Viral Structural Proteins Research Articles

COMPUTATIONAL PREDICTION OF BIOACTIVE COMPOUNDS AS POTENTIAL INHIBITORS OF COVID-19 MAIN PROTEASE, SPIKE GLYCOPROTEIN RECEPTOR-BINDING DOMAIN, AND RNA-DEPENDENT RNA POLYMERASE

Objectives: It has been known for ages that natural products have potent antiviral activity and hence show inhibitory effects on SARS-CoV-2 infections. In this study, some promising bioactive compounds from natural sources for drug development against SARS-CoV-2 were studied. Methods: The study was based on a computational approach using different phytochemicals for evaluating their potential against non-structural (main protease [MPro], RNA-dependent RNA polymerase [RdRp], and structural [spike [S] glycoprotein receptor-binding domain]) viral proteins. Molecular docking was conducted systematically using PyRx and AutoDock 4.2 to determine the binding affinities between bioactive compounds and Mpro, spike RBD, and RdRp. Twenty-two ligands were selected in this study from different sources including three known inhibitors of the virus remdesivir, favipiravir, and nelfinavir. The pharmacological assessment of the ligands was achieved using ADMET filters. Results: The docking results revealed that β-carotene, piperine, and cianidanol were the best antagonists for Mpro, isovitexin, quercitin, β-carotene, piperine, and cianidanol were the best antagonists for RdRp, and in case of the spike RBD, capsaicin, cianidanol, curcumin, gingerol, isovitexin, piperine, quercitin, rhapontin, and riboflavin were found to be best. Conclusion: All of these bioactive compounds could be considered potential drug candidates for COVID-19 inhibition due to their promising binding affinities with the viral structural and non-structural proteins.

An impedimetric biosensor for COVID-19 serology test and modification of sensor performance via dielectrophoresis force

Coronavirus disease 2019 (COVID-19) has caused significant global morbidity and mortality. The serology test that detects antibodies against the disease causative agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has often neglected value in supporting immunization policies and therapeutic decision-making. The ELISA-based antibody test is time-consuming and bulky. This work described a gold micro-interdigitated electrodes (IDE) biosensor for COVID antibody detection based on Electrochemical Impedance Spectroscopy (EIS) responses. The IDE architecture allows easy surface modification with the viral structure protein, Spike (S) protein, in the gap of the electrode digits to selectively capture anti-S antibodies in buffer solutions or human sera. Two strategies were employed to resolve the low sensitivity issue of non-faradic impedimetric sensors and the sensor fouling phenomenon when using the serum. One uses secondary antibody-gold nanoparticle (AuNP) conjugates to further distinguish anti-S antibodies from the non-specific binding and obtain a more significant impedance change. The second strategy consists of increasing the concentration of target antibodies in the gap of IDEs by inducing an AC electrokinetic effect such as dielectrophoresis (DEP). AuNP and DEP methods reached a limit of detection of 200 ng/mL and 2 μg/mL, respectively using purified antibodies in buffer, while the DEP method achieved a faster testing time of only 30 min. Both strategies could qualitatively distinguish COVID-19 antibody-positive and -negative sera. Our work, especially the impedimetric detection of COVID-19 antibodies under the assistance of the DEP force presents a promising path toward rapid, point-of-care solutions for COVID-19 serology tests.

SARS-CoV-2 Nucleocapsid Protein is Associated With Lower Testosterone Levels: An Experimental Study.

The ongoing COVID-19 pandemic represents an extra burden in the majority of public and private health systems worldwide beyond the most pessimistic expectations, driving an urgent rush to develop effective vaccines and effective medical treatments against the SARS-CoV-2 pandemic. The Nucleocapsid structural viral protein is remarkably immunogenic and hugely expressed during infection. High IgG antibodies against Nucleocapsid protein (N protein) levels were detected in the serum of COVID-19 patients, confirming its pivotal antigen role for a T lymphocyte response in a vaccine microenvironment. Currently, adverse events associated with immunizations have raised some degree of concern, irrespective of its huge benefits in dealing with disease severity and decreasing mortality and morbidity. This hitherto study evaluates histological changes in rats’ testes, epididymis, prostate, and seminal vesicles and analyzes hormone levels after solely N protein inoculation. Therefore, we exposed a group of Lewis rats to weekly injections of the recombinant N protein for 28 days, while a control group was inoculated with a buffer solution. The N group revealed a more significant number of spermatozoa. Spermatozoa in the seminiferous tubules were counted in twenty 400 × microscopy fields (mean of 9.2 vs. 4.6 in the control group; p < 0,01), but significantly lower testosterone levels (mean of 125.70 ng/dl vs. 309,00 ng/dl in the control group; p < 0,05) were found. No other histological and biochemical changes were displayed. Conclusively, these data suggest testicular hormonal imbalance mediated by the SARS-CoV-2 N protein that could be linked to reported post-COVID-19 syndrome hypogonadism. More relevant research might be performed to confirm this viral antigen’s deleterious mechanism in the human testicular microenvironment, particular in Leydig cell function.

Enterovirus 71 VP1 promotes 5-HT release by upregulating the expression of ERICH3 and methyltransferase ZC3H13

Background and aimThe effect of structural viral protein 1 (VP1) on neurological damage caused by enterovirus 71 (EV71) infection is unclear. This study aimed to explore the transcriptome changes in EV infected patients and the role of VP1 on the cell secretion pathway of neuron cells. MethodsIn our cohort, EV infected patients were enrolled, and RNA-seq analysis was used to evaluate the distinct transcript patterns of cerebrospinal fluid (CSF). The EV71 VP1-overexpressing vector (pEGFP-c3-VP1) was generated and transfected into neuron cells. The relationship between Glutamate Rich 3 (ERICH3) and methyltransferase Zinc Finger CCCH-Type Containing 13 (ZC3H13) and their effect on the serotonin (5-HT) release of neuron cells were explored using small interfering RNA. The expression of ERICH3 and ZC3H13 and concentration of 5-HT were determined using real-time PCR, Western blot, and ELISA, respectively. ResultThe expression of ERICH3 and ZC3H13 were significantly upregulated in EV infected patients with neurological symptoms compared to those without (P < 0.05). The ERICH3 gene had many N6-methyladenosine (m6A) binding sites that can be regulated by m6A modification. Further, the expression of ERICH3 and ZC3H13 were elevated significantly in EV71-VP1 overexpressing neuron cells (P < 0.05). Moreover, ERICH3 or ZC3H13 deficiency could significantly downregulate the release of 5-HT in VP1-overexpressing cells (P < 0.05). Nonetheless, ERICH3 expression was significantly suppressed when ZC3H13 was silenced in neuron cells and vice versa (P < 0.05). ConclusionsEV71-VP1 can promote 5-HT release by upregulating the expression of ERICH3 and ZC3H13. 5-HT might be a novel therapeutic target for EV71 infection-induced fatal neuronal damage.

Reverse-Phase Ultra-Performance Chromatography Method for Oncolytic Coxsackievirus Viral Protein Separation and Empty to Full Capsid Quantification.

Oncolytic virus immunotherapy is emerging as a novel therapeutic approach for cancer treatment. Immunotherapy clinical drug candidate V937 is currently in phase I/II clinical trials and consists of a proprietary formulation of Coxsackievirus A21 (CVA21), which specifically infects and lyses cells with overexpressed ICAM-1 receptors in a range of tumors. Mature Coxsackievirus virions, consisting of four structural virion proteins, (VPs) VP1, VP2, VP3, and VP4, and the RNA genome, are the only viral particles capable of being infectious. In addition to mature virions, empty procapsids with VPs, VP0, VP1, and VP3, and other virus particles are produced in V937 production cell culture. Viral protein VP0 is cleaved into VP2 and VP4 after RNA genome encapsidation to form mature virions. Clearance of viral particles containing VP0, and quantification of viral protein distribution are important in V937 downstream processing. Existing analytical methods for the characterization of viral proteins and particles may lack sensitivity or are low throughput. We developed a sensitive and robust reverse-phase ultra-performance chromatography method to separate, identify, and quantify all five CVA21 VPs. Quantification of virus capsid concentration and empty/full capsid ratio was achieved with good linearity, accuracy, and precision. ClinicalTrials.gov ID: NCT04521621 and NCT04152863.

Invasion and Propagation of White Spot Syndrome Virus: Hijacking of the Cytoskeleton, Intracellular Transport Machinery, and Nuclear Import Transporters.

