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1.
Sci Rep ; 11(1): 17422, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465838

RESUMO

The SARS-CoV-2 pandemic has raised concerns in the identification of the hosts of the virus since the early stages of the outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting viral genomic features automatically, to predict the host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool, reaching a satisfactory AUC of 0.975 in the five-classification, and could make a reliable prediction for the novel viruses without close neighbors in phylogeny. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existing tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of the COVID-19 pandemic, we inferred that minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, a large-scale genome analysis, based on DeepHoF's computation for the later pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.


Assuntos
COVID-19/virologia , Gatos/virologia , Quirópteros/virologia , Cães/virologia , Vison/virologia , SARS-CoV-2/classificação , Algoritmos , Animais , COVID-19/transmissão , Aprendizado Profundo , Especificidade de Hospedeiro , Humanos , RNA Viral/genética , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Análise de Sequência de RNA
2.
Arch Virol ; 166(10): 2887-2894, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34347170

RESUMO

The complete genome sequence of the virulent bacteriophage PMBT3, isolated on the proteolytic Pseudomonas grimontii strain MBTL2-21, showed no significant similarity to other known phage genome sequences, making this phage the first reported to infect a strain of P. grimontii. Electron microscopy revealed PMBT3 to be a member of the family Siphoviridae, with notably long and flexible whiskers. The linear, double-stranded genome of 87,196 bp has a mol% G+C content of 60.4 and contains 116 predicted protein-encoding genes. A putative tellurite resistance (terB) gene, originally reported to occur in the genome of a bacterium, was detected in the genome of phage PMBT3.


Assuntos
Pseudomonas/virologia , Animais , Bacteriólise , Composição de Bases , Sequência de Bases , DNA Viral/genética , Genoma Viral/genética , Especificidade de Hospedeiro , Leite/microbiologia , Filogenia , Fagos de Pseudomonas/classificação , Fagos de Pseudomonas/genética , Fagos de Pseudomonas/fisiologia , Fagos de Pseudomonas/ultraestrutura , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/fisiologia , Siphoviridae/ultraestrutura , Proteínas Virais/genética , Vírion/ultraestrutura
3.
Viruses ; 13(7)2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34372554

RESUMO

Urinary tract infections (UTIs) are among the events that most frequently need medical intervention. Uropathogenic Escherichia coli are frequently their causative agents and the infections are sometimes complicated by the presence of polyresistant nosocomial strains. Phage therapy is a tool that has good prospects for the treatment of these infections. In the present study, we isolated and characterized two bacteriophages with broad host specificity against a panel of local uropathogenic E. coli strains and combined them into a phage cocktail. According to genome sequencing, these phages were closely related and belonged to the Tequatrovirus genus. The newly isolated phages showed very good activity on a panel of local clinical E. coli strains from urinary tract infections. In the form of a two-phage cocktail, they were active on E. coli strains belonging to phylogroups B2 and D, with relatively lower activity in B1 and no response in phylogroup A. Our study is a preliminary step toward the establishment of a national phage bank containing local, well-characterized phages with therapeutic potential for patients in Slovakia.


Assuntos
Myoviridae/genética , Terapia por Fagos/métodos , Escherichia coli Uropatogênica/genética , Antibacterianos/farmacologia , Bacteriófagos/genética , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/terapia , Especificidade de Hospedeiro/genética , Humanos , Eslováquia , Infecções Urinárias/microbiologia , Infecções Urinárias/terapia , Escherichia coli Uropatogênica/efeitos dos fármacos , Escherichia coli Uropatogênica/isolamento & purificação , Fatores de Virulência/genética
4.
Arch Virol ; 166(10): 2789-2801, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34370094

RESUMO

Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.


Assuntos
Genoma Viral/genética , Especificidade de Hospedeiro/genética , Nepovirus/genética , Evolução Molecular , Variação Genética , Metagenômica , Nepovirus/classificação , Fases de Leitura Aberta/genética , Filogenia , Filogeografia , Plantas/classificação , Plantas/virologia , RNA Viral/genética , Recombinação Genética
5.
Adv Virus Res ; 110: 59-102, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34353482

RESUMO

Within only one year after the first detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), nearly 100 million infections were reported in the human population globally, with more than two million fatal cases. While SARS-CoV-2 most likely originated from a natural wildlife reservoir, neither the immediate viral precursor nor the reservoir or intermediate hosts have been identified conclusively. Due to its zoonotic origin, SARS-CoV-2 may also be relevant to animals. Thus, to evaluate the host range of the virus and to assess the risk to act as potential animal reservoir, a large number of different animal species were experimentally infected with SARS-CoV-2 or monitored in the field in the last months. In this review, we provide an update on studies describing permissive and resistant animal species. Using a scoring system based on viral genome detection subsequent to SARS-CoV-2 inoculation, seroconversion, the development of clinical signs and transmission to conspecifics or humans, the susceptibility of diverse animal species was classified on a semi-quantitative scale. While major livestock species such as pigs, cattle and poultry are mostly resistant, companion animals appear moderately susceptible, while several model animal species used in research, including several Cricetidae species and non-human primates, are highly susceptible to SARS-CoV-2 infection. By natural infections, it became obvious that American minks (Neovison vison) in fur farms, e.g., in the Netherlands and Denmark are highly susceptible resulting in local epidemics in these animals.


Assuntos
COVID-19/veterinária , SARS-CoV-2/fisiologia , Animais , Animais Selvagens/virologia , COVID-19/diagnóstico , COVID-19/transmissão , COVID-19/virologia , Reservatórios de Doenças/veterinária , Reservatórios de Doenças/virologia , Suscetibilidade a Doenças/diagnóstico , Suscetibilidade a Doenças/veterinária , Suscetibilidade a Doenças/virologia , Especificidade de Hospedeiro , Gado/virologia , Modelos Animais , Animais de Estimação/virologia , SARS-CoV-2/isolamento & purificação
6.
Viruses ; 13(7)2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34372577

RESUMO

A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.


Assuntos
Bacteriófagos/genética , Enterobacter cloacae/genética , Enterobacter cloacae/virologia , DNA Viral/genética , Enterobacter cloacae/metabolismo , Genoma Viral/genética , Genômica , Especificidade de Hospedeiro , Filogenia , Proteômica , Siphoviridae/genética , Proteínas Virais/genética , Vírion/metabolismo
7.
J Gen Virol ; 102(8)2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34356002

RESUMO

The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6-9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.


Assuntos
Genoma Viral , Filogenia , Vírus de RNA/classificação , Vírus de RNA/genética , Animais , Proteínas do Capsídeo , Eucariotos , Especificidade de Hospedeiro , Hidrobiologia , Metagenômica , Infecções por Vírus de RNA/virologia , Vírus de RNA/ultraestrutura , RNA Viral , Vírion/classificação , Vírion/genética , Vírion/ultraestrutura , Replicação Viral
8.
PLoS Pathog ; 17(7): e1009381, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34197564

RESUMO

Clearance of viral infections, such as SARS-CoV-2 and influenza A virus (IAV), must be fine-tuned to eliminate the pathogen without causing immunopathology. As such, an aggressive initial innate immune response favors the host in contrast to a detrimental prolonged inflammation. The complement pathway bridges innate and adaptive immune system and contributes to the response by directly clearing pathogens or infected cells, as well as recruiting proinflammatory immune cells and regulating inflammation. However, the impact of modulating complement activation in viral infections is still unclear. In this work, we targeted the complement decay-accelerating factor (DAF/CD55), a surface protein that protects cells from non-specific complement attack, and analyzed its role in IAV infections. We found that DAF modulates IAV infection in vivo, via an interplay with the antigenic viral proteins hemagglutinin (HA) and neuraminidase (NA), in a strain specific manner. Our results reveal that, contrary to what could be expected, DAF potentiates complement activation, increasing the recruitment of neutrophils, monocytes and T cells. We also show that viral NA acts on the heavily sialylated DAF and propose that the NA-dependent DAF removal of sialic acids exacerbates complement activation, leading to lung immunopathology. Remarkably, this mechanism has no impact on viral loads, but rather on the host resilience to infection, and may have direct implications in zoonotic influenza transmissions.


Assuntos
Antígenos CD55/fisiologia , Vírus da Influenza A Subtipo H1N1/isolamento & purificação , Pulmão/imunologia , Viremia/imunologia , Animais , Líquido da Lavagem Broncoalveolar/imunologia , Antígenos CD55/química , Antígenos CD55/deficiência , Quimiotaxia de Leucócito , Ativação do Complemento , Glicoproteínas de Hemaglutininação de Vírus da Influenza/fisiologia , Adaptação ao Hospedeiro , Especificidade de Hospedeiro , Interações Hospedeiro-Patógeno , Vírus da Influenza A Subtipo H1N1/enzimologia , Vírus da Influenza A Subtipo H1N1/patogenicidade , Vírus da Influenza A Subtipo H1N1/fisiologia , Interferon gama/análise , Pulmão/patologia , Pulmão/virologia , Camundongos , Camundongos Endogâmicos C57BL , Ácido N-Acetilneuramínico , Neuraminidase/fisiologia , Infecções por Orthomyxoviridae/imunologia , Infecções por Orthomyxoviridae/patologia , Carga Viral , Proteínas Virais/fisiologia , Virulência , Replicação Viral , Perda de Peso
9.
Arch Virol ; 166(10): 2911-2926, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34331585

RESUMO

The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).


