Determination of 50% endpoint titer using a simple formula

Ferritin nanoparticle complex with porcine epidemic diarrhea virus spike protein induces neutralizing antibody response against PEDV in mouse models

As the spike protein is the major antigen that contains various neutralizing epitopes against porcine epidemic diarrhea virus (PEDV), numerous vaccine trials employing the spike protein have been established. In this study, we developed a ferritin-based nanoparticle vaccine for PEDV by combining gene delivery functions of recombinant adenoviruses. To generate nanoparticles, the S1 subunit of the spike protein was genetically linked to the N-terminus of the human ferritin heavy chain (hFTHC), and recombinant adenoviruses were generated to deliver the genetic material. The efficacy of S1 conjugated human ferritin heavy chain (S1-hFTHC) adenoviruses against S1 adenoviruses was evaluated in BALB/c mice immunized intramuscularly without adjuvant. Two weeks after the final boost, we observed a significantly higher IgG response in S1-hFTHC immunized mice compared with the S1 immunized mice, and results from the virus neutralization assay revealed robust virus neutralization activity in the S1-hFTHC immunized group compared to the S1 immunized group. Furthermore, analysis of the serum based on IgG and neutralizing titers 40 days after the last vaccination revealed the significance and longevity of the immune response induced by S1-hFTCH compared to S1 only. This strategy elucidates the efficacy of combined vaccine strategies for developing promising vaccine candidates against PEDV.

Adapted hepatitis C virus clone infects innate immunity-deficient mouse hepatocytes with minimal human HCV entry factors

Background & Aims

Hepatitis C virus (HCV) has a narrow species tropism and cannot infect mice. To understand HCV species tropism and to develop better animal models, we adapted HCV to infect mouse cells deficient in innate immunity and with minimal human HCV host factors.

Methods

HCV was adapted via passaging an HCV infectious virus clone several times in human hepatoma cells, mouse liver cells, and eventually primary mouse hepatocytes deficient in innate immunity and ectopically expressing human occludin and human CD81. Using RNAseq the sequence of the adapted virus was analyzed, and several clones were generated to study replication and infection kinetics as well as neutralization assays in several human/mouse cell lines and primary hepatocytes from human, mouse, and macaques.

Results

Accumulation of 35 non-synonymous and 66 synonymous mutations correlated with >1,000-fold enhanced production of infectious progeny from primary mouse hepatocytes. These mutations did not confer drug resistance or evasion from innate immunity. They did not enhance fitness in human or macaque hepatocytes. We show that non-synonymous mutations are necessary and sufficient for adaptation, and that changes to the glycoproteins are not essential. Mutations outside of viral envelope proteins enhanced specific infectivity and facilitated viral spread in murine cells.

Conclusions

This study reveals key viral factors governing HCV species tropism. The mouse-adapted HCV opens up possibilities for the development of animal models to analyze HCV pathogenesis, immune control, and vaccine development.

Impact and implications

This work demonstrates the feasibility in principle of HCV adaptation to replication in and infection of non-human cells. This is made possible by a manageable number of non-synonymous mutations and opens up new ways to elucidate the principles of HCV species tropism and to develop important animal models for HCV research in the long term.

Optimization of an infectious subgenomic amplicons reverse genetics protocol for the rescue of synthetic coronaviruses

Reverse genetics (rg) systems are indispensable tools for investigating the pathogenesis of RNA viruses, facilitating vaccine design, and advancing antiviral therapeutic strategies. In this study, we optimized the Infectious Subgenomic Amplicons (ISA) method for generating synthetic r-wt SARS-CoV-2 Wuhan-Hu-1. This system was validated by demonstrating the successful rescue of infectious viral particles from overlapping DNA fragments and their propagation in vitro. Sequencing confirmed 100 % identity of the recovered virus with the Wuhan-Hu-1 reference genome. Importantly, in vivo experiments using K18-hACE2 mice revealed that the r-wt SARS-CoV-2 Wuhan-Hu-1 strain caused clinical symptoms, weight loss, and mortality comparable to those induced by a virulent SARS-CoV-2 field variant. This ISA rg method offers a rapid and reproducible approach to generating synthetic coronaviruses, with potential applications in pathogenesis studies, antiviral testing, and vaccine development.

Utilizing shRNA-expressing lentivectors for viral hemorrhagic septicemia virus suppression via NV gene targeting

Background

Viral hemorrhagic septicemia virus or VHSV, is a single-stranded negative-sense RNA virus that is a member of the Rhabdoviridae family's genus Novirhabdovirus. Its major host is rainbow trout. Severe clinical symptoms and a higher mortality rate in fish populations are caused by this virus. Regretfully, there is currently no medication or vaccination available to treat it. Recently, there has been a lot of interest in developing antiviral therapies employing interfering RNA (RNAi), particularly shRNA. This study used shRNAs targeting the NV gene of VHSV to test its effectiveness in preventing VHSV proliferation in cell culture. Using the VHSV-Fil3 strain, the appropriate oligonucleotide sequence for NV gene coding was chosen for this purpose. Subsequently, shRNA molecules were designed and synthesized with the aid of shRNA design tools. The shRNAs were transfected into HEK293T cells after being cloned into the suitable vectors using the third generation of lentiviral packaging system. The CS2-2 cell line was subsequently transduced with these shRNA-expressing lentiviruses in order to challenge the VHS virus. Finally, TCID50 was employed to calculate the viral infectious titer in order to assess the effectiveness of shRNAs.

Results

According to the final calculations, all shRNAs exhibited antiviral activity. When compared to the control groups, the shRNAs 1, 2, and 3 considerably lowered VHSV output in the TCID50 test (nearly 99.99, 99.99, and 99.99%, respectively, compared to cells with VHSV inoculation and nearly 99.98, 99.98, and 99.97%, respectively, compared to cells with VHSV and scrambled vector inoculation).

Conclusion

Thus, it can be declared that RNA interference (RNAi) has the potential to be an exceptionally effective therapeutic option against viruses like VHSV.

Isolation, molecular identification, and phylogenetic analysis of infectious bronchitis virus from commercial chicken farms in Mekele and Bishoftu, Ethiopia, 2023-2024

BACKGROUND

Avian infectious bronchitis (IB) is a highly contagious respiratory disease that affects the poultry industry globally. The disease is caused by avian infectious bronchitis virus (IBV), member of the genus Gammacoronavirus. In Ethiopia, IBV has been reported in both commercial and backyard chickens based on clinical observation. The objectives of this study were to isolate the virus, conduct molecular based identification, and phylogenetic analysis of the circulating IBV isolates.

METHODS AND MATERIALS

A cross-sectional study was conducted between November 2023 and May 2024 in Mekele and Bishoftu, Ethiopia. A total of 49 clinical samples were collected, comprising 12 tissue samples and 39 pooled swab samples. Of these, 6 samples-specifically, 5 swab samples and 1 tissue sample-tested positive for infectious bronchitis virus (IBV) through virus-specific conventional RT-PCR and real-time PCR. Nested PCR was performed using serotype-specific primers. The purified PCR products, which targeted the spike glycoprotein S1 subunit gene and the 3' UTR of the IBV, were sequenced, followed by phylogenetic tree analysis.

RESULTS

The six positive samples propagated into specific pathogen free embryonated eggs and exhibited characteristic IBV lesions and mortality observed over five consecutive passages. IBV isolates from Bishoftu (n = 4) and Mekele (n = 2) were amplified using one-step RT-PCR to target 466 bp of the S1 subunit gene and 433 bp of the 3'UTR. A BLAST search on the S1 partial gene and 3'UTR sequences, nested PCR, and phylogenetic analysis revealed that the present IBV isolates are genetically similar to the Massachusetts serotype. The S1 gene sequences of the five IBV isolates were deposited in GenBank with accession numbers PQ389500 to PQ389504.

CONCLUSIONS

This is the first detailed study on IB virus isolation, molecular detection, sequencing, and phylogenetic analysis in Ethiopia. The findings revealed that the outbreaks were caused by the IB virus, which created a serious health risk and economic losses in the chicken industry. To the author's knowledge, this is the first comprehensive study on the isolation and genetic analysis of IBV in Ethiopia. Further research on the economic impact of IBV in chicken production, farm biosecurity, serotyping of circulating IB virus, and vaccine development based on the local serotypes is recommended.

RAB5 is a host dependency factor for the generation of SARS-CoV-2 replication organelles

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a threat due to the emergence of variants with increased transmissibility and enhanced escape from immune responses. Like other coronaviruses before, SARS-CoV-2 likely emerged after its transmission from bats. The successful propagation of SARS-CoV-2 in humans might have been facilitated by usurping evolutionarily conserved cellular factors to execute crucial steps in its life cycle, such as the generation of replication organelles-membrane structures where coronaviruses assemble their replication-transcription complex. In this study, we found that RAB5, which is highly conserved across mammals, is a critical host dependency factor for the replication of the SARS-CoV-2 genome. Our results also suggest that SARS-CoV-2 uses RAB5+ membranes to build replication organelles with the aid of COPB1, a component of the COP-I complex, and that the virus protein NSP6 participates in this process. Hence, targeting NSP6 represents a promising approach to interfere with SARS-CoV-2 RNA synthesis and halt its propagation.IMPORTANCEIn this study, we sought to identify the host dependency factors that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses for the generation of replication organelles: cellular membranous structures that SARS-CoV-2 builds in order to support the replication and transcription of its genome. We uncovered that RAB5 is an important dependency factor for SARS-CoV-2 replication and the generation of replication organelles, and that the viral protein NSP6 participates in this process. Hence, NSP6 represents a promising target to halt SARS-CoV-2 replication.

