ViralZone 2024 provides higher-resolution images and advanced virus-specific resources.

ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses.

Virus replication in the honey bee parasite, Varroa destructor.

IMPORTANCE: The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.

Stem cells hint at how bats live with viruses.

Research team hits on formula to create stem cells from tissue of adult bats.

Vírus e fissuras orofaciais: um histórico isolado e de associação / Viruses and orofacial clefts: an isolated and associational history / Virus y fisuras orofaciales: una historia aislada y asociativa

Os vírus são microrganismos comumente associados as doenças e infectam todos os seres vivos. Atuam de forma direta e indireta levando a pressão seletiva, com papel significativo e ainda em exploração no planeta. As fissuras orofaciais são anomalias congênitas de etiologia complexa e multifatorial, sendo as infecções virais durante a gestação um dos possíveis fatores etiológicos. A história da humanidade frente aos vírus e fissuras orofaciais de forma isolada é vasta, remontando a períodos antes de Cristo, seja por meio de leis para o controle de pragas e/ou por lendas de míticas criaturas deificadas e/ou demonizadas, cuja criação está fundamentada na Teoria Alegórica do surgimento das mitologias, demonstrando assim o interesse do ser humano e sua curiosidade em inovação e explicação destes assuntos. Considerando a relevância histórica, bem como a possível relação etiológica destes dois elementos, uma revisão da literatura foi realizada para apresentar a história mitológica e científica dos vírus e fissuras orofaciais, de forma isolada e associadas para fins de comparação. Para isso, foram utilizadas as bases PubMed/Medline, SciElo, LILACS e Portal Periódicos (CAPES) com os descritores: Virus, Anomalias/Anomalies, Virus and Anomalias/Virus and Anomalies, A History of viruses/História dos vírus, Virus and History/História and Virus, Virus and Myth/Virus and Mito, Anomalias and Mitos/Anomalies and Myths, Vampires and Virus/Vampiros and Virus. Enquanto o histórico mitológico é cheio de teorias contraditórias, o histórico cientifico acadêmico se revela coerente, porém resistente as novas áreas de atuação, não ponderando novas possibilidades e limitando a exploração científica, que só pôde ser alcançada nos séculos atuais. Quanto a associação, a linha de pesquisa relacionando vírus e fissuras orofaciais não possui nem meio século de existência, propiciando um grande campo a ser explorado e na mesma medida limitando os benefícios em prevenção que poderiam ser obtidos através destes estudos.

Viruses are microorganisms commonly associated with diseases that infect all living beings, they act directly and indirectly leading to selective pressure, their role on the planet is significant and still under exploration. Orofacial clefts are congenital anomalies that have a complex multifactorial etiology, with viral infections during pregnancy being one of the possible etiological factors. The history of humanity in the face of viruses and orofacial clefts in isolation is vast, dating back to periods before Christ, whether through laws for pest control and/or legends of mythical deified and/or demonized creatures, whose creation is fundamentalized in the Allegorical Theory of the emergence of mythologies, thus demonstrating the interest of human beings and their curiosity in innovation and explanation of these subjects. Considering the historical relevance, as well as the possible etiology relationship of these two elements, we carried out a literature review to present the mythological and scientific history of viruses and orofacial clefts, isolated and associated for comparison purposes. For this intent, the bases PubMed/Medline, SciElo, LILACS and Portal Periódicos (CAPES) were selected with the descriptors: A History of viruses/História dos vírus, Virus and History/História and Virus, Virus and Myth/Virus and Mito, Anomalias and Mitos/Anomalies and Myths, Vampires and Virus/Vampiros and Virus. While the mythological history is full of contradictory theories, the academic, scientific history proves to be consistent, but resistant to new areas of action, not considering new possibilities and limiting scientific exploration, which can only be achieved in the present centuries. As for the association, the line of research relating viruses and orofacial clefts does not even have half a century of existence, providing a large field to be explored and at the same time limiting the benefits of prevention that could be obtained through these studies.

Los virus son microorganismos comúnmente asociados a enfermedades que infectan a todos los seres vivos, actúan directa e indirectamente provocando presión selectiva, su papel en el planeta es significativo y aún en exploración. Las hendiduras orofaciales son anomalías congénitas que tienen una compleja etiología multifactorial, siendo las infecciones virales durante el embarazo uno de los posibles factores etiológicos. La historia de la humanidad frente a los virus y las hendiduras orofaciales de forma aislada es vasta, remontándose a períodos anteriores a Cristo, ya sea a través de leyes para el control de plagas y/o leyendas de criaturas míticas deificadas y/o demonizadas, cuya creación se fundamentaliza en la Teoría Alegórica del surgimiento de las mitologías, demostrando así el interés del ser humano y su curiosidad en la innovación y explicación de estos temas. Considerando la relevancia histórica, así como la posible relación etiológica de estos dos elementos, realizamos una revisión bibliográfica para presentar la historia mitológica y científica de los virus y las hendiduras orofaciales, aislados y asociados para fines de comparación. Para ello, se seleccionaron las bases PubMed/Medline, SciElo, LILACS y Portal Periódicos (CAPES) con los descriptores: A History of viruses/História dos vírus, Virus and History/História and Virus, Virus and Myth/Virus and Mito, Anomalias and Mitos/Anomalías y Mitos, Vampiros and Virus/Vampiros y Virus. Mientras que la historia mitológica está llena de teorías contradictorias, la historia académica, científica, se muestra coherente, pero resistente a nuevos campos de actuación, no considerando nuevas posibilidades y limitando la exploración científica, que sólo puede alcanzarse en los siglos actuales. En cuanto a la asociación, la línea de investigación que relaciona virus y hendiduras orofaciales no tiene ni medio siglo de existencia, proporcionando un gran campo a ser explorado y al mismo tiempo limitando los beneficios de prevención que podrían ser obtenidos a través de estos estudios.

Enteric viruses replicate in salivary glands and infect through saliva.

Enteric viruses like norovirus, rotavirus and astrovirus have long been accepted as spreading in the population through fecal-oral transmission: viruses are shed into feces from one host and enter the oral cavity of another, bypassing salivary glands (SGs) and reaching the intestines to replicate, be shed in feces and repeat the transmission cycle1. Yet there are viruses (for example, rabies) that infect the SGs2,3, making the oral cavity one site of replication and saliva one conduit of transmission. Here we report that enteric viruses productively and persistently infect SGs, reaching titres comparable to those in the intestines. We demonstrate that enteric viruses get released into the saliva, identifying a second route of viral transmission. This is particularly significant for infected infants, whose saliva directly transmits enteric viruses to their mothers' mammary glands through backflow during suckling. This sidesteps the conventional gut-mammary axis route4 and leads to a rapid surge in maternal milk secretory IgA antibodies5,6. Lastly, we show that SG-derived spheroids7 and cell lines8 can replicate and propagate enteric viruses, generating a scalable and manageable system of production. Collectively, our research uncovers a new transmission route for enteric viruses with implications for therapeutics, diagnostics and importantly sanitation measures to prevent spread through saliva.

Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau.

Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.

Perspective on taxonomic classification of uncultivated viruses.

Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.

PDIA3: Structure, functions and its potential role in viral infections.

The catalysis of disulphide (SS) bonds is the most important characteristic of protein disulphide isomerase (PDI) family. Catalysis occurs in the endoplasmic reticulum, which contains many proteins, most of which are secretory in nature and that have at least one s-s bond. Protein disulphide isomerase A3 (PDIA3) is a member of the PDI family that acts as a chaperone. PDIA3 is highly expressed in response to cellular stress, and also intercept the apoptotic cellular death related to endoplasmic reticulum (ER) stress, and protein misfolding. PDIA3 expression is elevated in almost 70% of cancers and its expression has been linked with overall low cell invasiveness, survival and metastasis. Viral diseases present a significant public health threat. The presence of PDIA3 on the cell surface helps different viruses to enter the cells and also helps in replication. Therefore, inhibitors of PDIA3 have great potential to interfere with viral infections. In this review, we summarize what is known about the basic structure, functions and role of PDIA3 in viral infections. The review will inspire studies of pathogenic mechanisms and drug targeting to counter viral diseases.

Ethanol Susceptibility of SARS-CoV-2 and Other Enveloped Viruses.

