, 128 See prokoplab.com/n for additional information.

ORF10 has no solved protein structure, with ITASSERgenerated predictions, 39 and is unique to SARS-CoV-2. Very little is known of its molecular function or cellular expression. See prokoplab.com/orf10 for additional information.

■ SARS-COV-2 RISK FACTORS AND GENETICS BASED ON HUMAN PROTEIN INTERACTIONS SARS-CoV-2 infection exhibits more adverse effects and outcomes in those with other comorbidities, including hypertension, diabetes mellitus, and coronary heart disease. The other risk factors for mortality include older age, elevated D-dimer levels, and a higher Sequential Organ Failure Assessment (SOFA) score. 129 The mortality associated with SARS-CoV-2 infection is tied to the patient's progression to multiorgan dysfunction. The elderly are particularly susceptible to severe SARS-CoV-2 infection, which is most likely due to the immunosuppression and underlying comorbidities associated with advanced age.

Advanced age has been shown to have a depressive effect on both the innate and the adaptive immune system, known as immunosenescence. This is associated with decreased phagocytosis and the bactericidal effects of neutrophils 130 and is also associated with the downregulation of cytokine signaling 131,132 and innate immune receptors. 133 With SARS-CoV-2 infection, emphasis is placed on the adaptive immune system to aid in clearing virally infected cells. The elderly population has been shown to have a shift toward inhibitory pathways, particularly in CD8+ T cells and to a lesser degree in CD4+ T cells, 134 which may play a role in allowing disseminated viral spread. This reduction of T cell activity is also joined by the involution of the thymus with age, leading to less naive T cell output, 135 which further depresses immune functions. These accumulative effects on the immune system render the elderly population particularly susceptible to dispersed viral infection at baseline levels, which may ultimately result in viral sepsis.

With the immunosenescence and increased prevalence of comorbidities associated with older age, it makes sense that this population is being hit the hardest by SARS-CoV-2; however, many younger adults who lack the above immunosenescence have also been killed from the infection, some of whom displayed no prior medical history. This aspect points to the idea that genetics may play a role in determining the severity of SARS-CoV-2 infection.

The immune response to SARS-CoV-2 infection in severe cases characteristically induces lymphopenia, particularly of CD-8+ T cells, and increases IL-2, IL-6, IL-10, and interferon (IFN)-γ levels. 136 This work is backed by multiple proteomic studies identifying biomarkers of severity that connect to the immune system. 21, 22 The cytokine storm induced by SARS-CoV-2 is not a new phenomenon and has been demonstrated in the pathogenesis of other novel human coronaviruses, including MERS and SARS-CoV-1. 137 Similar consequences in severe coronavirus infections appear to stem from the cytokine storm of proinflammatory chemokines and cytokines, eventually resulting in Acute Respiratory Distress Syndrome (ARDS) and multiorgan dysfunction. 138 A previous study on sepsis and cytokine storm indicates the presence of genetic variants in multiple pathways that have a polygenetic contribution. 139 In many patients with SARS-CoV-2 that have severe infection, the identification of hyperferritinemic sepsis often occurs. Fever developed at day 1, sepsis developed at day 10, admission to the intensive care unit occurred at day 12 (for acute respiratory distress syndrome), and death occurred at day 19. Critically ill patients, defined as those with septic shock, multiple organ dysfunction/failure, and/or respiratory failure, accounted for approximately 5% of the study population, yet the study population displayed a case fatality rate of 49.0% in early reports from Wuhan, China. 129 Hyperferritinemia on day 4 and day 7 predicts mortality long before the development of sepsis and intensive care unit admission. Hyperferritinemia has been suggested to have genetic associations through pathogenic variants in genes targetable by IL1RAP and anti-C5 antibodies. 140 Type-1 interferonopathies, like heterozygous null variants in IRF7, have been shown to result in severe manifestations of seasonal influenza virus. 141 Similar monogenetic variants likely exist that lead to the individual risk of severe disease onset from SARS-CoV-2 in previously healthy patients. Much of the genetics around the immune activation leading to a cytokine storm and hyperferritinemic sepsis remains poorly defined and requires future initiatives and cohorts to define these genetic contributions adequately.

