Search

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent responsible for coronavirus disease (COVID-19), is an issue of global concern since March 2020. The respiratory manifestations of COVID-19 have widely been explained in the last couple of months of the pandemic. Initially, the virus was thought to be restricted to the pulmonary system; however, as time progressed and cases increased during the second wave of COVID-19, the virus affected other organs, including the nervous system. The neurological implication of SARS-CoV-2 infection is mounting, as substantiated by various reports, and in the majority of COVID-19 patients with neurological symptoms, the penetration of SARS-CoV-2 in the central nervous system (CNS) is likely. SARS-CoV-2 can enter the nervous system by exploiting the routes of olfactory mucosa, olfactory and sensory nerve endings, or endothelial and nerve tissues, thus crossing the neural-mucosal interface in the olfactory mucosa in the nose. Owing to multifactorial and complex pathogenic mechanisms, COVID-19 adds a large-scale risk to the entire nervous system. A thorough understanding of SARSCoV- 2 neurological damage is still vague; however, our comprehension of the virus is rapidly developing. The present comprehensive review will gain insights and provide neurological dimensions of COVID-19 and their associated anomalies. The review presents the entry routes of SARS-CoV-2 into the CNS to ascertain potential targets in the tissues owing to infection. We also discuss the molecular mechanisms involved, the array of clinical symptoms, and various nervous system diseases following the attack of SARS-CoV-2.

Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broad-spectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.

Introduction: The curve of spee plays an important role to create Christensen’s phenomenon in natural dentition. This study was performed to assess the difference in depth of the curve of Spee between normal and attrited dentition. Methods: An analytical cross-sectional study was performed to measure the depth of curve speed in a total of 80 willing participants who met the inclusion criteria, of which 40 had normal dentition and 40 had attrited dentition. Measurements were done on stone casts by using a rigid metal scale and a digital vernier caliper. Analytical statistical analysis (independent t-test) was done using SPSS Statistical Software Package (version 21.0). Results: There was a statistically significant difference in the depth of the curve of Spee between the two groups. Conclusions: The depth of the curve of spee decreases with the advancing of the age of human as attrition of the teeth occurs with age. Although there is a decrease in the depth of the curve of spee it should be maintained and created while performing full mouth rehabilitation and other extensive prosthodontic treatments.

Agradecimientos. Los autores desean agradecer el trabajo generoso de recogida de datos realizado por las maestras de educación infantil (Raquel, Isabel, Espe, Mª José, Carmen, Rus, Verónica, María, Emi, Aída y Charo) y el del alumnado participante. El estudio ha sido parcialmente realizado gracias a las ayudas del plan propio UCLM, de financia-ción de actividades de investigación, cofinanciadas por FEDER, concedida al grupo de investigación Botánica, Etnobiología y Educación (Ref: 2021-GRIN-30982) Este trabajo busca identificar qué conocimientos sobre los virus se generaron de modo informal durante la pandemia del SARS-CoV-2 entre los escolares de educación infantil. Para ello, se analizan las respuestas de una entrevista estructurada llevada a cabo por las tutoras en las aulas y los dibujos realizados por el alumnado. Los participantes fueron 241 escolares de las aulas de infantil de 3 a 5 años. Los resultados apuntan a que la pandemia ha favorecido un conocimiento más realista sobre los virus, aunque ligado a uno concreto, el coronavirus. Los virus son situados mayoritariamente en el medio exterior y entendidos como agentes dañinos. Por último, los medios de comunicación destacan como principal fuente de información. This paper seeks to identify what knowledge about viruses was generated informally during the SARS-CoV-2 pandemic among pre-school children. To this end, we analyzed the responses to a structured interview conducted by the tutors in the classrooms, and drawings made by the pupils. The participants were 241 children from early childhood education in 3- to 5-year-old classrooms. The results suggest that the pandemic has favored a more realistic knowledge of viruses, although linked to one specific virus, the coronavirus. Viruses are mostly located in the external environment and understood as harmful agents. Finally, the mass media stand out as the main source of information.

International audience; Molecular biology amplification enables sensitive detection of most respiratory viruses through nasopharyngeal swabbing. We developed an innovative approach to detect viral genomes on used facial tissues. In 2 communities of children, used tissues were collected once weekly for 1 year. Pooled analysis of tissues enabled detection of successive virus circulation in 4 age groups over time and forecasted by several weeks the circulation of influenza in the general population. At the individual level, in a proof-of-concept study of 30 volunteers with influenza-like signs/symptoms, we identified common respiratory viruses. The signals for SARS-CoV-2 obtained in parallel from 15 facial tissues and swab samples were similar and often higher for the tissues (11/15). Individual analysis of tissues offers a noninvasive, sensitive, and affordable alternative to self-sampling without a medical care requirement. Pooled analyses may be used to detect virus spread in specific communities, predict seasonal epidemics, and alert the population to viral infections. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.

The ongoing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has been proven to be more severe than the previous coronavirus outbreaks due to the virus’ high transmissibility. With the emergence of new variants, this global phenomenon took a more dramatic turn, with many countries recently experiencing higher surges of confirmed cases and deaths. On top of this, the inadequacy of effective treatment options for COVID-19 aggravated the problem. As a way to address the unavailability of target-specific viral therapeutics, computational strategies have been employed to hasten and systematize the search. The objective of this review is to provide initial data highlighting the utility of polyphenols as potential prophylaxis or treatment for COVID-19. In particular, presented here are virtually screened polyphenolic compounds which showed potential as either antagonists to viral entry and host cell recognition through binding with various receptor-binding regions of SARS-CoV-2 spike protein or as inhibitors of viral replication and post-translational modifications through binding with essential SARS-CoV-2 non-structural proteins.

COVID-19 is the disease caused by SARS-CoV-2 which has led to 2,643,000 deaths worldwide, a number which is rapidly increasing. Urgent studies to identify new antiviral drugs, repurpose existing drugs, or identify drugs that can target the overactive immune response are ongoing. Antiretroviral drugs (ARVs) have been tested in past human coronavirus infections, and also against SARS-CoV-2, but a trial of lopinavir and ritonavir failed to show any clinical benefit in COVID-19. However, there is limited data as to the course of COVID-19 in people living with HIV, with some studies showing a decreased mortality for those taking certain ARV regimens. We hypothesized that ARVs other than lopinavir and ritonavir might be responsible for some protection against the progression of COVID-19. Here, we used chemoinformatic analyses to predict which ARVs would bind and potentially inhibit the SARS-CoV-2 main protease (Mpro) or RNA-dependent-RNA-polymerase (RdRp) enzymes in silico. The drugs predicted to bind the SARS-CoV-2 Mpro included the protease inhibitors atazanavir and indinavir. The ARVs predicted to bind the catalytic site of the RdRp included Nucleoside Reverse Transcriptase Inhibitors, abacavir, emtricitabine, zidovudine, and tenofovir. Existing or new combinations of antiretroviral drugs could potentially prevent or ameliorate the course of COVID-19 if shown to inhibit SARS-CoV-2 in vitro and in clinical trials. Further studies are needed to establish the activity of ARVs for treatment or prevention of SARS-CoV-2 infection . Communicated by Ramaswamy H. Sarma

Hemagglutinins (HAs) are the receptor-binding and membrane fusion glycoproteins of influenza viruses. They recognize sialic acid-containing, cell-surface glycoconjugates as receptors but have limited affinity for them, and, as a consequence, virus attachment to cells requires their interaction with several virus HAs. Receptor-bound virus is transferred into endosomes where membrane fusion by HAs is activated at pH between 5 and 6.5, depending on the strain of virus. Fusion activity requires extensive rearrangements in HA conformation that include extrusion of a buried "fusion peptide" to connect with the endosomal membrane, form a bridge to the virus membrane, and eventually bring both membranes close together. In this review, we give an overview of the structures of the 16 genetically and antigenically distinct subtypes of influenza A HA in relation to these two functions in virus replication and in relation to recognition of HA by antibodies that neutralize infection.

While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.

Although it is clinically important for acute respiratory tract (co)infections to have rapid and accurate diagnosis, it is critical that respiratory medicine understand the advantages of current laboratory methods. In this study we tested nasopharyngeal samples (n=29) with a commercially available PCR assay and compared the results with hybridization capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct40% target coverage, median depth of 1X and RPKM>10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positive 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterize the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify® Platform for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompetent respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndromic-based tests and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration—with promise to reduce morbidity and mortality.HighlightsWhat are the main findings?Although there was a high concordance between methodologies, a hybridization capture-based mNGS workflow was able to detect 29 additional upper respiratory microorganisms versus PCR.Identified microorganisms were rapidly characterized into three phenotypic groups for infectivity and trafficking potential.What is the implication of the main finding?A hybridization capture-based mNGS workflow can provide a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infectionDeciphering upper respiratory microbiota with phenotypic grouping has potential to provide respiratory medicine a tool to better manage immunocompetent and complex respiratory cases.

The high economic impact and zoonotic potential of avian influenza call for detailed investigations of dispersal dynamics of epidemics. We integrated phylogeographic and epidemiologic analyses to investigate the dynamics of a low pathogenicity avian influenza (H3N1) epidemic that occurred in Belgium during 2019. Virus genomes from 104 clinical samples originating from 85% of affected farms were sequenced. A spatially explicit phylogeographic analysis confirmed a dominating northeast to southwest dispersal direction and a long-distance dispersal event linked to direct live animal transportation between farms. Spatiotemporal clustering, transport, and social contacts strongly correlated with the phylogeographic pattern of the epidemic. We detected only a limited association between wind direction and direction of viral lineage dispersal. Our results highlight the multifactorial nature of avian influenza epidemics and illustrate the use of genomic analyses of virus dispersal to complement epidemiologic and environmental data, improve knowledge of avian influenza epidemiologic dynamics, and enhance control strategies. ispartof: EMERGING INFECTIOUS DISEASES vol:29 issue:2 pages:351-359 ispartof: location:United States status: published

Abstract: The plant, Glycyrrhiza glabra species (liquorice or licorice), a flowering plant of the bean family Fabaceae, is of utmost importance as it contains glycyrrhizin an important antiviral compound along with other significant phytoconstituents like glycyrrhetinic acid, glabrin A&B, triterpene sterols, isoflavones, and many more. Glycyrrhiza glabra has been recognized since time immemorial for its ethnopharmacological values, as it exhibits various pharmacological activities. The crux of this review focuses on the antiviral activity of liquorice against several viruses that pose a severe threat to humankind like herpes simplex virus (HSV), Hepatitis C virus (HCV), H5N1 virus, human immunodeficiency virus (HIV), H3N2 virus, influenza, and influenza A virus, pseudorabies virus (PrV), etc. To recapitulate, this review article explains the compilation of data obtained from Scopus indexed journal articles over 5 years ranging from 2015 to 2020, which not only aims to shed light on the application of Glycyrrhiza glabra against human viruses but also on how to develop these responses further to improve the efficacy. Further the review also focuses on of Glycyrrhiza glabra for its potential commercial uses, such as for the treatment of porcine virus in pigs and piglets, is also verified.

4 Pág., Cetacean morbillivirus (CeMV) causes illness and death in cetaceans worldwide; the CeMV strains circulating in the Southern Hemisphere are poorly known. We detected a pilot whale CeMV strain in 3 short-finned pilot whales (Globicephala macrorhynchus) stranded in Brazil during July-October 2020. Our results confirm this virus circulates in this species., The Coordination for the Improvement of Higher Education Personnel (CAPES), National Council for Technological and Scientific Development (CNPq), and São Paulo Research Foundation (FAPESP) provided financial support. S.C.S. and A.C.E. received PhD fellowships by FAPESP (process nos. 2020/12434-9 and 2016/20956-0). L.B.K. received financial support from FAPESP (no. 2020/12434-9). J.L.C.-D., L.B.K. and M.J.C. are recipients of research productivity fellowships from CNPq (nos.304999-18, 315619/2021-0, and 313577/2020-0, respectively),C.S. is a recipient of a Juan de la Cierva incorporación fellowship (no. IJC2020-046019-I) and received a postdoctoral grant by FAPESP (no. 2018/25069-7)

Coronavirus disease 2019 has affected more than 4 million people throughout the world since December 2019. It seems this infection has been the most insidious virus of the coronavirus family. This virus causes severe respiratory failure and symptoms in patients and can result in death. Designing a restrict protocol to deal with infections from severe acute respiratory syndrome coronavirus type 2 is critical in cell therapy institutes. In this review, we present the important aspects related to this virus in cell therapy protocols.