The pathogenesis of white spot syndrome virus (WSSV) is largely unclear. In this study, we found that actin nucleation and clathrin-mediated endocytosis were recruited for internalization of WSSV into crayfish hematopoietic tissue (Hpt) cells. This internalization was followed by intracellular transport of the invading virions via endocytic vesicles and endosomes. After envelope fusion within endosomes, the penetrated nucleocapsids were transported along microtubules toward the periphery of the nuclear pores. Furthermore, the nuclear transporter CqImportin α1/β1, via binding of ARM repeat domain within CqImportin α1 to the nuclear localization sequences (NLSs) of viral cargoes and binding of CqImportin β1 to the nucleoporins CqNup35/62 with the action of CqRan for docking to nuclear pores, was hijacked for both targeting of the incoming nucleocapsids toward the nuclear pores and import of the expressed viral structural proteins containing NLS into the cell nucleus. Intriguingly, dysfunction of CqImportin α1/β1 resulted in significant accumulation of incoming nucleocapsids on the periphery of the Hpt cell nucleus, leading to substantially decreased introduction of the viral genome into the nucleus and remarkably reduced nuclear import of expressed viral structural proteins with NLS; both of these effects were accompanied by significantly inhibited viral propagation. Accordingly, the survival rate of crayfish post-WSSV challenge was significantly increased after dysfunction of CqImportin α1/β1, also showing significantly reduced viral propagation, and was induced either by gene silencing or by pharmacological blockade via dietary administration of ivermectin per os. Collectively, our findings improve our understanding of WSSV pathogenesis and support future antiviral designing against WSSV. IMPORTANCE As one of the largest animal DNA viruses, white spot syndrome virus (WSSV) has been causing severe economical loss in aquaculture due to the limited knowledge on WSSV pathogenesis for an antiviral strategy. We demonstrate that the actin cytoskeleton, endocytic vesicles, endosomes, and microtubules are hijacked for WSSV invasion; importantly, the nuclear transporter CqImportin α1/β1 together with CqRan were recruited, via binding of CqImportin β1 to the nucleoporins CqNup35/62, for both the nuclear pore targeting of the incoming nucleocapsids and the nuclear import of expressed viral structural proteins containing the nuclear localization sequences (NLSs). This is the first report that NLSs from both viral structure proteins and host factor are elaborately recruited together to facilitate WSSV infection. Our findings provide a novel explanation for WSSV pathogenesis involving systemic hijacking of host factors, which can be used for antiviral targeting against WSSV disease, such as the blockade of CqImportin α1/β1 with ivermectin.

Human Retrovirus Genomic RNA Packaging.

Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.

Duplex One-Step RT-qPCR Assays for Simultaneous Detection of Genomic and Subgenomic RNAs of SARS-CoV-2 Variants.

A hallmark of severe acute respiratory syndrome virus (SARS-CoV-2) replication is the discontinuous transcription of open reading frames (ORFs) encoding structural virus proteins. Real-time reverse transcription PCR (RT-qPCR) assays in previous publications used either single or multiplex assays for SARS-CoV-2 genomic RNA detection and a singleplex approach for subgenomic RNA detection. Although multiplex approaches often target multiple genomic RNA segments, an assay that concurrently detects genomic and subgenomic targets has been lacking. To bridge this gap, we developed two duplex one-step RT-qPCR assays that detect SARS-CoV-2 genomic ORF1a and either subgenomic spike or subgenomic ORF3a RNAs. All primers and probes for our assays were designed to bind to variants of SARS-CoV-2. In this study, our assays successfully detected SARS-CoV-2 Washington strain and delta variant isolates at various time points during the course of live virus infection in vitro. The ability to quantify subgenomic SARS-CoV-2 RNA is important, as it may indicate the presence of active replication, particularly in samples collected longitudinally. Furthermore, specific detection of genomic and subgenomic RNAs simultaneously in a single reaction increases assay efficiency, potentially leading to expedited lucidity about viral replication and pathogenesis of any variant of SARS-CoV-2.

The Nuclear DNA Sensor IFI16 Indiscriminately Binds to and Diminishes Accessibility of the HSV-1 Genome to Suppress Infection.

ABSTRACTHuman cells identify invading pathogens and activate immune signaling pathways through a wide array of pattern recognition receptors, including DNA sensors. The interferon-inducible protein 16 (IFI16) is a nuclear DNA sensor that recognizes double-stranded DNA from a number of viral sources, including genomes of nuclear-replicating viruses. Among these is the prevalent human pathogen herpes simplex virus 1 (HSV-1). Upon binding to the HSV-1 DNA genome, IFI16 both induces antiviral cytokine expression and suppresses virus gene expression. Here, we used a multiomics approach of DNA sequencing techniques paired with targeted mass spectrometry to obtain an extensive view of the interaction between IFI16 and the HSV-1 genome and how this binding affects the viral DNA structure and protein expression. Through chromatin immunoaffinity purification coupled with next-generation DNA sequencing (ChIP-seq), we found that IFI16 binds to the HSV-1 genome in a sequence-independent manner while simultaneously exhibiting broad enrichment at two loci: UL30, the viral DNA polymerase gene, and US1 to US7. The assay for transposase-accessible chromatin with sequencing (ATAC-seq) revealed that these two regions are among the most accessible stretches of DNA on the genome, thereby facilitating IFI16 binding. Accessibility of the entire HSV-1 genome is elevated upon IFI16 knockout, indicating that expression of IFI16 globally induces chromatinization of viral DNA. Deletion of IFI16 also results in a global increase in the expression of HSV-1 proteins, as measured by parallel reaction monitoring-mass spectrometry of viral proteins representing 80% of the HSV-1 genome. Altogether, we demonstrate that IFI16 interacts with the HSV-1 genome in a sequence-independent manner, coordinating epigenetic silencing of the viral genome and decreasing protein expression and virus replication.IMPORTANCE Mammalian host defense against viral infection includes broad-acting cellular restriction factors, as well as effectors of intrinsic and innate immunity. IFI16 is a critical nuclear host defense factor and intrinsic immune protein involved in binding viral DNA genomes, thereby repressing the replication of nucleus-replicating viruses, including the human herpes simplex virus 1. What has remained unclear is where on the viral genome IFI16 binds and how binding affects both viral DNA structural accessibility and viral protein expression. Our study provides a global view of where and how a nuclear restriction factor of DNA viruses associates with viral genomes to exert antiviral functions during early stages of an acute virus infection. Our study can additionally serve as a systems-level model to evaluate nuclear DNA sensor interactions with viral genomes, as well as the antiviral outcomes of transcriptionally silencing pathogen-derived DNA.

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein.

Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by three to four different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced coassembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.

MO869: SARS-COV-2 Neutralizing Antibodies in Patients on Hemodialysis After Vaccination