Initial SARS-CoV-2 infection is commonly associated with fever, cough, malaise, and fatigue. 142 In more severe cases, disseminated intravascular coagulation has been noted with elevated D-dimer levels in the serum of severe COVID-19 patients, placing them into thromboembolic risk. 143 Recent recommendations have been made to utilize thromboprophylaxis or full-anticoagulation therapy for patients in the thromboembolic risk category. 144 A specific protein−protein interaction was discovered between SARS-CoV-2's ORF8 and the tissue plasminogen activator (tPA) protein of hosts. 28 The tPA, which is encoded by the PLAT gene, plays a crucial role in thrombolysis by catalyzing the conversion of plasminogen to plasmin, the major enzyme involved in lysis of blood clots. Increased the activity of tPA can lead to excessive bleeding, whereas decreased activity is associated with thromboembolus formation, 145 increasing the chances of pulmonary embolism, stroke, and myocardial infarction. The extent to which ORF8 interacts with tPA is not well understood, but its involvement may render a patient at risk for thromboembolism, as has been seen in the clinical setting. In a study by Ladenvall et al., it was found that the discovered eight single nucleotide polymorphisms and the Alu insertion polymorphism at the PLAT locus were not significant contributors to plasma tPA levels. 146 This finding indicates that inherited variants of the PLAT gene may not be directly involved with the coagulopathy in SARS-CoV-2 patients; however, the polymorphisms may render the host's tPA protein to a tighter binding by ORF8, yielding greater repression during infection, placing the patient at higher risk for thromboembolism.

It has also been shown that sepsis involves upregulation of platelet adhesion molecules and increased circulation of platelet−leukocyte aggregates. 147 This may point toward more of an immune-system-catalyzed coagulopathy, resulting in the presentation of strokes, 148 pulmonary embolisms, 149 myocardial infarctions, 150 and microvascular injury, 151 which impact severe SARS-CoV-2 patients. As coagulopathy has mainly been investigated in both viral and bacterial sepsis, there may be a dual effect of both the immune-mediated response and the protein−protein interaction of ORF8 with the host tPA in cases of SARS-CoV-2 infection. Further investigation is warranted to determine the extent of the interaction of ORF8 with the host tPA to determine if it plays into the pathogenesis of SARS-CoV-2-related coagulopathy.

SARS-CoV-2 has been associated with cardiac dysfunction, including myocardial infarction and heart failure. The underlying mechanisms for cardiac injury currently being hypothesized are indirect cardiac injury from the cytokine storm and inflammatory response, 152 severe hypoxia as a result of ARDS, 153 and direct viral invasion of cardiomyocytes. 154 Interestingly, ACE2, the host receptor for SARS-CoV-2, is expressed in the heart, 155 indicating direct viral invasion could be a potential cause of myocardial dysfunction. SARS-CoV-2's nonstructural protein 9 (nsp9) was found to interact with the E3-ubiquitin ligase mindbomb homologue 1 (MIB1). 28 This ubiquitin ligase is a positive regulator of the Delta-mediated Notch signaling pathway, which is involved in multiple processes during cardiac development. 156 Mutations in the MIB1 have been associated with left ventricular noncompaction (LVNC) characterized by left ventricular trabeculations and reductions in cardiac systolic function. LVNC can range from being asymptomatic to presenting heart failure, depending on the extent the mutation has on the Notch pathway. 157 The prevalence of LVNC in the general population is estimated to be around 1/5000 to 1/ 30000. Patients with the asymptomatic form of LVNC may be at higher risk for exacerbation of cardiac dysfunction following SARS-CoV-2 due to involvement of this pathway, especially if they are unaware that they have this mutation. This may play a role in the cardiac dysfunction seen in younger SARS-CoV-2 patients who lack underlying comorbidities. Aside from cardiac development, the Notch pathway has also been implemented in cardiac repair, which was demonstrated in rat models where the Notch 3 and Notch 4 pathways were upregulated, thereby reducing postmyocardial infarctions in the setting of heart failure. 158 The mechanism behind the repair process is still under investigation; however, the disruption of the Notch signaling pathway by the interaction of nsp9 with MIB1 may prove to play a role in the cardiac involvement of SARS-CoV-2 infection. Furthermore, although vertical transmission of SARS-CoV-2 has not been seen, 159 neonates who have tested positive for the infection may need to have their cardiac function assessed over time due to MIB1's role in cardiogenesis and repair.

While we present a detailed assessment of two interaction partners' connections to pathology and risk factors, many more likely exist. We postulate that if function of any protein diverges from normal biology to contribute to SARS-CoV-2 biology, it could result in a similar disease state within the cell as a loss of function or deleterious genetic mutation. Thus, to Journal of Proteome Research pubs.acs.org/jpr Reviews understand the SARS-CoV-2-connected diseases through the human protein interactions, we assessed ClinVar, a database of clinically identified variants. A query of the 332 SARS-CoV-2 human interaction partners through ClinVar reveals 8311 protein-based variants within the list ( Figure 3A ). In total, 188 of the queried 332 genes have a ClinVar submission. Of these ClinVar-connected genes, there are a total of 111 that have a clinical annotation of pathogenic (pathogenic or likely pathogenic), with a total of 2386 different variants ( Figure  3B ). The gene with the most pathogenic variants is FBN1, which is known to interact with SARS-CoV-2 nsp9 and is involved in autosomal dominant familial thoracic aortic aneurysms and aortic dissections and Marfan syndrome. A further analysis of clinical disorders connected with those genes with 10 or more pathogenic-associated variants, excluding FBN1 (PKP2, ACADM, PPT1, WFS1, COL6A1,  PCNT, FBN2, BCS1L, NGLY1, CYB5R3, ACAD9, NEU1,  GNB1, NARS2, TCF12, NPC2, PIGO, CDK5RAP2, CENPF,  GGCX, FKBP10, TBK1, FBLN5, EXOSC3 , POR, GPAA1, and RHOA), reveals a high connection to cardiac, neurological, diabetic, and syndromic biology. The SARS-CoV-2 ORF8 has the most genes connected by interactions to pathogenic ClinVar returns from queried genes, followed by protein M, nsp13, nsp7, and ORF9c ( Figure 3C ). ORF8 is connected to 18 genes associated to human genetic diseases (COL6A1,  NGLY1, NEU1, NPC2, FKBP10, DNMT1, PLOD2, SMOC1,  IL17RA, ADAM9, SIL1, LOX, POFUT1, TOR1A, HYOU1 , EDEM3, EMC1, and HS6ST2), with significant enrichment of these genes to protein folding (false discovery rate (FDR) = 0.00095) and endoplasmic reticulum lumen (FDR = 2.99 × 10 −5 ). While only associated with 3 pathogenic interaction partners, the nucleocapsid (N) protein has interesting disease genetics based on previous observations of a process known as viral-induced genetics. 160 

The nucleocapsid (N) protein has the potential to impact and change cellular landscapes through the direct regulation of ribosomal biology. 161 The protein−protein interaction map by Gordon et al. 28 supports the hypothesis that SARS-CoV-2 N proteins interact with multiple mRNA-binding proteins and ribonucleoprotein complex proteins ( Figure 2 ). In multiple viruses, proteins have been shown to interact with these complexes to regulate a process known as nonsense-mediated decay (NMD). 162 NMD is a cellular process involved in the removal of mRNA that does not conform to the bulk of cellular mRNA, where proteins accumulate on the transcript and direct the cellular degradation of the mRNA. 163 The process is primarily used within cells to degrade mRNA molecules with nonsense and frameshift genetic variants and those with improper splicing to prevent the cell from producing truncated proteins that can drive dominant-negative or deleterious gain of function outcomes. 164 Viral RNA is usually suppressed and degraded within cells through NMD, acting as a cellular immune system process. 165−167 Thus, an evolutionary arms race has arisen where a virus can propagate more efficiently if it has a protein that can suppress NMD, keeping its RNA levels elevated. 168−171 Multiple lines of evidence for both SARS-CoV-2 and SARS-CoV suggested that the N protein is used to suppress NMD and evade cellular immune processes. Nearly all of the coronaviruses and the larger Nidovirales order genomes contain the N protein, which has been shown to interact with multiple ribosomal proteins, including crucial NMD factors. 28 directly inhibited by NMD, with the N protein expression blocking this inhibition. 162 Positive-sense single-stranded RNA viruses, including coronaviruses, are likely targets of NMD due to their many overlapping reading frames, retained introns, and long 3′ UTRs present within the cytoplasm of human cells. The N protein interacts with three proteins annotated to the mRNA surveillance pathway (UPF1, PABPC1, and PABPC4) and several proteins involved in mRNA binding and the ribonucleoprotein complex that are all known to have cellular interactions (Figure 2 ). While the fine details of the N protein interaction on the factors are poorly understood, the three mRNA surveillance genes are well-connected to NMD biology. PABPC1 is known to be critical for NMD, with its removal suppressing NMD. 175, 176 From plants to humans, UPF1 is considered a key regulator of NMD through its recruitment of multiple proteins to RNA. 177−180 The regulation switch of UPF1 is known to be regulated/activated through phosphorylation at various sites to allow its protein interactions, 181−183 while the N protein has been shown in multiple viral species to be phosphorylated 184−188 and likely dynamic in modifications throughout the RNA replication and viral lifecycle. 122, 189 These phosphorylation switches and the interaction of N to NMD proteins are potential sites of pharmaceutical or biological regulation that have been undervalued to this point.

Other notable interactions of the N protein are Ras GTPaseactivating protein-binding protein homologues (G3BP1/2) and casein kinase 2 alpha (CSNK2A2), 28 suggesting the regulation of stress granule formation. NMD is found at the intersection of a variety of cellular pathways beyond mRNA surveillance and viral control. Notably, it is closely associated with the integrated stress response requiring translation initiation factor EIF2S1 for function. 190 Cellular stresses such as hypoxia and ER stress lead to the inhibition of NMD via phosphorylation of EIF2S1. 190 This phosphorylation typically induces stress granule formation as well, which has been cited to aid viral replication in some cases and weaken them in others. 191 When G3BP1 is depleted within cells, there is a significant impairment of the replication for coronaviruses and respiratory syncytial viruses (RSVs). 191, 192 Multiple viruses have been shown to regulate phosphorylation of EIF2S1 at varying time points of infection with connection into NMD regulation. 193 Stress granule formation can enhance NMD inhibition, such as hypoxic conditions modulating UPF1 and EIF2S1. 194, 195 The interaction of SARS-CoV-2 N protein human interactors promotes the inhibition of NMD and enhancement of both viral replication and truncated host polypeptides that can enhance viral pathogenicity (Figure 4) .

The regulation of NMD by viral proteins is crucial for allowing the viral RNA to survive, but NMD processes within cells also regulate multiple endogenous transcripts, several in normal biology, and some based on genetic disease regulation. Many genes, including isoforms with early truncation (frameshifts and nonsense codons) and genes involved in amino acid homeostasis, tumorigenesis, and cell cycle control, are activated when NMD is inhibited within a cell. 196−199 In total, this amounts to about 10% of transcripts within a cell that are regulated by NMD processes and could be altered within the cell by SARS-CoV-2. 196 On top of this, most individuals contain at least one gene where a nonsense or frameshift variant within the genome is being suppressed, being either inherited or somatic. Assessments of human genomes reveal that every person has at least one variant regulated by NMD. 200 Recently, our group has shown a complex involvement of this regulation with rare human variants, driving adverse outcomes through a process we have termed viral-induced genetics (VIG). 160 In a patient with an Epstein−Barr virus (EBV) infection, they had an adverse immune response of classical hyperferritinemic sepsis like that of severe SARS-CoV-2 patients. This individual has both whole-exome sequencing in addition to multiple bloodbased RNaseq experiments performed throughout their clinical course. Sequencing revealed a heterozygous splicing variant in the gene RNASEH2B, which is associated with recessive Aicardi−Goutieres syndrome 201 and has been connected to Type-I IFN-mediated autoimmune disease. 202, 203 RNaseq of the patient, when healthy, showed that the splicing variant was present at very low levels, suggesting that the copy was being inhibited through NMD. While the patient was healthy for 16 years of life, the EBV was shown by RNaseq to inhibit NMD, resulting in the presence of the splice variant, which resulted in a dominant-negative RNASEH2B protein that drove cell dysfunction. This suggests that many human variants within genes connected to the immune system and viral response, which are usually suppressed by NMD and result in no cellular dysfunction, are activated by the virus through the inhibition of NMD and can give rise to severe viral outcomes. Just like in a computer virus, the antivirus of the computer is often targeted. When additional computer code contains a risk to system failure that is inhibited by the antivirus, if the antivirus is shut down, the other system vulnerabilities become present and often contribute to the computer failure. The full extent of these variants and the disease process remain to be elucidated but is a promising avenue for exploration of viral-induced outcomes in SARS-CoV-2.

The SARS-CoV-2 pandemic represents a unique challenge to scientists. Unlike previous pandemics, our knowledge of the genome and its coded proteins was gleaned within weeks of the outbreak, now with thousands of sequences within a short window. This level of insight has allowed for a pivot to a more robust insight into the viral proteome and how it interacts with host proteins. The advancement of protein-based bioinformatics and previous coronavirus research studies have proved useful in defining the function of each protein coded by the virus. Here, we show how many of these viral proteins interact with human proteins connected to biological pathways and disease connections, including numerous risk factors from immune to cardiovascular systems. Most notably, we highlight literature on the role of the viral nucleocapsid (N) protein in NMD regulation, where the inhibition of NMD allows for viral RNA stability while simultaneously activating genetics of cellular processes and viral-induced genetics. While we have seen thousands of publications on SARS-CoV-2 and other coronaviruses, the details of a proteome-wide knowledge base of SARS-CoV-2-coded proteins limit our ability to expand into the incredible potential of preventing and mitigating the current pandemic and future pandemics with a larger therapeutic toolset. 