Questions remain concerning the long-term efficacy, safety, and site(s) of transgene expression following adeno-associated vector (AAV) therapy. We report a long-term follow-up of 8 (male = 4, hemizygous, and female = 4, homozygous) dogs with severe hemophilia A treated with a single portal vein infusion of a B-domain–deleted (BDD)-canine FVIII (cFVIII) AAV vector (median dose = 1.25 × 1013 vg/kg, AAV2 = 4, AAV6 = 3, and AAV8 = 1). After a median follow-up of 10.8 years (8.2-12.0 years), persistent FVIII:C (median one-stage = 12.7%, chromogenic = 7.2%) was seen in all responding dogs (n = 6), with improvement in annualized bleed rates (pre = 3.9 vs post = 0.3 event per year; P = .003). Anti-AAV capsid neutralizing antibodies (nAbs) toward the dosed capsid were detected throughout the study, with limited cross-reactivity to other capsids. nAb titers for all capsid serotypes declined with time, although they remained at levels precluding redosing with the same capsid. AAV-BDD-cFVIII DNA was detected in the liver of all dogs (median = 0.15 vg per diploid genome), with lower levels in the spleen in 4 dogs (median = 0.005 vg per diploid genome). Consistent with the liver-specific promoter, BDD-cFVIII mRNA was only detected in the liver. Postmortem examination demonstrated no evidence of chronic liver disease or liver malignancy. Persistent FVIII expression and an improved bleeding phenotype was seen for more than a decade after vector delivery. This is the longest follow-up reported in a preclinical model supporting long-term efficacy and safety of AAV-mediated gene therapy.

Point-of-care detection of pathogens is critical to monitor and combat viral infections. Here, we demonstrate a plasmonic coupling assay (PCA) using gold nanourchins (AuNUs) as labels for the colorimetric quantification of viruses. The antibody functionalized AuNUs allow for rapid and highly specific identification of viruses and provide strong color change for sensitive detection. Using respiratory syncytial virus (RSV) as a target, we demonstrate that the AuNU-based PCA achieves a detection limit of 1,402 PFU/mL (equivalent to 17 copies/μL) that is 3.1- and 5.7-times lower than the rod- and sphere-based counterparts, respectively. The improved detection sensitivity arises from the higher virus binding capability and stronger plasmonic coupling at long distances (∼10 nm) by AuNU probes. The detection can be performed with a portable smartphone-based spectrometer and is validated by testing RSV-spiked nasal swab clinical samples. Our study reports a rapid and sensitive approach for intact virus detection and provides a potential toolkit at the point of care.Graphical abstract

Pre-existing SARS-CoV-2-specific T cells, but not antibodies, have been detected in some unexposed individuals. This may account for some of the diversity in clinical outcomes ranging from asymptomatic infection to severe COVID-19. Although age is a risk factor for COVID-19, how age affects SARS-CoV-2-specific T cell responses remains unknown. We found that some pre-existing T cell responses to specific SARS-CoV-2 proteins, Spike (S) and Nucleoprotein (N), were significantly lower in elderly donors (>70 years old) who were seronegative for S than in young donors. However, substantial pre-existing T cell responses to the viral membrane (M) protein were detected in some elderly donors. These responses likely compensate for loss of T cell responses specific to S and N. In contrast, young and elderly donors exhibited comparable T cell responses to S, N, and M proteins after infection with SARS-CoV-2. M-specific responses were mediated by CD4 T cells producing interferon-γ in both seronegative and seropositive individuals. T cells in seronegative elderly donors responded to various M-derived peptides, while the response after SARS-CoV-2 infection was apparently focused on a single peptide. These data suggest that diversity of target antigen repertoire for pre-existing SARS-CoV-2-specific T cells declines with age, but the magnitude of pre-existing T cell responses is maintained by T cells reactive to specific viral proteins such as M. A better understanding of the role of pre-existing SARS-CoV-2-specific T cells that are less susceptible to age-related loss may contribute to development of more effective vaccines for elderly people.

Bacteria, fungi, viruses, and protozoa are known to infect and induce diseases in the human central nervous system (CNS). Modeling the mechanisms of interaction between pathogens and the CNS microenvironment is essential to understand their pathophysiology and develop new treatments. Recent advancements in stem cell technologies have allowed for the creation of human brain organoids, which more closely resembles the human CNS microenvironment when compared to classical 2-dimensional (2D) cultures. Now researchers can utilize these systems to investigate and reinvestigate questions related to CNS infection in a human-derived brain organoid system. Here in this review, we highlight several infectious diseases which have been tested in human brain organoids and compare similarities in response to these pathogens across different investigations. We also provide a brief overview of some recent advancements which can further enrich this model to develop new and better therapies to treat brain infections.

Background Enhanced nonpharmaceutical interventions (NPIs) to prevent the Coronavirus Disease 2019 (COVID-19) have shown various levels of impact on common respiratory pathogens. We aimed to analyze the epidemiological changes seen in certain common respiratory viruses found in Taiwanese children (e.g., influenza virus, enterovirus, parainfluenza virus, adenovirus and respiratory syncytial virus (RSV)) after the implementation of public health measures, as well as interpret the possible meaning of these changes. Methods This retrospective observational study examined the viral isolation from children younger than 18 years at a medical center in central Taiwan during the period January 2015 – December 2020, a time frame of six years. Viral isolations prior to the COVID-19 pandemic (January 2015 – December 2019), along with those during the post-COVID-19 period (January – December 2020) were analyzed and compared. Results A total of 6,899 throat swab samples were collected during the pre-pandemic period of 2015 to 2019, with 2,681 of them having a positive result (38.86%). There were a total of 713 samples collected in 2020, with 142 of them showing positive results (19.92%). The overall positive rate of viral isolates significantly decreased in 2020 (p < 0.001). Declines in the isolation of the influenza virus, parainfluenza virus, adenovirus and enterovirus were observed. The RSV surprisingly became the leading isolate, with up to 47 (6.59%) instances in 2020, and showing an unusual peak in the winter of 2020. The rise began in September of 2020 and reached its plateau in November of that year. Conclusions Most respiratory viruses decreased under NPIs regarding SARS-CoV-2. However, the RSV outbreak in the winter of 2020 had shown the limitation of current NPIs. Possible explanations have been discussed in details and public preventive measures should be reinforced for RSV, particularly amongst people having young children both at home and in care centers.

Abstract: Favipiravir is a potential antiviral drug undergoing clinical trials to manage various viral infections, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Favipiravir possesses antiviral properties against RNA viruses, including SARS-CoV-2. Unfortunately, these viruses do not have authorized antiviral drugs for the management of diseases resulting from their infection, hence the dire need to accentuate the discovery of antiviral drugs that are efficacious and have a broad spectrum. Favipiravir acts primarily by blocking inward and outward movements of the virus from cells. Favipiravir is a prodrug undergoing intracellular phosphorylation and ribosylation to form an active form, favipiravir-RTP, which binds viral RNA-dependent RNA polymerase (RdRp). Considering the novel mechanism of favipiravir action, especially in managing viral infections, it is vital to pay more attention to the promised favipiravir hold in the management of SARS-CoV-2, its efficacy, and dosage regimen, and interactions with other drugs. In conclusion, favipiravir possesses antiviral properties against RNA viruses, including COVID- 19. Favipiravir is effective against SARS-CoV-2 infection through inhibition of RdRp. Pre-clinical and large-scalp prospective studies are recommended for efficacy and long-term safety of favipiravir in COVID-19.

The covalent attachment of ubiquitin and ubiquitin-like polypeptides to cellular and viral proteins regulates numerous processes that enable virus infection, viral genome replication, and the spread of viruses to new hosts. The importance of these protein modifications in the regulation of the life cycle of herpesviruses is underscored by the discovery that all known members of this virus family encode at least one protease that specifically recognizes and disassembles ubiquitin conjugates. The structural and functional characterization of the viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infection and increasing evidence suggests that the viral deconjugases may also play a role in malignant transformation.

The autumn and winter bronchiolitis epidemics have virtually disappeared in the first year of the COVID-19 pandemic.Our objectives were characterised bronchiolitis during fourth quarter of 2020 and the role played by SARS-CoV-2.Prospective multi-centre study performed in Madrid (Spain) between October and December 2020 including all children admitted with acute bronchiolitis. Clinical data were collected and multiplex PCR for respiratory viruses were performed.Thirty-three patients were hospitalised with bronchiolitis during the study period: 28 corresponded to rhinovirus (RV), 4 to SARS-CoV-2, and 1 had both types of infection. SAR-CoV-2 bronchiolitis were comparable to RV bronchiolitis except for a shorter hospital stay. A significant decrease in the admission rate for bronchiolitis was found and no RSV was isolated.SARS-CoV-2 infection rarely causes acute bronchiolitis and it is not associated with a severe clinical course. During COVID-19 pandemic period there was a marked decrease in bronchiolitis cases.La epidemia de bronquiolitis de otoño e invierno prácticamente desapareció durante el primer año de la pandemia de COVID-19.Nuestros objetivos eran caracterizar la bronquiolitis durante el cuarto trimestre de 2020 y determinar el papel desempeñado por el virus SARS-CoV-2.Estudio multicéntrico prospectivo realizado en Madrid (España) entre los meses de octubre y diciembre de 2020, que incluyó a todos los niños ingresados con bronquiolitis aguda. Se recogieron los datos clínicos y se realizó una PCR múltiple para virus respiratorios.Se hospitalizó a treinta y tres pacientes con bronquiolitis durante el periodo del estudio: 28 correspondieron a rinovirus, 4 a SARS-CoV-2 y uno presentaba ambos tipos de infección. Las bronquiolitis por SAR-CoV-2 fueron comparables a las bronquiolitis por rinovirus, salvo por una estancia hospitalaria más corta. Se detectó una reducción significativa en la tasa de ingresos por bronquiolitis y no se aisló VSR.Es raro que la infección por SARS-CoV-2 cause bronquiolitis aguda y no se asocia a una evolución clínica grave. Durante la pandemia de COVID-19 se produjo un descenso pronunciado de los casos de bronquiolitis.

Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.

Background: The novel coronavirus 2019 (COVID-19) infection has caused the global emergence of coronavirus in humans during the last 12 months. Till May 11, 2021, the confirmed global COVID-19 cases and deaths reached 158551526 and 3296855, respectively. Methods: Goblet cells and ciliated cells in the nose act as the initial infection site of SARS-CoV-2. Thus, mucus immunity is important to protect from infection. The outburst of SARS-CoV-2 infection can be halted only when an effective vaccine will be developed. Results: Globally, over 100 different vaccines are under investigation, including DNA vaccines, RNA vaccines, inactivated virus vaccines, adenovirus-based vaccines, recombinant/subunit protein vaccines, peptide vaccines, virus-like particles, etc. Inactivated virus vaccines and mRNA, and adenovirus-based vaccines have moved fast into clinical trials. Conclusion: Vaccines containing spike protein of SARS-CoV as subunit could effectively prevent binding of coronavirus to the host cell and membrane fusion. Thus, spike protein can be used as a major target for subunit vaccine preparation.

Well-established surveillance and monitoring systems for respiratory viruses need to be improved, and epidemiological data on respiratory viruses in China are scarce. This study aimed to investigate the epidemiological characteristics of respiratory viruses among hospitalized children aged ≤2 years with acute respiratory tract infections (ARTIs) in Xiamen, China, from October 2014 to September 2017. The clinical records of 7,248 children hospitalized for ARTIs were retrospectively analyzed. Respiratory syncytial virus (RSV) (22.3%) was the most common virus among hospitalized children aged ≤2 years, followed by parainfluenza (5.0%), adenovirus (3.5%), and influenza (1.7%). RSV-infected children had a higher disease burden, including a higher intensive care unit (ICU) admission rate (12.7%) and higher hospital charges ($635.36). Particularly, infants aged6 months had the highest risk of RSV infection (odds ratio = 2.4; 95% CI, 1.9-2.9) and a higher ICU admission rate (12.1% vs. 4.5%, 4.6%) and hospital cost ($923.3 vs. $785.5, $811.7) than the other age groups. Therefore, infants aged 0-6 months, particularly premature infants and children with congenital diseases, should receive more attention. There is an urgent need to develop effective immunization strategies to protect these infants during the first 6 months of life and in the RSV season.

Aims The aim of this study was to determine how the transfer efficiency of MS-2 coliphage from the toilet seat to hands and fingertip to lip differs according to the suspension of the inoculum. Methods and Results Hands were sampled after lifting a toilet seat which was inoculated with MS-2 on the underneath side. MS-2 was suspended in a spectrum of proteinaceous and non-proteinaceous solutions. Transfer efficiencies were greatest with the ASTM tripartite soil load (3.02% ± 4.03) and lowest with phosphate-buffered saline (PBS) (1.10% ± 0.81) for hand-to-toilet seat contacts. Finger-to-lip transfer rates were significantly different (p < 0.05) depending on suspension matrix, with PBS yielding the highest transfer (52.53% ± 4.48%) and tryptose soy broth (TSB) the lowest (23.15% ± 24.27%). Quantitative microbial risk assessment was used to estimate the probability of infection from adenovirus and norovirus from finger contact with a toilet seat. Conclusions The greatest transfer as well as the largest variation of transfer were measured for finger-to-lip contacts as opposed to toilet seat-to-finger contacts. These factors influence the estimation of the probability of infection from micro-activity, that is, toilet seat adjustment. Significance and Impact Viruses may be transferred from various human excreta with differing transfer efficiencies, depending on the protein content.

The possible impact of viral infections on the development or pathogenesis of neurodegenerative disorders remains largely unknown. However, there have been reports associating the influenza virus pandemic and long-term infection with the Japanese encephalitis virus with the development of post-encephalitic Parkinsonism or von Economo’s encephalitis. In the last couple of years, there has been a worldwide pandemic caused by the novel coronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV)-2, which causes a severe acute respiratory syndrome and is found to be associated with symptoms or complications of the central nervous system. Its possible involvement with the central nervous system is in line with emerging scientific evidence stating that the human respiratory coronaviruses can enter the brain, infect neural cells, persist in the brain, and cause activation of myelin-reactive T cells. Currently, there is a dearth of scientific information on the acute or possible long-term impact of infection with SARS-CoV-2 on the development of dementia and/or neurodegenerative diseases. This is related to the fact that the virus is ‘new,’ and its effects on humans are still being studied. This narrative review examines the extant literature for understanding the impact of coronavirus infections on the brain as there is a possibility that coronavirus disease 2019 (COVID-19) could increase the risk for the development of neurodegenerative diseases or hasten their progression.

The gut microbiome includes a series of microorganism genomes, such as bacteriome, virome, mycobiome, etc. The gut microbiota is critically involved in intestine immunity and diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC); however, the underlying mechanism remains incompletely understood. Clarifying the relationship between microbiota and inflammation may profoundly improve our understanding of etiology, disease progression, patient management, and the development of prevention and treatment. In this review, we discuss the latest studies of the influence of enteric viruses (i.e., commensal viruses, pathogenic viruses, and bacteriophages) in the initiation, progression, and complication of colitis and colorectal cancer, and their potential for novel preventative approaches and therapeutic application. We explore the interplay between gut viruses and host immune systems for its effects on the severity of inflammatory diseases and cancer, including both direct and indirect interactions between enteric viruses with other microbes and microbial products. Furthermore, the underlying mechanisms of the virome’s roles in gut inflammatory response have been explained to infer potential therapeutic targets with examples in specific clinical trials. Given that very limited literature has thus far discussed these various topics with the gut virome, we believe these extensive analyses may provide insight into the understanding of the molecular pathogenesis of IBD and CRC, which could help add the design of improved therapies for these important human diseases.

Abstract: The novel coronavirus disease (COVID-19) emerged in December 2019. It is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is still existent all over the world. Researchers worldwide are continuously conducting in silico studies or virtual screening on various phytochemicals and reporting potential candidates that can be developed against COVID-19 after in vitro and in vivo validation. Antiviral effects of several phytochemicals have been demonstrated against different kinds of coronavirus, including SARS-CoV. Using drug repurposing techniques, a number of phytochemicals have shown substantial antiviral efficacy against COVID 19. This article reviews the efficacy of lead phytochemicals in computational studies on different important targets of SARS-CoV-2 like main protease, ACE-2, papain-like protease, spike protein, nsp-1, nsp-15, RdRp, MTase, helicase, cathepsin, TMPRSS-2. This review discusses potential application of these phytochemicals, which can guide medicinal chemists to choose phytochemicals to proceed with further in vitro and in vivo testing for SARS-CoV-2, which may eventually lead to an effective therapeutic agent and thus can be used to control the current ongoing pandemic.

The intentional use of viruses for cancer therapy dates back over a century. As viruses are inherently immunogenic and naturally optimized delivery vehicles, repurposing viruses for drug delivery, tumor antigen presentation, or selective replication in cancer cells represents a simple and elegant approach to cancer treatment. While early virotherapy was fraught with harsh side effects and low response rates, virus-based therapies have recently seen a resurgence due to newfound abilities to engineer and tune oncolytic viruses, virus-like particles, and virus-mimicking nanoparticles for improved safety and efficacy. However, despite their great potential, very few virus-based therapies have made it through clinical trials. In this review, we present an overview of virus-inspired approaches for cancer therapy, discuss engineering strategies to enhance their mechanisms of action, and highlight their application for overcoming the challenges of traditional cancer therapies.

With the COVID-19 pandemic still ongoing, the annual season of influenza and other respiratory virus epidemics has arrived. Specimens from patients suspected of respiratory viruses infection were collected. Viral detection was performed following RNA extraction and real-time RT-PCR. During the study period, we received and tested a total of 606 specimens. Rhinovirus virus was the viral type most prevalent, detected in 186 (45.47%) specimens. The age range of patients positive for influenza A, influenza A (H1N1), and influenza B was 18 days to 13 years. With female prevalence for this viral type, cough and asthma were the main clinical manifestations presented by this viral type. Our results indicate that rhinoviruses, adenoviruses, metapneumoviruses, and influenza are among the most important agents of ARI in pediatrics. The epidemic period of respiratory infections observed in Goiânia can be useful for planning and implementing some prevention strategies.

1.AbstractTuatara (Sphenodon punctatus) are one of the most phylogenetically isolated species and provide a unique host system to study virus evolution. While the tuatara genome, sequenced in 2020, revealed many endogenous viral elements, we know little of the exogenous viruses that infect tuatara. We performed a metatranscriptomics study of tuatara cloaca samples from a wild population on Takapourewa (Stephens Island), Aotearoa New Zealand. From these data we identified 49 potentially novel viral species that spanned 20 RNA viral families and/or orders, the vast majority (48) of which were likely dietary related. Notably, using a protein structure homology search, we identified a highly divergent novel virus within the Picornaviridae which may directly infect tuatara. Additionally, two endogenous tuatara adintoviruses were characterised that exhibited long-term viral-host co-divergence. Overall, our results indicate that the tuatara cloacal virome is highly diverse likely due a large number of dietary related viruses.

Abstract: Viruses have been classified as non-living because they require a cellular host to support their replicative processes. Empirical investigations have significantly advanced our understanding of the many strategies employed by viruses to usurp and divert host regulatory and metabolic processes to drive the synthesis and release of infectious particles. The recent emergence of SARS-CoV-2 has permitted us to evaluate and discuss a potentially novel classification of viruses as living entities. The ability of SARS CoV-2 to engender comprehensive regulatory control of integrative cellular processes is strongly suggestive of an inherently dynamic informational registry that is programmatically encoded by linear ssRNA sequences responding to distinct evolutionary constraints. Responses to positive evolutionary constraints have resulted in a single-stranded RNA viral genome that occupies a threedimensional space defined by conserved base-paring resulting from a complex pattern of both secondary and tertiary structures. Additionally, regulatory control of virus-mediated infectious processes relies on extensive protein-protein interactions that drive conformational matching and shape recognition events to provide a functional link between complementary viral and host nucleic acid and protein domains. We also recognize that the seamless integration of complex replicative processes is highly dependent on the precise temporal matching of complementary nucleotide sequences and their corresponding structural and non-structural viral proteins. Interestingly, the deployment of concerted transcriptional and translational activities within targeted cellular domains may be modeled by artificial intelligence (AI) strategies that are inherently fluid, self-correcting, and adaptive at accommodating temporal changes in host defense mechanisms. An in-depth understanding of multiple self-correcting AIassociated viral processes will most certainly lead to novel therapeutic development platforms, notably the design of efficacious neuropharmacological agents to treat chronic CNS syndromes associated with long-COVID. In summary, it appears that viruses, notably SARS-CoV-2, are very much alive due to acquired genetic advantages that are intimately entrained to existential host processes via evolutionarily constrained AI-associated learning paradigms.

Many viruses induce shutoff of host gene expression (host shutoff) as a strategy to take over cellular machinery and evade host immunity. Without host shutoff activity, these viruses generally replicate poorly in vivo, attesting to the importance of this antiviral strategy. In this review, we discuss one particularly advantageous way for viruses to induce host shutoff: triggering widespread host messenger RNA (mRNA) decay. Viruses can trigger increased mRNA destruction either directly, by encoding RNA cleaving or decapping enzymes, or indirectly, by activating cellular RNA degradation pathways. We review what is known about the mechanism of action of several viral RNA degradation factors. We then discuss the consequences of widespread RNA degradation on host gene expression and on the mechanisms of immune evasion, highlighting open questions. Answering these questions is critical to understanding how viral RNA degradation factors regulate host gene expression and how this process helps viruses evade host responses and replicate.

In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.

The currently ongoing outbreak of monkeypox virus in many non-endemic countries around the world has also raised concerns about the safety of plasma-derived medicinal products. Based on what is known about the poxviridae, that is, that members are exceedingly large and carry a lipid envelope, effective removal and inactivation by plasma product manufacturing processes is expected. For the widely used solvent-detergent (S/D) treatments, however, poxviruses have been reported as potentially being a bit more resistant.Using a S/D mixture comprising tri-n-butyl-phosphate, polysorbate 80 and Triton X-100 (TX-100), inactivation of vaccinia virus (a model closely resembling monkeypox virus, both within the same genus, i.e., Orthopoxvirus) in a plasma-derived process intermediate was analyzed over 60 min. As use of Triton X-100 will, based on environmental concerns, be restricted, similar experiments were conducted with a physicochemically virtually identical alternative, Nereid.Fast inactivation of vaccinia virus to the assay detection limit, that is, reduction of infectivity by greater than 4 logAs for other lipid-enveloped viruses, treatment of process intermediates with S/D mixtures containing TX-100 or the closely related detergent Nereid are highly effective in inactivating poxviruses. Thus, the current spread of monkeypox virus does not compromise the viral safety margins of plasma-derived medicines.

Pretransplant respiratory virus infections (RVIs) have been shown to negatively affect hematopoietic cell transplantation (HCT) outcomes. The impact of and need for delay of HCT for pretransplant infection with human rhinovirus (HRV) or endemic human coronavirus (HCoV; 229E, OC43, NL63, and HKU1) remain controversial. We analyzed the impact of symptomatic RVI within ≤90 days before HCT on overall mortality, posttransplant lower respiratory tract disease (LRD), and days alive and out of hospital (DAOH) by day 100 post-HCT in multivariable models. Among 1,643 adult HCT recipients (58% allogeneic recipients), 704 (43%) were tested for RVI before HCT, and 307 (44%) tested positive. HRV was most commonly detected (56%). Forty-five (15%) of 307 HCT recipients had LRD with the same virus early after HCT. Pretransplant upper respiratory tract infection (URI) with influenza, respiratory syncytial virus, adenovirus, human metapneumovirus, parainfluenza virus, HRV, or endemic HCoV was not associated with increased overall mortality or fewer DAOH. However, in allogeneic recipients who received myeloablative conditioning, LRD due to any respiratory virus, including HRV alone, was associated with increased overall mortality (adjusted hazard ratio, 10.8 [95% confidence interval, 3.29-35.1] for HRV and 3.21 [95% confidence interval, 1.15-9.01] for all other viruses). HRV LRD was also associated with fewer DAOH. Thus, the presence of LRD due to common respiratory viruses, including HRV, before myeloablative allogeneic HCT was associated with increased mortality and hospitalization. Pretransplant URI due to HRV and endemic HCoV was not associated with these outcomes. Improved management strategies for pretransplant LRD are warranted.

Treatment with RNAi against HIV-1 transcripts efficiently inhibits viral replication but induces selection of escape mutants; therefore, the CCR5 coreceptor was suggested as an additional target. Blocking viral and host transcripts improved the antiviral effect. We have used short hairpin RNA (shRNA) targeting the human CCR5 (shCCR5) or the HIV-1 rev (shRev) transcripts to demonstrate distinctive properties of anti-CCR5 shRNA: shCCR5 induced more sustained protection than shRev; partial reduction in CCR5 expression substantially decreased HIV-1 infection, and shCCR5 performed better than shRev in the mixed shRNA-treated and untreated cultures. These observations indicate that CCR5 inhibitors should be conveniently included in HIV-1 gene silencing treatment schedules when only a certain cell fraction is protected to further reduce endogenous virus in a properly ART-treated HIV-1 infected individual.

The refractive index (RI) is a fundamental physical property of materials. Although measurement of the RI of biological nanoparticles (BNPs) in aqueous media is of great importance to basic research and biomedical applications, it is hampered by their tiny size, large intrinsic heterogeneity, and weak scattering. Here, we report the development of a label-free technique that can determine the RI of individual viruses and small extracellular vesicles (sEVs) with high precision and an analysis rate up to 10 000 particles per minute. This was achieved via the combination of high-sensitivity light-scattering detection by nanoflow cytometry (nFCM) and the Mie theory calculation. With the measured RIs for T7 virions, T7 capsids, and sEVs, the concentrations of nucleic acid in viral particles and protein in the lumen of sEVs were estimated. Furthermore, building upon a simplified core-shell model, the RIs of sEVs ranging from 40 to 200 nm were obtained. By using these RIs, a statistically robust size distribution of sEVs was acquired in minutes with accuracy and resolution matched closely with those of cryo-TEM measurements. Our approach could become an important tool in the RI determination of single BNPs.

Research on plant–virus–vector interactions has revealed that viruses can enhance their spread to new host plants by attracting nonviruliferous vectors to infected plants or driving viruliferous vectors to noninfected plants. However, whether viruses can also modulate the feeding preference of viruliferous vectors for different plant parts remains largely unknown. Here, by using rice stripe virus (RSV) and its vector, the small brown planthopper (SBPH), as a model, the effect of the virus on the feeding preference of its vector was studied by calculating the number of nonviruliferous and viruliferous SBPHs settling on different parts of rice plants. The results showed that the RSV-free SBPHs significantly preferred feeding on the stems of rice plants, whereas RSV-carrying SBPHs fed more on rice leaves. Moreover, the rice plants inoculated with RSV on the leaves showed more severe symptoms, with enhanced disease incidence and virus accumulation compared with rice plants inoculated at the top and bottom of stems, suggesting that the leaves are more susceptible to RSV than the stems of rice plants. These results demonstrate that RSV modulates the feeding preference of its transmitting vector SBPH from the stems to leaves of rice plants to promote virus infection. Interestingly, we also found that the leaves were more susceptible than the stems to rice black-streaked dwarf virus. This study proves that the feeding preference of insect vectors can be modulated by plant viruses to facilitate virus transmission.

Infections because of chikungunya and other mosquito-borne viruses, such as dengue and Zika, represent an area of significant unmet medical need. There are currently no approved medicines for prophylaxis or treatment of these diseases, and the development and implementation of vaccines against these viruses have proved problematic. Although antiviral molecules with treatment and prophylactic potential against the chikungunya virus have been identified, no successful field trials have been reported. Chemoprophylaxis may be attractive for unvaccinated at-risk populations; however, performing a successful chemoprophylaxis trial during a chikungunya outbreak will require a clearly identifiable at-risk population. We propose the application of a household transmission model as used in testing drugs against respiratory viruses. Current evidence on household clustering of chikungunya and other Aedes mosquito-borne viral infections is supportive. We suggest that this model may improve prophylaxis trial feasibility and focus research and future treatment on a population likely to benefit.

Spodoptera frugiperda is a new invasive pest in Indonesia and its severity in maize ranges from 26.50 to 100%. However, information on the strains or genetic diversity of the S. frugiperda in Indonesia is still very limited. This research aimed to identify the genetic diversity of S. frugiperda from South Sumatra and determine its damage in maize. Surveys from January to June 2021 were carried out from the lowlands to highlands of South Sumatra. The field scouting was performed to calculate the incidence of damage and to estimate the severity caused by S. frugiperda larvae. The severity was assessed using a visual rating scale from 1 (no damage) to 5 (plant stunting and funnel damaged severely). The S. frugiperda larvae was identified based on morphological characters and molecular techniques using sequence analysis of Cytochrome c Oxidase subunit I (COI) gene. All larvae collected from South Sumatra showed identical morphological characteristics identified as S. frugiperda. The sequence analysis results showed that the 6 isolates of S. frugiperda shared 100% of sameness as the rice strain haplotype 1, S. frugiperda isolate from Lampung Province. The other 3 isolates of S. frugiperda shared 100% sameness as the corn strain haplotype I and IS 1 (obtained from sugarcane in Japan). All isolates have been deposited in the GenBank. This study confirmed the presence of rice and corn strains of Spodoptera frugiperda and this is the first report of the occurrence of both strains in South Sumatra. We also found that outbreaks of S. frugiperda have occured in the South Sumatra. The incidence and severity of S. frugiperda reached 100% and 65% respectively. Comprehensive further study should be performed to confirm the presence of both strains and their damage in all corn producing areas in Indonesia.

We established a split nanoluciferase complementation assay to rapidly screen for inhibitors that interfere with binding of the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein with its target receptor, angiotensin-converting enzyme 2 (ACE2). After a screen of 1,200 US Food and Drug Administration (FDA)-approved compounds, we identified bifonazole, an imidazole-based antifungal agent, as a competitive inhibitor of RBD-ACE2 binding. Mechanistically, bifonazole binds ACE2 around residue K353, which prevents association with the RBD, affecting entry and replication of spike-pseudotyped viruses as well as native SARS-CoV-2 and its variants of concern (VOCs). Intranasal administration of bifonazole reduces lethality in K18-hACE2 mice challenged with vesicular stomatitis virus (VSV)-spike by 40%, with a similar benefit after live SARS-CoV-2 challenge. Our screen identified an antiviral agent that is effective against SARS-CoV-2 and VOCs such as Omicron that employ the same receptor to infect cells and therefore has high potential to be repurposed to control, treat, or prevent coronavirus disease 2019 (COVID-19).

Background In this study, the time and path of transmission of H1N1 serotype influenza A viruses in Iran and neighboring countries have been investigated by using Bayesian phylogeography analysis on the sequences extracted from the gene bank. Methods We obtained all hemagglutinin (HA) and neuraminidase (NA) nucleotide sequences of influenza H1N1 available up to December 25, 2020, from Iran and its neighboring countries (i.e., Pakistan, Afghanistan, Turkmenistan, Armenia, Azerbaijan, Turkey, and Iraq). We also performed a Bayesian Markov chain Monte Carlo method to infer the evolutionary dynamic and the most recent common ancestor for the HA and NA sequences. Results Based on the extracted sequences, the age of emergence of H1N1 influenza virus serotype was older in Iran compared to neighboring countries, and Tehran had a key role and epicenter of transmission to other cities within Iran. The mean time of the most recent common ancestor of H1N1 viruses was 1989 (95% HPD: 1980-1994) for HA and NA as well. Conclusions Along with ordinary measures like resource management, diagnostic approaches, and preparedness to fight against viruses that were in place, continuous monitoring, and screening of H1N1 serotype influenza virus in the country, especially by implementation of feasible, effective, and innovative measures at border line should be initiated and identified gaps and shortage that should be a priority for virus control. It is also important for countries to have a regional monitoring program in addition to internal monitoring programs, as well as to start a virus molecular care program.

The production of common bean (Phaseolus vulgaris L.) is adversely affected by virus-like diseases globally, but little is known about the occurrence, distribution, and diversity of common bean-infecting viruses in Zambia. Consequently, field surveys were conducted during the 2018 season in 128 fields across six provinces of Zambia and 640 common bean leaf tissue samples were collected with (n = 585) or without (n = 55) symptoms. The prevalence of symptomatic fields was 100%, but incidence of symptomatic plants ranged from 32 to 67.5%. Metagenomic analyses of nine composite samples and a single plant sample of interest revealed the occurrence of isolates of Bean common mosaic necrosis virus, Bean common mosaic virus, Cowpea aphid-borne mosaic virus, Peanut mottle virus, Southern bean mosaic virus (SBMV), Cucumber mosaic virus, Phaseolus vulgaris alphaendornavirus 1 (PvEV-1), PvEV-2, Ethiopian tobacco bushy top virus (ETBTV), and a novel strain of Cowpea polerovirus 1 (CPPV1-Pv) of 5,902 nt in length. While CPPV1-Pv was consistently detected in mixed infection with ETBTV and its satellite RNA molecule, based on results of mechanical transmission assays it does not appear to be involved in disease etiology, suggesting that its role may be limited to being a helper virus for the umbravirus. Screening of the survey samples by real-time PCR for the viruses detected by high-throughput sequencing revealed the prevalence of single (65.2% or 417/640) over mixed (1.9% or 12/640) infections in the samples. SBMV was the most frequently detected virus, occurring in ∼29.4% (188/640) of the samples and at a prevalence rate of 58.6% (75/128) across fields. The results showed that diverse virus species are present in Zambian common bean fields and the information will be useful for the management of common bean viral diseases.

A 52-year-old woman with HIV and recent antiretroviral therapy non-adherence presented with a 5-day history of widespread painful vesicular skin lesions. Direct fluorescent antibody testing of the skin lesions was positive for varicella zoster virus (VZV). On day 3, she developed profound right upper extremity weakness. MRI of the brain and cervical spine was suggestive of VZV myelitis. Lumbar puncture was positive for VZV PCR in the cerebrospinal fluid (CSF) and CSF HIV viral load was detected at 1030 copies/mL, indicating ‘secondary’ HIV CSF escape. She was treated with intravenous acyclovir for 4 weeks and subsequent oral therapy with famciclovir then valacyclovir for 6 weeks. She also received dexamethasone. The patient had an almost full recovery at 6 months. Myelitis is a rare complication of reactivated VZV infection that can have atypical presentation in immunocompromised patients. Such ‘secondary’ HIV CSF escape should be considered in immunosuppressed patients with concomitant central nervous system infection.

Chikungunya virus (CHIKV) is a mosquito-transmitted pathogen that causes chikungunya disease (CHIK); the disease is characterized by fever, muscle ache, rash, and arthralgia. This arthralgia can be debilitating and long-lasting, seriously impacting quality of life for years. Currently, there is no specific therapy available for CHIKV infection. We have developed a despeciated equine polyclonal antibody (CHIKV-EIG) treatment against CHIKV and evaluated its protective efficacy in mouse models of CHIKV infection. In immunocompromised (IFNAR−/−) mice infected with CHIKV, daily treatment for five consecutive days with CHIKV-EIG administered at 100 mg/kg starting on the day of infection prevented mortality, reduced viremia, and improved clinical condition as measured by body weight loss. These beneficial effects were seen even when treatment was delayed to 1 day after infection. In immunocompetent mice, CHIKV-EIG treatment reduced virus induced arthritis (including footpad swelling), arthralgia-associated cytokines, viremia, and tissue virus loads in a dose-dependent fashion. Collectively, these results suggest that CHIKV-EIG is effective at preventing CHIK and could be a viable candidate for further development as a treatment for human disease.

Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.

Stroke leads to gut bacterial dysbiosis that impacts the post-stroke outcome. The gut microbiome also contains a high abundance of viruses which might play a crucial role in disease progression and recovery by modulating the metabolism of both host and host’s gut bacteria. We presently analyzed the virome composition (viruses and phages) by shotgun metagenomics in the fecal samples obtained at 1 day of reperfusion following transient focal ischemia in adult mice. Viral genomes, viral auxiliary metabolic genes, and viral protein networks were compared between stroke and sham conditions (stroke vs sham, exclusive to sham and exclusive to stroke). Following focal ischemia, abundances of 2 viral taxa decreased, and 5 viral taxa increased compared with the sham. Furthermore, the abundance of Clostridia-like phages and Erysipelatoclostridiaceae-like phages were altered in the stroke compared with the sham cohorts. This is the first report to show that the gut virome responds acutely to stroke.