Testing the Tenacity of Small Ruminant Lentiviruses In Vitro to Assess the Potential Risk of Indirect Fomites' Transmission

In 2011-2013, we isolated and characterized small ruminant lentiviruses (SRLVs) from two flocks, one of goats and the other of sheep, that had never been in direct contact. Phylogenetic analysis of these viruses indicated a common origin, which led us to hypothesize indirect transmission of these viruses between the two flocks. Since, to our knowledge, there are no published data on the tenacity of these viruses, we started this work. In the first part, we monitored the loss of infectivity of two prototypic SRLV strains, MVV 1514 and CAEV-CO, over time, in liquid suspension. As expected, the suspensions stored at 4 °C better preserved the infectivity of the viruses. Additionally, viruses resuspended in milk, the medium mirroring the in vivo situation, proved more tenacious than those maintained in a cell culture medium. These viruses, subjected to harsh treatments such as drying and resuspending, partially maintained their replication capacity. After an immediate loss of nearly 1 log10 TCID50 immediately after desiccation, the viruses maintained their replication capacity for at least three weeks when desiccated in milk. These results suggest that fomites, clothing, or pastures contaminated with secretions or milk from infected animals might mediate the infection of animals independently of direct contact.

Assessment of the preventive effect of knockdown of cellular genes NXF1, PRPS1PRPS1 and NAA10 in influenza infection in an in vitro model

INTRODUCTION

Influenza is an acute respiratory viral infectious disease caused by the influenza viruses. Current preventive and therapeutic approaches are of great anti-epidemic importance, but there are a number of problems, such as the rapid emergence of resistant strains, the lack of cross-immunity and the effectiveness of vaccines. One of the approaches to the development of anti-influenza agents is the use of RNA interference and small interfering RNAs complementary to the mRNA target of viral and cellular genes. Aim ‒ to evaluate the prophylactic anti-influenza effect of siRNAs directed to the cellular genes NXF1, PRPS1 and NAA10 in an in vitro model.

MATERIALS AND METHODS

Antigenic variants of influenza A virus: A/California/7/09 (H1N1), A/WSN/33 (H1N1) and A/Brisbane/59/07 (H1N1); cell cultures A549 and MDCK. The study was performed using molecular genetic (transfection, NC isolation, RT-PCR-RV) and virological (cell culture infection, titration by visual CPE, viral titer assessment using the Ramakrishnan method) methods.

RESULTS

It was shown that siRNAs targeting the cellular genes NXF1, PRPS1 and NAA10, when used prophylactically in cell culture at a concentration of 0.25 μg per well, during infection with influenza virus strains A/California/7/09 (H1N1), A/WSN/33 (H1N1) and A/Brisbane/59/07 (H1N1) at a multiplicity of infection of 0.01, reduced viral replication to a level of 220 TCID50 per 1 ml of cell medium, whereas in control untreated cells the viral yield was ~106 TCID50 per 1 ml of medium.

CONCLUSIONS

Reproduction of influenza A viruses directly depends on the protein products of the NXF1, PRPS1, and NAA10 genes. Reduced expression of these genes disrupts the life cycle and activity of influenza viruses. Such an approach can potentially be studied and used for closely and distantly related representatives of other virus families.

Age-based host response to Turkey arthritis reovirus in commercial Turkeys in the presence of maternally derived antibodies

BACKGROUND

Turkey arthritis reovirus (TARV) causes arthritic lameness in market-age turkeys. Since 2011, highly pathogenic TARV strains have caused significant economic losses in the turkey industry due to increased culling, reduced market weights, and decreased carcass quality, necessitating more effective control measures. Autogenous vaccine prevention strategies have been inefficacious partly due to a limited understanding of age-related susceptibility of turkeys to TARV. This study investigated age-related host and gut microbiota responses to TARV infection in commercial turkeys derived from vaccinated breeder hens. Poults with known maternally derived antibody titers were orally challenged with TARV O'Neil strain at 1-, 3-, and 7- weeks of age (WOA) and monitored for cloacal virus shedding, gastrocnemius tendon viral tropism, tendon inflammation, weight gain, and changes in gut microbiota.

RESULTS

A transient TARV-induced weight gain suppression was evident in poults infected at 1- and 3- WOA during the first 3 weeks post-infection. Age-dependent variations in cloacal viral shedding, virus isolation from tendons, and tendon inflammation severity were also observed. There was significant dissimilarity in ileal and cecal bacterial communities between mock and infected groups, but the effect of age of infection was unclear.

CONCLUSIONS

Age dependent host response was observed to TARV based on cloacal virus shedding, weight gain suppression and viral tendon tropism. Our study also indicates that maternally derived antibodies appeared insufficient to prevent virus translocation to the tendons and subsequent pathological changes. This study lays the groundwork for future investigations of better vaccines/vaccination strategies and alternative preventive measures.

IMPORTANCE

Turkey arthritis reovirus (TARV) causes lameness due to arthritis and tenosynovitis, commonly in market-age turkeys, resulting in significant economic losses. As a control strategy, the turkey industry used autogenous vaccines, prepared from field TARV isolates in breeder hens, to protect the poults in the early stage of life through maternally derived antibodies (MDAs). This study establishes the level of protection provided by MDAs in young poults with age-based responses to TARV O'Neil reovirus strain. Additionally, this study reveals the dynamics of gut dysbiosis in infected poults at different timepoints, paving the way to ground-breaking investigations into gut microbiome modulation interventions that could potentially improve vaccine efficacy and reduce virus transmission and disease severity.

Characteristics of viral ovarian tumor domain protease from two emerging orthonairoviruses and identification of Yezo virus human infections in northeastern China as early as 2012

Emerging tick-borne orthonairovirus infections pose a growing global concern, with limited understanding of the viral ovarian tumor-like cysteine proteases (vOTUs) encoded by novel orthonairoviruses. These vOTUs, a group of deubiquinylases (DUBs), disrupt the innate immune response. Yezo virus (YEZV), a recently discovered pathogenic orthonairovirus, was first reported in Japan in 2021. In this study, we successfully isolated and identified YEZV and a new orthonairovirus, Jiànchuān tick virus (JCTV), from Ixodes persulcatus and Haemaphysalis montgomeryi ticks, respectively, in China. We found that the vOTU domains encoded by YEZV and JCTV exhibited both DUB and deISGylase activities, though with potentially less broad deISGylation compared to that of Crimean-Congo hemorrhagic fever virus (CCHFV) during natural infection. Phylogenetic analysis of global vOTUs, including 83 new sequences, revealed a high diversity of this domain. Interestingly, retrospective screening of tick-bite patients from 2012 to 2016 in northeastern China traced YEZV infections as far back as 2012, identifying four cases. Additionally, YEZV primarily infected I. persulcatus (31.4%) and Dermacentor nuttalli (10.5%) in northern China, while JCTV exhibited high infection rates in H. montgomeryi (81.3%) in southern China. In summary, our work emphasizes the active surveillance of orthonairovirus infections and the imperative need for the development of vOTU domain-targeted anti-virals, offering potential therapeutic solutions for a broad spectrum of orthonairoviruses.IMPORTANCEThe vOTUs, a group of DUBs, mimic the functions of host DUBs to enhance viral infectivity and may serve as potential drug targets. vOTUs from different orthonairoviruses exhibit distinct preferences toward ubiquitin (Ub) and ubiquitin-like protein interferon stimulated gene 15 (ISG15). In this study, we investigated the deubiquitinase and deISGylase functions of various orthonairoviral vOTUs using both an overexpression system and natural viral infections in vitro. Our findings illustrate that the vOTUs from YEZV and JCTV can cleave both Ub and ISG15 in an overexpression system, but these viruses exhibit potentially narrower deISGylation capacity than CCHFV during natural infection. This suggests that the diversity of vOTUs may have a potential relationship with the pathogenesis.

InP-Based Quantum Dots as Photosensitizers in Photodynamic Antimicrobial Materials

Ligand-functionalized InP-based quantum dots (QDs) have been developed as an innovative class of nontoxic photosensitizer suitable for antimicrobial applications, aimed at reducing or preventing pathogen transmission from one host to another via high contact surfaces. A hot injection method followed by functionalization via ligand exchange with 9-anthracene carboxylic acid (ACA) yielded the desired core/shell InP/ZnSe/ZnS QDs. Transmission electron microscopy (TEM) revealed these QDs to be uniform in size (∼3.2 nm), with light absorption across the entire visible spectrum (λmax ∼550 nm). Under light excitation at 550 nm, the generation of singlet oxygen (1O2) was evidenced by its characteristic phosphorescence signal at 1278 nm, indicating successful energy transfer from the QDs to surface-anchored ACA ligands, in accordance with a type II mechanism for a photodynamically generated singlet oxygen. The InP/ZnSe/ZnS core/shell QDs were applied to cellulose via dip coating, and the resultant QDs-loaded material was assessed for antimicrobial photodynamic inactivation (aPDI) of both Gram-positive [methicillin-resistant Staphylococcus aureus (MRSA; ATCC-44), vancomycin-resistant Enterococcus faecium (VRE; ATCC-2320)] and Gram-negative [multidrug-resistant Acinetobacter baumannii (MDRAB; ATCC-1605), NDM-1 positive Klebsiella pneumoniae (KP; ATCC-2146)] bacteria under illumination (400-700 nm; 85 mW/cm2; 90 min). The highest inactivation was observed for MRSA, achieving at least 99.999% inactivation (5 log units). Antiviral photodynamic inactivation on human coronavirus 229E (HCoV-229E) and feline calicivirus (FCV) demonstrated complete viral inactivation (to the detection limit). Cytotoxicity studies showed that the QDs are nontoxic to mammalian cells in the dark. Together, these results confirm the promising potential of ligand-functionalized InP-based QDs to be employed as nontoxic photosensitizers as materials in self-sterilizing surfaces.

Effect of Inoculation Volume on a Mouse Model of Influenza Virus Infected with the Same Viral Load

BACKGROUND

Influenza is a highly contagious respiratory disease that poses significant health and economic burdens. Mice are commonly used as animal models for studying influenza virus pathogenesis and the development of vaccines and drugs. However, the viral volume used for nasal inoculation varies substantially in reported mouse influenza infection models, and the appropriate viral dose is crucial for reproducing experimental results.

METHODS

Mice were inoculated with mouse lung-adapted strains of influenza virus A/Puerto Rico/8/34 (H1N1) via intranasal administration of 10 μL, 20 μL, and 40 μL at doses of 200 plaque-forming units (PFU) and 2000 PFU. This study investigated the impact of varying viral inoculum volumes on murine outcomes at identical doses and assessed the disparities across diverse dosage levels.

RESULTS

Regarding weight change trajectories, mortalities, lung tissue viral titers, and pathological manifestations, the group that received the 40 μL inoculation volume within the low-dose infection mice (200 PFU) manifested a statistically significant divergence from those inoculated with both the 10 μL and 20 μL volumes. Within the context of high-dose infections (2000 PFU), groups that received inoculation volumes of 20 μL and 40 μL exhibited marked disparities when compared to those receiving the 10 μL volume.

CONCLUSIONS

Disparities in inoculation volume, even under uniform infection dosages, engender differential outcomes in pathogenicity. Of particular note, the viral replication efficacy at a 20 μL inoculation volume demonstrates conspicuous fluctuations across diverse infection dose regimens.

Preferential apical infection of Caco-2 intestinal cell monolayers by SARS-CoV-2 is associated with damage to cellular barrier integrity: Implications for the pathophysiology of COVID-19

SARS-CoV-2 can infect different organs, including the intestine. In an in vitro model of Caco-2 intestinal cell line, we previously found that SARS-CoV-2 modulates the ACE2 receptor expression and affects the expression of molecules involved in intercellular junctions. To further explore the possibility that the intestinal epithelium can serve as an alternative infection route for SARS-CoV-2, we used a model of polarized monolayers of Caco-2 cells (or co-cultures of two intestinal cell lines: Caco-2 and HT29) grown on the polycarbonate membrane of Transwell inserts, inoculated with the virus either in the upper or lower chamber of culture to determine the tropism of the virus for the apical or basolateral pole of these cells. In both polarized Caco-2 cell monolayers and co-culture Caco-2/HT29 cell monolayer, apical SARS-CoV-2 inoculation was found to be much more effective in establishing infection than basolateral inoculation. In addition, apical SARS-CoV-2 infection triggers monolayer degeneration, as shown by histological examination, measurement of trans-epithelial electrical resistance, and cell adhesion molecule expression. During apical infection, the infectious viruses reach the lower chamber, suggesting either a transcytosis mechanism from the apical side to the basolateral side of cells, a paracellular trafficking of the virus after damage to intercellular junctions in the epithelial barrier, or both. Taken together, these data indicate a preferential tropism of SARS-CoV-2 for the apical pole of the human intestinal tract and suggest that infection via the intestinal lumen leads to a systemic infection.

An analytical, numerical and experimental study of in-vitro SARS-CoV-2 evolution in Vero B4 cells

We derive a numerical model representing the emergence and evolution of SARS-CoV-2 variants, informed by data from in-vitro passaging experiments in Vero B4 cells. We compare our numerical simulation results against probabilistic derivations of the expected probability of and time until the fittest variant becomes fixed in the population. Contrary to literature surrounding DNA viruses and eukaryotes where probabilities of fitness extremes are often modelled by exponential decaying tail, we show that above wildtype fitness differences for SARS-CoV-2 are actually best modelled by a heavy-tailed Fréchet distribution. Furthermore, we find that SARS-CoV-2 variants evolve through an essentially deterministic process rather than a diffusional one, with the dynamics driven by the fitness difference between the top variants rather than by the sampling/dilution process. An interesting consequence of this setting is that the number of variant virions, rather than their proportion, is a better predictor of the probability of fixation for a given variant.

Targeting Cytokines: Evaluating the Potential of Mesenchymal Stem Cell Derived Extracellular Vesicles in the Management of COVID-19

The Coronavirus Disease 2019 (COVID-19), caused by virus SARS-CoV-2, is characterized by massive inflammation and immune system imbalance. Despite the implementation of vaccination protocols, the accessibility of treatment remains uneven. Furthermore, the persistent threat of new variants underscores the urgent need for expanded research into therapeutic options for SARS-CoV-2. Mesenchymal stem cells (MSCs) are known for their immunomodulatory potential through the release of molecules into the extracellular space, either as soluble elements or carried by extracellular vesicles (EVs). The aim of this study was to evaluate the anti-inflammatory potential of EVs obtained from human adipose tissue (ASC-EVs) against SARS-CoV-2 infection. ASC-EVs were purified by size-exclusion chromatography, and co-culture assays confirmed that ASC-EVs were internalized by human lung cells and could colocalize with SARS-CoV-2 into early and late endosomes. To determine the functionality of ASC-EVs, lung cells were infected with SARS-CoV-2 in the presence of increasing concentrations of ASC-EVs, and the release of cytokines, chemokines and viruses were measured. While SARS-CoV-2 replication was significantly reduced only at the highest concentrations tested, multiplex analysis highlighted that lower concentrations of ASC-EV sufficed to prevent the production of immune modulators. Importantly, ASC-EVs did not contain detectable inflammatory cytokines, nor did they trigger inflammatory mediators, nor affect cellular viability. In conclusion, this work suggests that ASC-EVs have the potential to attenuate inflammation by decreasing the production of pro-inflammatory cytokines in lung cells following SARS-CoV-2 infection.

Antimicrobial efficacy of an experimental UV-C robot in controlled conditions and in a real hospital scenario

BACKGROUND

Among no-touch automated disinfection devices, ultraviolet-C (UV-C) radiation has been proven to be one of the most effective against a broad spectrum of micro-organisms causing healthcare-associated infections.

AIM

To evaluate the antimicrobial efficacy of an experimental UV-C robotic platform, under controlled conditions and in a real hospital scenario, when used to implement the standard cleaning operating protocol (SOP).

METHODS

In vitro, following dose calibration tests, bactericidal and virucidal efficacy were tested in accordance with American Society for Testing and Materials International Standard E3135-18. In hospital settings, 12 high-touch surfaces were sampled after healthcare activity (dirty condition), after SOP alone, and after SOP + UV-C treatment, with a total of 180 samples.

FINDINGS

In vitro, <4 mJ/cm2 was required to remove Staphylococcus aureus and Pseudomonas aeruginosa completely, 194 mJ/cm2 was required to inactivate adenovirus HadV5 completely, and 38.8 mJ/cm2 was sufficient to inactivate coronavirus 229E completely. In the real hospital scenario, the mean UV-C dose emitted on the sampled surfaces was 29.31 mJ/cm2. A significant difference was found after SOP alone (P=0.022) and after SOP + UV-C treatment (P=0.007) compared with the dirty condition. The average percentage reduction in the total viable count (TVC) was 67% after SOP alone and 96% after SOP + UV-C treatment.

CONCLUSIONS

Comparison of the tests conducted in vitro and in the real hospital scenario showed that the efficacy of the UV-C robot was reduced in the hospital setting, as a higher dose was needed to obtain a reduction in the TVC.

Low Neutralization of SARS-CoV-2 Omicron BA5248, XBB15 and JN1 by Homologous Booster and Breakthrough Infection

Immunity against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be induced through either infection with the virus or vaccination, providing protection against reinfection or reducing the risk of severe clinical outcomes. In this study, we recruited 172 volunteers who received different vaccination regimens, including 124 individuals who had recovered from breakthrough infections caused by the Omicron variant (27 with 2 doses, 49 with 3 doses, and 48 with 4 doses) and 48 healthy donors who did not experience breakthrough infections (all of whom received a fourth dose during the infection wave). We measured neutralizing antibody levels against Omicron BA.5.2.48, XBB.1.5, and JN.1 and found no significant differences in neutralizing antibody titers between natural infection and homologous booster vaccination at 6 months (p > 0.05), with geometric mean titers declining by over 100-fold for some variants relative to the prototype strain.

Disinfection effect of ozonated water on SARS-CoV-2 in the presence of salivary proteins

BACKGROUND

Ozonated water is expected to be an effective disinfectant for SARS-CoV-2 present on environmental fomites; however, ozone is consumed by organic substances, resulting in attenuation of its effect. SARS-CoV-2 present in saliva can contaminate environmental surfaces; therefore, it is essential to understand the effect of organic substances in saliva on the disinfectant properties of ozonated water.

AIM

To assess organic factors in saliva and the extent to which they diminish the effect of ozonated water on SARS-CoV-2.

METHODS

Ozonated water was exposed to salivary organic factors and residual ozone concentrations were measured. SARS-CoV-2 was exposed to a salivary factor and virus inactivation by ozonated water was measured.

FINDINGS

Amylase and mucin consumed ozone in a concentration-dependent manner. Urea did not. Ozonated water appeared to inactivate SARS-CoV-2 within 30 s. The amount of inactivated SARS-CoV-2 decreased as the protein concentration increased. Virus inactivation was stronger by 1.5 mg/L ozonated water than by 0.5 mg/L ozonated water.

CONCLUSION

This study suggests that the salivary amylase and mucin decay ozone in a concentration-dependent manner, thereby attenuating the disinfection properties of ozonated water for SARS-CoV-2. An increase of the initial amount of ozone can ameliorate the disinfection effect of ozonated water on SARS-CoV-2. Ozone consumption should be taken into consideration for virus infection control. These results provide fundamental information about the effect of ozonated water when used to decontaminate surfaces harbouring SARS-CoV-2 in saliva.

Selective and complementary antimicrobial and antiviral activity of silver, copper, and selenium nanoparticle suspensions in deep eutectic solvent

Metallic and nonmetallic nanoparticles are bioactive compounds that exhibit broad resistance to bacteria, fungi, and even viruses. In this paper, a deep eutectic solvent (DES) based on betaine, glucose, and ethylene glycol was used to obtain suspensions of silver, copper, and selenium nanoparticles. Depending on the nanoparticle precursor used, Ag, Cu, and Se nanoparticles (NPs) with an average particle size of 50-100 nm were prepared, and the properties of the products were confirmed by the STEM, XPS, DLS, and UV-VIS methods. The use of a DES, without the need for additional reactants, allowed the production of stable nanoparticles with increased bioactivity against microorganisms. The obtained systems showed high bioactivity against strains of S. aureus, E. coli, and C. albicans. Nanosuspensions, by generating reactive oxygen species (ROSs), caused enzyme inactivation and the inhibition of the metabolic processes of microorganisms. Particle-generated cell degradation processes were investigated through ROS generation assays, API assays, the determination of the MIC/MBC, and cell decomposition rate assays in the early logarithmic growth phase. Copper nanoparticles derived from copper(II) acetate were also highly active against the human influenza A/H1N1 viruses, human coronavirus (HCoV-OC43, Betacoronavirus 1), and vesicular stomatitis virus (VSV, Rhabdoviridae), showing a virus titer reduction of more than 93.7-99.96%.

Inhibitors of dihydroorotate dehydrogenase synergize with the broad antiviral activity of 4'-fluorouridine

RNA viruses present a constant threat to human health, often with limited options for vaccination or therapy. Notable examples include influenza viruses and coronaviruses, which have pandemic potential. Filo- and henipaviruses cause more limited outbreaks, but with high case fatality rates. All RNA viruses rely on the activity of a virus-encoded RNA-dependent RNA polymerase (RdRp). An antiviral nucleoside analogue, 4'-Fluorouridine (4'-FlU), targets RdRp and diminishes the replication of several RNA viruses, including influenza A virus and SARS-CoV-2, through incorporation into nascent viral RNA and delayed chain termination. However, the effective concentration of 4'-FlU varied among different viruses, raising the need to fortify its efficacy. Here we show that inhibitors of dihydroorotate dehydrogenase (DHODH), an enzyme essential for pyrimidine biosynthesis, can synergistically enhance the antiviral effect of 4'-FlU against influenza A viruses, SARS-CoV-2, henipaviruses, and Ebola virus. Even 4'-FlU-resistant mutant influenza A virus was re-sensitized towards 4'-FlU by DHODH inhibition. The addition of uridine rescued influenza A virus replication, strongly suggesting uridine depletion as a mechanism of this synergy. 4'-FlU was also highly effective against SARS-CoV-2 in a hamster model of COVID. We propose that the impairment of endogenous uridine synthesis by DHODH inhibition enhances the incorporation of 4'-FlU into viral RNAs. This strategy may be broadly applicable to enhance the efficacy of pyrimidine nucleoside analogues for antiviral therapy.

In-vitro and in-silico evaluation of rue herb for SARS-CoV-2 treatment

SARS-CoV-2, a β-coronavirus responsible for the COVID-19 pandemic, has resulted in approximately 4.9 million fatalities worldwide. Despite the urgent need, there is currently no specific therapeutic developed for treating or preventing SARS-CoV-2 infections. The virus enters the host by engaging in a molecular interaction between the viral Spike glycoprotein (S protein) and the host ACE2 receptor, facilitating membrane fusion and initiating infection. Inhibiting this interaction could impede viral activity. Therefore, this study aimed to identify natural small molecules from perennial rue herb (Ruta graveolens) as potential inhibitors against the S protein, thus preventing virus infection. Initially, a screening process was conducted on 53 compounds identified from rue herbs, utilizing pharmacophore-based virtual screening approaches. This analysis resulted in the identification of 12 hit compounds. Four compounds, namely Amentoflavone (CID: 5281600), Agathisflavone (CID: 5281599), Vitamin P (CID: 24832108), and Daphnoretin (CID: 5281406), emerged as potential S protein inhibitors through molecular docking simulations, exhibiting binding energies in kcal/mol of -9.2, -8.8, -8.2, and -8.0, respectively. ADMET analysis revealed favorable pharmacokinetics and toxicity profiles for these compounds. The compounds' stability with respect to the target S protein was evaluated using MD simulation and MM-GBSA approaches. The analysis revealed the stability of the selected compounds with the target protein. Also, PCA revealed distinctive movement patterns in four selected compounds, offered valuable insights into their functional behaviors and potential interactions. In-vitro assays revealed that rue herb extracts containing these compounds displayed potential inhibitory properties against the virus, with an IC50 value of 1.299 mg/mL and a cytotoxic concentration (CC50) value of 11.991 mg/mL. The compounds derived from rue herb, specifically Amentoflavone, Agathisflavone, Vitamin P, and Daphnoretin, show promise as candidates for the therapeutic intervention of SARS-CoV-2-related complications.

Phage-resistance alters Lipid A reactogenicity: a new strategy for LPS-based conjugate vaccines against Salmonella Rissen

Salmonella enterica serovar Rissen (S. Rissen) is an emerging causative agent of foodborne diseases. The current emergence of antibiotic resistance makes necessary alternative therapeutic strategies. In this study, we investigated the potential of a phage-resistant strain of S. Rissen (RR) as a tool for developing an effective lipopolysaccharide (LPS)-based vaccine. The LPS O-antigen is known to play critical roles in protective immunity against Salmonella. However, the high toxicity of the LPS lipid A moiety limits its use in vaccines. Here, we demonstrated that the acquisition of bacteriophage resistance by S. Rissen leads to structural modifications in the LPS structure. Using NMR and mass spectrometry, we characterized the LPS from phage-resistant strains as a smooth variant bearing under-acylated Lipid A portions (penta- and tetra-acylated forms). We then combined RT-qPCR and NMR-based metabolomics to explore the effects of phage resistance and LPS modification on bacterial fitness and virulence. Finally, we conducted in vivo studies to determine whether lysogeny-induced remodeling of LPS affects the host immune response. Results revealed that the under-acylated variant of LPS from RR attenuates the inflammatory response in BALB/c mice, while eliciting a specific antibody response that protects against S. Rissen (RW) infection. In conclusion, our findings suggest that phage resistance, through lipid A modification, may offer a novel strategy for reducing LPS toxicity, highlighting its potential as a promising biological approach for developing LPS-based vaccines against Salmonella infections.

Evolution and zoonotic risk of O1:K1 and O2:K1 avian pathogenic Escherichia coli

The O1 and O2 serogroups of avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (huExPEC) are closely related, but their evolutionary relationships need to be further elucidated. This study classified nineteen O1 and O2 APEC into rpoB sequence types (RSTs) and compared them with reference huExPEC using molecular prophage typing, virulence and antibiotic resistance gene profiling, and comparative genomics. Most O1:K1 and O2:K1 APEC (73.7 %) were classified as RST46-1 and RST47-9. RST47-9 is unique to Korean O1 APEC and likely derives from RST46-1 APEC. The six APEC showed high genome coverage/identity with the Korean RST46-1 huExPEC. Based on RST network and comparative genomics, we hypothesized that the O1 antigen first appeared in RST19-1 and O2 in RST24-1 E. coli in humans. Then, O1 and O2-antigen horizontally transferred to human RST46-1, where a unique K1 capsule (K1-cps) first appeared. The Korean APEC and huExPEC share evolutionary CRISPR spacers but differ in molecular antibiograms and prophage contents. Thus, RST46-1 huExPEC transmitted and evolved in poultry. The zoonotic risks remain unknown, but the substantial virulence of the RST46-1 APEC indicates that the reverse zoonotic risk of huExPEC in poultry is alarming.

Inhibition of RAN attenuates influenza a virus replication and nucleoprotein nuclear export

Nuclear export of the viral ribonucleoprotein (vRNP) is a critical step in the influenza A virus (IAV) life cycle and may be an effective target for the development of anti-IAV drugs. The host factor ras-related nuclear protein (RAN) is known to participate in the life cycle of several viruses, but its role in influenza virus replication remains unknown. In the present study, we aimed to determine the function of RAN in influenza virus replication using different cell lines and subtype strains. We found that RAN is essential for the nuclear export of vRNP, as it enhances the binding affinity of XPO1 toward the viral nuclear export protein NS2. Depletion of RAN constrained the vRNP complex in the nucleus and attenuated the replication of various subtypes of influenza virus. Using in silico compound screening, we identified that bepotastine could dissociate the RAN-XPO1-vRNP trimeric complex and exhibit potent antiviral activity against influenza virus both in vitro and in vivo. This study demonstrates the important role of RAN in IAV replication and suggests its potential use as an antiviral target.

Bivalent Omicron BA.1 vaccine booster increases memory B cell breadth and neutralising antibodies against emerging SARS-CoV-2 variants

BACKGROUND

Current literature informs us that bivalent vaccines will generate a broader serum neutralizing antibody response to multiple SARS-CoV-2 variants, but studies on how this breadth relates to the memory B cell (MBC) and T cell responses are sparse. This study compared breadth of neutralising antibody, and memory B and T cell responses to monovalent or a bivalent ancestral/Omicron BA.1 COVID-19 booster vaccine.

METHODS

At baseline and 1-month post-booster, neutralisation activity and frequencies of receptor binding domain (RBD)-specific MBCs and Spike-specific memory T cells were measured against a panel of variants.

FINDINGS

Both vaccines boosted neutralising antibodies to 5 variants - Wuhan-Hu-1, Delta, BA.1, BA.5 and JN.1, the latter of which had not yet emerged at the time of sample collection. The bivalent vaccine induced a significantly larger increase in nAb against BA.1 and JN.1. Both vaccines boosted RBD-specific MBC responses to Wuhan-Hu-1, Delta, BA.1 and BA.5 variants with a significantly greater increase for BA.1 in the bivalent group. The breadth of MBCs was significantly higher in those who received the bivalent boost and correlated with nAb breadth. Both vaccines significantly boosted Spike-specific T cell responses to the Wuhan-Hu-1 and BA.5 variants, but only the bivalent vaccine boosted BA.1 responses.

INTERPRETATION

These results suggest that the bivalent vaccine confers an advantage against future novel variants due to increased frequency of broadly reactive RBD-specific B cells.

FUNDING

Work supported by NSW Health for the NSW Vaccine, Infection and Immunology Collaborative (VIIM).

Circulation of tick-borne pathogens in wildlife of the Republic of Korea

Habitat loss of wildlife and increased human activities in their habitat provide more opportunities for human-wild animal contact. These artificial environments influence humans by facilitating the transmission of tick-borne pathogens. Therefore, we aimed to detect and understand circulating tick-borne pathogens in the natural environment by analyzing blood and spleen samples of wild animals admitted to wildlife rescue centers in the Republic of Korea. In total, 376 samples were collected from 355 rescued wild animals immediately after their arrival or death. After DNA deoxyribonucleic acid and RNA extractions, reverse transcription polymerase chain reaction (RT-PCR) and nested PCR were conducted to detect target tick-borne pathogens. This study detected six positive samples of severe fever with thrombocytopenia syndrome virus (SFTSV), 146 Anaplasma phagocytophilum, 55 Anaplasma bovis, 19 Rickettsia spp., 45 Borrelia theileri, and 4 Bartonella schoenbuchensis. Among the positive samples, SFTSV was detected in one spleen sample from a Korean water deer, from which SFTSV was successfully isolated. After full genome sequencing, the L, M, and S segments all belonged to genotype B-3 and indicated 99.84 % ∼ 99.94 % similarity with SFTSV isolated from human serum. In conclusion, wild animals are potential reservoirs of tick-borne pathogens. Therefore, surveillance systems to prevent transmission among ticks, animals, and humans must be developed using the One Health concept.

A screening study on the detection strain of Coxsackievirus A6: the key to evaluating neutralizing antibodies in vaccines

The increasing incidence of diseases caused by Coxsackievirus A6 (CV-A6) and the presence of various mutants in the population present significant public health challenges. Given the concurrent development of multiple vaccines in China, it is challenging to objectively and accurately evaluate the level of neutralizing antibody response to different vaccines. The choice of the detection strain is a crucial factor that influences the detection of neutralizing antibodies. In this study, the National Institutes for Food and Drug Control collected a prototype strain (Gdula), one subgenotype D1, as well as 13 CV-A6 candidate vaccine strains and candidate detection strains (subgenotype D3) from various institutions and manufacturers involved in research and development. We evaluated cross-neutralization activity using plasma from naturally infected adults (n = 30) and serum from rats immunized with the aforementioned CV-A6 strains. Although there were differences between the geometric mean titer (GMT) ranges of human plasma and murine sera, the overall trends were similar. A significant effect of each strain on the neutralizing antibody test (MAX/MIN 48.0 ∼16410.3) was observed. Among all strains, neutralization of the S112 strain by 15 different sera resulted in higher neutralizing antibody titers (GMTS112 = 132.0) and more consistent responses across different genotypic immune sera (MAX/MIN = 48.0). Therefore, S112 may serve as a detection strain for NtAb testing in various vaccines, minimizing bias and making it suitable for evaluating the immunogenicity of the CV-A6 vaccine.

Cross-sectional and longitudinal genotype to phenotype surveillance of SARS-CoV-2 variants over the first four years of the COVID-19 pandemic

BACKGROUND

Continued phenotyping and ongoing molecular epidemiology are important in current and future monitoring of emerging SARS-CoV-2 lineages. Herein we developed pragmatic strategies to track the emergence, spread and phenotype of SARS-CoV-2 variants in Australia in an era of decreasing diagnostic PCR testing and focused cohort-based studies. This was aligned to longitudinal studies that span 4 years of the COVID-19 pandemic.

METHODS

Throughout 2023, we partnered with diagnostic pathology providers and pathogen genomics teams to identify relevant emerging or circulating variants in the New South Wales (NSW) community. We monitored emerging variants through viral culture, growth algorithms, neutralisation responses and changing entry requirements defined by ACE2 and TMPRSS2 receptor use. To frame this in the context of the pandemic stage, we continued to longitudinally track neutralisation responses at the population level using pooled Intravenous Immunoglobulins (IVIG) derived from in excess of 700,000 donations.

FINDINGS

In antibodies derived from recent individual donations and thousands of donations pooled in IVIGs, we observed continued neutralisation across prior and emerging variants with EG.5.1, HV.1, XCT and JN.1 ranked as the most evasive SARS-CoV-2 variants. Changes in the type I antibody site at Spike positions 452, 455 and 456 were associated with lowered neutralisation responses in XBB lineages. In longitudinal tracking of population immunity spanning three years, we observed continued maturation of neutralisation breadth to all SARS-CoV-2 variants over time. Whilst neutralisation responses initially displayed high levels of imprinting towards Ancestral and early pre-Omicron lineages, this was slowly countered by increased cross reactive breadth to all variants. We predicted JN.1 to have a marked transmission advantage in late 2023 and this eventuated globally at the start of 2024. We could not attribute this advantage to neutralisation resistance but rather propose that this growth advantage arises from the preferential utilisation of ACE2 pools that cannot engage TMPRSS2 at its Collectrin-Like Domain (CLD).

INTERPRETATION

The emergence of many SARS-CoV-2 lineages documented at the end of 2023 was found to be initially associated with lowered neutralisation responses. This continued to be countered by the gradual maturation of cross-reactive neutralisation responses over time. The later appearance and dominance of the divergent JN.1 lineage cannot be attributed to a lack of neutralisation responses alone, and our data supports that its dominance is a culmination of both lowered neutralisation and changes in ACE2/TMPRSS2 entry preferences.

FUNDING

This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).

Saturation mutagenesis-reinforced functional assays for disease-related genes

Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.

A highly immunogenic UVC inactivated Sabin based polio vaccine

Despite their efficacy, the currently available polio vaccines, oral polio vaccine (OPV) and inactivated polio vaccine (IPV), possess inherent flaws posing significant challenges in the global eradication of polio. OPV, which uses live Sabin attenuated strains, carries the risk of reversion to pathogenic forms and causing vaccine-associated paralytic poliomyelitis (VAPP) and vaccine-derived polio disease (VDPD) in incompletely vaccinated or immune-compromised individuals. Conventional IPVs, which are non-replicative, are more expensive to manufacture and introduce biohazard and biosecurity risks due to the use of neuropathogenic strains in production. These types of limitations have led to a call by the Global Polio Eradication Initiative and others for the development of updated polio vaccines. We are developing a novel Ultraviolet-C radiation (UVC) inactivation method that preserves immunogenicity and is compatible with attenuated strains of polio. The method incorporates an antioxidant complex, manganese-decapeptide-phosphate (MDP), derived from the radioresistant bacterium Deinococcus radiodurans. The inclusion of MDP protects the immunogenic neutralizing epitopes from damage during UVC inactivation. The novel vaccine candidate, ultraIPVTM, produced using these methods demonstrates three crucial attributes: complete inactivation, which precludes the risk of vaccine-associated disease; use of non-pathogenic strains to reduce production risks; and significantly enhanced yield of doses per milligram of input virus, which could increase vaccine supply while reducing costs. Additionally, ultraIPVTM retains antigenicity post-freeze-thaw cycles, a testament to its robustness.

Pro-inflammatory macrophages suppress HIV replication in humanized mice and ex vivo co-cultures

Introduction

Very little is known about the role of macrophages as immune mediators during natural HIV infection. Humanized mice are an extremely valuable in vivo model for studying HIV pathogenesis. However, the presence of murine mononuclear phagocytes in these models represents a significant limitation for studying their human counterpart. Therefore, we have developed a novel humanized mouse model that allows selective depletion of human myeloid cells at a time point of our choosing.

Methods

We genetically engineered human hematopoietic stem and progenitor cells (HSPCs) to express an inducible caspase-9 (iCas9) suicide system under a synthetic myeloid promoter. Using these HSPCs, we generated humanized mice. iCasp9 induction in vivo resulted in selective human myeloid cell death in this inducible human myeloid depletion (iHMD) mouse model. In addition, we co-cultured monocyte-derived macrophages with ex vivo HIV-infected PBMCs to further mechanistically investigate the effect of macrophages on HIV replication using flow cytometry, cytokine analysis, and RNA sequencing of both macrophages and CD4+ T cells.

Results

HIV infection induced a pro-inflammatory phenotype in HIV-infected humanized NSG mice during the early and late stages of HIV infection. Myeloid cell depletion in HIV-infected iHMD-NSG mice resulted in a rapid increase in HIV RNA replication, which was accompanied by a loss of pro-inflammatory cytokines. Co-culture of macrophages with ex vivo HIV-infected PBMCs reproduced their anti-HIV effects observed in vivo. Transcriptomic data showed macrophages upregulate antiviral cytokines and chemokines in co-culture, while inducing CD4+ T cells to upregulate HIV restriction factors and downregulate pathways involved in protein expression and cell replication.

Discussion

This study describes a novel role of macrophages as effector cells, both ex vivo and in vivo, acting against HIV replication and limiting disease progression.

Production of Oncolytic Measles Virus in Vero Cells: Impact of Culture Medium and Multiplicity of Infection

Oncolytic measles virus (MeV) is a promising anti-cancer treatment. However, the production of high titers of infectious MeV (typically 107-109 TCID50 per dose) is challenging because the virus is unstable under typical production conditions. The objective of this study was to investigate how the multiplicity of infection (MOI) and different media-a serum-containing medium (SCM), a serum-free medium (SFM) and two chemically defined media (CDM)-affect MeV production. We infected Vero cells at MOIs of 0.02, 0.2 or 2 TCID50 cell-1 and the lowest MOI resulted in the largest number of infected cells towards the end of the production period. However, this did not equate to higher maximum MeV titers, which were similar for all the MOIs. The medium had a moderate effect, generating maximum titers of 0.89-2.17 × 106, 1.08-1.25 × 106 and 4.58-9.90 × 105 TCID50 mL-1 for the SCM, SFM and CDM, respectively. Infection at a low MOI often required longer process times to reach maximum yields. On the other hand, a high MOI requires a large amount of MeV stock. We would therefore recommend a mid-range MOI of 0.2 TCID50 cell-1 for MeV production. Our findings show that SCM, SFM and CDM are equally suitable for MeV production in terms of yield and process time. This will allow MeV production in serum-free conditions, addressing the safety risks and ethical concerns associated with the use of serum.

Development of quaternized agar-based materials for the coronavirus inactivation

The COVID-19 pandemic has revealed weaknesses in healthcare systems and underscored the need for advanced antimicrobial materials. This study investigates the quaternization of agar, a seaweed-derived polysaccharide, and the development of electrospun membranes for air filtration in facemasks and biomedical applications. Using the betacoronavirus MHV-3 as a model, quaternized agar and membranes achieved a 90-99.99 % reduction in viral load, without associated cytotoxicity. The quaternization process reduced the viscosity of the solution from 1.19 ± 0.005 to 0.64 ± 0.005 Pa.s and consequently the electrospun fiber diameter ranged from 360 to 185 nm. Membranes synthesized based on polyvinyl alcohol and thermally cross-linked with citric acid exhibited lower water permeability. Avoiding organic solvents in the electrospinning technique ensured eco-friendly production. This approach offers a promising way to develop biocompatible and functional materials for healthcare and environmental applications.

Electrospun nonwoven fabric of poly(ε-caprolactone)/n-phosphonium chitosan for antiviral applications: Fabrication, characterization, and potential efficacy

This work reports the virucidal properties of nonwoven fibers developed via electrospinning with polycaprolactone (PCL) and chitosan quaternized with phosphonium salt (NPCS), emphasizing the influence of NPCS concentration on the structure of fibers and their performance against the MHV-3 coronavirus. The addition of NPCS enhances solutions conductivity and viscosity, leading to fibers containing a finer porous structure with a more hydrophilic and smoother surface, thereby making them a potent barrier against respiratory particles, which is a key factor for protective face masks. In terms of degradation, NPCS paced-up the process, suggesting potential environmental benefits. PCL/NPCS (90/10) fibers exhibit a 99 % coronavirus inhibition within a five-minute exposure without cellular toxicity, while also meeting breathability standards for medical masks. These findings suggest the use of NPCS as a promising strategy to design materials with remarkable virucidal performance and physical characteristics that reinforce their use in the field of biomaterials engineering.

Multidrug Combinations against SARS-CoV-2 Using GS-441524 or Ivermectin with Molnupiravir and/or Nirmatrelvir in Reconstituted Human Nasal Airway Epithelia

Background. The emergence, global spread, and persistence of SARS-CoV-2 resulted in an unprecedented need for effective antiviral drugs. Throughout the pandemic, various drug development and treatment strategies were adopted, including repurposing of antivirals designed for other viruses along with a multitude of other drugs with varying mechanisms of action (MoAs). Furthermore, multidrug treatment against COVID-19 is an ongoing topic and merits further investigation. Method/Objectives. We assessed the efficacy of multidrug treatment against SARS-CoV-2 in reconstituted human nasal epithelia, using combinations of molnupiravir and nirmatrelvir as a baseline, adding suboptimal concentrations of either GS-441524 or ivermectin, attempting to increase overall antiviral activity while lowering the overall therapeutic dose. Results. Nirmatrelvir combined with molnupiravir, GS-441524, or ivermectin at suboptimal concentrations show increased antiviral activity compared to single treatment. No triple combinations showed improved inhibition of SARS-CoV-2 replication beyond what was observed for double treatments. Conclusions. In general, we observed that the addition of a third compound is not beneficial for antiviral activity, while various double combinations exhibit increased antiviral activity over single treatment.

A Single-Component Multilayered Self-Assembling Protein Nanoparticle Vaccine Based on Extracellular Domains of Matrix Protein 2 against Both Influenza A and B

The development of an effective and broadly protective influenza vaccine against circulating and emerging strains remains elusive. In this study, we evaluated a potentially universal influenza vaccine based on single-component self-assembling protein nanoparticles (1c-SApNPs) presenting the conserved matrix protein 2 ectodomain (M2e) from influenza A and B viruses (IAV and IBV, respectively). We previously designed a tandem antigen comprising three IAV M2e domains of human, avian/swine, and human/swine origins (termed M2ex3). The M2ex3-presenting 1c-SApNPs conferred complete protection in mice against sequential lethal challenges with H1N1 and H3N2. To broaden this protection to cover IBVs, we designed a series of antigens incorporating different arrangements of three IAV M2e domains and three copies of IBV M2e. Tandem repeats of IAV and IBV (termed influenza A-B) M2e arrayed on the I3-01v9a 60-mer 1c-SApNP, when formulated with an oil-in-water emulsion adjuvant, generated greater M2e-specific immunogenicity and protective efficacy than the soluble influenza A-B M2e trimer, indicated by higher survival rates and reduced weight loss post-challenge. Importantly, one of the influenza A-B M2e SApNP constructs elicited 100% protection against a lethal influenza A/Puerto Rico/8/1934 (H1N1) challenge in mice and 70% protection against a lethal influenza B/Florida/4/2006 (Yamagata lineage) challenge, the latter of which has not been reported in the literature to date. Our study thus provides a promising M2e-based single-component universal vaccine candidate against the two major types of influenza virus circulating in humans.

Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern

The high mutation rate of SARS-CoV-2 leads to the emergence of multiple variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors, e.g. cellular proteins required for viral replication, would help prevent the development of resistance. However, it remains unclear whether different SARS-CoV-2 variants induce conserved cellular responses and exploit the same core host factors. To this end, we compared three variants of concern and found that the host transcriptional response was conserved, differing only in kinetics and magnitude. Clustered regularly interspaced short palindromic repeats screening identified host genes required for each variant during infection. Most of the genes were shared by multiple variants. We validated our hits with small molecules and repurposed the US Food and Drug Administration-approved drugs. All the drugs were highly active against all the tested variants, including new variants that emerged during the study (Delta and Omicron). Mechanistically, we identified reactive oxygen species production as a key step in early viral replication. Antioxidants such as N-acetyl cysteine (NAC) were effective against all the variants in both human lung cells and a humanized mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.

Enhanced Effects of ISA 207 Adjuvant via Intradermal Route in Foot-and-Mouth Disease Vaccine for Pigs

In South Korea, a mandatory nation-wide foot-and-mouth disease (FMD) vaccination policy is in place. However, a major side effect of the current method of intramuscular (IM) administration of oil-adjuvanted FMD vaccines is the formation of granulomas in the muscles of pigs. To address this issue, we assessed the possible application of intradermal (ID) vaccination. Initially, we compared the serological immune response in specific pathogen-free pigs inoculated with FMD vaccines formulated with eight different adjuvants, administered twice at the neck site using a syringe with a needle via the ID route. Among the formulations (water-in-oil-in-water (W/O/W), oil-in-water (O/W), and polymer nanomaterials), ISA 207 of W/O/W was the most effective in inducing immunogenicity followed by ISA 201 of W/O/W. ISA 207 was further tested in formulations of different antigen doses (12 or 1.2 μg) delivered via both IM and ID routes. All four treatments successfully protected the pigs against FMD virus challenges. To assess the feasibility of the field application of the vaccines with ISA 207, we conducted ID vaccination of conventional pigs using a needle-free device, resulting in the detection of significant levels of neutralizing antibodies. ISA 207 was shown to be superior to ISA 201 in inducing immunogenicity via the ID route. In conclusion, ISA 207 could be a suitable adjuvant for ID vaccination in terms of vaccine efficacy for FMD, allowing for alternate use of ID vaccination and subsequent reduction in the incidences of granuloma formation in the field.

Exploring the potency of polyphenol-rich blend from Lonicera caerulea var. Kamtschatica sevast., Aronia melanocarpa, and Echinacea purpurea: Promising anti-inflammatory, antioxidant, and antiviral properties

Previous studies have highlighted the beneficial properties of plants rich in polyphenols, such as Lonicera caerulea var. Kamtschatica Sevast. (LCK), Aronia melanocarpa (AM), and Echinacea purpurea (EP). These plants have demonstrated antioxidant, immunomodulatory, and potential antiviral effects. Thus, the objective of this study was to investigate the impact of the ELA blend, a polyphenol-rich blend containing EP, LCK, and AM, on the cellular mechanisms involved in viral infection. To assess the effects of the ELA blend, various experiments were conducted using A549 cells and a mucociliary tissue 3D model called EpiAirway™. Inflammation and oxidative stress induced by LPS were evaluated through measurements of SOD activity, ELISA, and qPCR analysis. Additionally, antiviral assays were performed in a cell-present environment to examine the blend's effectiveness against HCoV-OC43. The results showed that the ELA blend-treated group exhibited reduced expression of IL1B, CXCL8, ICAM1, MCP1, and RELA in both A549 cells and EpiAirway™. Moreover, the blend enhanced the expression of CAT, HMOX1, SOD1, and SOD2 in A549 cells. The antiviral activity of the ELA blend was also investigated, i.e. its influence on viral replication cycle, to determine the potential as an antiviral preparation. At the highest non-cytotoxic concentration, the ELA blend demonstrated a 87.5 % reduction in viral titer when administered simultaneously with HCoV-OC43. It emphasize potential ability of the preparation to block viral entry to the host cells. At the same time, ELA blend did not express virucidal activity, i.e. inactivation of free viral particles, against HCoV-OC43. In conclusion, ELA blend displayed antiviral activity and exhibited immunomodulatory and antioxidant effects. Based on these findings, it can be concluded that ELA blend has potential for the prevention and treatment of viral infections.

Ventilation does not affect close-range transmission of influenza virus in a ferret playpen setup

Sustained community spread of influenza viruses relies on efficient person-to-person transmission. Current experimental transmission systems do not mimic environmental conditions (e.g., air exchange rates, flow patterns), host behaviors, or exposure durations relevant to real-world settings. Therefore, results from these traditional systems may not be representative of influenza virus transmission in humans. To address this pitfall, we developed a close-range transmission setup that implements a play-based scenario and used it to investigate the impact of ventilation rates on transmission. In this setup, four immunologically naive recipient ferrets were exposed to a donor ferret infected with a genetically barcoded 2009 H1N1 virus (H1N1pdm09) for 4 h. The ferrets interacted in a shared space that included toys, similar to a childcare setting. Transmission efficiency was assessed under low and high ventilation, with air exchange rates of ~1.3 h-1 and 23 h-1, respectively. Transmission efficiencies observed in three independent replicate studies were similar between ventilation conditions. The presence of infectious virus or viral RNA on surfaces and in air throughout the exposure area was also not impacted by the ventilation rate. While high viral genetic diversity in donor ferret nasal washes was maintained during infection, recipient ferret nasal washes displayed low diversity, revealing a narrow transmission bottleneck regardless of ventilation rate. Examining the frequency and duration of ferret physical touches revealed no link between these interactions and a successful transmission event. Our findings indicate that exposures characterized by frequent, close-range interactions and the presence of fomites can overcome the benefits of increased ventilation.

Activation of Antiviral Host Responses against Avian Influenza Virus and Remodeling of Gut Microbiota by rLAB Vector Expressing rIL-17A in Chickens

Low-pathogenic avian influenza virus (LPAIV) remains the most common subtype of type-A influenza virus that causes moderate to severe infection in poultry with significant zoonotic and pandemic potential. Due to high mutability, increasing drug resistance, and limited vaccine availability, the conventional means to prevent intra- or interspecies transmission of AIV is highly challenging. As an alternative to control AIV infections, cytokine-based approaches to augment antiviral host defense have gained significant attention. However, the selective application of cytokines is critical since unregulated expression of cytokines, particularly proinflammatory ones, can cause substantial tissue damage during acute phases of immune responses. Moreover, depending on the type of cytokine and its impact on intestinal microbiota, outcomes of cytokine-gut microflora interaction can have a critical effect on overall host defense against AIV infections. Our recent study demonstrated some prominent roles of chicken IL-17A (ChIL-17A) in regulating antiviral host responses against AIV infection, however, in an in vitro model. For more detailed insights into ChIL-17A function, in the present study, we investigated whether ChIL-17A-meditated elevated antiviral host responses can translate into effective immune protection against AIV infection in an in vivo system. Moreover, considering the role of gut health in fostering innate or local host responses, we further studied the contributory relationships between gut microbiota and host immunity against AIV infection in chickens. For this, we employed a recombinant lactic acid-producing bacterial (LAB) vector, Lactococcus lactis, expressing ChIL-17A and analyzed the in vivo functionality in chickens against an LPAIV (A/H9N2) infection. Our study delineates that mucosal delivery of rL. lactis expressing ChIL-17A triggers proinflammatory signaling cascades and can drive a positive shift in phylum Firmicutes, along with a marked decline in phylum Actinobacteriota and Proteobacteria, favoring effective antiviral host responses against AIV infection in chickens. We propose that ChIL-17A-mediated selective expansion of beneficial gut microbiota might form a healthy microbial community that augments the effective immune protection against AIV infections in chickens.

Herpes Simplex Virus Type 1 Infection of Human Periodontal Ligament

The periodontal ligament (PDL) is a complex connective tissue that connects the tooth root to the dental alveolar bone and plays crucial mechanical roles. PDL also exhibits regenerative roles and regulatory functions to maintain periodontium integrity and homeostasis. While PDL exposure to oral microbial pathogens is common, virtually nothing is known regarding viral infections of PDL. In particular, human herpes simplex virus type 1 (HSV-1) persistently infects the oral cavity through infections of the oral epithelium, connective tissue and neurons. While the oral spread of HSV-1 is generally asymptomatic, this virus has also been implicated in various oral pathologies. In this study, using a primary cell model derived from PDL (PDL cells), and whole surgical fragments of PDL, we provide evidence supporting the efficient infection of PDL by HSV-1 and the promotion of cytopathic effects. Infection of PDL by HSV-1 was also associated with an acute innate inflammatory response, as illustrated by the production of antiviral interferons and pro-inflammatory cytokines. Furthermore, this inflammatory response to HSV-1 was exacerbated in the presence of bacterial-derived products, such as peptidoglycans. This work therefore highlights the ability of HSV-1 to infect mesenchymal cells from PDL, suggesting that PDL may serve as a viral reservoir for the periodontal spread of HSV-1. Moreover, this raises questions about HSV-1 oral pathogenesis, as HSV-1-associated cytopathic and inflammatory effects may contribute to profound alterations of PDL integrity and functioning.

Evaluation of a novel intramuscular prime/intranasal boost vaccination strategy against influenza in the pig model

Live-attenuated influenza vaccines (LAIV) offer advantages over the commonly used inactivated split influenza vaccines. However, finding the optimal balance between sufficient attenuation and immunogenicity has remained a challenge. We recently developed an alternative LAIV based on the 2009 pandemic H1N1 virus with a truncated NS1 protein and lacking PA-X protein expression (NS1(1-126)-ΔPAX). This virus showed a blunted replication and elicited a strong innate immune response. In the present study, we evaluated the efficacy of this vaccine candidate in the porcine animal model as a pertinent in vivo system. Immunization of pigs via the nasal route with the novel NS1(1-126)-ΔPAX LAIV did not cause disease and elicited a strong mucosal immune response that completely blocked replication of the homologous challenge virus in the respiratory tract. However, we observed prolonged shedding of our vaccine candidate from the upper respiratory tract. To improve LAIV safety, we developed a novel prime/boost vaccination strategy combining primary intramuscular immunization with a haemagglutinin-encoding propagation-defective vesicular stomatitis virus (VSV) replicon, followed by a secondary immunization with the NS1(1-126)-ΔPAX LAIV via the nasal route. This two-step immunization procedure significantly reduced LAIV shedding, increased the production of specific serum IgG, neutralizing antibodies, and Th1 memory cells, and resulted in sterilizing immunity against homologous virus challenge. In conclusion, our novel intramuscular prime/intranasal boost regimen interferes with virus shedding and transmission, a feature that will help combat influenza epidemics and pandemics.

Mechanisms and fitness of ceftazidime/avibactam-resistant Klebsiella pneumoniae clinical strains in Taiwan

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection is a global public health issue, and ceftazidime/avibactam is recommended by international guidelines as the preferred treatment for KPC- and OXA-48-producing CRKP. Since its introduction in Taiwan in 2019, ceftazidime/avibactam-resistant strains have emerged. Our aim is to investigate the mechanisms of ceftazidime/avibactam resistance in CRKP in Taiwan and study their associated fitness costs.

METHODS

Ceftazidime/avibactam-resistant CRKP strains with exposure to ceftazidime/avibactam isolated from clinical specimens were consecutively collected at Taipei Veterans General Hospital in 2020. The serial strains exhibiting ceftazidime/avibactam-susceptible and ceftazidime/avibactam-resistant phenotypes isolated from the same patient were characterized using whole-genome sequencing and tested for their growth rates and competitive abilities.

RESULTS

A total of 35 ceftazidime/avibactam-resistant CRKP strains were identified, with 20 being metallo-β-lactamase producers. Ten strains harboured KPC variants, exhibiting MIC for ceftazidime/avibactam ranging from 64 to ≥256 mg/L. The 10 strains demonstrating high-level ceftazidime/avibactam resistance possessed mutated KPC variants: KPC-33 (n = 3), KPC-31 (n = 1), KPC-39 (n = 1), KPC-44 (n = 1), KPC-58 (n = 1), KPC-90 (n = 1), and two novel KPC variants. Ceftazidime/avibactam-resistant strains with KPC-33 and KPC-39 showed a significant fitness cost and lower growth rate compared to their parental strains. In contrast, ceftazidime/avibactam-resistant strains with KPC-58 and KPC-58 plus D179Y showed similar growth rates and competitive abilities compared to their parental strains.

CONCLUSIONS

Mutated KPC variants conferred high-level ceftazidime/avibactam resistance in Taiwan. Significant fitness costs were observed in both the ceftazidime/avibactam-resistant KPC-33 and KPC-39 strains. Despite conferring a similar level of ceftazidime/avibactam resistance, different KPC variants could entail varying degrees of fitness costs.

Zika virus replication is impaired by a selective agonist of the TRPML2 ion channel

The flavivirus genus includes human pathogenic viruses such as Dengue (DENV), West Nile (WNV) and Zika virus (ZIKV) posing a global health threat due to limited treatment options. Host ion channels are crucial for various viral life cycle stages, but their potential as targets for antivirals is often not fully realized due to the lack of selective modulators. Here, we observe that treatment with ML2-SA1, an agonist for the human endolysosomal cation channel TRPML2, impairs ZIKV replication. Upon ML2-SA1 treatment, levels of intracellular genomes and number of released virus particles of two different ZIKV isolates were significantly reduced and cells displayed enlarged vesicular structures and multivesicular bodies with ZIKV envelope protein accumulation. However, no increased ZIKV degradation in lysosomal compartments was observed. Rather, the antiviral effect of ML2-SA1 seemed to manifest by the compound's negative impact on genome replication. Moreover, ML2-SA1 treatment also led to intracellular cholesterol accumulation. ZIKV and many other viruses including the Orthohepevirus Hepatitis E virus (HEV) rely on the endolysosomal system and are affected by intracellular cholesterol levels to complete their life cycle. Since we observed that ML2-SA1 also negatively impacted HEV infections in vitro, this compound may harbor a broader antiviral potential through perturbing the intracellular cholesterol distribution. Besides indicating that TRPML2 may be a promising target for combatting viral infections, we uncover a tentative connection between this protein and cholesterol distribution within the context of infectious diseases.

Inhibitory effects of Belamcanda extract on inflammatory response and antiviral mechanism in H9N2 Avian influenza virus: insights from in vitro and in vivo studies

Avian influenza, particularly the H9N2 subtype, presents significant challenges to poultry health, underscoring the need for effective antiviral interventions. This study explores the antiviral capabilities of Belamcanda extract, a traditional Chinese medicinal herb, against H9N2 Avian influenza virus (AIV) in specific pathogen-free (SPF) chicks. Through a comprehensive approach, we evaluated the impact of the extract on cytokine modulation and crucial immunological signaling pathways, essential for understanding the host-virus interaction. Our findings demonstrate that Belamcanda extract significantly modulates the expression of key inflammatory cytokines, including tumor necrosis factor alpha (TNF-α), interleukin-1 (IL-1), interleukin-2 (IL-2), and interleukin-6 (IL-6), which are pivotal to the host's response to H9N2 AIV infection. Western blot analysis further revealed that the extract markedly reduces the expression of critical immune signaling molecules such as toll-like receptor 3 (TLR3), TIR-domain-containing adapter-inducing interferon-β (TRIF), and nuclear factor kappa B (NF-κB). These insights into the mechanisms by which Belamcanda extract influences host immune responses and hinders viral replication highlight its potential as an innovative antiviral agent for poultry health management. The study advances our comprehension of natural compounds' antiviral mechanisms and lays the groundwork for developing strategies to manage viral infections in poultry. The demonstrated ability of Belamcanda extract to modulate immune responses and inhibit viral replication establishes it as a promising candidate for future antiviral therapy development, especially in light of the need for effective treatments against evolving influenza virus strains and the critical demand for enhanced poultry health management strategies.

Design and testing of Hepatitis Delta Ribozymes for suppression of Chikungunya virus infection in cell cultures

Chikungunya virus is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates following the introduction of its major vector, Aedes albopictus. Recent cases have been documented in Europe, the Caribbean, and the Americas. Chikungunya virus causes a disease frequently misdiagnosed as Dengue fever, with potentially life-threatening symptoms that can result in long term debilitating arthritis. There have been ongoing investigations of possible therapeutic interventions for both acute and chronic symptoms, but to date none have proven effective in reducing the severity or lasting effects of this disease. Recently, a promising vaccine candidate has received accelerated approval, indicating the importance of remedies to this emerging worldwide health threat. Nonetheless, therapeutic interventions for Chikungunya and other mosquito borne virus diseases are urgently needed yet remain elusive. The increasing risk of spread from endemic regions via human travel and commerce, coupled with the absence of a vaccine or approved therapeutic, puts a significant proportion of the world population at risk for this disease. In this report we explore the possibility of using Specific On/oFf Adapter Hepatitis Delta Virus Ribozymes as antivirals in cells infected with Chikungunya virus. The results we obtained suggest there could be some role in using these ribozyme molecules as antiviral therapies for not only Chikungunya virus, but potentially other viruses as well.

mRNA Profiling and Transcriptomics Analysis of Chickens Received Newcastle Disease Virus Genotype II and Genotype VII Vaccines

Newcastle Disease Virus (NDV) genotype VII (GVII) is becoming the predominant strain of NDV in the poultry industry. It causes high mortality even in vaccinated chickens with a common NDV genotype II vaccine (GII-vacc). To overcome this, the killed GVII vaccine has been used to prevent NDV outbreaks. However, the debate about vaccine differences remains ongoing. Hence, this study investigated the difference in chickens' responses to the two vaccines at the molecular level. The spleen transcriptomes from vaccinated chickens reveal that GVII-vacc affected the immune response by downregulating neuroinflammation. It also enhanced a synaptogenesis pathway that operates typically in the nervous system, suggesting a mechanism for the neurotrophic effect of this strain. We speculated that the down-regulated immune system regulation correlated with protecting the nervous system from excess leukocytes and cytokine activity. In contrast, GII-vacc inhibited apoptosis by downregulating PERK/ATF4/CHOP as part of the unfolded protein response pathway but did not affect the expression of the same synaptogenesis pathway. Thus, the application of GVII-vacc needs to be considered in countries where GVII is the leading cause of NDV outbreaks. The predicted molecular signatures may also be used in developing new vaccines that trigger specific genes in the immune system in combating NDV outbreaks.

An Intrinsic Host Defense against HSV-1 Relies on the Activation of Xenophagy with the Active Clearance of Autophagic Receptors

Autophagy engulfs cellular components in double-membrane-bound autophagosomes for clearance and recycling after fusion with lysosomes. Thus, autophagy is a key process for maintaining proteostasis and a powerful cell-intrinsic host defense mechanism, protecting cells against pathogens by targeting them through a specific form of selective autophagy known as xenophagy. In this context, ubiquitination acts as a signal of recognition of the cargoes for autophagic receptors, which direct them towards autophagosomes for subsequent breakdown. Nevertheless, autophagy can carry out a dual role since numerous viruses including members of the Orthoherpesviridae family can either inhibit or exploit autophagy for its own benefit and to replicate within host cells. There is growing evidence that Herpes simplex virus type 1 (HSV-1), a highly prevalent human pathogen that infects epidermal keratinocytes and sensitive neurons, is capable of negatively modulating autophagy. Since the effects of HSV-1 infection on autophagic receptors have been poorly explored, this study aims to understand the consequences of HSV-1 productive infection on the levels of the major autophagic receptors involved in xenophagy, key proteins in the recruitment of intracellular pathogens into autophagosomes. We found that productive HSV-1 infection in human neuroglioma cells and keratinocytes causes a reduction in the total levels of Ub conjugates and decreases protein levels of autophagic receptors, including SQSTM1/p62, OPTN1, NBR1, and NDP52, a phenotype that is also accompanied by reduced levels of LC3-I and LC3-II, which interact directly with autophagic receptors. Mechanistically, we show these phenotypes are the result of xenophagy activation in the early stages of productive HSV-1 infection to limit virus replication, thereby reducing progeny HSV-1 yield. Additionally, we found that the removal of the tegument HSV-1 protein US11, a recognized viral factor that counteracts autophagy in host cells, enhances the clearance of autophagic receptors, with a significant reduction in the progeny HSV-1 yield. Moreover, the removal of US11 increases the ubiquitination of SQSTM1/p62, indicating that US11 slows down the autophagy turnover of autophagy receptors. Overall, our findings suggest that xenophagy is a potent host defense against HSV-1 replication and reveals the role of the autophagic receptors in the delivery of HSV-1 to clearance via xenophagy.

Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles

Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles.

IMPORTANCE

In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.