Characterization of Coding/Noncoding Variants For SHROOM3 in Patients with CKD

Molecular Modeling in the Age of Clinical Genomics, the Enterprise of the next Generation

SARS-CoV-2 (COVID-19) Structural and Evolutionary Dynamicome: Insights into Functional Evolution and Human Genomics

Expression of the SARS-CoV-2 Cell Receptor Gene ACE2 in a Wide Variety of Human Tissues

ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia

Receptor ACE2 and TMPRSS2 Are Primarily Expressed in Bronchial Transient Secretory Cells

HCA Lung Biological Network. SARS-CoV-2 Entry Factors Are Highly Expressed in Nasal Epithelial Cells Together with Innate Immune Genes

Proteomics of SARS-CoV-2-Infected Host Cells Reveals Therapy Targets

Single-Cell Landscape of Bronchoalveolar Immune Cells in Patients with COVID-19

Eils, R. COVID-19 Severity Correlates with Airway Epithelium-Immune Cell Interactions Identified by Single-Cell Analysis

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Transcriptomic Characteristics of Bronchoalveolar Lavage Fluid and Peripheral Blood Mononuclear Cells in COVID-19 Patients

Proteomic and Metabolomic Characterization of COVID-19

Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome

The SARS Coronavirus Nucleocapsid Protein-Forms and Functions

Nucleocapsid Phosphorylation and RNA Helicase DDX1 Recruitment Enables Coronavirus Transition from Discontinuous to Continuous Transcription

Virus-Host Interactomes-Antiviral Drug Discovery

Host Factors in Coronavirus Replication

Novel Beta-Barrel Fold in the Nuclear Magnetic Resonance Structure of the Replicase Nonstructural Protein 1 from the Severe Acute Respiratory Syndrome Coronavirus

SARS Coronavirus Nsp1 Protein Induces Template-Dependent Endonucleolytic Cleavage of MRNAs: Viral MRNAs Are Resistant to Nsp1-Induced RNA Cleavage

Suppression of Host Gene Expression by Nsp1 Proteins of Group 2 Bat Coronaviruses

A Two-Pronged Strategy to Suppress Host Protein Synthesis by SARS Coronavirus Nsp1 Protein

Severe Acute Respiratory Syndrome Coronavirus Protein Nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation

Severe Acute Respiratory Syndrome Coronavirus Evades Antiviral Signaling: Role of Nsp1 and Rational Design of an Attenuated Strain

Unique SARS-CoV Protein Nsp1: Bioinformatics, Biochemistry and Potential Effects on Virulence

Coronavirus Nonstructural Protein 1: Common and Distinct Functions in the Regulation of Host and Viral Gene Expression

Protein Structure and Sequence Reanalysis of 2019-NCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

The Nsp2 Proteins of Mouse Hepatitis Virus and SARS Coronavirus Are Dispensable for Viral Replication

Identification of Severe Acute Respiratory Syndrome Coronavirus Replicase Products and Characterization of Papain-like Protease Activity

A Noncovalent Class of Papain-like Protease/Deubiquitinase Inhibitors Blocks SARS Virus Replication

Deubiquitinating Activity of the SARS-CoV Papainlike Protease

The Papain-like Protease from the Severe Acute Respiratory Syndrome Coronavirus Is a Deubiquitinating Enzyme

Severe Acute Respiratory Syndrome Coronavirus Papain-like Protease: Structure of a Viral Deubiquitinating Enzyme

SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6

Coronavirus Papain-like Proteases Negatively Regulate Antiviral Innate Immune Response through Disruption of STING-Mediated Signaling

SARS Coronavirus Papain-like Protease Inhibits the Type I Interferon Signaling Pathway through Interaction with the STING-TRAF3-TBK1 Complex

The Papain-like Protease Determines a Virulence Trait That Varies among Members of the SARS-Coronavirus Species

Structure and Cleavage Specificity of the Chymotrypsin-like Serine Protease (3CLSP/Nsp4) of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

Mutation in Murine Coronavirus Replication Protein Nsp4 Alters Assembly of Double Membrane Vesicles

Localization and Membrane Topology of Coronavirus Nonstructural Protein 4: Involvement of the Early Secretory Pathway in Replication

Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

3C-like Proteinase from SARS Coronavirus Catalyzes Substrate Hydrolysis by a General Base Mechanism

Dissection Study on the Severe Acute Respiratory Syndrome 3C-like Protease Reveals the Critical Role of the Extra Domain in Dimerization of the Enzyme: Defining the Extra Domain as a New Target for Design of Highly Specific Protease Inhibitors

Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs

Biosynthesis, Purification, and Substrate Specificity of Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase

The Substrate Specificity of SARS Coronavirus 3C-like Proteinase

Topology and Membrane Anchoring of the Coronavirus Replication Complex: Not All Hydrophobic Domains of Nsp3 and Nsp6 Are Membrane Spanning

Coronavirus Nsp6 Proteins Generate Autophagosomes from the Endoplasmic Reticulum via an Omegasome Intermediate

Evolutionary Analysis of SARS-CoV-2: How Mutation of Non-Structural Protein 6

Could Affect Viral Autophagy

Coronavirus NSP6 Restricts Autophagosome Expansion

Structure of the SARS-CoV Nsp12 Polymerase Bound to Nsp7 and Nsp8 Co-Factors

Insights into SARS-CoV Transcription and Replication from the Structure of the Nsp7-Nsp8 Hexadecamer

Nonstructural Proteins 7 and 8 of Feline Coronavirus Form a 2:1 Heterotrimer That Exhibits Primer-Independent RNA Polymerase Activity

The SARS-Coronavirus Nsp7+nsp8 Complex Is a Unique Multimeric RNA Polymerase Capable of Both de Novo Initiation and Primer Extension

The Nonstructural Protein 8 (Nsp8) of the SARS Coronavirus Interacts with Its ORF6 Accessory Protein

Severe Acute Respiratory Syndrome Coronavirus Nsp9 Dimerization Is Essential for Efficient Viral Growth

Virus-Host Interactome and Proteomic Survey of PMBCs from COVID-19 Patients Reveal Potential Virulence Factors Influencing SARS-CoV-2

The Nsp9 Replicase Protein of SARS-Coronavirus, Structure and Functional Insights

The Severe Acute Respiratory Syndrome-Coronavirus Replicative Protein Nsp9 Is a Single-Stranded RNA-Binding Subunit Unique in the RNA Virus World

Crystal Structure of Nonstructural Protein 10 from the Severe Acute Respiratory Syndrome Coronavirus Reveals a Novel Fold with Two Zinc-Binding Motifs

RNA 3′-End Mismatch Excision by the Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein Nsp10/ Nsp14 Exoribonuclease Complex

Structural Basis and Functional Analysis of the SARS Coronavirus Nsp14-Nsp10 Complex

In Vitro Reconstitution of SARS-Coronavirus MRNA Cap Methylation

Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase Nsp10/Nsp16 Complex

Coronavirus Nsp10, a Critical Co-Factor for Activation of Multiple Replicative Enzymes

Dodecamer Structure of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein Nsp10

Coronavirus Nsp10/Nsp16 Methyltransferase Can Be Targeted by Nsp10-Derived Peptide In Vitro and In Vivo To Reduce Replication and Pathogenesis

Molecular Anatomy of Viral RNA-Directed RNA Polymerases

Multiple Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase

The Severe Acute Respiratory Syndrome (SARS) Coronavirus NTPase/Helicase Belongs to a Distinct Class of 5′ to 3′ Viral Helicases

The Human Coronavirus 229E Superfamily 1 Helicase Has RNA and DNA Duplex-Unwinding Activities with 5′-to-3′ Polarity

Structure-Function Analysis of Severe Acute Respiratory Syndrome Coronavirus RNA Cap Guanine-N7-Methyltransferase

Functional Screen Reveals SARS Coronavirus Nonstructural Protein Nsp14 as a Novel Cap N7 Methyltransferase

Characterization of the Guanine-N7 Methyltransferase Activity of Coronavirus Nsp14 on Nucleotide GTP

The Cellular RNA Helicase DDX1 Interacts with Coronavirus Nonstructural Protein 14 and Enhances Viral Replication

Crystal Structure and Mechanistic Determinants of SARS Coronavirus Nonstructural Protein 15 Define an Endoribonuclease Family

Crystal Structure of a Monomeric Form of Severe Acute Respiratory Syndrome Coronavirus Endonuclease Nsp15 Suggests a Role for Hexamerization as an Allosteric Switch

Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus

Binding of the Methyl Donor S-Adenosyl-l-Methionine to Middle East Respiratory Syndrome Coronavirus 2′-O-Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10

Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2′O)-Methyltransferase Activity

Ribose 2′-O-Methylation Provides a Molecular Signature for the Distinction of Self and Non-Self MRNA Dependent on the RNA Sensor Mda5

Assembly of Coronavirus Spike Protein into Trimers and Its Role in Epitope Expression

Cryo-Electron Microscopy Structure of a Coronavirus Spike Glycoprotein Trimer

The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex

Coronavirus Spike Proteins in Viral Entry and Pathogenesis

Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor

Characterization of Severe Acute Respiratory Syndrome-Associated Coronavirus (SARS-CoV) Spike Glycoprotein-Mediated Viral Entry

Mechanisms of Coronavirus Cell Entry Mediated by the Viral Spike Protein

Severe Acute Respiratory Syndrome Coronavirus Spike Protein Expressed by Attenuated Vaccinia Virus Protectively Immunizes Mice

Potent Binding of 2019 Novel Coronavirus Spike Protein by a SARS Coronavirus-Specific Human Monoclonal Antibody

Severe Acute Respiratory Syndrome Coronavirus Orf3a Protein Interacts with Caveolin

Severe Acute Respiratory Syndrome Coronavirus 3a Protein Is a Viral Structural Protein

The Severe Acute Respiratory Syndrome Coronavirus 3a Is a Novel Structural Protein

G1 Phase Cell Cycle Arrest Induced by SARS-CoV 3a Protein via the Cyclin D3/PRb Pathway

Nucleocapsid-Independent Assembly of Coronavirus-like Particles by Co-Expression of Viral Envelope Protein Genes

Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel

Expression of SARS-Coronavirus Envelope Protein in Escherichia Coli Cells Alters Membrane Permeability

Coronavirus Particle Assembly: Primary Structure Requirements of the Membrane Protein

Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame (ORF) 3b, ORF 6, and Nucleocapsid Proteins Function as Interferon Antagonists

Severe Acute Respiratory Syndrome Coronavirus ORF6 Antagonizes STAT1 Function by Sequestering Nuclear Import Factors on the Rough Endoplasmic Reticulum/Golgi Membrane

ORF-6, Induces Caspase-3 Mediated, ER Stress and JNK-Dependent Apoptosis

Structure and Intracellular Targeting of the SARS-Coronavirus Orf7a Accessory Protein

SARS Coronavirus 7a Protein Blocks Cell Cycle Progression at G0/G1 Phase via the Cyclin D3/PRb Pathway

Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8

Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

Selective Replication of Coronavirus Genomes That Express Nucleocapsid Protein

The Coronavirus Nucleocapsid Is a Multifunctional Protein

The Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein Is Phosphorylated and Localizes in the Cytoplasm by 14−3-3-Mediated Translocation

Sequence Comparison of the N Genes of Five Strains of the Coronavirus Mouse Hepatitis Virus Suggests a Three Domain Structure for the Nucleocapsid Protein

The Nucleocapsid Protein of Coronavirus Infectious Bronchitis Virus: Crystal Structure of Its N-Terminal Domain and Multimerization Properties

Modular Organization of SARS Coronavirus Nucleocapsid Protein

Coronavirus Nucleocapsid Protein Is an RNA Chaperone

Characterization of Protein-Protein Interactions between the Nucleocapsid Protein and Membrane Protein of the SARS Coronavirus

The SARS-CoV Nucleocapsid Protein: A Protein with Multifarious Activities

Clinical Course and Risk Factors for Mortality of Adult Inpatients with COVID-19 in Wuhan, China: A Retrospective Cohort Study

Effect of Age on Human Neutrophil Function

Innate Immunosenescence: Effect of Aging on Cells and Receptors of the Innate Immune System in Humans

Altered Cytokine Production in the Elderly

Cutting Edge: Impaired Toll-like Receptor Expression and Function in Aging

Signaling Pathways in Aged T Cells -a Reflection of T Cell Differentiation

The Effect of Age on Thymic Function

Human Coronavirus Infections: Causes and Consequences of Cytokine Storm and Immunopathology

Molecular Immune Pathogenesis and Diagnosis of COVID-19

Understanding the Inflammatory Cytokine Response in Pneumonia and Sepsis: Results of the Genetic and Inflammatory Markers of Sepsis (GenIMS) Study

Adults with Septic Shock and Extreme Hyperferritinemia Exhibit Pathogenic Immune Variation

Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics

COVID-19) in China: A Systematic Review and Meta-Analysis

Changes in Blood Coagulation in Patients with Severe Coronavirus Disease 2019 (COVID-19): A Meta-Analysis

Thromboembolic Risk and Anticoagulant Therapy in COVID-19 Patients: Emerging Evidence and Call for Action

Tissue Plasminogen Activator

Genetic Variation at the Human Tissue-Type Plasminogen Activator (TPA) Locus: Haplotypes and Analysis of Association to Plasma Levels of TPA

The Coagulopathy of Acute Sepsis

COVID-19 Presenting as Stroke

Pulmonary Embolism in Patients with COVID-19: Time to Change the Paradigm of Computed Tomography

COVID-19 and the Cardiovascular System: Implications for Risk Assessment

Complement Associated Microvascular Injury and Thrombosis in the Pathogenesis of Severe COVID-19 Infection: A Report of Five Cases

Novel Coronavirus Outbreak Research Team. Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in

The Cardiovascular Burden of Coronavirus Disease 2019 (COVID-19) with a Focus on Congenital Heart Disease

Associated with Acute Respiratory Distress Syndrome

Receptor Recognition by the Novel Coronavirus from Wuhan: An Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

Notch Signaling in Cardiac Development and Disease

Mutations in the NOTCH Pathway Regulator MIB1 Cause Left Ventricular Noncompaction Cardiomyopathy

Activation of Notch Signaling in Cardiomyocytes during Post-Infarction Remodeling

Vertical Transmission of Coronavirus Disease 19 (COVID-19) from Infected Pregnant Mothers to Neonates: A Review

