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1.
Microbiome ; 9(1): 51, 2021 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-33610182

RESUMO

BACKGROUND: The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS: A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS: The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS: The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.


Assuntos
/isolamento & purificação , Vírus/isolamento & purificação , Zoonoses/diagnóstico , Animais , DNA Viral/genética , Genoma Viral , Humanos , RNA Viral/genética , Vírus/classificação
2.
Molecules ; 26(3)2021 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-33503834

RESUMO

Plants have had historical significance in medicine since the beginning of civilization. The oldest medical pharmacopeias of the African, Arabian, and Asian countries solely utilize plants and herbs to treat pain, oral diseases, skin diseases, microbial infections, multiple types of cancers, reproductive disorders among a myriad of other ailments. The World Health Organization (WHO) estimates that over 65% of the world population solely utilize botanical preparations as medicine. Due to the abundance of plants, plant-derived medicines are more readily accessible, affordable, convenient, and have safer side-effect profiles than synthetic drugs. Plant-based decoctions have been a significant part of Jamaican traditional folklore medicine. Jamaica is of particular interest because it has approximately 52% of the established medicinal plants that exist on earth. This makes the island particularly welcoming for rigorous scientific research on the medicinal value of plants and the development of phytomedicine thereof. Viral infections caused by the human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2), hepatitis virus B and C, influenza A virus, and the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) present a significant global burden. This is a review of some important Jamaican medicinal plants, with particular reference to their antiviral activity.


Assuntos
Antivirais/farmacologia , Plantas Medicinais/química , Vírus/efeitos dos fármacos , Antivirais/efeitos adversos , Antivirais/química , Jamaica , Testes de Sensibilidade Microbiana , Vírus/classificação
3.
BMC Infect Dis ; 21(1): 43, 2021 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-33422002

RESUMO

BACKGROUND: Acute respiratory infections (ARIs) are a worldwide public health problem. It is estimated that up to 80% of cases of ARIs are caused by viruses. In Central America, however, we identified few epidemiologic studies on the main ARI-related viruses in hospitalized children. METHODS: This study retrospectively analyzed the clinical charts of patients ages 29 days to 14 years admitted with diagnoses of ARIs in a pediatric reference hospital in central Panama during 2016. The variables analyzed were age, sex, signs, symptoms, and diagnosis at admission. Samples of patients to whom a viral panel was indicated were analyzed via quantitative polymerase chain reaction, qPCR. RESULTS: The most common virus was respiratory syncytial virus (RSV; 25.9%), followed by influenza A virus (10.6%), rhinovirus (10.6%), parainfluenza type 3 (PIV-3; 8.2%) and adenovirus (5.9%). However, virus detection varied with patient age and season. RSV and Influenza virus were respectively identified mainly during July-November and May-July. All cases of viral co-infection occurred in children < 5-years-old. Both influenza A (H1N1) pdm09 and rhinovirus were detected in all pediatric ages analyzed in this study, unlike RSV and PIV-3, which were only present in children < 5-years-old. CONCLUSIONS: This study analyzed the epidemiological patterns of different respiratory viruses in pediatric patients with ARI from central Panama and found that the prevalence of the specific respiratory viruses identified varied with season and age. The most common viruses were RSV, influenza A, and rhinovirus. There were no reports of human metapneumovirus associated with ARI, which may be explained by the time and geographic location of the study. Knowledge of the local epidemiology of respiratory viruses in tropical countries is helpful in forecasting the peaks of hospitalizations due to ARIs and may help improve prevention efforts aiming at respiratory disease control in these settings.


Assuntos
Infecções Respiratórias/virologia , Viroses/virologia , Vírus/isolamento & purificação , Adolescente , Criança , Pré-Escolar , Coinfecção/epidemiologia , Coinfecção/virologia , Feminino , Hospitalização , Hospitais/estatística & dados numéricos , Humanos , Lactente , Masculino , Metapneumovirus/genética , Panamá/epidemiologia , Pediatria , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/epidemiologia , Estudos Retrospectivos , Estações do Ano , Viroses/epidemiologia , Vírus/classificação , Vírus/genética
4.
Pediatr Infect Dis J ; 40(1): e12-e17, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33165274

RESUMO

BACKGROUND: Human coronaviruses (HCoVs) are a significant cause of acute respiratory illness (ARI) in children; however, the role of HCoVs in ARI among hospitalized children in the Middle East is not well defined. METHODS: Children under 2 years admitted with fever and/or respiratory symptoms were enrolled from 2010 to 2013 in Amman, Jordan. Nasal/throat swabs were collected and stored for testing. Demographic and clinical characteristics were collected through parent/guardian interviews and medical chart abstractions. Prior stored specimens were tested for HCoVs (HKU1, OC43, 229E and NL63) by qRT-PCR. RESULTS: Of the 3168 children enrolled, 6.7% were HCoVs-positive. Among HCoV-positive children, the median age was 3.8 (1.9-8.4) months, 59% were male, 14% were premature, 11% had underlying medical conditions and 76% had viral-codetection. The most common presenting symptoms were cough, fever, wheezing and shortness of breath. HCoVs were detected year-round, peaking in winter-spring months. Overall, 56%, 22%, 13% and 6% were OC43, NL63, HKU1 and 229E, respectively. There was no difference in disease severity between the species, except higher intensive care unit admission frequency in NL63-positive subjects. CONCLUSIONS: HCoVs were detected in around 7% of children enrolled in our study. Despite HCoV detection in children with ARI with highest peaks in respiratory seasons, the actual burden and pathogenic role of HCoVs in ARI merits further evaluation given the high frequency of viral codetection.