Assuntos
Vírus de DNA/classificação , Animais , Sequência de Bases , Vírus de DNA/genética , Vírus de DNA/fisiologia , DNA Circular , DNA de Cadeia Simples , Genoma Viral/genética , Especificidade de Hospedeiro , Filogenia , Terminologia como Assunto , Proteínas Virais/genética
10.
Emerg Microbes Infect ; 10(1): 1507-1514, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34263709

RESUMO

Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the Sarbecovirus phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from Rhinolophus affinis, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.


Assuntos
Enzima de Conversão de Angiotensina 2/fisiologia , Linhagem da Célula , Quirópteros/virologia , Vírus da SARS/isolamento & purificação , SARS-CoV-2/classificação , Animais , Especificidade de Hospedeiro , Filogenia , Vírus da SARS/classificação
11.
Arch Virol ; 166(9): 2505-2520, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34236511

RESUMO

In this study, a novel Escherichia coli-specific bacteriophage, vB_EcoM_IME392, was isolated from chicken farm sewage in Qingdao, China. The genome of IME392 was found by next-generation sequencing to be 116,460 base pairs in length with a G+C content of 45.4% (GenBank accession number MH719082). BLASTn results revealed that only 2% of the genome sequence of IME392 shows sequence similarity to known phage sequences in the GenBank database, which indicates that IME392 is a novel bacteriophage. Transmission electron microscopy showed that IME392 belongs to the family Myoviridae. The host range, the multiplicity of infection, and a one-step growth curve were also determined.


Assuntos
Colífagos/genética , Escherichia coli/virologia , Myoviridae/genética , Sequenciamento Completo do Genoma , Composição de Bases , Sequência de Bases , China , Mapeamento Cromossômico , Colífagos/classificação , DNA Viral/genética , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Especificidade de Hospedeiro , Concentração de Íons de Hidrogênio , Myoviridae/classificação , Filogenia , Proteômica , Esgotos/virologia , Temperatura
12.
Front Cell Infect Microbiol ; 11: 686090, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34222050

RESUMO

Capsular polysaccharides enable clinically important clones of Klebsiella pneumoniae to cause severe systemic infections in susceptible hosts. Phage-encoded capsule depolymerases have the potential to provide an alternative treatment paradigm in patients when multiple drug resistance has eroded the efficacy of conventional antibiotic chemotherapy. An investigation of 164 K. pneumoniae from intensive care patients in Thailand revealed a large number of distinct K types in low abundance but four (K2, K51, K1, K10) with a frequency of at least 5%. To identify depolymerases with the capacity to degrade capsules associated with these common K-types, 62 lytic phage were isolated from Thai hospital sewage water using K1, K2 and K51 isolates as hosts; phage plaques, without exception, displayed halos indicative of the presence of capsule-degrading enzymes. Phage genomes ranged in size from 41-348 kb with between 50 and 535 predicted coding sequences (CDSs). Using a custom phage protein database we were successful in applying annotation to 30 - 70% (mean = 58%) of these CDSs. The largest genomes, of so-called jumbo phage, carried multiple tRNAs as well as CRISPR repeat and spacer sequences. One of the smaller phage genomes was found to contain a putative Cas type 1E gene, indicating a history of host DNA acquisition in these obligate lytic phage. Whole-genome sequencing (WGS) indicated that some phage displayed an extended host range due to the presence of multiple depolymerase genes; in total, 42 candidate depolymerase genes were identified with up to eight in a single genome. Seven distinct virions were selected for further investigation on the basis of host range, phage morphology and WGS. Candidate genes for K1, K2 and K51 depolymerases were expressed and purified as his6-tagged soluble protein and enzymatic activity demonstrated against K. pneumoniae capsular polysaccharides by gel electrophoresis and Anton-Paar rolling ball viscometry. Depolymerases completely removed the capsule in K-type-specific fashion from K. pneumoniae cells. We conclude that broad-host range phage carry multiple enzymes, each with the capacity to degrade a single K-type, and any future use of these enzymes as therapeutic agents will require enzyme cocktails for utility against a range of K. pneumoniae infections.


Assuntos
Bacteriófagos , Infecções por Klebsiella , Cápsulas Bacterianas , Bacteriófagos/genética , Genoma Viral , Especificidade de Hospedeiro , Humanos , Klebsiella pneumoniae/genética , Tailândia
13.
J Gen Virol ; 102(7)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34227934

RESUMO

Members of the family Inoviridae are non-enveloped flexible filamentous bacteriophages (600-2500×6-10 nm) with supercoiled, circular, positive-sense, single-stranded DNA genomes of 5.5-10.6 kb, encoding 7-15 proteins. They absorb to the pili of Gram-negative bacteria and replicate their DNA by a rolling-circle mechanism with progeny released from cells by extrusion without killing the host. Phage DNA can persist extra-chromosomally or integrate into the bacterial genome. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Inoviridae, which is available at ictv.global/report/inoviridae.


Assuntos
Bactérias Gram-Negativas/virologia , Inoviridae/classificação , Genoma Viral , Especificidade de Hospedeiro , Inoviridae/genética , Inoviridae/fisiologia , Inoviridae/ultraestrutura , Vírion/ultraestrutura , Replicação Viral
14.
J Gen Virol ; 102(7)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34227935

RESUMO

Members of the family Bornaviridae produce enveloped virions containing a linear negative-sense non-segmented RNA genome of about 9 kb. Bornaviruses are found in mammals, birds, reptiles and fish. The most-studied viruses with public health and veterinary impact are Borna disease virus 1 and variegated squirrel bornavirus 1, both of which cause fatal encephalitis in humans. Several orthobornaviruses cause neurological and intestinal disorders in birds, mostly parrots. Endogenous bornavirus-like sequences occur in the genomes of various animals. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Bornaviridae, which is available at ictv.global/report/bornaviridae.


Assuntos
Vírus da Doença de Borna/classificação , Bornaviridae/classificação , Animais , Doença de Borna/virologia , Vírus da Doença de Borna/genética , Vírus da Doença de Borna/fisiologia , Vírus da Doença de Borna/ultraestrutura , Bornaviridae/genética , Bornaviridae/fisiologia , Bornaviridae/ultraestrutura , Genoma Viral , Especificidade de Hospedeiro , Humanos , Vírion/ultraestrutura , Replicação Viral
15.
Arch Virol ; 166(10): 2817-2823, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34279720

RESUMO

Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.


Assuntos
Amaryllidaceae/virologia , Vírus de Plantas/isolamento & purificação , Amaryllidaceae/classificação , Sequência de Aminoácidos , Genoma Viral/genética , Especificidade de Hospedeiro , Doenças das Plantas/virologia , Vírus de Plantas/classificação , Vírus de Plantas/genética , África do Sul , Proteínas Virais/genética
16.
J Gen Virol ; 102(7)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34328827

RESUMO

Members of the family Thaspiviridae have linear dsDNA genomes of 27 to 29 kbp and are the first viruses known to infect mesophilic ammonia-oxidizing archaea of the phylum Thaumarchaeota. The spindle-shaped virions of Nitrosopumilus spindle-shaped virus 1 possess short tails at one pole and measure 64±3 nm in diameter and 112±6 nm in length. This morphology is similar to that of members of the families Fuselloviridae and Halspiviridae. Virus replication is not lytic but leads to growth inhibition of the host. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Thaspiviridae, which is available at ictv.global/report/thaspiviridae.


Assuntos
Archaea/virologia , Vírus de Archaea/classificação , Vírus de DNA/classificação , Vírus de Archaea/genética , Vírus de Archaea/fisiologia , Vírus de Archaea/ultraestrutura , Vírus de DNA/genética , Vírus de DNA/fisiologia , Vírus de DNA/ultraestrutura , Genoma Viral , Especificidade de Hospedeiro , Vírion/ultraestrutura , Replicação Viral
17.
Science ; 373(6554)2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34326207

RESUMO

Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.


Assuntos
Farmacorresistência Bacteriana/genética , Sequências Repetitivas Dispersas , Myoviridae/fisiologia , Vibrio cholerae/efeitos dos fármacos , Vibrio cholerae/virologia , Bacteriólise , Cólera/microbiologia , Conjugação Genética , Epigênese Genética , Fezes/microbiologia , Fezes/virologia , Gammaproteobacteria/genética , Gammaproteobacteria/virologia , Genes Bacterianos , Genes Virais , Genoma Bacteriano , Genoma Viral , Especificidade de Hospedeiro , Humanos , Interações Microbianas , Myoviridae/genética , Myoviridae/isolamento & purificação , Vibrio cholerae/genética , Vibrio cholerae/isolamento & purificação , Proteínas Virais/genética , Proteínas Virais/metabolismo
18.
Cell ; 184(13): 3438-3451.e10, 2021 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-34139177

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide, causing a global pandemic. Bat-origin RaTG13 is currently the most phylogenetically related virus. Here we obtained the complex structure of the RaTG13 receptor binding domain (RBD) with human ACE2 (hACE2) and evaluated binding of RaTG13 RBD to 24 additional ACE2 orthologs. By substituting residues in the RaTG13 RBD with their counterparts in the SARS-CoV-2 RBD, we found that residue 501, the major position found in variants of concern (VOCs) 501Y.V1/V2/V3, plays a key role in determining the potential host range of RaTG13. We also found that SARS-CoV-2 could induce strong cross-reactive antibodies to RaTG13 and identified a SARS-CoV-2 monoclonal antibody (mAb), CB6, that could cross-neutralize RaTG13 pseudovirus. These results elucidate the receptor binding and host adaption mechanisms of RaTG13 and emphasize the importance of continuous surveillance of coronaviruses (CoVs) carried by animal reservoirs to prevent another spillover of CoVs.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , Sítios de Ligação/fisiologia , COVID-19/metabolismo , Quirópteros/virologia , SARS-CoV-2/patogenicidade , Sequência de Aminoácidos , Animais , Anticorpos Monoclonais/imunologia , COVID-19/imunologia , Quirópteros/imunologia , Quirópteros/metabolismo , Especificidade de Hospedeiro/imunologia , Humanos , Filogenia , Ligação Proteica/fisiologia , Receptores Virais/metabolismo , SARS-CoV-2/imunologia , Alinhamento de Sequência
19.
Zootaxa ; 4991(1): 36-72, 2021 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-34186736

RESUMO

Species of Astiotrema Looss, 1900 (sensu lato) infect a wide range of fishes, amphibians and reptilians. They also possess a considerably wide spectrum of morphological features. Several species were recognized for variable, confusing, overlapping and unspecialized morphological characters rather than for unique distinguishing features, causing continuing dispute around the validity of several species. Following comprehensive review, a revised restricted concept of Astiotrema is proposed including a morphologically strict definition. Both Tremiorchis Mehra Negi, 1926 and Astioglossimetra Bilqees, Khatoon Khan, 2002 are synonymized with Astiotrema (sensu stricto). Several nominal species are synonymized, others are excluded and characters for each recognized species are presented and explained. Only eight species are recognized: Astiotrema cyclemysi Siddiqi, 1965, Astiotrema emydis Ejsmont, 1930, Astiotrema fotedari Dhar, 1977, Astiotrema impletum (Looss, 1899) Looss, 1900, Astiotrema karachiensis (Bilqees, Khatoon Khan, 2002) n. comb., Astiotrema odhneri Bhalerao, 1936, Astiotrema ranarum (Mehra Negi, 1926) Fotedar, 1971 and Astiotrema reniferum (Looss, 1898) Looss, 1900. A key to the species of Astiotrema (sensu stricto) is presented, a comprehensive list of all host-locality records is included and host-parasite specificity is elucidated.


Assuntos
Peixes , Trematódeos , Distribuição Animal , Animais , Peixes/parasitologia , Especificidade de Hospedeiro , Especificidade da Espécie , Trematódeos/anatomia & histologia , Trematódeos/classificação , Trematódeos/fisiologia
20.
Ticks Tick Borne Dis ; 12(5): 101758, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34153869

RESUMO

The southern paralysis tick, Ixodes cornuatus, is a tick of veterinary and medical importance in Australia. We use two methods, CLIMEX, and an envelope-model approach which we name the 'climatic-range method' to study the climatic requirements of I. cornuatus and thus to attempt to account for the geographic distribution of I. cornuatus. CLIMEX and our climatic-range method allowed us to account for 94% and 97% of the records of I. cornuatus respectively. We also studied the host preferences of I. cornuatus which we subsequently used in conjunction with our species distribution methods to account for the presence and the absences of I. cornuatus across Australia. Our findings indicate that the actual geographic distribution of I. cornuatus is smaller than the potential geographic range of this tick, and thus, that there are regions in Australia which may be suitable for I. cornuatus where this tick has not been recorded. Although our findings indicate that I. cornuatus might be able to persist in these currently unoccupied regions, our findings also indicate that the potential geographic range of I. cornuatus may shrink by 51 to 76% by 2090, depending on which climate change scenario comes to pass.


Assuntos
Distribuição Animal , Mudança Climática/estatística & dados numéricos , Marsupiais/parasitologia , Modelos Estatísticos , Animais , Austrália , Especificidade de Hospedeiro , Interações Hospedeiro-Parasita , Humanos , Ixodes , Mamíferos/parasitologia , Paralisia por Carrapato/epidemiologia , Paralisia por Carrapato/veterinária
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