A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses.

Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of the phylum Nucleocytoviricota. However, they were not classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus Alphacedratvirus, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.

Gene duplication as a major force driving the genome expansion in some giant viruses.

IMPORTANCE: Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.

Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses.

The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.

Analysis of the Genomic Features and Evolutionary History of Pithovirus-Like Isolates Reveals Two Major Divergent Groups of Viruses.

New representatives of the phylum Nucleocytoviricota have been rapidly described in the last decade. Despite this, not all viruses of this phylum are allocated to recognized taxonomic families, as is the case for orpheovirus, pithovirus, and cedratvirus, which form the proposed family Pithoviridae. In this study, we performed comprehensive comparative genomic analyses of 8 pithovirus-like isolates, aiming to understand their common traits and evolutionary history. Structural and functional genome annotation was performed de novo for all the viruses, which served as a reference for pangenome construction. The synteny analysis showed substantial differences in genome organization between these viruses, with very few and short syntenic blocks shared between orpheovirus and its relatives. It was possible to observe an open pangenome with a significant increase in the slope when orpheovirus was added, alongside a decrease in the core genome. Network analysis placed orpheovirus as a distant and major hub with a large fraction of unique clusters of orthologs, indicating a distant relationship between this virus and its relatives, with only a few shared genes. Additionally, phylogenetic analyses of strict core genes shared with other viruses of the phylum reinforced the divergence of orpheovirus from pithoviruses and cedratviruses. Altogether, our results indicate that although pithovirus-like isolates share common features, this group of ovoid-shaped giant viruses presents substantial differences in gene contents, genomic architectures, and the phylogenetic history of several core genes. Our data indicate that orpheovirus is an evolutionarily divergent viral entity, suggesting its allocation to a different viral family, Orpheoviridae. IMPORTANCE Giant viruses that infect amoebae form a monophyletic group named the phylum Nucleocytoviricota. Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established. With advances in isolation techniques, the speed at which new giant viruses are described has increased, escalating the need to establish criteria to define the emerging viral taxa. In this work, we performed a comparative genomic analysis of representatives of the putative family Pithoviridae. Based on the dissimilarity of orpheovirus from the other viruses of this putative family, we propose that orpheovirus be considered a member of an independent family, Orpheoviridae, and suggest criteria to demarcate families consisting of ovoid-shaped giant viruses.

A Brief History of Giant Viruses' Studies in Brazilian Biomes.

Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil.

Functional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates.

Chloroviruses (family Phycodnaviridae) are large double-stranded DNA (dsDNA) viruses that infect unicellular green algae present in inland waters. These viruses have been isolated using three main chlorella-like green algal host cells, traditionally called NC64A, SAG, and Pbi, revealing extensive genetic diversity. In this study, we performed a functional genomic analysis on 36 chloroviruses that infected the three different hosts. Phylogenetic reconstruction based on the DNA polymerase B family gene clustered the chloroviruses into three distinct clades. The viral pan-genome consists of 1,345 clusters of orthologous groups of genes (COGs), with 126 COGs conserved in all viruses. Totals of 368, 268, and 265 COGs are found exclusively in viruses that infect NC64A, SAG, and Pbi algal hosts, respectively. Two-thirds of the COGs have no known function, constituting the "dark pan-genome" of chloroviruses, and further studies focusing on these genes may identify important novelties. The proportions of functionally characterized COGs composing the pan-genome and the core-genome are similar, but those related to transcription and RNA processing, protein metabolism, and virion morphogenesis are at least 4-fold more represented in the core genome. Bipartite network construction evidencing the COG sharing among host-specific viruses identified 270 COGs shared by at least one virus from each of the different host groups. Finally, our results reveal an open pan-genome for chloroviruses and a well-established core genome, indicating that the isolation of new chloroviruses can be a valuable source of genetic discovery. IMPORTANCE Chloroviruses are large dsDNA viruses that infect unicellular green algae distributed worldwide in freshwater environments. They comprise a genetically diverse group of viruses; however, a comprehensive investigation of the genomic evolution of these viruses is still missing. Here, we performed a functional pan-genome analysis comprising 36 chloroviruses associated with three different algal hosts in the family Chlorellaceae, referred to as zoochlorellae because of their endosymbiotic lifestyle. We identified a set of 126 highly conserved genes, most of which are related to essential functions in the viral replicative cycle. Several genes are unique to distinct isolates, resulting in an open pan-genome for chloroviruses. This profile is associated with generalist organisms, and new insights into the evolution and ecology of chloroviruses are presented. Ultimately, our results highlight the potential for genetic diversity in new isolates.

GASTRIC RESIDUAL VOLUME FACTORS AFTER BOWEL PREPARATION WITH MANNITOL EXPRESS.

BACKGROUND: Bowel preparation with mannitol is a well-established method in Brazil. However, factors that interfere with the gastric emptying time period are yet to be known. Knowing these factors may favor the examination scheduling logistics and the individualized orientation for each patient. OBJECTIVE: Know the factors that can contribute to the gastric emptying time after intestinal preparation with express mannitol. METHODS: This is a prospective observational study to know factors that may contribute on the gastric emptying timing: predominant type of diet, comorbidities, medication usage, previous surgeries, number of evacuation per week, bearer of bowel obstipation, fecal type, diet type, number of evacuations after the home usage of bisacodyl before the ingestion of mannitol and number of evacuations after the ingestion of mannitol until reaching a proper bowel preparation. Before starting the colonoscopy exam, an upper digestive endoscopy exam was made to aspirate the gastric content. RESULTS: Sample was composed of 103 patients, 55 (53.4%) women, medium age 61 (±12.1) years, medium weight 75.3 (±14.1) kg, medium height 1.7 (±10) m and medium BMI of 26.6 (±3.9) kg/m2. Average gastric residual volume was 120.9 (0-900) mL. Gastric residual volume (GRV) below 100 mL (GRV ≤100 mL) occurred in 45 (43.6%) patients, 24 (53.3%) women, medium age of 61.0 years and medium BMI of 26.7 kg/m2. Gastric residual volume above 100 mL (GRV >100 mL) occurred on 58 (56.3%) patients, 29 (50%) women, medium age of 61.0 years and medium BMI of 26.2 kg/m2. Comparing both groups, average fasting time period after the ingestion of mannitol was significantly higher on the group with GRV ≤100 mL than group with GRV >100 mL, 123.1 (60-246) vs 95.3 (55-195) minutes, respectively. There was also statistical significance concerning the usage of ezetimibe 6 (13.7%) in the group with GRV ≤100 mL and statistical significance in the group with GRV >100 mL concerning the usage of paroxetine 3 (6.7%) and tadalafil 3 (6.7%) and surgical history of prostatectomy 3 (6.7%) and bridle withdrawal 3 (6.7%). CONCLUSION: We may conclude in this study that the usage of ezetimibe and fasting above 2 hours after the ingestion of mannitol decrease significantly the incidence of a GRV >100 mL. The usage of paroxetine, tadalafil and surgical history of prostatectomy or bridle withdrawal may contribute to increase de incidence of a GRV >100 mL.

Fatores predisponentes do volume residual gástrico após preparo expresso com manitol / Gastric residual volume factors after bowel preparation with mannitol express

ABSTRACT BACKGROUND: Bowel preparation with mannitol is a well-established method in Brazil. However, factors that interfere with the gastric emptying time period are yet to be known. Knowing these factors may favor the examination scheduling logistics and the individualized orientation for each patient. OBJECTIVE: Know the factors that can contribute to the gastric emptying time after intestinal preparation with express mannitol. METHODS: This is a prospective observational study to know factors that may contribute on the gastric emptying timing: predominant type of diet, comorbidities, medication usage, previous surgeries, number of evacuation per week, bearer of bowel obstipation, fecal type, diet type, number of evacuations after the home usage of bisacodyl before the ingestion of mannitol and number of evacuations after the ingestion of mannitol until reaching a proper bowel preparation. Before starting the colonoscopy exam, an upper digestive endoscopy exam was made to aspirate the gastric content. RESULTS: Sample was composed of 103 patients, 55 (53.4%) women, medium age 61 (±12.1) years, medium weight 75.3 (±14.1) kg, medium height 1.7 (±10) m and medium BMI of 26.6 (±3.9) kg/m2. Average gastric residual volume was 120.9 (0-900) mL. Gastric residual volume (GRV) below 100 mL (GRV ≤100 mL) occurred in 45 (43.6%) patients, 24 (53.3%) women, medium age of 61.0 years and medium BMI of 26.7 kg/m2. Gastric residual volume above 100 mL (GRV >100 mL) occurred on 58 (56.3%) patients, 29 (50%) women, medium age of 61.0 years and medium BMI of 26.2 kg/m2. Comparing both groups, average fasting time period after the ingestion of mannitol was significantly higher on the group with GRV ≤100 mL than group with GRV >100 mL, 123.1 (60-246) vs 95.3 (55-195) minutes, respectively. There was also statistical significance concerning the usage of ezetimibe 6 (13.7%) in the group with GRV ≤100 mL and statistical significance in the group with GRV >100 mL concerning the usage of paroxetine 3 (6.7%) and tadalafil 3 (6.7%) and surgical history of prostatectomy 3 (6.7%) and bridle withdrawal 3 (6.7%). CONCLUSION: We may conclude in this study that the usage of ezetimibe and fasting above 2 hours after the ingestion of mannitol decrease significantly the incidence of a GRV >100 mL. The usage of paroxetine, tadalafil and surgical history of prostatectomy or bridle withdrawal may contribute to increase de incidence of a GRV >100 mL.

RESUMO CONTEXTO: O preparo intestinal com manitol é um método bem estabelecido no Brasil. No entanto, os fatores que interferem no tempo de esvaziamento gástrico ainda não são conhecidos. O conhecimento desses fatores pode favorecer a logística de agendamento do exame e a orientação individualizada para cada paciente. OBJETIVO: Estudar os fatores que podem contribuir para o tempo de esvaziamento gástrico após o preparo intestinal com manitol expresso. MÉTODOS: Trata-se de um estudo observacional prospectivo com o objetivo de conhecer os seguintes fatores que podem contribuir no tempo de esvaziamento gástrico: tipo de dieta predominante, comorbidades, uso de medicamentos, cirurgias anteriores, número de evacuações por semana, portador de obstipação intestinal, tipo fecal, tipo de dieta, número de evacuações após o uso domiciliar de bisacodil antes da ingestão de manitol e número de evacuações após a ingestão de manitol até atingir o preparo intestinal adequado. Antes de iniciar o preparo intestinal, os pacientes responderam a um questionário clínico. O endoscópio foi introduzido para aspirar o conteúdo gástrico, antes de iniciar a colonoscopia. RESULTADOS: A amostra foi composta por 103 pacientes, sendo 55 mulheres, com média de idade de 61 anos, peso médio de 75,3 kg, altura média de 1,7 m e IMC médio de 26,6 kg/m2. O volume residual gástrico médio medido foi 120,9 (0-900) mL. Volume residual gástrico inferior a 100 mL (VRG ≤100 mL) foi encontrado em 45 (43,6%) pacientes, sendo 24 (53,3%) mulheres, com média de idade de 61,0 anos e IMC médio de 26,7 kg/m2. Volume residual gástrico acima de 100 mL (VRG >100 mL) ocorreu em 58 (56,3%) pacientes, sendo 29 (50%) mulheres, com idade média de 61,0 anos e IMC médio de 26,2 kg/m2. Comparando os dois grupos, notou-se que o tempo médio de jejum após a ingestão de manitol foi significativamente maior no grupo com VRG ≤100 mL do que no grupo com VRG> 100 mL, 123,1 (60-246) vs 95,3 (55-195) minutos, respectivamente. Também houve significância estatística em relação ao uso de ezetimiba 6 (13,7%), sendo maior no grupo com VRG ≤100 mL. Além disso, houve significância estatística no grupo com VRG >100 mL quanto ao uso de paroxetina 3 (6,7%) e tadalafil 3 (6,7%) e história cirúrgica de prostatectomia 3 (6,7%) e retirada de bridas 3 (6,7%). CONCLUSÃO: Podemos concluir neste estudo que o uso de ezetimiba e o jejum acima de 2 horas após a ingestão de manitol diminuem significativamente a incidência de um VRG> 100 mL. O uso de paroxetina, tadalafil e história cirúrgica de prostatectomia ou retirada de bridas podem contribuir para o aumento da incidência de um VRG >100 mL.

Ubiquitous giants: a plethora of giant viruses found in Brazil and Antarctica.

BACKGROUND: Since the discovery of giant viruses infecting amoebae in 2003, many dogmas of virology have been revised and the search for these viruses has been intensified. Over the last few years, several new groups of these viruses have been discovered in various types of samples and environments.In this work, we describe the isolation of 68 giant viruses of amoeba obtained from environmental samples from Brazil and Antarctica. METHODS: Isolated viruses were identified by hemacolor staining, PCR assays and electron microscopy (scanning and/or transmission). RESULTS: A total of 64 viruses belonging to the Mimiviridae family were isolated (26 from lineage A, 13 from lineage B, 2 from lineage C and 23 from unidentified lineages) from different types of samples, including marine water from Antarctica, thus being the first mimiviruses isolated in this extreme environment to date. Furthermore, a marseillevirus was isolated from sewage samples along with two pandoraviruses and a cedratvirus (the third to be isolated in the world so far). CONCLUSIONS: Considering the different type of samples, we found a higher number of viral groups in sewage samples. Our results reinforce the importance of prospective studies in different environmental samples, therefore improving our comprehension about the circulation anddiversity of these viruses in nature.

An Anthropocentric View of the Virosphere-Host Relationship.

For over a century, viruses have been known as the most abundant and diverse group of organisms on Earth, forming a virosphere. Based on extensive meta-analyses, we present, for the first time, a wide and complete overview of virus-host network, covering all known viral species. Our data indicate that most of known viral species, regardless of their genomic category, have an intriguingly narrow host range, infecting only 1 or 2 host species. Our data also show that the known virosphere has expanded based on viruses of human interest, related to economical, medical or biotechnological activities. In addition, we provide an overview of the distribution of viruses on different environments on Earth, based on meta-analyses of available metaviromic data, showing the contrasting ubiquity of head-tailed phages against the specificity of some viral groups in certain environments. Finally, we uncovered all human viral species, exploring their diversity and the most affected organic systems. The virus-host network presented here shows an anthropocentric view of the virology. It is therefore clear that a huge effort and change in perspective is necessary to see more than the tip of the iceberg when it comes to virology.

Antidiarrheal activity of extracts from Maytenus gonoclada and inhibition of Dengue virus by lupeol.

Diarrhea is an infectious disease caused by bacterial, virus, or protozoan, and dengue is caused by virus, included among the neglected diseases in several underdeveloped and developing countries, with an urgent demand for new drugs. Considering the antidiarrheal potential of species of Maytenus genus, a phytochemical investigation followed by antibacterial activity test with extracts of branches and heartwood and bark of roots from Maytenus gonoclada were conducted. Moreover, due the frequency of isolation of lupeol from Maytenus genus the antiviral activity against Dengue virus and cytotoxicity of lupeol and its complex with ß-cyclodextrins were also tested. The results indicated the bioactivity of ethyl acetate extract from branches and ethanol extract from heartwood of roots of M. gonoclada against diarrheagenic bacteria. The lupeol showed potent activity against Dengue virus and low cytotoxicity in LLC-MK2 cells, but its complex with ß-cyclodextrin was inactive. Considering the importance of novel and selective antiviral drug candidates the results seem to be promising.

Antidiarrheal activity of extracts from Maytenus gonoclada and inhibition of Dengue virus by lupeol

ABSTRACT Diarrhea is an infectious disease caused by bacterial, virus, or protozoan, and dengue is caused by virus, included among the neglected diseases in several underdeveloped and developing countries, with an urgent demand for new drugs. Considering the antidiarrheal potential of species of Maytenus genus, a phytochemical investigation followed by antibacterial activity test with extracts of branches and heartwood and bark of roots from Maytenus gonoclada were conducted. Moreover, due the frequency of isolation of lupeol from Maytenus genus the antiviral activity against Dengue virus and cytotoxicity of lupeol and its complex with β-cyclodextrins were also tested. The results indicated the bioactivity of ethyl acetate extract from branches and ethanol extract from heartwood of roots of M. gonoclada against diarrheagenic bacteria. The lupeol showed potent activity against Dengue virus and low cytotoxicity in LLC-MK2 cells, but its complex with β-cyclodextrin was inactive. Considering the importance of novel and selective antiviral drug candidates the results seem to be promising.

Subcutaneous Emphysema, Pneumothorax and Pneumomediastinum Following Endoscopic Sphincterotomy.

Retroperitoneal perforation during therapeutic endoscopic retrograde cholangiopancreatography (ERCP) is uncommon and is usually manifested by abdominal pain, fever and leukocytosis. We report the case of a patient with post-ERCP subcutaneous emphysema, pneumomediastinum and pneumothorax treated conservatively. A 79-year-old woman with a diagnosis of choledocholitiasis was referred to our institution for an elective outpatient therapeutic ERCP. At the end of the procedure, subcutaneous emphysema was observed, and a thoracic computed tomography revealed a right pneumothorax and pneumomediastinum. Supportive care was instituted and she was discharged asymptomatic after 10 days of hospitalization. Subcutaneous emphysema, pneumothorax and pneumomediastinum are potencial complications of ERCP and sphincterotomy. We review the other cases previously reported and discuss the management.