Abstract BACKGROUND Patients on hemodialysis (HD) are at high risk of a severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection, which causes coronavirus disease 2019 (COVID-19), and humoral and cellular response data in these patients are limited. SARS-CoV-2 has four major structural proteins: spike (S), membrane, envelope and nucleocapsid (N) proteins. The S protein consists of the S1 and S2 subunits, which mediate cell surface binding via the receptor-binding domain, and induce viral-host cell membrane fusion, respectively. Approximately, 90% of the SARS-CoV-2-specific neutralizing antibodies (nAbs) target the highly immunogenic receptor-binding domain, but there is little evidence of nAbs targeting other viral structural proteins, such as the N protein. Speer et al. reported reduced Ab responses to the first and second doses of the mRNA vaccine, BNT162b2 (BioNTech), in patients on long-term HD. The majority (82%) of patients developed nAbs after the second dose, but at lower levels than healthy controls (HCs) [1]. Since data on the efficacy of COVID-19 vaccination in patients on HD are limited, we investigated the SARS-CoV-2 nAbs in Japanese patients on HD. METHOD Forty-two patients (24 males and 18 females) on HD for an average of 4.5 years (0–21), with a mean age of 68 years (28–92), who received two doses of the mRNA vaccine, BNT162b2, between May 1 and 30 November 2021 were included. In addition, 10 HCs (6 males and 4 females with mean age of 55 (26–75) and 41 (28–63) years, respectively) with normal renal function who received two doses of the mRNA vaccine BNT162b2 in the same period were tested for SARS-CoV-2 nAbs at 4, 8, 12, 16 and 20 weeks (W) after vaccination. We measured SARS-CoV-2 Abs in human plasma qualitatively with a fully automated Cobas e801 analyzer, an Elecsys® Anti-SARS-CoV-2 electrochemiluminescence immunoassay, and an Elecsys® Anti-SARS-CoV-2 S RUO electrochemiluminescence immunoassay (Roche Diagnostics International Ltd, Rotkreuz, Switzerland) according to the manufacturer's instructions. RESULTS Approximately, 97.6% (41/42) of patients on HD tested positive for SARS-CoV-2 nAbs. The mean titer of SARS-CoV-2 nAbs after BNT162b2 vaccination in all individuals was 490.1 (0.4–5116) U/mL. The mean titers of SARS-CoV-2 nAbs after BNT162b2 vaccination in patients on HD aged between 56–92 years and 28–53 years were 266.7 (0.4–1131) U/mL and 1320.4 (44.8–5116) U/mL, respectively. The levels of nAbs were lower in the older group than in the younger group. Patients on HD are associated with premature aging of the immune systems. Progressive immunosenescence may be associated with reduced T cell activity and humoral response, potentially leading to reduced vaccine protection. During the follow-up period, Abs against N protein were not detected in all individuals. Over 90% of patients on HD wore face masks, washed their hands and maintained a 2 m social distance in the dialysis facilities. Almost all patients avoided the three Cs (closed spaces with poor ventilation, crowded places with nearby people and close-contact settings, such as close-range conversations). In contrast, the mean SARS-CoV-2 nAb titers in the older (55–73 years) HCs were 1006, 643, 520, 464 and 390 U/mL at 4, 8, 12, 16 and 20 W post-vaccination. Contrastingly, the mean SARS-CoV-2 nAb titers in the younger (26–45 years) HCs were 2685, 2032, 1731, 1609 and 1527 U/mL at 4, 8, 12, 16 and 20 W post-vaccination. The nAb levels decreased gradually and were lower in the older group than in the younger group. CONCLUSION Japanese patients on HD had SARS-CoV-2 neutralizing capacities after BNT162b2 vaccination. The majority (97.6%) developed nAb after the second dose. The levels of neutralizing antibodies were lower in the older group than in the younger group.

Inactivation mechanisms of human adenovirus by e-beam irradiation in water environments.

This study aims to study the kinetics and mechanisms of human adenovirus inactivation by electron beam. Human adenovirus type 5 (HAdV-5) was inoculated in two types of aqueous substrates (phosphate-buffered saline - PBS, domestic wastewater - WW) treated by electron beam at a dose range between 3 and 21kGy. Samples were evaluated for virus infectivity, PCR amplification of fragments of HAdV-5 genome and abundance and antigenicity of the virion structural proteins. The maximum reduction in viral titre, in plaque-forming units (PFU) per millilitre, was about 7 and 5 log PFU/mL for e-beam irradiation at 20kGy in PBS and 19kGy in wastewater, respectively. Among the virion structural proteins detected, the hexon protein showed the higher radioresistance. Long (10.1 kbp) genomic DNA fragments were differently PCR amplified, denoting a substrate effect on HAdV-5 genome degradation by e-beam. The differences observed between the two substrates can be explained by the protective effect that the organic matter present in the substrate may have on viral irradiation. According to the obtained results, the decrease in viral viability/infectivity may be due to DNA damage and to protein alterations. In summary, electron beam irradiation at a dose of 13kGy is capable of reducing HAdV-5 viral titres by more than 99.99% (4 log PFU/mL) in both substrates assayed, indicating that this type of technology is effective for viral wastewater disinfection and may be used as a tertiary treatment in water treatment plants. KEY POINTS: • The substrate in which the virus is suspended has an impact on its sensitivity to e-beam treatment. • E-beam irradiation at 13 kGy is capable of reducing by 4 Log PFU/mL the HAdV-5 viral titre. • The decrease in viral viability/infectivity may be due to DNA damage and to protein alterations.

Protein engineering and biochemical/biophysical approaches for structural studies of small membrane proteins and their complexes: Application to viroporins

We study the structure and function of small viral membrane proteins, which are expressed in the host and function in cellular membranes. Typically, they are multi‐domain multi‐functional proteins aiding virus adaptation and proliferation. Detailed characterization of the structure‐function relationship of these proteins will help to better understand virus‐host interactions and possibly develop protein inhibitors. However, such characterization is challenging due to the proteins’ small size and dynamic nature. Our focus is on viroporins, namely the Vpu, p7 and E proteins from HIV‐1, HCV, and CoV, respectively. Viroporins form ion‐conducting oligomers in cellular membranes leading to increased membrane permeability affecting ion homeostasis in infected cells. In addition, these proteins have soluble domains involved in interactions with host proteins. Currently, the structures of full‐length viroporins are largely uncharacterized and the information about the mechanism of oligomer formation and inter‐domain communication is very limited. Here, we report our effort to produce and solve the structure of stable viroporin oligomers in lipid environment. We use protein engineering to generate a range of fusion constructs aiming to increase the protein/oligomer size and reduce the conformational heterogeneity, thus making the protein amenable for structural determination by electron microscopy (EM) techniques. We produced, expressed in E. coli and purified, several soluble constructs of Vpu, p7 and E proteins fused at their N‐terminals to maltose binding protein (MBP). Thereafter, we interacted these proteins with lyso lipid mixtures of PC and PG, and their oligomerization was observed by negative staining EM and pulse electron paramagnetic resonance (EPR). We further use size‐exclusion chromatography (SEC) to assess the heterogeneity of viroporin oligomers in lyso PC/PG. Indeed, the protein elution exhibits a relatively broad chromatographic profile, indicating the presence of more than one oligomeric form. We further use SEC to test different protein‐to‐lipid molar ratios and the effect of viroporin inhibitor binding, aiming to shift the equilibrium toward stable functional viroporin oligomers. We will also discuss results from EM studies on these stable oligomers and EPR studies on spin‐labeled viroporin assembly. The progress we made in generating protein constructs and assessing protein oligomerization and stability in lipid provides a great promise for the development of successful methodology to determine the structure of full‐length viroporin. This methodology could also be applicable to other small oligomeric membrane proteins.

Exploring Protein Structures of SARS‐CoV‐2 Variants of Concern within an Undergraduate Research Course

Lane College is a Historically Black College with a legacy of educating underserved minority students. As a primarily undergraduate teaching college, faculty and students have limited opportunities to engage in undergraduate research. To address this concern, the biology department created the undergraduate research course sequence (Undergraduate Research I and II) to provide course‐based undergraduate research experiences for students. During the Spring 2021 semester, to limit the spread of COVID‐19, the College began the first few weeks with complete online instruction before switching to hybrid or face‐to‐face modality. For the biology undergraduate research students, the projects were redesigned based on input from the students to explore the viral protein structural changes in newly emerging SARS‐CoV‐2 variants of concern (VOC). First, students explored the virology of SARS‐CoV‐2 and structures of key viral proteins using curriculum available from Rutgers University on the Protein Data Bank during the online instruction period. Then the students selected a variant of concern, B.1.1.7 (Alpha), B.1.351 (Beta), or P.1 (Gamma), and a specific viral protein containing at least one mutation for further study. During the hybrid instruction period, using open‐source bioinformatics tools, including NCBI SARS‐CoV‐2 genome sequences, PANGO Lineage VOC data, UCSC Genome Browser and SNAP Gene, the students mapped the location of the VOC mutation on their chosen protein’s known structure. They then modeled the effect of the mutation on the protein structure using Chimera or iCN3D, since Chimera is not compatible with Chromebooks. Students determined that the mutations found in nsp3 in Alpha variant and ORF8 in Gamma variant did not have a large impact on the overall structure of the proteins and predicted that there would not be significant effects on protein function. In contrast, several mutations found in Beta variant spike protein likely impact receptor binding domain interactions with angiotensin converting enzyme 2 receptor. The methods developed here will be useful for further investigations of protein structures from emerging variants of concern. This experience demonstrates the utility of bioinformatics research projects in online and hybrid courses and the importance of consideration of compatibility of various open‐source tools with student devices.

Development of DNA Aptamers Against Structural Proteins of SARS‐CoV‐2

The severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) is a positive‐sense single strand (ss) RNA virus responsible for causing the COVID‐19 disease. With the continuous incidence of infections by SARS‐CoV‐2 and the appearance of strains that may evade existing vaccines and treatments, it is imperative to implement strategies that allow an effective and rapid diagnosis of this disease. Due to their high‐abundance in viral particles, structural proteins (i.e., nucleocapsid (N) and spike glycoprotein (S)) are logical targets for diagnostic tests. Aptamers are single‐stranded DNA or RNA oligonucleotides, ~100 bases long, that interact with high‐affinity binding and specificity with a wide variety of molecules including proteins. Aptamers can be generated through an in vitro selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). This research aims to use SELEX process to select DNA‐aptamers targeting structural proteins of SARS‐CoV‐2. The developed aptamers resulting from this work will be incorporated on a sensitive and cost‐effective rapid antigen test to detect the presence of SARS‐CoV‐2.