Ethanol is an effective disinfectant against the novel coronavirus SARS-CoV-2. However, its effective concentration has not been shown, and we therefore analyzed the effects of different concentrations of ethanol on SARS-CoV-2. When SARS-CoV-2 was treated with varying ethanol concentrations and examined for changes in infectivity, the ethanol concentration at which 99% of the infectious titers were reduced was 24.1% (w/w) [29.3% (v/v)]. For reference, ethanol susceptibility was also examined with other envelope viruses, including influenza virus, vesicular stomatitis virus in the family Rhabdoviridae, and Newcastle disease virus in the family Paramyxoviridae, and the 99% inhibitory concentrations were found to be 28.8%(w/w) [34.8% (v/v)], 24.0% (w/w) [29.2% (v/v)], and 13.3% (w/w) [16.4% (v/v)], respectively. Some differences from SARS-CoV-2 were observed, but the differences were not significant. It was concluded that ethanol at a concentration of 30%(w/w) [36.2% (v/v)] almost completely inactivates SARS-CoV-2.

Sphingolipids: Effectors and Achilles Heals in Viral Infections?

As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.

Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways.

APOBEC3A is a cytidine deaminase driving mutagenesis in tumors. While APOBEC3A-induced mutations are common, APOBEC3A expression is rarely detected in cancer cells. This discrepancy suggests a tightly controlled process to regulate episodic APOBEC3A expression in tumors. In this study, we find that both viral infection and genotoxic stress transiently up-regulate APOBEC3A and pro-inflammatory genes using two distinct mechanisms. First, we demonstrate that STAT2 promotes APOBEC3A expression in response to foreign nucleic acid via a RIG-I, MAVS, IRF3, and IFN-mediated signaling pathway. Second, we show that DNA damage and DNA replication stress trigger a NF-κB (p65/IkBα)-dependent response to induce expression of APOBEC3A and other innate immune genes, independently of DNA or RNA sensing pattern recognition receptors and the IFN-signaling response. These results not only reveal the mechanisms by which tumors could episodically up-regulate APOBEC3A but also highlight an alternative route to stimulate the immune response after DNA damage independently of cGAS/STING or RIG-I/MAVS.

Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.

BACKGROUND & AIMS: The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS: We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS: We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS: We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.

A two-transcript biomarker of host classifier genes for discrimination of bacterial from viral infection in acute febrile illness: a multicentre discovery and validation study.

BACKGROUND: Acute febrile illness is one of the main reasons for outpatient hospital visits worldwide. However, differential diagnosis between bacterial and viral causes is challenging and misdiagnosis can result in antimicrobial overuse and hinder prompt treatment. We aimed to build and validate a diagnostic model to discriminate bacterial from viral infection in acute febrile illness by evaluating the expression of potential classifier host genes. METHODS: In this multicentre discovery and validation study, we included patients aged 14-85 years with acute febrile illness (fever for ≤14 days, axillary temperature of ≥38°C, and confirmed bacterial infection, viral infection, or non-infectious inflammatory disease), and healthy control participants (no significant medical history and no fever within the past 90 days) from four hospitals in Shandong province, China. Patients from the first hospital were divided into the screening, discovery, and internal validation groups, and patients from the three other hospitals comprised the external validation group. We measured expression of candidate genes in peripheral blood by RT-PCR, and patients for whom a successful RT-PCT result was recorded were included in the next-step analysis. For patients from the first hospital, those enrolled during the early phase of the study were assigned to the screening group, which was used to identify the optimal transcripts (IFI44L and PI3) for discrimination between bacterial and viral infections by screening four candidate genes (FAM89A, IFI44L, PI3, and ITGB2) by RT-PCR. The remaining patients were then randomly assigned (1:1) to discovery and internal validation groups by time of admission and blood drawing via the equidistant random sampling method. A logistic regression model integrating the mRNA levels of IFI44L and PI3 was built by use of the discovery group, and the diagnostic performance of the model was evaluated in the internal and external validation groups using area under the receiver operating curve (AUC), sensitivity, and specificity. FINDINGS: Between March 1, 2018, and Aug 31, 2019, we assessed 1658 individuals for inclusion in the study. After exclusion of ineligible participants, 458 participants were enrolled (178 patients with acute febrile illness caused by bacterial infection, 212 with acute febrile illness caused by viral infection, 38 with non-infectious inflammatory diseases, and 30 healthy controls). The 390 patients with bacterial or viral infections were assigned to one of four groups: screening (n=64, 33 with bacterial infections and 31 with viral infections), discovery (n=124, 55 with bacterial infections and 69 with viral infections), internal validation (n=124, 55 with bacterial infections and 69 with viral infections), and external validation (n=78, 35 with bacterial infections and 43 with viral infections). Of the four candidate host genes (FAM89A, IFI44L, PI3, and ITGB2), IFI44L and PI3 showed the most discriminative expression pattern and were used to build the logistic regression model. We established the optimal cutoff of the bacterial infection likelihood score to be 0·547598. With the diagnostic result from the gold standard tests (culture and PCR) as the reference, the two-transcript classifier model had an AUC of 0·969 (95% CI 0·937-1·000), sensitivity of 0·891 (0·782-0·949), and specificity of 0·971 (0·900-0·992) to discriminate bacterial and viral infections in the internal validation group. The model showed similar results in the external validation group (AUC 0·986, 95% CI 0·968-1·000; sensitivity 0·857, 0·706-0·937; and specificity 0·954, 0·845-0·987). INTERPRETATION: IFI44L and PI3 transcripts, measured by RT-PCR, are robust classifiers to discriminate bacterial from viral infection in acute febrile illness. This two-transcript biomarker has the potential to be transformed into a commercial panel and applied universally. FUNDING: None.

Variantes de vírus são esperadas, mas vigilância deve continuar monitorando possíveis mudanças nos padrões clínicos, dizem especialistas

Nas Américas, uma rede de laboratórios de 22 países contribui para a detecção de variantes do SARS-CoV-2. Até agora, 37 países e territórios confirmaram a presença de uma ou mais das quatro variantes de preocupação. Monitorá-las é a chave para detectar quaisquer mudanças incomuns ou inesperadas que possam afetar as medidas de controle, incluindo as vacinas

The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.

The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.

Using the near field optical trapping effect of a dielectric metasurface to improve SERS enhancement for virus detection.

In this paper, we report the effect of optical trapping on the enhancement factor for Raman spectroscopy, using a dielectric metasurface. It was found that a higher enhancement factor (up to 275%) can be obtained in a substrate immersed in water, where particles are freee to move, compared to a dried substrate, where the particles (radius [Formula: see text] nm, refractive index [Formula: see text]) are fixed on the surface. The highest enhancement is obtained at low concentrations because, this case, the particles are trapped preferentially in the regions of highest electric field (hotspots). For high concentrations, it was observed that the hotspots become saturated with particles and that additional particles are forced to occupy regions of lower field. The dielectric metasurface offers low optical absorption compared to conventional gold substrates. This aspect can be important for temperature-sensitive applications. The method shows potential for applications in crystal nucleation, where high solute supersaturation can be achieved near the high-field regions of the metasurface. The high sensitivity for SERS (surface-enhanced Raman spectroscopy) at low analyte concentrations makes the proposed method highly promising for detection of small biological particles, such as proteins or viruses.

The antiviral immunity of ticks against transmitted viral pathogens.

Ticks, being obligate hematophagous arthropods, are exposed to various blood-borne pathogens, including arboviruses. Consequently, their feeding behavior can readily transmit economically important viral pathogens to humans and animals. With this tightly knit vector and pathogen interaction, the replication and transmission of tick-borne viruses (TBVs) must be highly regulated by their respective tick vectors to avoid any adverse effect on the ticks' biological development and viability. Knowledge about the tick-virus interface, although gaining relevant advances in recent years, is advancing at a slower pace than the scientific developments related to mosquito-virus interactions. The unique and complicated feeding behavior of ticks, compared to that of other blood-feeding arthropods, also limits the studies that would further elaborate the antiviral immunity of ticks against TBVs. Hence, knowledge of molecular and cellular immune mechanisms at the tick-virus interface, will further elucidate the successful viral replication of TBVs in ticks and their effective transmission to human and animal hosts.

The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity.

RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the 'knowns' and 'unknowns' regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses.