Decay of infectious adenovirus and coliphages in freshwater habitats is differentially affected by ambient sunlight and the presence of indigenous protozoa communities

Genetic landscape for majority and minority HIV-1 drug resistance mutations in antiretroviral therapy naive patients in Accra, Ghana

Background

The successful detection of drug-resistance mutations (DRMs) in HIV-1 infected patients has improved the management of HIV infection. Next-generation sequencing (NGS) to detect low-frequency mutations is predicted to be useful for efficiently testing minority drug resistance mutations, which could contribute to virological failure. This study employed Sanger sequencing and NGS to detect and compare minority and majority drug resistance mutations in HIV-1 strains in treatment-naive patients from Ghana.

Method

From a previous study, 20 antiretroviral therapy (ART)-naive participants were selected for a cross-sectional study. Sanger sequencing and NGS techniques were used to detect the majority and minority HIV drug resistance (HIVDR) mutations, respectively, in the protease (PR) and partial reverse transcriptase (RT) genes. NGS detected mutations at 1 % and 5 % frequencies and Sanger sequencing at ≥20 % frequencies. The sequences obtained from NGS and Sanger sequencing platforms were submitted to the Stanford HIV drug resistance database for subtyping, mutation identification, and interpretations.

Results

Sequences from the twenty participants where the CRF02_AG was the predominant strain (16, 80 %) were analyzed. NGS detected 25 mutations in the RT and PR genes, compared to 21 mutations by Sanger sequencing. Minority DRMs were detected at the prevalence of 55.0 % with NGS against 35 % DRMs by Sanger sequencing. One of the patients had eight different HIVDR variants, with two minority variants. These mutations were directed against PI (K20I and D30DN), NNRTI (Y181C, M23LM and V108I) and NRTI (K65R, M184I, and D67N).

Conclusion

The study affirms the usefulness of genomic sequencing for drug resistance testing in HIV. It further shows that Sanger sequencing alone may not be adequate to detect mutations and that NGS capacity should be developed and deployed in the Ghanaian clinical settings for patients living with HIV.

Assessing the nucleic acid decay of human wastewater markers and enteric viruses in estuarine waters in Sydney, Australia

This research investigated the in-situ decay rates of four human wastewater-associated markers (Bacteroides HF183 (HF183), Lachnospiraceae Lachno3 (Lachno3), cross-assembling phage (crAssphage), pepper mild mottle virus (PMMoV) and three enteric viruses (human adenovirus 40/41 (HAdV 40/41), enterovirus (EV) and human norovirus GII (HNoV GII) in two estuarine water environments (Davidson Park (DP) and Hen and Chicken Bay (HCB) in temperate Sydney, NSW, Australia, employing qPCR and RT-qPCR assays. The study also aimed to compare decay rates observed in mesocosms with previously published laboratory microcosms, providing insights into the persistence of markers and viruses in estuarine environments. Results indicated varying decay rates between DP and HCB mesocosms, with HF183 exhibiting relatively faster decay rates compared to other markers and enteric viruses in sunlight and dark mesocosms. In DP mesocosms, HF183 decayed the fastest, contrasting with PMMoV, which exhibited the slowest. Sunlight induced higher decay rates for all markers and viruses in DP mesocosms. In HCB sunlight mesocosms, HF183 nucleic acid decayed most rapidly compared to other markers and enteric viruses. In dark mesocosms, crAssphage showed the fastest decay, while PMMoV decayed at the slowest rate in both sunlight and dark mesocosms. Comparisons with laboratory microcosms revealed faster decay of markers and enteric viruses in laboratory microcosms than the mesocosms, except for crAssphage and HAdV 40/41 in dark, and PMMoV in sunlight mesocosms. The study concludes that decay rates of markers and enteric viruses vary between estuarine mesocosms, emphasizing the impact of sunlight exposure, which was potentially influenced by the elevated turbidity at HCB estuarine waters. The generated decay rates contribute valuable insights for establishing site-specific risk-based thresholds of human wastewater-associated markers.

Hussein S, Abdalhabib EK, Nabi SU. The critical impacts of cytokine storms in respiratory disorders

Cytokine storm (CS) refers to the spontaneous dysregulated and hyper-activated inflammatory reaction occurring in various clinical conditions, ranging from microbial infection to end-stage organ failure. Recently the novel coronavirus involved in COVID-19 (Coronavirus disease-19) caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has been associated with the pathological phenomenon of CS in critically ill patients. Furthermore, critically ill patients suffering from CS are likely to have a grave prognosis and a higher case fatality rate. Pathologically CS is manifested as hyper-immune activation and is clinically manifested as multiple organ failure. An in-depth understanding of the etiology of CS will enable the discovery of not just disease risk factors of CS but also therapeutic approaches to modulate the immune response and improve outcomes in patients with respiratory diseases having CS in the pathogenic pathway. Owing to the grave consequences of CS in various diseases, this phenomenon has attracted the attention of researchers and clinicians throughout the globe. So in the present manuscript, we have attempted to discuss CS and its ramifications in COVID-19 and other respiratory diseases, as well as prospective treatment approaches and biomarkers of the cytokine storm. Furthermore, we have attempted to provide in-depth insight into CS from both a prophylactic and therapeutic point of view. In addition, we have included recent findings of CS in respiratory diseases reported from different parts of the world, which are based on expert opinion, clinical case-control research, experimental research, and a case-controlled cohort approach.

Favipiravir does not improve viral clearance in mild to moderate COVID-19 - A systematic review and meta-analysis of randomized controlled trials

Purpose

Favipiravir has been used in the therapy of COVID-19, including patients with mild to moderate symptoms in certain countries. The aim of our systematic review and meta-analysis was to investigate its efficacy and safety in mild-to-moderate COVID-19 infections.

Methods

The PubMed, Embase, Web of Science, and Cochrane databases were systematically reviewed for articles reporting the results of randomized controlled trials published until January 6, 2023, resulting in the identification of 20 eligible studies.

Results

There were no significant differences in viral clearance time (HR = 1.20, p = 0.09) compared to those without favipiravir therapy. However, in the subgroup analyses, favipiravir treatment significantly increased viral clearance by 59 % (HR = 1.59, p < 0.01) and 42 % (HR = 1.42, p < 0.01], I2 = 20 %) compared to the comparator group in patients with moderate severity of COVID-19 and in the inpatient care setting, respectively. Favipiravir had no beneficial effects in the case of patients with mild symptoms and treated in ambulatory care.

Conclusions

The use of favipiravir is questionable in the treatment of outpatients with COVID-19 with mild symptoms. Moderate beneficial effects in the case of patients with moderate symptoms and inpatients should be treated with care due to the limitations of the analysed trials.

Oncolytic viruses improve cancer immunotherapy by reprogramming solid tumor microenvironment

Immunotherapies using immune checkpoint inhibitors (ICIs) and chimeric antigen receptor (CAR) T-cell therapy have achieved successful results against several types of human tumors, particularly hematological malignancies. However, their clinical results for the treatment of solid tumors remain poor and unsatisfactory. The immunosuppressive tumor microenvironment (TME) plays an important role by interfering with intratumoral T-cell infiltration, promoting effector T-cell exhaustion, upregulating inhibitory molecules, inducing hypoxia, and so on. Oncolytic viruses are an encouraging biocarrier that could be used in both natural and genetically engineered platforms to induce oncolysis in a targeted manner. Oncolytic virotherapy (OV) contributes to the reprogramming of the TME, thus synergizing the functional effects of current ICIs and CAR T-cell therapy to overcome resistant barriers in solid tumors. Here, we summarize the TME-related inhibitory factors affecting the therapeutic outcomes of ICIs and CAR T cells and discuss the potential of OV-based approaches to alleviate these barriers and improve future therapies for advanced solid tumors.

Improved virus concentration methods for wash waters from decontamination of permeable and non-permeable surfaces

Surface decontamination is a method of using wash water to decontaminated surfaces preventing transmission of biological contaminants that can pose potential health risks to responders and the public. However, the risks associated with handling used wash water are largely unknown due to the lack of effective methodology to screen for pathogenic microorganisms present in these samples, especially viral pathogens. This study adapted the dead-end hollow-fiber ultrafiltration (D-HFUF) system to wash waters, including a separate procedure for recovering particle attached viruses. Simulated wash water was created using dechlorinated tap water containing a mild surfactant (0.05 % Tween 80). To determine virus recovery efficiencies, measured amounts of somatic and F+ coliphage were spiked into 2-liter volumes of wash water under the following scenarios: (1) wash water was amended with a measured amount of sterile river sediment with no sediment separation prior to filter concentration; or (2) sediment added to wash water was allowed to settle prior to filter concentrating clarified liquid portions, while precipitated sediment was subjected to viral extraction techniques to recover particle attached virus; and (3) the optimized method was deployed on non-porous and porous surfaces to simulate a decontamination clean-up event. Separation of sediment prior to D-HFUF significantly increased recovery of coliphages, (P = <0.0001) versus filtration of sediment and liquids simultaneously. A tryptic soy broth (TSB) elution solution was significantly more effective (P = ≤0.010) for recovery of both somatic and F+ coliphage, (108 ± 9 % and 92 ± 9 %, respectively), compared to elution buffers containing various surfactants (sodium hexametaphosphate, Tween 80) for recovering particle attached virus. Simulating a biocontaminate clean-up event (using the optimized sediment separation and elution protocol) resulted in coliphage recoveries of 75-96 % (permeable surface) and 71-92 % (non-permeable surface). This procedure can be used to effectively detect viruses in used wash waters aiding in reducing risks to human health during site decontamination.

Estimation of alkali dosage and contact time for treating human excreta containing viruses as an emergency response: a systematic review

Water, sanitation, and hygiene provisions are essential during emergencies to prevent infectious disease outbreaks caused by improper human excreta management in settlements for people affected by natural disasters and conflicts. Human excreta disinfection is required when long-term containment in latrines is not feasible on-site. Alkali additives, including lime, are effective disinfectants for wastewater and faecal sludge containing large amounts of solid and dissolved organic matter. The aim of this study was to determine the minimum dose and contact time of alkali additives for treating virus-containing human excreta in emergency situations. We used literature data collected by searching Google Scholar and Web of Science. The date of the last search for each study was 31th May 2023. Only peer-reviewed articles that included disinfection practices in combination with quantitative data for the physicochemical data of a matrix and viral decay were selected for data extraction. Two reviewers independently collected data from each study. We extracted datasets from 14 studies that reported quantitative information about their disinfection tests, including viral decay over time, matrix types, and physicochemical properties. Three machine learning algorithms were applied to the collected dataset to determine the time required to achieve specified levels of virus inactivation under different environmental conditions. The best model was used to estimate the contact time to achieve a 3-log10 inactivation of RNA virus in wastewater and faeces. The most important variables for predicting the contact time were pH, temperature, and virus type. The estimated contact time for 3 log inactivation of RNA virus was <2 h at pH 12, which was achieved by adding 1.8 and 3.1% slaked lime to wastewater and faeces, respectively. The contact time decreased exponentially with the pH of the sludge and wastewater. In contrast, the pH of the sludge and wastewater increased linearly with the slaked lime dosage. Lime treatment is a promising measure where long-term containment in latrine is not feasible in densely populated areas, as 1 day is sufficient to inactivate viruses. The relationship we have identified between required contact time and lime dosage is useful for practitioners in determining appropriate treatment conditions of human waste.

Promising role of Vitamin D and plant metabolites against COVID-19: Clinical trials review

Vitamin D possesses immunomodulatory qualities and is protective against respiratory infections. Additionally, it strengthens adaptive and cellular immunity and boosts the expression of genes involved in oxidation. Experts suggested taking vitamin D supplements to avoid and treat viral infection and also COVID-19, on the other hand, since the beginning of time, the use of plants as medicines have been vital to human wellbeing. The WHO estimates that 80 % of people worldwide use plants or herbs for therapeutic purposes. Secondary metabolites from medicinal plants are thought to be useful in lowering infections from pathogenic microorganisms due to their ability to inhibit viral protein and enzyme activity by binding with them. As a result, this manuscript seeks to describe the role of vitamin D and probable plant metabolites that have antiviral activities and may be complementary to the alternative strategy against COVID-19 in a single manuscript through reviewing various case studies.

Involving stemness factors to improve CAR T-cell-based cancer immunotherapy

Treatment with chimeric antigen receptor (CAR) T cells indicated remarkable clinical responses with liquid cancers such as hematological malignancies; however, their therapeutic efficacy faced with many challenges in solid tumors due to severe toxicities, antigen evasion, restricted and limited tumor tissue trafficking and infiltration, and, more importantly, immunosuppressive tumor microenvironment (TME) factors that impair the CAR T-cell function adds support survival of cancer stem cells (CSCs), responsible for tumor recurrence and resistance to current cancer therapies. Therefore, in-depth identification of TME and development of more potent CAR platform targeting CSCs may overcome the raised challenges, as presented in this review. We also discuss recent stemness-based innovations in CAR T-cell production and engineering to improve their efficacy in vivo, and finally, we propose solutions and strategies such as oncolytic virus-based therapy and combination therapy to revive the function of CAR T-cell therapy, especially in TME of solid tumors in future.

Two Predators, One Prey - the Interaction Between Bacteriophage, Bacterivorous Ciliates, and Escherichia coli

Bacterivorous ciliates and lytic bacteriophages are two major predators in aquatic environments, competing for the same type of prey. This study investigated the possible interaction of these different microorganisms and their influence on the activity of each other. Therefore, two bacterivorous ciliates, Paramecium sp. RB1 and Tetrahymena sp. RB2, were used as representative ciliates; a T4-like Escherichia coli targeting lytic bacteriophage as a model virus; and E. coli ATCC 25922 as a susceptible bacterial host and prey. The growth of the two ciliates with E. coli ATCC 25922 as prey was affected by the presence of phage particles. The grazing activity of the two ciliates resulted in more than a 99% reduction of the phage titer and bacterial cell numbers. However, viable phage particles were recovered from individual washed cells of the two ciliates after membrane filtration. Therefore, ciliates such as Paramecium sp. RB1 and Tetrahymena sp. RB2 can remove bacteriophages present in natural and artificial waters by ingesting the viral particles and eliminating bacterial host cells required for viral replication. The ingestion of phage particles may marginally contribute to the nutrient supply of the ciliates. However, the interaction of phage particles with ciliate cells may contribute to the transmission of bacteriophages in aquatic environments.

An overview on medicinal plants used for combating coronavirus: Current potentials and challenges

Worldwide, Severe acute respiratory syndrome Coronavirus (SARS-CoV-2) pandemic crisis, causing many morbidities, mortality, and devastating impact on economies, so the current outbreak of the CoV-2 is a major concern for global health. The infection spread quickly and caused chaos in many countries around the world. The slow discovery of CoV-2 and the limited treatment options are among the main challenges. Therefore, the development of a drug that is safe and effective against CoV-2 is urgently needed. The present overview briefly summarizes CoV-2 drug targets ex: RNA-dependent RNA polymerase (RdRp), papain-like protease (PLpro), 3-chymotrypsin-like protease (3CLpro), transmembrane serine protease enzymes (TMPRSS2), angiotensin-converting enzyme 2 (ACE2), structural protein (N, S, E, and M), and virulence factors (NSP1, ORF7a, and NSP3c) for which drug design perspective can be considered. In addition, summarize all anti-COVID-19 medicinal plants and phytocompounds and their mechanisms of action to be used as a guide for further studies.

Uptake without inactivation of human adenovirus type 2 by Tetrahymena pyriformis ciliates

Human adenoviruses are ubiquitous contaminants of surface water. Indigenous protists may interact with adenoviruses and contribute to their removal from the water column, though the associated kinetics and mechanisms differ between protist species. In this work, we investigated the interaction of human adenovirus type 2 (HAdV2) with the ciliate Tetrahymena pyriformis. In co-incubation experiments in a freshwater matrix, T. pyriformis was found to efficiently remove HAdV2 from the aqueous phase, with ≥4 log₁₀ removal over 72 hours. Neither sorption onto the ciliate nor secreted compounds contributed to the observed loss of infectious HAdV2. Instead, internalization was shown to be the dominant removal mechanism, resulting in the presence of viral particles inside food vacuoles of T. pyriformis, as visualized by transmission electron microscopy. The fate of HAdV2 once ingested was scrutinized and no evidence of virus digestion was found over the course of 48 hours. This work shows that T. pyriformis can exert a dual role in microbial water quality: while they remove infectious adenovirus from the water column, they can also accumulate infectious viruses.

Disinfection of the air and surfaces in the dental clinic using hydroxyl radical (OH-) based technology: A systematic review

Background

A systematic review was carried out to compare the disinfectant capacity of hydroxyl radicals (OH-) versus other products commonly used for disinfecting the air and surfaces.

Material and Methods

A literature search was made of the Cochrane Library, PubMed (MEDLINE) and Scopus databases. "In vitro" studies evaluating disinfection methods applicable to several surfaces and room air were included in the search. The search was carried out in April 2022, with no restrictions in terms of language or publication date.

Results

Of the 308 articles identified from the initial search, 8 were included for the quantitative analysis. All publications corresponded to experimental "in vitro" studies. Seven of them evaluated biocidal action against bacteria, and only two assessed activity against viral loads. The generation of contaminants secondary to application of the disinfectants was only analyzed in one of the studies, with the conclusion that the production of peroxyl radicals (RO2) derived from the oxidation of volatile organic compounds (VOCs) is greater when chemical surface disinfectants are used versus air disinfection systems.

Conclusions

The disinfection capacities of the currently available methods are similar, and none of them are able to replace the use of additional physical protection measures. Key words:Disinfection methods, hydroxyl radical, environment, surfaces, dentistry.

Combinational administration of mesenchymal stem cell-derived exosomes and metformin reduces inflammatory responses in an in vitro model of insulin resistance in HepG2 cells

Diabetes is a highly common metabolic disorder in advanced societies. One of the causes of diabetes is insulin resistance, which is associated with a loss of sensitivity to insulin-sensitive cells. Insulin resistance develops in the body of a person prone to diabetes many years before diabetes development. Insulin resistance is associated with complications such as hyperglycemia, hyperlipidemia, and compensatory hyperinsulinemia and causes liver inflammation, which, if left untreated, can lead to cirrhosis, fibrosis, and even liver cancer. Metformin is the first line of treatment for patients with diabetes, which lowers blood sugar and increases insulin sensitivity by inhibiting gluconeogenesis in liver cells. The use of metformin has side effects, including a metallic taste in the mouth, vomiting, nausea, diarrhea, and upset stomach. For this reason, other treatments, along with metformin, are being developed. Considering the anti-inflammatory role of mesenchymal stem cells (MSCs) derived exosomes, their use seems to help improve liver tissue function and prevent damage caused by inflammation. This study investigated the anti-inflammatory effect of Wharton's jelly MSCs derived exosomes in combination with metformin in the HepG2 cells insulin resistance model induced by high glucose. This study showed that MSCs derived exosomes as an anti-inflammatory agent in combination with metformin could increase the therapeutic efficacy of metformin without needing to change metformin doses by decreasing inflammatory cytokines production, including IL-1, IL-6, and TNF-α and apoptosis in HepG2 cells.

Using compartmental models and Particle Swarm Optimization to assess Dengue basic reproduction number R 0 for the Republic of Panama in the 1999-2022 period

Nowadays, the ability to make data-driven decisions in public health is of utmost importance. To achieve this, it is necessary for modelers to comprehend the impact of models on the future state of healthcare systems. Compartmental models are a valuable tool for making informed epidemiological decisions, and the proper parameterization of these models is crucial for analyzing epidemiological events. This work evaluated the use of compartmental models in conjunction with Particle Swarm Optimization (PSO) to determine optimal solutions and understand the dynamics of Dengue epidemics. The focus was on calculating and evaluating the rate of case reproduction, R 0 , for the Republic of Panama. Three compartmental models were compared: Susceptible-Infected-Recovered (SIR), Susceptible-Exposed-Infected-Recovered (SEIR), and Susceptible-Infected-Recovered Human-Susceptible-Infected Vector (SIR Human-SI Vector, SIR-SI). The models were informed by demographic data and Dengue incidence in the Republic of Panama between 1999 and 2022, and the susceptible population was analyzed. The SIR, SEIR, and SIR-SI models successfully provided R 0 estimates ranging from 1.09 to 1.74. This study provides, to the best of our understanding, the first calculation of R 0 for Dengue outbreaks in the Republic of Panama.

Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage

Wastewater-based epidemiology during the COVID-19 pandemic has proven useful for public health decision-making but is often hampered by sampling methodology constraints, particularly at the building- or neighborhood-level. Time-weighted composite samples are commonly used; however, autosamplers are expensive and can be affected by intermittent flows in sub-sewershed contexts. In this study, we compared time-weighted composite, grab, and passive sampling via Moore swabs, at four locations across a college campus to understand the utility of passive sampling. After optimizing the methods for sample handling and processing for viral RNA extraction, we quantified SARS-CoV-2 N1 and N2, as well as a fecal strength indicator, PMMoV, by ddRT-PCR and applied tiled amplicon sequencing of the SARS-CoV-2 genome. Passive samples compared favorably with composite samples in our study area: for samples collected concurrently, 42 % of the samples agreed between Moore swab and composite samples and 58 % of the samples were positive for SARS-CoV-2 using Moore swabs while composite samples were below the limit of detection. Variant profiles from Moore swabs showed a shift from variant BA.1 to BA.2, consistent with in-person saliva samples. These data have implications for the broader implementation of sewage surveillance without advanced sampling technologies and for the utilization of passive sampling approaches for other emerging pathogens.

Efficacy and safety of add-on Viola odorata L. in the treatment of COVID-19: A randomized double-blind controlled trial

ETHNOPHARMACOLOGICAL RELEVANCE

Severe Acute Respiratory Syndrome (SARS) due to the novel coronavirus has become the highest priority that threatens human health. This situation demands widespread vaccination and the innovation of new therapeutic methods. Despite drug discoveries, the need for approving new medicaments is felt because of adverse effects and lack of efficacy. Several medicinal plants including Viola odorata L. are recommended in traditional Persian medicine for alleviating respiratory infection symptoms. Recent studies showed anti-inflammatory, antioxidant, anti-asthmatic, antitussive, analgesic, and antibacterial activities of sweet violet. These enhance respiratory functions, reduce pulmonary inflammation, and decline mucous membrane edema. This study aimed to evaluate the efficacy of sweet violet syrup in alleviating the manifestations of COVID-19 infection.

MATERIAL AND METHODS

A randomized parallel-group double-blind controlled trial was conducted at Al-Zahra general hospital, Isfahan, Iran. A total of 108 outpatients were enrolled in the study. The patients were randomly allocated to intervention and placebo groups, with 54 patients in each group. The allocation was concealed using sealed opaque envelopes. The intervention group received violet syrup and the control group received placebo syrup, an add-on to the conventional treatment. The outcomes were COVID-19 manifestations, such as dyspnea, cough, myalgia, headache, and diarrhea, considered as outcomes of the study and were evaluated twice using a visual analog scale before the intervention and after 7 days, at the end of the study. Patients were followed daily by phone calls to monitor proper drug consumption and possible side effects.

RESULTS

No significant difference was between groups regarding demographic characteristics and vital signs before and after the treatment. Although all symptoms have improved significantly in both groups, patients who received violet syrup recovered faster and the mean severity scores of cough (P = 0.025), myalgia (P = 0.036), headache (P = 0.037), and diarrhea (P = 0.044) decreased greater in comparison to control group.

CONCLUSION

This study, the first clinical trial on the effectiveness of Viola odorata on SARS-CoV-2 patients, showed that Viola odorata L. effectively controls prevalent manifestations of COVID-19 including cough, myalgia, headache, and diarrhea. Regarding this survey, the violet syrup can be mentioned as a complementary treatment for viral influenza-like infections in which cough, myalgia, headache, and diarrhea are prominent.

The Effect of Protozoa Indigenous to Lakewater and Wastewater on Decay of Fecal Indicator Bacteria and Coliphage

Fecal indicator bacteria (FIB: Escherichia coli and enterococci) are used to assess recreational water quality. Viral indicators (i.e., somatic and F+ coliphage), could improve the prediction of viral pathogens in recreational waters, however, the impact of environmental factors, including the effect of predatory protozoa source, on their survival in water is poorly understood. We investigated the effect of lakewater or wastewater protozoa, on the decay (decreasing concentrations over time) of culturable FIB and coliphages under sunlight and shaded conditions. FIB decay was generally greater than the coliphages and was more rapid when indicators were exposed to lake vs. wastewater protozoa. F+ coliphage decay was the least affected by experimental variables. Somatic coliphage decayed fastest in the presence of wastewater protozoa and sunlight, though their decay under shaded conditions was-10-fold less than F+ after 14 days. The protozoa source consistently contributed significantly to the decay of FIB, and somatic, though not the F+ coliphage. Sunlight generally accelerated decay, and shade reduced somatic coliphage decay to the lowest level among all the indicators. Differential responses of FIB, somatic, and F+ coliphages to environmental factors support the need for studies that address the relationship between the decay of coliphages and viral pathogens under environmentally relevant conditions.

Detection and genome characterisation of SARS-CoV-2 P.6 lineage in dogs and cats living with Uruguayan COVID-19 patients

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in domestic animals have occurred from the beginning of the pandemic to the present time. Therefore, from the perspective of One Health, investigating this topic is of global scientific and public interest.

OBJECTIVES

The present study aimed to determine the presence of SARS-CoV-2 in domestic animals whose owners had coronavirus disease 2019 (COVID-19).

METHODS

Nasopharyngeal and faecal samples were collected in Uruguay. Using quantitative polymerase chain reaction (qPCR), we analysed the presence of the SARS-CoV-2 genome. Complete genomes were obtained using ARTIC enrichment and Illumina sequencing. Sera samples were used for virus neutralisation assays.

FINDINGS

SARS-CoV-2 was detected in an asymptomatic dog and a cat. Viral genomes were identical and belonged to the P.6 Uruguayan SARS-CoV-2 lineage. Only antiserum from the infected cat contained neutralising antibodies against the ancestral SARS-CoV-2 strain and showed cross-reactivity against the Delta but not against the B.A.1 Omicron variant.

MAIN CONCLUSIONS

Domestic animals and the human SARS-CoV-2 P.6 variant comparison evidence a close relationship and gene flow between them. Different SARS-CoV-2 lineages infect dogs and cats, and no specific variants are adapted to domestic animals. This first record of SARS-CoV-2 in domestic animals from Uruguay supports regular surveillance of animals close to human hosts.

Assessment of SARS-CoV-2 Stability in human and environmental matrices, and potential hazards

In the context of the ongoing pandemic of COVID-19, SARS-CoV-2 was detected in human excreta and environmental matrices. The occurrence of SARS-CoV-2 in environmental compartments raises questions on its fate and stability in these matrices and its potential to spread in the exposed communities. This review focused on the stability of the SARS-CoV-2 in human excreta, wastewater, soils, crops, and other environmental matrices, that may be reached through human excreta and sewage products spreading. Little is known about the persistence and survival of SARS-CoV-2 in the environment. Up to now sewage sludge, soil and crops are seldom investigated implying the convenience of considering future researches focusing on SARS-CoV-2 in soils receiving wastewater and sewage sludge, as well as on grown crops. Information regarding SARS-CoV-2 persistence in environmental media is crucial to establish and implement effective policies and measures for mitigating the transmission of COVID-19 and tackling eventual future outbreaks.

A Review: The Antiviral Activity of Cyclic Peptides

In the design and development of therapeutic agents, macromolecules with restricted structures have stronger competitive edges than linear biological entities since cyclization can overcome the limitations of linear structures. The common issues of linear peptides include susceptibility to degradation of the peptidase enzyme, off-target effects, and necessity of routine dosing, leading to instability and ineffectiveness. The unique conformational constraint of cyclic peptides provides a larger surface area to interact with the target at the same time, improving the membrane permeability and in vivo stability compared to their linear counterparts. Currently, cyclic peptides have been reported to possess various activities, such as antifungal, antiviral and antimicrobial activities. To date, there is emerging interest in cyclic peptide therapeutics, and increasing numbers of clinically approved cyclic peptide drugs are available on the market. In this review, the medical significance of cyclic peptides in the defence against viral infections will be highlighted. Except for chikungunya virus, which lacks specific antiviral treatment, all the viral diseases targeted in this review are those with effective treatments yet with certain limitations to date. Thus, strategies and approaches to optimise the antiviral effect of cyclic peptides will be discussed along with their respective outcomes. Apart from isolated naturally occurring cyclic peptides, chemically synthesized or modified cyclic peptides with antiviral activities targeting coronavirus, herpes simplex viruses, human immunodeficiency virus, Ebola virus, influenza virus, dengue virus, five main hepatitis viruses, termed as type A, B, C, D and E and chikungunya virus will be reviewed herein.

Graphical Abstract

Sociodemographic and medical characteristics of liver cirrhosis deaths in a Ghanaian tertiary hospital

Objective

Cirrhosis is common in Ghana because of its high risk factors prevalence. However, information on cirrhosis in Ghana is lacking. This study aimed to study the clinical, and laboratory characteristics of cirrhotic patients in a tertiary hospital in Ghana.

Design

This was a retrospective study of sociodemographic characteristics, symptoms and signs, biochemical and fibrotic indices, treatments, and complications data of 247 patients with cirrhosis who died on admission.

Setting

This study was carried out at the Gastroenterology Unit of the Korle-Bu Teaching Hospital, Ghana.

Results

Two-thirds (68.0%) of the patients were within 30 to 60 years, with more than half (73.7%) being males. The most common aetiological factors among the patients were Hepatitis B virus infection (53.8%), alcohol use (31.6%) and Hepatitis C virus infection (4.9%). More than half (55.0%) of the patients reported late for admission, and 67.2% died within the first two weeks of admission. The most common clinical feature was abdominal distension (61.1% of patients), and the least was upper-abdominal mass (14.2%). The levels of most liver test parameters were elevated, fibrotic indices were high, and haemoglobin and albumin levels were reduced. More than half (53.8%) of the patients were in Child Pugh class B. The most common complication was hepatic encephalopathy; the least was hepato-renal syndrome. Definite treatment for complications of cirrhosis was lacking.

Conclusion

Deaths from cirrhosis at the hospital were mostly of young males with chronic hepatitis B infection. Implementation of hepatitis B prevention and treatment guidelines can help reduce cirrhosis deaths.

Funding

None declared.

Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform

Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.

Reprogramming the tumor microenvironment to improve the efficacy of cancer immunotherapies

The immunotherapeutic approaches based on checkpoint inhibitors, tumor vaccination, immune cell-based therapy, and cytokines were developed to engage the patient's immune system against cancer and better survival of them. While potent, however, preclinical and clinical data have identified that abnormalities in the tumor microenvironment (TME) can affect the efficacy of immunotherapies in some cancers. It is therefore imperative to develop new therapeutic interventions that will enable to overcome tumor-supportive TME and restrain anti-tumor immunity in patients that acquire resistance to current immunotherapies. Therefore, recognition of the essential nature of the tolerogenic TME may lead to a shift from the immune-suppressive TME to an immune-stimulating phenotype. Here, we review the composition of the TME and its effect on tumor immunoediting and then present how targeted monotherapy or combination therapies can be employed for reprogramming educated TME to improve current immunotherapies outcomes or elucidate potential therapeutic targets.

Escherichia coli removal in a treatment wetland - pond system: A mathematical modelling experience

A full-scale treatment wetland (TW) (100 inhabitants, 14 m³·d^-1), composed of two horizontal subsurface flow wetlands (TW1-400 m² and TW2-200 m²) and a small pond (13 m²), has been evaluated for Escherichia coli (E. coli) removal. The results indicate a global removal from 1.74·10⁶ to 685 MPN·100 mL^-1 (3.41 log units), reducing E. coli sufficiently to reach values suitable for reuse purposes such as agricultural reuse, without energy and reagent consumption. The small pond at the end of the treatment train plays an important role in E. coli removal and biodiversity enhancement. Data from TW1 and TW2 have been fitted to the P-k-C* model, giving values of 134 and 100 m·yr^-1 for the first-order kinetic reaction coefficient. For the pond, a process-based model using continuous stirred-tank reactor (CSTR) and a 3d-CFD model have been implemented and compared. The models indicate that solar disinfection and predation by daphnids are the most important mechanisms in the studied pond, representing 65% and 25% of the removal respectively. It can be concluded that CSTR can provide good results for small ponds and 3d-CFD model provides extra information, useful to enhance their design.

Prevalence of cervicovaginal human papillomavirus infection and genotype distribution in Shanghai, China

Background

The evaluation of human papillomavirus (HPV) prevalence rate dynamics and genotype distribution could support the adoption of more targeted prevention and treatment of cervical cancer. We aimed to assess the infection status and genotype characteristics of HPV among gynecological outpatients in Shanghai, China.

Methods

Clinical specimens were collected from patients attending gynaecological department of the Putuo Hospital, Shanghai University of Traditional Chinese Medicine, between January 2015 and December 2019. The cervicovaginal infection of 17 high-risk genotypes and 10 low-risk genotypes were analyzed by Luminex-based multiple assays.

Results

The overall HPV infection rate was 18.81% (95% CI 18.31–19.30%) in Shanghai city, with high-risk, low-risk and mixed high- and low-risk HPV prevalence being 11.65% (95% CI 11.24–12.06%), 4.19% (95% CI 3.94–4.44%) and 2.96% (95% CI 2.74–3.17%), respectively. The five most prevalent high-risk genotypes were HPV-52 (2.95%), HPV-16 (2.34%), HPV-58 (2.07%), HPV-53 (1.67%) and HPV-39 (1.36%). The most common low-risk genotype was HPV-61 (1.52%), followed by HPV-6 (1.29%) and HPV-81 (1.19%). Moreover, the coverage of HPV genotype by nonavalent vaccine was 10.42%, and non-vaccine-covered high-risk genotype was 7.70%. The 15–24 years age group demonstrated the highest HPV prevalence (43.14%), and significant differences were observed among different age groups (P < 0.001).

Conclusions

This study revealed the HPV prevalence and genotype distribution among women in Shanghai city, which could serve as guidance for HPV vaccination and preventative strategies against cervical cancer in this area.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01879-y.

Quantification of human adenovirus in irrigation water-soil-crop continuum: are consumers of wastewater-irrigated vegetables at risk?

Because of health concerns regarding the presence of enteric viruses in wastewater effluents, this study was designed to investigate the occurrence of human adenovirus (HAdV) in the irrigation water-soil-crop continuum. Viral particles were extracted from wastewater and wastewater- or water-irrigated soil and crop samples and analyzed using real-time PCR. Concentration of fecal indicator bacteria (FIB) were also determined. Quantitative microbial risk assessment was performed to determine the HAdV illness risk associated with the consumption of wastewater-irrigated vegetables. HAdV-F was detected in 74% of wastewater effluent samples with a mean concentration of 38 Genomic Copy (GC)/mL. HAdV was also detected in wastewater-irrigated soil (2 × 102 GC/g) and crop (< 10 GC/g) samples, with no statistically significant difference in concentrations between wastewater- and freshwater-irrigated samples. The results showed no correlation between concentrations of FIB and HAdV in the analyzed samples. Mean probability of illness risk from consumption of wastewater-irrigated vegetables was 4 × 10-1 per person per year (pppy) which was about two orders of magnitude higher than the proposed value by WHO (10-3 pppy) for safe reuse of wastewater. This finding suggests that the wastewater reuse for irrigation of vegetables eaten raw could pose a threat to human health with respect to the risk of viral illness, signifying stricter management of wastewater reuse. However, because of uncertainties in the QMRA model, particularly the ratio of infectious to non-infectious virus particles, more data is required to validate the predicted risk. This information is especially important in arid and semi-arid regions where high temperatures, UV radiation intensity, and desiccation can efficiently inactivate microorganisms in the environment.

N-terminus of flagellin enhances vaccine efficacy against Actinobacillus pleuropneumoniae

BACKGROUND

Flagellin elicits potent immune response and may serve as a vaccine adjuvant. We previously reported that the N-terminus of flagellin (residues 1-99, nFliC) is sufficient for vaccine efficacy enhancement against Pasteurella multocida challenge in chickens. In this study, we futher tested the adjuvancy of nFliC in a subunit vaccine against the pig pathogen Actinobacillus pleuropneumoniae in a mice model. For vaccine formulation, the antigen ApxIIPF (the pore-forming region of the exotoxin ApxII) was combined with nFliC, either through genetic fusion or simple admixture.

RESULTS

Immune analysis showed that nFliC, introduced through genetic fusion or admixture, enhanced both humoral (antibody levels) and cellular (T cell response and cytokine production) immunity. In a challenge test, nFliC increased vaccine protective efficacy to 60-80%, vs. 20% for the antigen-only group. Further analysis showed that, even without a supplemental adjuvant such as mineral salt or oil emulsion, genetically linked nFliC still provided significant immune enhancement.

CONCLUSIONS

We conclude that nFliC is a versatile and potent adjuvant for vaccine formulation.

Assessing the potential impact of COVID-19 Omicron variant: Insight through a fractional piecewise model

We consider a new mathematical model for the COVID-19 disease with Omicron variant mutation. We formulate in details the modeling of the problem with omicron variant in classical differential equations. We use the definition of the Atangana-Baleanu derivative and obtain the extended fractional version of the omicron model. We study mathematical results for the fractional model and show the local asymptotical stability of the model for infection-free case if R 0 < 1 . We show the global asymptotically stable of the model for the disease free case when R 0 ≤ 1 . We show the existence and uniqueness of solution of the fractional model. We further extend the fractional order model into piecewise differential equation system and give a numerical algorithm for their numerical simulation. We consider the real cases of COVID-19 in South Africa of the third wave March 2021-Sep 2021 and estimate the model parameters and get R 0 ≈ 1 . 4004 . The real parameters values are used to show the graphical results for the fractional and piecewise model.

New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae

Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.

A bioinformatic approach of targeting SARS-CoV-2 replication by silencing a conserved alternative reserve of the orf8 gene using host miRNAs

The causative agent of the COVID-19 pandemic, the SARS-CoV-2 virus has yielded multiple relevant mutations, many of which have branched into major variants. The Omicron variant has a huge similarity with the original viral strain (first COVID-19 strain from Wuhan). Among different genes, the highly variable orf8 gene is responsible for crucial host interactions and has undergone multiple mutations and indels. The sequence of the orf8 gene of the Omicron variant is, however, identical with the gene sequence of the wild type. orf8 modulates the host immunity making it easier for the virus to conceal itself and remain undetected. Variants seem to be deleting this gene without affecting the viral replication. While analyzing, we came across the conserved orf7a gene in the viral genome which exhibits a partial sequence homology as well as functional similarity with the SARS-CoV-2 orf8. Hence, we have proposed here in our hypothesis that, orf7a might be an alternative reserve of orf8 present in the virus which was compensating for the lost gene. A computational approach was adopted where we screened various miRNAs targeted against the orf8 gene. These miRNAs were then docked onto the orf8 mRNA sequences. The same set of miRNAs was then used to check for their binding affinity with the orf7a reference mRNA. Results showed that miRNAs targeting the orf8 had favorable shape complementarity and successfully docked with the orf7a gene as well. These findings provide a basis for developing new therapeutic approaches where both orf8 and orf7a can be targeted simultaneously.

Bottom-Up Control of the Groundwater Microbial Food-Web in an Alpine Aquifer

Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.

Hepatitis E in a Portuguese cohort of human immunodeficiency virus positive patients: High seroprevalence but no chronic infections

Introduction

Hepatitis E virus (HEV) infection causes zoonotic hepatitis in Europe, with a higher risk of complications in immunocompromised hosts. HEV natural history in human immunodeficiency virus (HIV) positive patients is not fully understood, and its prevalence is unknown.

Objectives

To study the seroprevalence of HEV and prevalence of chronic HEV in HIV‐positive patients from Porto, Portugal.

Methods

We randomly selected patients from the cohort of HIV‐positive patients followed in our hospital. We performed an enzyme‐linked immunosorbent assay to search for immunoglobulin G for HEV. When the absorbance/cut‐off was inferior to 3.5, the test was repeated, and a confirmatory test executed in that sample. For reactive tests and for immunosuppressed patients (CD4 count < 200/mm³) with nonreactive test, a polymerase chain reaction (PCR) test was also performed.

Results

We included 299 patients. The mean age was 48 and 75.3% were men. Regarding HIV infection, the median follow‐up time was 10 years, the acquisition was mainly heterosexual contact, and 94% were on antiretroviral therapy. Seventy‐six patients (25.4%) had reactive immunoglobulin G (IgG) hepatitis E serology. Patients with a reactive test were older (statistically significant difference). Otherwise, there was no difference between groups concerning birthplace, rural residence, chronic viral hepatitis coinfection, or cirrhosis. Nadir and actual T_CD4+ lymphocyte counts did not differ significantly from patients with HEV reactive and nonreactive serology. Gamma‐glutamyl‐transferase (GGT) was higher in patients with reactive IgG HEV. All serum HEV PCR tests were negative.

Conclusions

Seroprevalence of HEV was 25.4% in HIV‐positive patients. Older age and higher GGT correlated to HEV reactive IgG test. No cases of current hepatitis E were found.

Rapid and simple detection of influenza virus via isothermal amplification lateral flow assay

Respiratory illness caused by influenza virus is a serious public health problem worldwide. As the symptoms of influenza virus infection are similar to those of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is essential to distinguish these two viruses. Therefore, to properly respond to a pathogen, a detection method that is capable of rapid and accurate diagnosis in a hospital or at home is required. To satisfy this need, we applied loop-mediated isothermal amplification (LAMP) and an isothermal nucleic acid amplification technique, along with a system to analyze the results without specialized equipment, a lateral flow assay (LFA). Using the platform developed in this study, all processes, from sample preparation to detection, can be performed without special equipment. Unlike existing PCR methods, the nucleic acid amplification can be performed in the field because hot packs do not require electricity. Thus, the designed platform can provide rapid results without the need to transport the samples to a laboratory or hospital. These advantages are not limited to operations in developing countries with poor access to medical systems. In conclusion, the developed technology is a promising tool for infectious disease management that allows for rapid identification of infectious diseases and appropriate treatment of patients.

There is no "origin" to SARS-CoV-2

Since the beginning of the COVID-19 pandemic in 2020 caused by SARS-CoV-2, the question of the origin of this virus has been a highly debated issue. Debates have been, and are still, very disputed and often violent between the two main hypotheses: a natural origin through the "spillover" model or a laboratory-leak origin. Tenants of these two options are building arguments often based on the discrepancies of the other theory. The main problem is that it is the initial question of the origin itself which is biased. Charles Darwin demonstrated in 1859 that all species are appearing through a process of evolution, adaptation and selection. There is no determined origin to any animal or plant species, simply an evolutionary and selective process in which chance and environment play a key role. The very same is true for viruses. There is no determined origin to viruses, simply also an evolutionary and selective process in which chance and environment play a key role. However, in the case of viruses the process is slightly more complex because the "environment" is another living organism. Pandemic viruses already circulate in humans prior to the emergence of a disease. They are simply not capable of triggering an epidemic yet. They must evolve in-host, i.e. in-humans, for that. The evolutionary process which gave rise to SARS-CoV-2 is still ongoing with regular emergence of novel variants more adapted than the previous ones. The real relevant question is how these viruses can emerge as pandemic viruses and what the society can do to prevent the future emergence of pandemic viruses.

Persistence of wastewater-associated antibiotic resistant bacteria in river microcosms

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 h. Both types of wastewater amendments significantly increased the initial abundance of ARB compared to microcosms containing only river water (all p < 0.03). The increase was greatest with untreated wastewater, but that effect decreased steadily over time. In contrast, microcosms amended with treated wastewater saw a smaller initial increase and more complex temporal dynamics. Following a brief lag, ARB abundance bloomed for all three of the antibiotics that we considered. This suggests that ARB that survive wastewater treatment are particularly hardy and may proliferate in riverine conditions after a short recovery period. To determine how interactions with the native river microbial community impacted the persistence of wastewater-associated ARB, an additional set of microcosms was prepared using filter-sterilized river water. Peak abundance in these microcosms was significantly higher by 1-2 orders of magnitude compared to microcosms containing an intact river microbial community (all p < 0.05), which suggests that biotic interactions play a significant role in regulating the persistence and proliferation of ARB. The data presented in this paper are among the first available that specifically consider persistence of viable ARB and represent an important step toward understanding AR-related human health risks downstream from wastewater discharge points and following sewer overflow events. Additional studies that consider longer time scales and the interplay of biotic and abiotic variables are essential for modeling public health risks associated with wastewater inputs of ARB to rivers and other aquatic environments.

Diagnostic Accuracy of Rapid Antigen Tests for COVID-19 Detection: A Systematic Review With Meta-analysis

Introduction

Reverse transcription-polymerase chain reaction (RT-PCR) to detect SARS-CoV-2 is time-consuming and sometimes not feasible in developing nations. Rapid antigen test (RAT) could decrease the load of diagnosis. However, the efficacy of RAT is yet to be investigated comprehensively. Thus, the current systematic review and meta-analysis were conducted to evaluate the diagnostic accuracy of RAT against RT-PCR methods as the reference standard.

Methods

We searched the MEDLINE/Pubmed and Embase databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures [i.e., sensitivity, specificity, diagnostic odds ratio (DOR), positive likelihood ratios (PLR), negative likelihood ratios (NLR), and the area under the curve (AUC)] were pooled with a random-effects model. All statistical analyses were performed with Meta-DiSc (Version 1.4, Cochrane Colloquium, Barcelona, Spain).

Results

After reviewing retrieved records, we identified 60 studies that met the inclusion criteria. The pooled sensitivity and specificity of the rapid antigen tests against the reference test (the real-time PCR) were 69% (95% CI: 68–70) and 99% (95% CI: 99–99). The PLR, NLR, DOR and the AUC estimates were found to be 72 (95% CI: 44–119), 0.30 (95% CI: 0.26–0.36), 316 (95% CI: 167–590) and 97%, respectively.

Conclusion

The present study indicated that using RAT kits is primarily recommended for the early detection of patients suspected of having COVID-19, particularly in countries with limited resources and laboratory equipment. However, the negative RAT samples may need to be confirmed using molecular tests, mainly when the symptoms of COVID-19 are present.

ERp57/PDIA3: new insight

The ERp57/PDIA3 protein is a pleiotropic member of the PDIs family and, although predominantly located in the endoplasmic reticulum (ER), has indeed been found in other cellular compartments, such as the nucleus or the cell membrane. ERp57/PDIA3 is an important research target considering it can be found in various subcellular locations. This protein is involved in many different physiological and pathological processes, and our review describes new data on its functions and summarizes some ligands identified as PDIA3-specific inhibitors.

Vitamin D attenuates COVID-19 complications via modulation of proinflammatory cytokines, antiviral proteins, and autophagy

INTRODUCTION

Global emergence of coronavirus disease-19 (COVID-19) has clearly shown variable severity, mortality, and frequency between and within populations worldwide. These striking differences have made many biological variables attractive for future investigations. One of these variables, vitamin D, has been implicated in COVID-19 with rapidly growing scientific evidence.

AREAS COVERED

The review intended to systematically explore the sources, and immunomodulatory role of vitamin D in COVID-19. Search engines and data sources including Google Scholar, PubMed, NCBI, Scopus, and Web of Science were used for data collection. The search terms used were Vitamin D, COVID-19, immune system, and antiviral mechanism. Overall, 232 sources of information were collected and 188 were included in this review.

EXPERT OPINION

Interaction of vitamin D and vitamin D receptor (VDR) triggers the cellular events to modulate the immune system by regulation of many genes. Vitamin D operates as a double-edged sword against COVID-19. First, in macrophages, it promotes the production of antimicrobial and antiviral proteins like β-defensin 2 and cathelicidin, and these proteins inhibit the replication of viral particles and promote the clearance of virus from the cells by autophagy. Second, it suppresses cytokine storm and inflammatory processes in COVID-19.

Computational peptidology approach to the study of the chemical reactivity and bioactivity properties of Aspergillipeptide D, a cyclopentapeptide of marine origin

Aspergillipeptide D is a cyclic pentapeptide isolated from the marine gorgonian Melitodes squamata-derived fungus Aspergillus sp. SCSIO 41501 that it has been shown to present moderate activity against herpes virus simplex type 1 (HSV-1). Thus, this paper presents the results of a computational study of this cyclopentapeptide's chemical reactivity and bioactivity properties using a CDFT-based computational peptidology (CDFT-CP) methodology, which is derived from combining chemical reactivity descriptors derived from Conceptual Density Functional Theory (CDFT) and some Cheminformatics tools which may be used. This results in an improvement of the virtual screening procedure by a similarity search allowing the identification and validation of the known ability of the peptide to act as a possible useful drug. This was followed by an examination of the drug's bioactivity and pharmacokinetics indices in relation to the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics. The findings provide further evidence of the MN12SX density functional's superiority in proving the Janak and Ionization Energy theorems using the proposed KID approach. This has proven to be beneficial in accurately predicting CDFT reactivity characteristics, which aid in the understanding of chemical reactivity. The Computational Pharmacokinetics study revealed the potential ability of Aspergillipeptide D as a therapeutic drug through the interaction with different target receptors. The ADMET indices confirm this assertion through the absence of toxicity and good absorption and distribution properties.

Treatment outcomes of HIV patients with hepatitis B and C virus co-infections in Southwest China: an observational cohort study

Background

Antiretroviral therapy (ART) has reduced mortality among people living with HIV (PLWH) in China, but co-infections of hepatitis B virus (HBV) and hepatitis C virus (HCV) may individually or jointly reduce the effect of ART. This study aimed to evaluate the impacts of HBV/HCV coinfections on treatment drop-out and mortality among PLWH on ART.

Methods

A retrospective cohort study analysis of 58 239 people living with HIV (PLWH) who initiated antiretroviral therapy (ART) during 2010–2018 was conducted in Guangxi Province, China. Data were from the observational database of the National Free Antiretroviral Treatment Program. Cox proportional hazard models were fitted to evaluate the effects of baseline infection of HBV or HCV or both on death and treatment attrition among PLWH.

Results

Our study showed high prevalence of HBV (11.5%), HCV (6.6%) and HBV-HCV (1.5%) co-infections. The overall mortality rate and treatment attrition rate was 2.95 [95% confidence interval (CI) 2.88–3.02] and 5.92 (95% CI 5.82–6.01) per 100 person-years, respectively. Compared with HIV-only patients, HBV-co-infected patients had 42% higher mortality [adjusted hazard ratio (aHR) = 1.42; 95% CI 1.32–1.54], HCV-co-infected patients had 65% higher mortality (aHR = 1.65; 95% CI 1.47–1.86), and patients with both HCV and HBV co-infections had 123% higher mortality (aHR = 2.23; 95% CI 1.87–2.66).

Conclusions

HBV and HCV coinfection may have an additive effect on increasing the risk of all-cause death among PLWH who are on ART. It is suggested that there is need for primary prevention and access to effective hepatitis treatment for PLWH.

Graphical Abstract

ALD based nanostructured zinc oxide coated antiviral silk fabric

The COVID-19 pandemic has underscored the importance of research and development in maintaining public health. Facing unprecedented challenges, the scientific community developed antiviral drugs, virucides, and vaccines to combat the infection within the past two years. However, an ever-increasing list of highly infectious SARS-CoV-2 variants (gamma, delta, omicron, and now ba.2 stealth) has exacerbated the problem: again raising the issues of infection prevention strategies and the efficacy of personal protective equipment (PPE). Against this backdrop, we report an antimicrobial fabric for PPE applications. We have fabricated a nanofibrous silk-PEO material using electrospinning followed by zinc oxide thin film deposition by employing the atomic layer deposition technique. The composite fabric has shown 85% more antibacterial activity than the control fabric and was found to possess substantial superoxide dismutase–mimetic activity. The composite was further subjected to antiviral testing using two different respiratory tract viruses: coronavirus (OC43: enveloped) and rhinovirus (RV14: non-enveloped). We report a 95% reduction in infectious virus for both OC43 and RV14 from an initial load of ∼1 × 10⁵ (sample size: 6 mm dia. disk), after 1 h of white light illumination. Furthermore, with 2 h of illumination, ∼99% reduction in viral infectivity was observed for RV14. High activity in a relatively small area of fabric (3.5 × 10³ viral units per mm²) makes this antiviral fabric ideal for application in masks/PPE, with an enhanced ability to prevent antimicrobial infection overall.

This study presents an antiviral self-cleaning fabric for masks/PPE applications with protection against human coronavirus.

In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2

The COVID-19 epidemic, caused by virus SARS-CoV-2, has been a pandemic and threatening everyone's health in the past two years. In SARS-CoV-2, ORF8 is one of the most important accessory...

Therapeutic effects of stem cells in different body systems, a novel method that is yet to gain trust: A comprehensive review

Stem cell therapy has been used to treat several types of diseases, and it is expected that its therapeutic uses shall increase as novel lines of evidence begin to appear. Furthermore, stem cells have the potential to make new tissues and organs. Thus, some scientists propose that organ transplantation will significantly rely on stem cell technology and organogenesis in the future. Stem cells and its robust potential to differentiate into specific types of cells and regenerate tissues and body organs, have been investigated by numerous clinician scientists and researchers for their therapeutic effects. Degenerative diseases in different organs have been the main target of stem cell therapy. Neurodegenerative diseases such as Alzheimer's, musculoskeletal diseases such as osteoarthritis, congenital cardiovascular diseases, and blood cell diseases such as leukemia are among the health conditions that have benefited from stem cell therapy advancements. One of the most challenging parts of the process of incorporating stem cells into clinical practice is controlling their division and differentiation potentials. Sometimes, their potential for  uncontrolled growth will make these cells tumorigenic. Another caveat in this process is the ability to control the differentiation process. While stem cells can easily differentiate into a wide variety of cells,  a paracrine effect controlled activity, being in an appropriate medium will cause abnormal differentiation leading to treatment failure. In this review, we aim to provide an overview of the therapeutic effects of stem cells in diseases of various organ systems. In order to advance this new treatment to its full potential, researchers should focus on establishing methods to control the differentiation process, while policymakers should take an active role in providing adequate facilities and equipment for these projects. Large population clinical trials are a necessary tool that will help build trust in this method. Moreover, improving social awareness about the advantages and adverse effects of stem cell therapy is required to develop a rational demand in the society, and consequently, healthcare systems should consider established stem cell-based therapeutic methods in their treatment algorithms.

Graphene-based nanomaterials as antimicrobial surface coatings: A parallel approach to restrain the expansion of COVID-19

The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a significant and topmost global health challenge of today. SARS-CoV-2 can propagate through several direct or indirect means resulting in its exponential spread in short times. Consequently, finding new research based real-world and feasible solutions to interrupt the spread of pathogenic microorganisms is indispensable. It has been established that this virus can survive on a variety of available surfaces ranging from a few hours to a few days, which has increased the risk of COVID-19 spread to large populations. Currently, available surface disinfectant chemicals provide only a temporary solution and are not recommended to be used in the long run due to their toxicity and irritation. Apart from the urgent development of vaccine and antiviral drugs, there is also a need to design and develop surface disinfectant antiviral coatings for long-term applications even for new variants. The unique physicochemical properties of graphene-based nanomaterials (GBNs) have been widely investigated for antimicrobial applications. However, the research work for their use in antimicrobial surface coatings is minimal. This perspective enlightens the scope of using GBNs as antimicrobial/antiviral surface coatings to reduce the spread of transmittable microorganisms, precisely, SARS-CoV-2. This study attempts to demonstrate the synergistic effect of GBNs and metallic nanoparticles (MNPs), for their potential antiviral applications in the development of surface disinfectant coatings. Some proposed mechanisms for the antiviral activity of the graphene family against SARS-CoV-2 has also been explained. It is anticipated that this study will potentially lead to new insights and future trends to develop a framework for further investigation on this research area of pivotal importance to minimize the transmission of current and any future viral outbreaks.

Review of sheep and goat pox disease: current updates on epidemiology, diagnosis, prevention and control measures in Ethiopia

Sheep pox, goat pox, and lumpy skin diseases are economically significant and contagious viral diseases of sheep, goats and cattle, respectively, caused by the genus Capripoxvirus (CaPV) of the family Poxviridae. Currently, CaPV infection of small ruminants (sheep and goats) has been distributed widely and are prevalent in Central Africa, the Middle East, Europe and Asia. This disease poses challenges to food production and distribution, affecting rural livelihoods in most African countries, including Ethiopia. Transmission occurs mainly by direct or indirect contact with infected animals. They cause high morbidity (75-100% in endemic areas) and mortality (10-85%). Additionally, the mortality rate can approach 100% in susceptible animals. Diagnosis largely relies on clinical symptoms, confirmed by laboratory testing using real-time PCR, electron microscopy, virus isolation, serology and histology. Control and eradication of sheep pox virus (SPPV), goat pox virus (GTPV), and lumpy skin disease (LSDV) depend on timely recognition of disease eruption, vector control, and movement restriction. To date, attenuated vaccines originating from KSGPV O-180 strains are effective and widely used in Ethiopia to control CaPV throughout the country. This vaccine strain is clinically safe to control CaPV in small ruminants but not in cattle which may be associated with insufficient vaccination coverage and the production of low-quality vaccines.

Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review

Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.