Flavivirus NS1: Structure and Function of an Enigmatic Virulence Factor

Viruses employ a variety of molecular strategies to carve out an existence in their host and to thwart host defenses. Crystal structures of viral proteins and of the host proteins deployed as molecular weapons contribute enormously to our understanding of viral pathogenesis and our efforts to combat viral infection. Mosquito‐borne flaviviruses, including the dengue, Zika, yellow fever, Japanese encephalitis and West Nile viruses, cause serious human diseases in much of the world. A growing number of diverse functions has been discovered for the enigmatic virulence factor known as NS1: it is an essential cofactor in viral genome replication, a mediator of the host immune response, and a trigger of host vascular leakage. NS1 lacks precedent in the structure and sequence databases, so an accurate 3D structure was key to understanding the basis for its various functions. A high‐throughput survey of expression conditions in baculovirus‐infected insect cells was essential to identifying conditions for production of recombinant NS1 in its natural glycosylated, disulfide‐linked form. We solved a crystal structure of West Nile virus NS1 from the anomalous scattering of the native sulfur atoms using an 18‐crystal data set [1,2]. The structure revealed a previously unknown protein fold with a fundamentally dimeric architecture, and led to assigned functions for two of the three NS1 structural domains. Subsequent structures of NS1 from dengue virus and Zika viruses established the basis for its membrane association in cells and its lipid encapsidation when secreted [3]. Recently discovered functions of this remarkable virulence factor emerged in follow‐up studies that built upon the crystal structures. Prime among these is the discovery that the NS1 protein, in a mouse model of dengue disease and in absence of virus, can induce the vascular leak that is a hallmark of severe dengue disease [4,5]. Clues to the molecular mechanism of NS1‐induced endothelial dysfunction emerged from a study of the protection afforded by a monoclonal antibody and the structure of the Fab fragment bound to the NS1 epitope [6].[1] Akey DL et al. &amp; Smith JL (2014) Science 343, 881‐885.[2] Akey DL et al. &amp; Smith JL (2014) Acta Crystallogr D70, 2719‐2729.[3] Brown WC et al. &amp; Smith JL (2016) Nature Struct Molec Biol 23, 856‐867.[4] Beatty PR et al. &amp; Harris E (2015) Science Trans Med 7, 304ra141.[5] Modhiran N et al. &amp; Young PR (2015) Science Trans Med 7, 304ra142.[6] Biering SB, Akey DL et al. Smith JL &amp; Harris E (2021) Science 371, 194‐200.

Targeting of Silver Cations, Silver-Cystine Complexes, Ag Nanoclusters, and Nanoparticles towards SARS-CoV-2 RNA and Recombinant Virion Proteins.

Background: Nanosilver possesses antiviral, antibacterial, anti-inflammatory, anti-angiogenesis, antiplatelet, and anticancer properties. The development of disinfectants, inactivated vaccines, and combined etiotropic and immunomodulation therapy against respiratory viral infections, including COVID-19, remains urgent. Aim: Our goal was to determine the SARS-CoV-2 molecular targets (genomic RNA and the structural virion proteins S and N) for silver-containing nanomaterials. Methods: SARS-CoV-2 gene cloning, purification of S2 and N recombinant proteins, viral RNA isolation from patients’ blood samples, reverse transcription with quantitative real-time PCR ((RT)2-PCR), ELISA, and multiplex immunofluorescent analysis with magnetic beads (xMAP) for detection of 17 inflammation markers. Results: Fluorescent Ag nanoclusters (NCs) less than 2 nm with a few recovered silver atoms, citrate coated Ag nanoparticles (NPs) with diameters of 20–120 nm, and nanoconjugates of 50–150 nm consisting of Ag NPs with different protein envelopes were constructed from AgNO3 and analyzed by means of transmission electron microscopy (TEM), atomic force microscopy (AFM), ultraviolet-visible light absorption, and fluorescent spectroscopy. SARS-CoV-2 RNA isolated from COVID-19 patients’ blood samples was completely cleaved with the artificial RNase complex compound Li+[Ag+2Cys2−(OH−)2(NH3)2] (Ag-2S), whereas other Ag-containing materials provided partial RNA degradation only. Treatment of the SARS-CoV-2 S2 and N recombinant antigens with AgNO3 and Ag NPs inhibited their binding with specific polyclonal antibodies, as shown by ELISA. Fluorescent Ag NCs with albumin or immunoglobulins, Ag-2S complex, and nanoconjugates of Ag NPs with protein shells had no effect on the interaction between coronavirus recombinant antigens and antibodies. Reduced production of a majority of the 17 inflammation biomarkers after treatment of three human cell lines with nanosilver was demonstrated by xMAP. Conclusion: The antiviral properties of the silver nanomaterials against SARS-CoV-2 coronavirus differed. The small-molecular-weight artificial RNase Ag-2S provided exhaustive RNA destruction but could not bind with the SARS-CoV-2 recombinant antigens. On the contrary, Ag+ ions and Ag NPs interacted with the SARS-CoV-2 recombinant antigens N and S but were less efficient at performing viral RNA cleavage. One should note that SARS-CoV-2 RNA was more stable than MS2 phage RNA. The isolated RNA of both the MS2 phage and SARS-CoV-2 were more degradable than the MS2 phage and coronavirus particles in patients’ blood, due to the protection with structural proteins. To reduce the risk of the virus resistance, a combined treatment with Ag-2S and Ag NPs could be used. To prevent cytokine storm during the early stages of respiratory infections with RNA-containing viruses, nanoconjugates of Ag NPs with surface proteins could be recommended.

Oligomers of hepatitis A virus (HAV) capsid protein VP1 generated in a heterologous expression system

BackgroundThe quasi-enveloped picornavirus, Hepatitis A Virus (HAV), causes acute hepatitis in humans and infects approximately 1.5 million individuals a year, which does not include the asymptomatically infected population. Several severe outbreaks in developing nations in recent years have highlighted the reduction in HAV endemicity, which increases the risk of infections in the vulnerable population. The current HAV vaccines are based on growing wildtype or attenuated virus in cell culture, which raises the cost of production. For generation of cheaper, subunit vaccines or strategies for antibody-based diagnostics, production of viral structural proteins in recombinant form in easily accessible expression systems is a priority.ResultsWe attempted several strategies for recombinant production of one of the major capsid proteins VP1, from HAV, in the E. coli expression system. Several efforts resulted in the formation of soluble aggregates or tight association of VP1 with the bacterial chaperone GroEL. Correctly folded VP1 was eventually generated in a discrete oligomeric form upon purification of the protein from inclusion bodies and refolding. The oligomers resemble oligomers of capsid proteins from other picornaviruses and appear to have the correct secondary and antigenic surface structure.ConclusionsVP1 oligomers generated in the bacterial expression system can be utilized for understanding the molecular pathway of HAV capsid assembly and may also have potential biomedical usages in prevention and diagnostics of HAV infections.

Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging

RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5′ untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5′ UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS–SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.

Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic

Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on public health, continuous molecular epidemiology is of vital importance. The current study has been designed to investigate the major SARS-CoV-2 variants and emerging mutations in virus structural and non-structural proteins (NSP) during the fourth wave in September 2021 from the Punjab province of Pakistan. Twenty SARS-CoV-2 positive samples have been collected from major cities were subjected to next-generation sequencing. Among the 20 whole genomes (GenBank Accession SRR16294858-SRR16294877), 2 samples failed to be completely sequenced. These genome sequences harbored 207 non-synonymous mutations, among which 19 were unique to GISAID. The genome sequences were detected: Delta 21I, 21J variants (B.1.617.2). Mutation’s spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. These genomic sequences also harbored 129 non-synonymous mutations in NSP. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. Numerous other unique mutations have been detected in the virus papain-like protease (NSP3), main protease (NSP5), and RNA-dependent RNA polymerase (NSP12). The most common non-synonymous mutations in the spike protein were subjected to stability analysis, exhibiting a stabilizing effect on structures. The presence of Delta variants may affect therapeutic efforts and vaccine efficacy. Continuous genomic epidemiology of SARS-CoV-2 in Pakistan may be useful for better management of SARS-CoV-2 infections.