Viral-Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow Applicable to COVID-19

Nucleocapsid Protein Recruitment to Replication-Transcription Complexes Plays a Crucial Role in Coronaviral Life Cycle

Interplay between Coronavirus, a Cytoplasmic RNA Virus, and Nonsense-Mediated MRNA Decay Pathway

Nonsense-Mediated MRNA Decay (NMD) Mechanisms

The Nonsense-Mediated Decay RNA Surveillance Pathway

The Host Nonsense-Mediated MRNA Decay Pathway Restricts Mammalian RNA Virus Replication

Nonsense-Mediated MRNA Decay: Novel Mechanistic Insights and Biological Impact

Beyond Quality Control: The Role of Nonsense-Mediated MRNA Decay (NMD) in

A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated MRNA Decay

Virus Escape and Manipulation of Cellular Nonsense-Mediated MRNA Decay

RNA Virus Evasion of Nonsense-Mediated Decay

How Retroviruses Escape the Nonsense-Mediated MRNA Decay

An Interactome Map of the Nucleocapsid Protein from a Highly Pathogenic North American Porcine Reproductive and Respiratory Syndrome Virus Strain Generated Using SILAC-Based Quantitative Proteomics

Function of a Retrotransposon Nucleocapsid Protein

The Cellular Interactome of the Coronavirus Infectious Bronchitis Virus Nucleocapsid Protein and Functional Implications for Virus Biology

Interaction of PABPC1 with the Translation Initiation Complex Is Critical to the NMD Resistance of AUG-Proximal Nonsense Mutations

A Conserved Role for Cytoplasmic Poly(A)-Binding Protein 1 (PABPC1) in Nonsense-Mediated MRNA Decay

UPF1 Is Required for Nonsense-Mediated MRNA Decay (NMD) and RNAi in Arabidopsis

Mammalian Staufen1 Recruits Upf1 to Specific MRNA 3′UTRs so as to Elicit MRNA Decay

NMD Factors UPF2 and UPF3 Bridge UPF1 to the Exon Junction Complex and Stimulate Its RNA Helicase Activity

Interactions between UPF1, ERFs, PABP and the Exon Junction Complex Suggest an Integrated Model for Mammalian NMD Pathways

Upf1 Phosphorylations Create Binding Platforms for SMG-6 and SMG-5:SMG-7 during NMD

Binding of a Novel SMG-1-Upf1-ERF1-ERF3 Complex (SURF) to the Exon Junction Complex Triggers Upf1 Phosphorylation and Nonsense-Mediated MRNA Decay

A Post-Translational Regulatory Switch on UPF1 Controls Targeted MRNA Degradation

Phosphorylation of the Porcine Reproductive and Respiratory Syndrome Virus Nucleocapsid Protein

Phosphorylation and Subcellular Localization of Transmissible Gastroenteritis Virus Nucleocapsid Protein in Infected Cells

Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein Expressed by an Adenovirus Vector Is Phosphorylated and Immunogenic in Mice

Phosphorylation of the Mouse Hepatitis Virus Nucleocapsid Protein

Effects of Phosphorylation of Avian Retrovirus Nucleocapsid Protein Pp12 on Binding of Viral RNA

Regulation of Hepadnavirus Reverse Transcription by Dynamic Nucleocapsid Phosphorylation

Nonsense-Mediated MRNA Decay at the Crossroads of Many Cellular Pathways

Valiente-Echeverría, F. Strategies for Success. Viral Infections and Membraneless Organelles

Innate Immune Evasion by Human Respiratory RNA Viruses

Mouse Hepatitis Coronavirus Replication Induces Host Translational Shutoff and MRNA Decay, with Concomitant Formation of Stress Granules and Processing Bodies

Hypoxic Inhibition of Nonsense-Mediated RNA Decay Regulates Gene Expression and the Integrated Stress Response

Possible Roles in the Control of Translation and MRNA Degradation. Cold Spring Harbor Perspect

Nonsense Surveillance Regulates Expression of Diverse Classes of Mammalian Transcripts and Mutes Genomic Noise

Nonsense-Mediated RNA Decay Regulation by Cellular Stress: Implications for Tumorigenesis

Nonsense-Mediated MRNA Decay Factors Act in Concert to Regulate Common MRNA Targets

Nonsense-Mediated MRNA Decay in Health and Disease

The Rules and Impact of Nonsense-Mediated MRNA Decay in Human Cancers

A Novel RNASEH2B Splice Site Mutation Responsible for Aicardi-Goutieres Syndrome in the Faroe Islands

Genetically Defined Autoinflammatory Diseases

Rare ADAR and RNASEH2B Variants and a Type I Interferon Signature in Glioma and Prostate Carcinoma Risk and Tumorigenesis