Vaccines have saved more lives than any other medical intervention throughout human history by preventing the spread of infectious diseases. However, despite several decades of research, there is no effective vaccine against fast evolving viruses such as the human immunodeficiency virus (HIV) and the hepatitis C virus (HCV). A confounding factor in the development of a HIV or HCV vaccine is that these viruses have a unique ability to make a lot of mutations in their genetic code. This enables them to escape the human immune system while retaining their ability to propagate infection. For developing a vaccine against such viruses, scientists are developing novel strategies which seek to target specific parts of the virus that are most vulnerable (i.e., where it is difficult for the virus to survive mutations) in order to induce a focused and potentially effective immune response. To determine the existence and location of such parts of HIV and HCV, initial studies have leveraged recently-available sequence data for these viruses, and looked for those positions in the genome for which the frequency of mutation was lowest. Unfortunately, vaccines based on such first-order statistics have not enjoyed much success, and there is increasing evidence suggesting that interactions between mutations is also important and must be considered when designing an effective vaccine against HIV and HCV. It is almost impossible to determine effects of interactions between all mutations experimentally as it requires performing billions of experiments. In this article, we explain how by leveraging virus sequence data, mutational interactions can be estimated using statistical techniques and incorporated in designing novel and potentially effective vaccine strategies against such fast-evolving viruses.

Convalescent plasma samples that can be collected from individuals after the resolution of infection and vaccination are an invaluable source of neutralization antibodies against the virus. Although plaque reduction assay with replicative virus is the gold standard of analyzing neutralization potency of convalescent plasma, it is a technically demanding procedure requiring high biosafety level (BSL-3/4) laboratory and equipment. The abundance of neutralizing antibodies varies among individuals, therefore fast and reliable methods to identify neutralization potency of plasma samples are needed. In this paper, G-protein deficient vesicular stomatitis virus (VSV-ΔG) carrying a C-terminal 21 amino acid truncated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was generated for pseudovirus neutralization assay. We analyzed SARS-CoV-2 neutralizing potency of vaccinated human convalescent plasma samples (n=13) and plasma samples of healthy people (n=2). Human convalescent plasma samples were examined against the ancestral Wuhan strain and two SARS-CoV-2 variants (B.1.1.7, and B.1.351) using a VSV-ΔG-Sdel21 pseudovirus and Vero E6 cell line. Neutralization values against pseudotyped virus were compared to those of plaque reduction assay against authentic virus. The serum neutralizing titer of convalescent plasma measured by pseudovirus assay has a good correlation with that measured by plaque reduction assay (R 2= 0.7). The pseudovirus assay is safer and timesaving than the replicative virus-based plaque reduction assay, and has several advantages in evaluating a new vaccine, newly emergent variants, and approved vaccine efficacy against variants of concern as well as in viral fusion-focused treatment analysis that can be performed under BSL-2 conditions.

Background Respiratory syncytial virus (RSV) infection in infants is a major cause of viral bronchiolitis and hospitalisation. We have previously shown in a murine model that ongoing infection with the gut helminth Heligmosomoides polygyrus ( H. polygyrus) protects against RSV infection through type I interferon (IFN-I) dependent reduction of viral load. Yet, the cellular basis for this protection has remained elusive. Given that recruitment of mononuclear phagocytes to the lung is critical for early RSV infection control, we assessed their role in this coinfection model. Methods Mice were infected by oral gavage with H. polygyrus. Myeloid immune cell populations were assessed by flow cytometry in lung, blood and bone marrow throughout infection and after secondary infection with RSV. Monocyte numbers were depleted by anti-CCR2 antibody or increased by intravenous transfer of enriched monocytes. Results H. polygyrus infection induces bone marrow monopoiesis, increasing circulatory monocytes and lung mononuclear phagocytes in a IFN-I signalling dependent manner. This expansion causes enhanced lung mononuclear phagocyte counts early in RSV infection that may contribute to the reduction of RSV load. Depletion or supplementation of circulatory monocytes prior to RSV infection confirms that these are both necessary and sufficient for helminth induced antiviral protection. Conclusions H. polygyrus infection induces systemic monocytosis contributing to elevated mononuclear phagocyte numbers in the lung. These cells are central to an anti-viral effect that reduces the peak viral load in RSV infection. Treatments to promote or modulate these cells may provide novel paths to control RSV infection in high risk individuals.

A document by Saumik Basu. Click on the document to view its contents.

While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds, but also allergens and viruses, fall within the ‘pollutant’ definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied; for example, respiratory viral infection induces hyperresponsiveness to allergens, as well as irritants. However, a lot is missing in respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing, and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real-life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats.

Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and protein-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies, and community diversity metrics. The vAMPirus pipelines additionally include optional approaches that can increase the biological signal-to-noise ratio in results by leveraging tools not yet commonly applied to virus amplicon data analyses. In this paper, we validate the vAMPirus analytical framework and illustrate its implementation into the general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is incorporated with the Nextflow workflow manager, offering straightforward scalability, standardization, and communication of virus lineage-specific analyses. The vAMPirus framework itself is also designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.

Background and Purpose: The previous humanized mouse model for HIV/AIDS study loses the superiority of easy operation and justifiable cost. In this study, an economical and easy-to-operate small animal model supporting SIV replication in vivo was established. Experimental approach: Three-week-old male BALB/c nude mice were transplanted with SIV infected MT-2 cells by single intraperitoneal injection to establish the SIV infection model. The change in plasma viral load and the colonization of MT-2 cells in vivo were investigated. Changes of the immune system were evaluated by ELISA assay and flow cytometry assay. Results: The success rates of this model were 100% and all mice in the model group had detectable plasma viral loads (4.98±0.35 ~ 5.39±0.31 log10 SIV RNA copies / mL) in peripheral blood. It is our speculation that the virus replication in mice was mainly due to the proliferation of SIV-infected MT-2 cells that distributed and colonized in abdominal cavities as well as lymph nodes, releasing free virions to maintain infection. It is worth mentioning that there was a statistically significant downtrend in the plasma viral loads of the HAART group. Administration of HAART somewhat reversed this trend of SIV-associated B cell exhaustion and immune collapse. Conclusions and Implications: Therefore, it is reasonable to believe that the model proposed in this study could be a valuable tool to evaluate antiviral effects and immune regulation efficacy in vivo.

BACKGROUND Severe acute respiratory syndrome corona virus (SARS-CoV-2) infection frequently causes severe and prolonged disease but only few specific treatments are available. We aimed to investigate safety and efficacy of a SARS-CoV-2-specific siRNA-peptide dendrimer formulation (MIR 19 ®) targeting a conserved sequence in known SARS-CoV-2 variants for treatment of COVID-19. METHODS We conducted an open-label, randomized controlled multicenter phase II trial (NCT05184127) evaluating safety and efficacy of inhaled MIR 19 ® (3.7mg and 11.1 mg/day: groups 1 and 2, respectively) in comparison with standard etiotropic drug treatment (group 3) in patients hospitalized with moderate COVID-19. The primary endpoint was the time to clinical improvement according to predefined criteria within 14 days of randomization. RESULTS Patients from group1 had a significantly reduced (median 6 days (95% confidence interval [CI]: 5-7, HR 1.75, P=0.0005) time to clinical improvement compared to patients from group 3 (8 days (95% CI: 7-10). Normalized oxygen saturation (SpO 2>94%) occurred quicker in the group 1 (median 5 days (95% CI: 4–5, HR 1.59, P=0.0033) than in the group 3 (6 days, 95% CI: 5–8). Treatment with MIR 19® was well tolerated and safe. CONCLUSIONS MIR 19 ®, a SARS-CoV-2-specific siRNA-peptide dendrimer formulation is safe and significantly reduces time to clinical improvement in hospitalized moderate COVID-19 patients compared to standard therapy in a randomized controlled trial. MIR 19 ® treatment targets a sequence which is identical in all SARS-CoV-2 variants known so far and hence should be applicable for all of them.

Title:A rare case of eczema herpeticum after subcutaneous immunotherapy

A document by Alessandro Farsi. Click on the document to view its contents.

The present work argues the involvement of zinc chelation ability of some non-steroidal anti-inflammatory drugs as an additive mechanism able to increase their efficacy against COVID-19.