Assuntos
Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Coronavirus/isolamento & purificação , Doença Aguda , Coinfecção/epidemiologia , Coinfecção/patologia , Coinfecção/virologia , Coronavirus/classificação , Coronavirus/genética , Infecções por Coronavirus/patologia , Feminino , Hospitalização , Humanos , Lactente , Jordânia/epidemiologia , Masculino , Vigilância da População , Estudos Prospectivos , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/patologia , Infecções Respiratórias/virologia , Fatores de Risco , Estações do Ano , Vírus/classificação , Vírus/genética , Vírus/isolamento & purificação
5.
Arch Virol ; 165(12): 2847-2856, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33034764

RESUMO

Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we detected a novel polyomavirus (RabPyV), and phylogenetic analysis based on the large T antigen, VP1 and VP2 regions indicated that the novel strain might have undergone a recombination event. Recombination analysis based on related genomes confirmed that RabPyV is a multiple recombinant between rodent-like and avian-like polyomaviruses. In fecal samples, three partial or complete genome sequences of viruses belonging to the families Picobirnaviridae, Parvoviridae, Microviridae and Coronaviridae were characterized, and phylogenetic trees were constructed based on the predicted amino acid sequences of viral proteins. This study increases the amount of genetic information on viruses present in laboratory rabbits.


Assuntos
Metagenoma , Polyomavirus/isolamento & purificação , Coelhos/virologia , Proteínas Virais/genética , Vírus/classificação , Animais , Animais de Laboratório/virologia , Sangue/virologia , Fezes/virologia , Genoma Viral , Boca/virologia , Filogenia , Pele/virologia , Vírus/isolamento & purificação , Sequenciamento Completo do Genoma
6.
Arch Virol ; 165(12): 3073-3077, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33025195

RESUMO

The species concept used in virology is based on the logic of the Linnaean hierarchy, which views a species class as the lowest abstract category that is included in all the higher categories in the classification, such as genera and families. As a result of this class inclusion, the members of a species class are always less numerous than the members of higher classes, which become more numerous as one moves up in the hierarchy. Because species classes always have fewer members than any of the higher classes, logic requires that they need more qualifications for establishing membership than any of the higher classes. This invalidates the claim that a species could be defined by a single property present in all its members. Species were only accepted in virus classification in 1991, because virologists assumed that it would lead to the use of Latin species names, which they rejected. Anglicized binomial species names have been used by virologists for more the 40 years and are popular because they consist of a virus name followed by a genus name that most virologists are familiar with. The ICTV has proposed to introduce a new Latinized virus species binomial nomenclature using the genus name followed by a hard-to-remember Latinized species epithet that bears little resemblance to the name of the virus itself. However, the proposal did not clarify what the advantage is of having to learn hundreds of new unfamiliar virus species names. In 2013, the ICTV changed the definition of a virus species as an abstract class and defined it as a group of physical objects, which induced virologists to believe that a virus species could be defined by a few characteristics of the viral genome. In recent years, thousands of viral sequences have been discovered in metagenomic databases, and the ICTV has suggested that it should be possible to incorporate these sequences in the current ICTV virus classification. Unfortunately, the relational properties of these hypothetical viruses that result from their biological interactions with hosts and vectors remain in the vast majority of cases totally unknown. The absence of this information makes it in fact impossible to incorporate these metagenomic sequences in the current classification of virus species.


Assuntos
Virologia/história , Vírus/classificação , Gerenciamento de Dados , Bases de Dados como Assunto , Genoma Viral , História do Século XX , História do Século XXI
7.
Arch Virol ; 165(12): 3079-3083, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33025196

RESUMO

On several occasions over the past century it has been proposed that Latinized (Linnaean) binomial names (LBs) should be used for the formal names of virus species, and the opinions expressed in the early debates are still valid. The use of LBs would be sensible for the current Taxonomy if confined to the names of the specific and generic taxa of viruses of which some basic biological properties are known (e.g. ecology, hosts and virions); there is no advantage in filling the literature with formal names for partly described viruses or virus-like gene sequences. The ICTV should support the time-honoured convention that LBs are only used with biological (phylogenetic) classifications. Recent changes have left the ICTV Taxonomy and its Code uncoordinated, and its aims and audience uncertain.


Assuntos
Virologia/tendências , Vírus/classificação , Classificação/métodos , Terminologia como Assunto
8.
Viruses ; 12(9)2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32967229

RESUMO

As evidence has mounted that virus-infected cells, such as cancer cells, negatively regulate the function of T-cells via immune checkpoints, it has become increasingly clear that viral infections similarly exploit immune checkpoints as an immune system escape mechanism. Although immune checkpoint therapy has been successfully used in cancer treatment, numerous studies have suggested that such therapy may also be highly relevant for treating viral infection, especially chronic viral infections. However, it has not yet been applied in this manner. Here, we reviewed recent findings regarding immune checkpoints in viral infections, including COVID-19, and discussed the role of immune checkpoints in different viral infections, as well as the potential for applying immune checkpoint blockades as antiviral therapy.


Assuntos
Fatores Imunológicos/imunologia , Viroses/imunologia , Vírus/imunologia , Animais , Antivirais/uso terapêutico , Doença Crônica , Humanos , Fatores Imunológicos/antagonistas & inibidores , Imunoterapia , Ativação Linfocitária/efeitos dos fármacos , Linfócitos T/imunologia , Linfócitos T/patologia , Viroses/terapia , Vírus/classificação
9.
Nat Commun ; 11(1): 4620, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32934242

RESUMO

Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.


Assuntos
Entamoeba/virologia , Giardia/virologia , Adulto , Estudos de Coortes , Fezes/parasitologia , Fezes/virologia , Feminino , Genoma Viral , