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1.
PLoS Comput Biol ; 20(1): e1011795, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38271457

RESUMO

The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/genética , Pandemias , Mutação , Antivirais/farmacologia
2.
PLoS Biol ; 19(9): e3001352, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34491982

RESUMO

Antiviral defenses can sense viral RNAs and mediate their destruction. This presents a challenge for host cells since they must destroy viral RNAs while sparing the host mRNAs that encode antiviral effectors. Here, we show that highly upregulated interferon-stimulated genes (ISGs), which encode antiviral proteins, have distinctive nucleotide compositions. We propose that self-targeting by antiviral effectors has selected for ISG transcripts that occupy a less self-targeted sequence space. Following interferon (IFN) stimulation, the CpG-targeting antiviral effector zinc-finger antiviral protein (ZAP) reduces the mRNA abundance of multiple host transcripts, providing a mechanistic explanation for the repression of many (but not all) interferon-repressed genes (IRGs). Notably, IRGs tend to be relatively CpG rich. In contrast, highly upregulated ISGs tend to be strongly CpG suppressed. Thus, ZAP is an example of an effector that has not only selected compositional biases in viral genomes but also appears to have notably shaped the composition of host transcripts in the vertebrate interferome.


Assuntos
Fosfatos de Dinucleosídeos , Fatores Reguladores de Interferon/genética , RNA Viral , Proteínas de Ligação a RNA/metabolismo , Células A549 , Linhagem Celular , Humanos , Interferon beta/farmacologia , RNA Mensageiro , Proteínas de Ligação a RNA/genética , Fenômenos Fisiológicos Virais , Vírus
3.
Proc Natl Acad Sci U S A ; 118(3)2021 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-33397804

RESUMO

Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing so, HDV enhances the virulence of HBV. How this seemingly improbable hyperparasitic lifestyle emerged is unknown, but it underpins the likelihood that HDV and related deltaviruses may alter other host-virus interactions. Here, we show that deltaviruses diversify by transmitting between mammalian species. Among 96,695 RNA sequence datasets, deltaviruses infected bats, rodents, and an artiodactyl from the Americas but were absent from geographically overrepresented Old World representatives of each mammalian order, suggesting a relatively recent diversification within the Americas. Consistent with diversification by host shifting, both bat and rodent-infecting deltaviruses were paraphyletic, and coevolutionary modeling rejected cospeciation with mammalian hosts. In addition, a 2-y field study showed common vampire bats in Peru were infected by two divergent deltaviruses, indicating multiple introductions to a single host species. One vampire bat-associated deltavirus was detected in the saliva of up to 35% of individuals, formed phylogeographically compartmentalized clades, and infected a sympatric bat, illustrating horizontal transmission within and between species on ecological timescales. Consistent absence of HBV-like viruses in two deltavirus-infected bat species indicated acquisitions of novel viral associations during the divergence of bat and human-infecting deltaviruses. Our analyses support an American zoonotic origin of HDV and reveal prospects for future cross-species emergence of deltaviruses. Given their peculiar life history, deltavirus host shifts will have different constraints and disease outcomes compared to ordinary animal pathogens.


Assuntos
Vírus da Hepatite B/genética , Vírus Delta da Hepatite/genética , Especificidade de Hospedeiro/genética , Vírus Satélites/genética , Animais , Quirópteros/virologia , Transmissão de Doença Infecciosa , Variação Genética/genética , Genoma Viral/genética , Hepatite B/genética , Hepatite B/transmissão , Hepatite B/virologia , Vírus da Hepatite B/patogenicidade , Hepatite D/genética , Hepatite D/transmissão , Hepatite D/virologia , Vírus Delta da Hepatite/patogenicidade , Interações Hospedeiro-Patógeno/genética , Humanos , Mamíferos/virologia , Filogenia , Roedores/virologia , Vírus Satélites/patogenicidade
4.
Mol Biol Evol ; 39(4)2022 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-35325204

RESUMO

Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.


Assuntos
COVID-19 , Glicoproteína da Espícula de Coronavírus , COVID-19/genética , Humanos , Mutação , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética
5.
PLoS Pathog ; 17(9): e1009929, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34534263

RESUMO

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.


Assuntos
Monofosfato de Adenosina/análogos & derivados , Alanina/análogos & derivados , Antivirais/farmacologia , Tratamento Farmacológico da COVID-19 , RNA-Polimerase RNA-Dependente de Coronavírus/genética , Resistência Microbiana a Medicamentos/genética , SARS-CoV-2/efeitos dos fármacos , Monofosfato de Adenosina/farmacologia , Alanina/farmacologia , Animais , Evolução Biológica , Chlorocebus aethiops , Humanos , Mutação , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Células Vero
6.
Vet Res ; 53(1): 107, 2022 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-36510312

RESUMO

Bovine respiratory syncytial virus (BRSV) is a major cause of respiratory disease in cattle. Genomic sequencing can resolve phylogenetic relationships between virus populations, which can be used to infer transmission routes and potentially inform the design of biosecurity measures. Sequencing of short (<2000 nt) segments of the 15 000-nt BRSV genome has revealed geographic and temporal clustering of BRSV populations, but insufficient variation to distinguish viruses collected from herds infected close together in space and time. This study investigated the potential for whole-genome sequencing to reveal sufficient genomic variation for inferring transmission routes between herds. Next-generation sequencing (NGS) data were generated from experimental infections and from natural outbreaks in Jämtland and Uppsala counties in Sweden. Sufficient depth of coverage for analysis of consensus and sub-consensus sequence diversity was obtained from 47 to 20 samples respectively. Few (range: 0-6 polymorphisms across the six experiments) consensus-level polymorphisms were observed along experimental transmissions. A much higher level of diversity (146 polymorphic sites) was found among the consensus sequences from the outbreak samples. The majority (144/146) of polymorphisms were between rather than within counties, suggesting that consensus whole-genome sequences show insufficient spatial resolution for inferring direct transmission routes, but might allow identification of outbreak sources at the regional scale. By contrast, within-sample diversity was generally higher in the experimental than the outbreak samples. Analyses to infer known (experimental) and suspected (outbreak) transmission links from within-sample diversity data were uninformative. In conclusion, analysis of the whole-genome sequence of BRSV from experimental samples discriminated between circulating isolates from distant areas, but insufficient diversity was observed between closely related isolates to aid local transmission route inference.


Assuntos
Doenças dos Bovinos , Infecções por Vírus Respiratório Sincicial , Vírus Sincicial Respiratório Bovino , Bovinos , Animais , Vírus Sincicial Respiratório Bovino/genética , Filogenia , Doenças dos Bovinos/epidemiologia , Infecções por Vírus Respiratório Sincicial/epidemiologia , Infecções por Vírus Respiratório Sincicial/veterinária , Anticorpos Antivirais
7.
Arch Virol ; 167(11): 2429-2440, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35999326

RESUMO

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.


Assuntos
Vírus , Membro de Comitê , Vírus/genética
8.
J Gen Virol ; 102(10)2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34704922

RESUMO

Members of the family Herpesviridae have enveloped, spherical virions with characteristic complex structures consisting of symmetrical and non-symmetrical components. The linear, double-stranded DNA genomes of 125-241 kbp contain 70-170 genes, of which 43 have been inherited from an ancestral herpesvirus. In general, herpesviruses have coevolved with and are highly adapted to their hosts, which comprise many mammalian, avian and reptilian species. Following primary infection, they are able to establish lifelong latent infection, during which there is limited viral gene expression. Severe disease is usually observed only in the foetus, the very young, the immunocompromised or following infection of an alternative host. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Herpesviridae, which is available at ictv.global/report/herpesviridae.


Assuntos
Genoma Viral , Herpesviridae , Animais , Evolução Molecular , Herpesviridae/classificação , Herpesviridae/genética , Herpesviridae/fisiologia , Herpesviridae/ultraestrutura , Infecções por Herpesviridae/veterinária , Infecções por Herpesviridae/virologia , Adaptação ao Hospedeiro , Vírion/química , Vírion/ultraestrutura , Latência Viral , Replicação Viral
9.
Arch Virol ; 166(9): 2633-2648, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34231026

RESUMO

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes.


Assuntos
Classificação/métodos , Filogenia , Vírus não Classificados/classificação , Vírus/classificação , Cooperação Internacional , Viroides/classificação , Vírus/genética , Vírus/isolamento & purificação , Vírus não Classificados/genética , Vírus não Classificados/isolamento & purificação
10.
J Virol ; 93(14)2019 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-31043525

RESUMO

The gammacoronavirus infectious bronchitis virus (IBV) causes an acute, highly contagious respiratory disease of poultry. Live attenuated vaccines are traditionally generated by serial passage of a virulent strain in embryonated chicken eggs; however, the molecular mechanism of attenuation is unknown. M41-CK, a virulent lab-adapted strain of IBV, was egg passaged over 100 times in four parallel independent replicates. All four final egg-passaged viruses were attenuated in vivo and exhibited similar growth phenotypes in adult chicken kidney cells and ex vivo tracheal organ cultures. The virus populations were sequenced by 454 pyrosequencing at the end of passaging, and the results showed that overall sequence diversity in the IBV population increased but the four replicates only had between 11 and 17 consensus-level single nucleotide polymorphisms (SNPs). Although hot spots of variation were identified in spike and nucleocapsid structural proteins as well as the 3' untranslated region, each attenuated virus possessed a different pattern of genomic variation. Overall, only a small number of consensus-level SNPs were acquired during egg passage, leaving a potentially short route back to virulence. These results highlight the unpredictable nature of attenuation by serial egg passage and the need to develop mechanisms to rationally attenuate IBV for the next generation of effective vaccines.IMPORTANCE Infectious bronchitis remains a major problem in the global poultry industry, despite the existence of many different vaccines. IBV vaccines are currently developed by serial passage of a virulent strain on embryonated hen's eggs until attenuation; however, little is known about the evolution of the viral population during the process of attenuation. High-throughput sequencing of four replicates of a serially egg-passaged IBV revealed a different pattern of genomic variation in each attenuated replicate and few consensus-level SNPs. This raises concerns that only a small number of genomic mutations are required to revert to a virulent phenotype, which may result in vaccine breakdown in the field. The observed hot spots of variation in the attenuated viruses have the potential to be used in the rational attenuation of virulent IBV for next-generation vaccine design.


Assuntos
Ovos/virologia , Vírus da Bronquite Infecciosa , Polimorfismo de Nucleotídeo Único , Vacinas Virais , Animais , Linhagem Celular , Galinhas , Infecções por Coronavirus/genética , Infecções por Coronavirus/imunologia , Vírus da Bronquite Infecciosa/genética , Vírus da Bronquite Infecciosa/imunologia , Doenças das Aves Domésticas/genética , Doenças das Aves Domésticas/imunologia , Doenças das Aves Domésticas/virologia , Vacinas Atenuadas/genética , Vacinas Atenuadas/imunologia , Vacinas Virais/genética , Vacinas Virais/imunologia
11.
Mol Ecol ; 29(1): 26-39, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31561274

RESUMO

Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.


Assuntos
Biodiversidade , Quirópteros/virologia , Doenças Transmissíveis/virologia , Ecologia , Metagenoma , Vírus/genética , Animais , Demografia , Ecossistema , Meio Ambiente , Humanos , Metagenômica , América do Sul
12.
PLoS Biol ; 15(12): e2004086, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-29253856

RESUMO

The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I 'interferome' have mainly been carried out at a single species level, often lacking the power necessary to understand key evolutionary features of this pathway. Here, using a single experimental platform, we determined the properties of the interferomes of multiple vertebrate species and developed a webserver to mine the dataset. This approach revealed a conserved 'core' of 62 ISGs, including genes not previously associated with IFN, underscoring the ancestral functions associated with this antiviral host response. We show that gene expansion contributes to the evolution of the IFN system and that interferomes are shaped by lineage-specific pressures. Consequently, each mammal possesses a unique repertoire of ISGs, including genes common to all mammals and others unique to their specific species or phylogenetic lineages. An analysis of genes commonly down-regulated by IFN suggests that epigenetic regulation of transcription is a fundamental aspect of the IFN response. Our study provides a resource for the scientific community highlighting key paradigms of the type I IFN response.


Assuntos
Imunidade Inata , Fatores Reguladores de Interferon/fisiologia , Interferon Tipo I/fisiologia , Mamíferos/imunologia , Animais , Mineração de Dados , Fatores Reguladores de Interferon/genética , Fatores Reguladores de Interferon/metabolismo , Interferon Tipo I/metabolismo , Especificidade da Espécie , Viroses/imunologia
13.
Arch Virol ; 165(11): 2737-2748, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32816125

RESUMO

This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.


Assuntos
Classificação/métodos , Vírus/classificação , Terminologia como Assunto , Virologia/organização & administração , Vírus/isolamento & purificação
14.
Nucleic Acids Res ; 46(D1): D708-D717, 2018 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-29040670

RESUMO

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.


Assuntos
Bases de Dados Factuais , Vírus/classificação , Previsões , Filogenia , Terminologia como Assunto , Vírus/genética
15.
PLoS Comput Biol ; 13(4): e1005470, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28369082

RESUMO

The role of host movement in the spread of vector-borne diseases of livestock has been little studied. Here we develop a mathematical framework that allows us to disentangle and quantify the roles of vector dispersal and livestock movement in transmission between farms. We apply this framework to outbreaks of bluetongue virus (BTV) and Schmallenberg virus (SBV) in Great Britain, both of which are spread by Culicoides biting midges and have recently emerged in northern Europe. For BTV we estimate parameters by fitting the model to outbreak data using approximate Bayesian computation, while for SBV we use previously derived estimates. We find that around 90% of transmission of BTV between farms is a result of vector dispersal, while for SBV this proportion is 98%. This difference is a consequence of higher vector competence and shorter duration of viraemia for SBV compared with BTV. For both viruses we estimate that the mean number of secondary infections per infected farm is greater than one for vector dispersal, but below one for livestock movements. Although livestock movements account for a small proportion of transmission and cannot sustain an outbreak on their own, they play an important role in establishing new foci of infection. However, the impact of restricting livestock movements on the spread of both viruses depends critically on assumptions made about the distances over which vector dispersal occurs. If vector dispersal occurs primarily at a local scale (99% of transmission occurs <25 km), movement restrictions are predicted to be effective at reducing spread, but if dispersal occurs frequently over longer distances (99% of transmission occurs <50 km) they are not.


Assuntos
Vírus Bluetongue/patogenicidade , Doenças dos Bovinos/transmissão , Interações Hospedeiro-Patógeno , Insetos Vetores , Gado , Modelos Teóricos , Vírus de RNA/patogenicidade , Doenças dos Ovinos/transmissão , Animais , Teorema de Bayes , Bovinos , Doenças dos Bovinos/virologia , Surtos de Doenças , Ovinos , Doenças dos Ovinos/virologia
16.
Arch Virol ; 162(5): 1441-1446, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28078475

RESUMO

We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.


Assuntos
Vírus/classificação , Vírus/genética , Biologia Computacional , História do Século XX , História do Século XXI , Metagenômica , Filogenia , Sociedades Científicas
17.
BMC Genomics ; 16: 229, 2015 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-25886445

RESUMO

BACKGROUND: RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial. RESULTS: We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site's coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone. CONCLUSIONS: These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Frequência do Gene , Sequenciamento de Nucleotídeos em Larga Escala/normas , Modelos Teóricos , Mutação , Vírus de RNA/genética , RNA Viral/análise , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Análise de Sequência de RNA/normas
18.
PLoS Pathog ; 8(11): e1003008, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23209404

RESUMO

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers.


Assuntos
Genoma Bacteriano , Modelos Biológicos , Mycobacterium bovis , Polimorfismo de Nucleotídeo Único , Tuberculose Bovina , Animais , Bovinos , Estudo de Associação Genômica Ampla , Humanos , Mycobacterium bovis/genética , Mycobacterium bovis/patogenicidade , Tuberculose Bovina/epidemiologia , Tuberculose Bovina/genética , Tuberculose Bovina/transmissão
19.
Viruses ; 15(6)2023 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-37376548

RESUMO

Nanopore sequencing is becoming increasingly commonplace in clinical settings, particularly for diagnostic assessments and outbreak investigations, due to its portability, low cost, and ability to operate in near real-time. Although high sequencing error rates initially hampered the wider implementation of this technology, improvements have been made continually with each iteration of the sequencing hardware and base-calling software. Here, we assess the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) in high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior knowledge of the sequences. We utilised a hybrid bioinformatic approach that involved assembling the reads de novo, improving the consensus sequence by aligning reads to the best-matching genome from a collated set of published sequences, and polishing the improved consensus sequence. The final genomes from a urine sample and a lung sample, the former with an HCMV to human DNA load approximately 50 times greater than the latter, achieved 99.97 and 99.93% identity, respectively, to the benchmark genomes obtained independently by Illumina sequencing. Thus, we demonstrated that nanopore sequencing is capable of determining HCMV genomes directly from high-viral-load clinical samples with a high accuracy.


Assuntos
Citomegalovirus , Sequenciamento por Nanoporos , Humanos , Análise de Sequência de DNA , Citomegalovirus/genética , Biologia Computacional , Software , Sequenciamento de Nucleotídeos em Larga Escala
20.
Viruses ; 15(8)2023 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-37632111

RESUMO

Although domestic cats are susceptible to infection with SARS-CoV-2, the role of the virus in causing feline disease is less well defined. We conducted a large-scale study to identify SARS-CoV-2 infections in UK pet cats, using active and passive surveillance. Remnant feline respiratory swab samples, submitted for other pathogen testing between May 2021 and February 2023, were screened using RT-qPCR. In addition, we appealed to veterinarians for swab samples from cats suspected of having clinical SARS-CoV-2 infections. Bespoke testing for SARS-CoV-2 neutralising antibodies was also performed, on request, in suspected cases. One RT-qPCR-positive cat was identified by active surveillance (1/549, 0.18%), during the Delta wave (1/175, 0.57%). Passive surveillance detected one cat infected with the Alpha variant, and two of ten cats tested RT-qPCR-positive during the Delta wave. No cats tested RT-qPCR-positive after the emergence of Omicron BA.1 and its descendants although 374 were tested by active and eleven by passive surveillance. We describe four cases of SARS-CoV-2 infection in pet cats, identified by RT-qPCR and/or serology, that presented with a range of clinical signs, as well as their SARS-CoV-2 genome sequences. These cases demonstrate that, although uncommon in cats, a variety of clinical signs can occur.


Assuntos
COVID-19 , SARS-CoV-2 , Animais , Gatos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/veterinária , Anticorpos Antivirais , Reino Unido/epidemiologia
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