The pandemic situation of the new corona virus (SARS-COV-2) forces drug designers to formulate a new intelligent drug for this disease effective to treat all mutations of the virus. One way to control all mutations of virus is inhibition of spike protein (binding with Angiotensin converting enzyme 2 (ACE-2)) duo to inhibit the viral entry. Viral entry is the first step for virus to start infection. In this work the interactions of SARS-COV-2 spike protein and ACE-2 are evaluated Insilico by docking process and four different Ligands are estimated to simulate those interactions, so as to avoid bindings with ACE-2 needed for viral entry in reality. All Ligand – receptor interactions are considered. Results approves the suggested Ligands in this work, have definite inhibitory effect on SARS-COV-2 spike protein based on the interactions which they make with receptor binding domain (RBD). Docking process are done repeatedly to assure conclusions.

Background and Purpose Codonopsis lanceolata (CL) has long been used as a medicinal herb in East Asian countries to treat inflammatory diseases of the respiratory system but its antiviral activity has not been investigated. Here, we evaluated the potential inhibitory activity of CL extracts and their active compounds on SARS-CoV-2. Experimental Approach Pseudotyped SARS-CoV-2 entry assay and dose-response curve analysis with authentic SARS-CoV-2 and recombinant SARS-CoV-2 reporter virus expressing the nanoluciferase were carried out to investigate the effects of compounds against SARS-CoV-2 entry into host cells. Filipin cholesterol staining, SARS-CoV-2 Spike (S)-ACE2 binding assay, and S-mediated cell fusion assay using time-lapse imaging, flow cytometry, and split-GFP fusion were conducted to understand the inhibitory mechanisms. Key Results Lancemaside A (LA), a triterpenoid saponin isolated from CL, impeded the endosomal entry pathway of SARS-CoV-2 and its variants including Alpha, Beta, Delta, and Omicron with similar IC50 values of 2.23 ~ 3.37 μM as well as the TMPRSS2-mediated viral entry pathway with IC50 value of 3.92 μM. LA was also able to prevent the formation of S-induced multinucleated syncytia. Mechanically, LA altered the distribution of host cell membrane cholesterol and blocked the membrane fusion between SARS-CoV-2 and host cells. Conclusion and implications LA can be a broad-spectrum antiviral drug not only against SARS-CoV-2 but also against other novel enveloped viral pathogens that might arise in the future by targeting viral envelope fusion with the host cell membrane. Keywords SARS-CoV-2, Omicron, COVID-19, Lancemaside A, triterpenoid saponin, membrane fusion

Background: From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses, shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort. Methods: Peripheral blood mononuclear cells from 51 children (32 asthmatics, 19 healthy controls), participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analyzed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high troughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis. Results: High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile, however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed amongst immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations. Conclusions: Antiviral cytokines responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not affected by TLR-induced immune responses.

Virus infections and T cell-mediated drug hypersensitivity reactions (DHR) can influence each other. In most instances, systemic virus infections appear first. They may prime the reactivity to drugs in two ways: First, by virus-induced second signals: certain drugs like β-lactam antibiotics are haptens and covalently bind to various soluble and tissue proteins, thereby forming novel antigens. Under homeostatic conditions, these neo-antigens do not induce an immune reaction, probably because co-stimulation is missing. During a virus infection, the hapten-modified peptides are presented in an immune-stimulatory environment with co-stimulation. A drug-specific immune reaction may develop and manifest as exanthema. Second, by increased pharmacological interactions with immune receptors (p-i) : drugs tend to bind to proteins and may even bind to immune receptors. In the absence of viral infections, this low affine binding may be insufficient to elicit T cell activation. During a viral infection immune receptors are more abundantly expressed and allow more interactions to occur. This increases the overall avidity of p-i reactions and may even be sufficient for T cell activation and symptoms. There is a situation, where the virus-DHR sequence of events is inversed: in drug reaction with eosinophilia and systemic symptoms (DRESS), a severe DHR can precede reactivation and viremia of various herpes viruses. One could explain this phenomenon by the massive p-i mediated immune stimulation during acute DRESS, which coincidentally acvitates many herpes virus-specific T cells. Through p-i stimulation, they develop a cytotoxic activity with killing of herpes peptide-expressing cells and release of herpes viruses. These concepts could explain the often transient nature of DHR occurring during viral infections and the often asymptomatic herpes-virus viraemia after DRESS.

This article introduces current status of COVID-19 and its side-effects, and reviews emerging protective measures and strategies from lifestyle to traditional Chinese medicine (TCM) for fighting against the SARS-CoV-2 and its major variants (Delta and Omicron) as well as the global COVID-19 pandemic, which include “Carassius auratus lifestyle” for high effective isolation, social and high-tech related medical strategies, traditional Chinese herbs “Bark-Flower-Fruit-Grass-Leaf-Nucleolus-Root (BFFGLNR)”, as well the combination of Chinese and western medicine. As a choice, little is known whether Chinese acupuncture is an effective method for confirmed and suspected COVID-19 patients, which include imported and asymptomatic cases. Definitely, acupuncture is effective for the recovery of COVID-19 cases. However, its effects and related mechanisms need further animal experiments and clinical trials to confirm and disclose. In conclusion, these emerging protective measures and strategies for COVID-19 will help to effectively combat the SARS-CoV-2 and its variants during the pandemic and post-COVID-19 era.

Logical deductions from experimental data have been unable to explain the origin of the current monkeypox outbreaks in multiple countries. But upon illustrating the reality in which these outbreaks occur, it was found to be that in which different diseases of the same immunological nature, the nature that permits them to be rendered asymptomatic simultaneously without the elimination of their different causes, appear simultaneously when conditions that permitted immune mechanisms to bring about such protection disappear. An outbreak of such immunologically equivalent diseases therefore does not require the spread of those that are pathogens among the causes of such diseases to occur. And the manifestations of such diseases will become widespread in a population when factors that cause the disappearance of conditions that permitted them to be rendered asymptomatic by immune mechanisms become widespread in the population. If we will escape the threat that the catastrophically widespread appearance of manifestations such as Ebola and malignancies will pose to our species, our topmost research priority ought to be the immunological nature of the pathological effects of the pathogens that are linked with them.

Xenotransplantation with porcine organs has been recognized as a promising solution to alleviate the shortage of organs for human transplantation. Porcine endogenous retrovirus (PERV), whose proviral DNAs are buried in the genome of all pig breeds, is a main microbiological risk for xenotransplantation. Over the last decades, some advances on PERVs’ study have been achieved. Here we reviewed the current progress of PERVs including the classification, molecular structure, regulation , function in immune system and potential risk in xenotransplantation. We also discussed the problem of insufficient research on PERVs as well as the questions need to be answered in the future work.

This article introduces briefly current status of the Covid-19 pandemic and discusses “antidotes” of coronavirus (SARS-CoV-2 and its variants), that is, “ISISI” barriers from locals, nations or regions to the globe, namely, [Isolation with Masks, Unit protective clothing, Stay at “home”, and Travel restriction (MUST); Screening and testing; Individual immunity by healthy E(e)SEEDi lifestyle, bio-agents (chemical agents, convalescent plasma, neutralizing antibody, and Chinese medicine), and vaccination; Social and medical supports; International cooperation and information sharing]. Since there are several major coronavirus variants with more infectious, such as Delta and Omicron, many more cases with cardiac injury and cardiac arrest need better cardiovascular prevention and protection. With further understanding of the pathogenesis of Covid-19 and development of novel mRNA vaccines and discovery of new antiviral drugs, such as Molnupiravir and Paxlovid, people will do better in fighting against SARS-CoV-2 and its variants and cardiovascular protection in the pandemic and post-Covid-19 era.

The COVID-19 pandemic is still continuing. Current major variants of SARS-CoV-2 (Delta and Omicron) have lead to new uncertainties. Since the infection of SARS-CoV-2 and its major variants has been a high risk factor of cardiovascular health due to major adverse cardiovascular events (MACCE) and outcomes. Thus, the more coverage of vaccination, enough health workers, and related medical resources as well as the “ISISI” barriers from locals or regions to the globe play a critical role in combating COVID-19 and protection of human cardiovascular health.

In this study, a specific and simple method based on the dual priming oligonucleotide (DPO) system was developed to simultaneously detect transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine rotavirus A (PRV-A), porcine delta coronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), associated with the major enteric RNA viruses in pigs. The multiplex RT-PCR method based on the DPO system simplified the primer design and did not require optimization of the annealing temperature. Specificity analysis revealed that the method could specifically detect TGEV, PEDV, PRV-A, PDCoV, and SADS-CoV without any cross-amplification of other circulating swine viruses. The limit of detection of the method was as low as 103–104 copies/μL plasmid of each virus. The method also had good repeatability, and obvious results were seen in three repeat experiments with an interval of 45 days. This optimized multiplex RT-PCR method was used to evaluate 181 clinical swine samples that were collected from four provinces of China between September 2016 and August 2018. The results showed that the positive detection rates of PEDV, PDCoV, SADS-CoV, PRV-A, and TGEV were 30.94% (56/181), 17.67% (32/181), 11.6% (21/181), 9.39% (17/181), and 0.55% (1/181), respectively. Mixed infection of two or more viruses was also common. The DPO system-based multiplex RT-PCR could be a useful tool for detecting enteric virus infections. This method has the advantages of easy operation, low cost, high detection efficiency, and short running time for early diagnosis in clinical cases.

Japanese encephalitis (JE) is the major cause of viral encephalitis (VE) in most Asian-Pacific countries. In Vietnam, there is no nationwide surveillance system for JE due to lack of medical facilities and diagnoses. Culex tritaeniorhynchus, Culex Vishnui, and Culex quinquefasciatus have been identified as the major JE vectors in Vietnam. The main objective of this study was to forecast a risk map of Culex mosquitoes in Hanoi, which is one of the most densely populated cities in Vietnam. A total of 10,775 female adult Culex mosquitoes were collected from 513 trapping locations. We collected temperature and precipitation information during the study period and its preceding month. In addition, the other predictor variables (e.g., normalized difference vegetation index [NDVI], land use/land cover and human population density), were collected for our analysis. All the collected data was pre-processed with the same study extent and spatial resolution of 30 m. The final model selected for estimating the Culex mosquito abundance included centered rainfall, quadratic term rainfall, rice cover ratio, forest cover ratio, and human population density variables. The estimated spatial distribution of Culex mosquito abundance ranged from 0 to 200. Our model estimated that 87% of the Hanoi area had an abundance of mosquitoes from 0 to 50, whereas approximately 1.2% of the area showed more than 150 mosquitoes, which was mostly in the rural/peri-urban districts. Our findings may provide better insight into understanding the spatial distribution of Culex mosquitoes and its associated environmental risk factors. Such information can assist local clinicians and public health policymakers to identify the potential areas of risk for JE virus. Risk maps can be an efficient way of raising public awareness about the virus and further preventive measures need to be considered in order to prevent outbreaks and onwards transmission of the JE virus.

The ongoing COVID-19 pandemic has highlighted the central role of diagnostic tests in pandemic control. Although reverse transcriptase quantitative real-time PCR (RT-qPCR) is the gold standard for the diagnosis of COVID-19, several rapid antigen tests (RAT) have been commercialized as rapid point-of-care diagnostics. To the best of our knowledge, there are limited data on the effect of patient’s clinical and laboratory parameters on RAT performance and no studies exist that tested the importance of combining laboratory measurements in patient’s blood in enhancing the performance of RAT. Here we tried to fill these gaps by evaluating the diagnostic performance of the RAT “Standard ™ Q COVID-19 Ag” in participant’s subgroups studying the influence of viral load, sampling time-post symptoms, clinical and laboratory features on test performance. Eighty-three nasopharyngeal and oropharyngeal swabs were tested for sever acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) by both RT-qPCR and RAT. Diagnostic accuracy of the RAT was evaluated for participant’s subgroups that have various features. Support vector machine model was then used to investigate whether laboratory measurements in subject’s blood would enhance the predictive accuracy of this RAT. The sensitivity, specificity and accuracy of the RAT were 78.2, 64.2 and 75.9%, respectively. Samples with high viral load and those that were collected within one week post-symptom showed the highest sensitivity and accuracy. Measuring Laboratory indices did not enhance the predictive accuracy of this RAT. It is concluded that “Standard ™ Q COVID-19 Ag” should not be used alone for COVID-19 diagnosis due to its low diagnostic performance. This RAT is best used at early disease stage and in patients with high viral load.

Seneca Valley Virus (SVV) infection was recently spread the pig farm in the Canada, American and China, human, mice and housefly have been the host and reservoirs. Although such cross-species transmission events result in limited onward in the new cross-species transmission, sustained outbreak have posed a new mammalian host. Thus, to determine whether mink was one of a new mammalian host in our study with the molecular characteristics of isolated SVA genomes, challenge, pathological study, and immune respond. Here, our research was the first systemic analysis on a new isolation strain of SVV from pig, the new strain infected the mink in oral and intestine, which produced the pathological change in the intestine. And the SVV could stimulate the specific neutralizing antibody. This study highlights the importance of identifying SVV infection in the mink and host as a mutational pressure for the virus evolution that could threaten livestock, public health and economic growth.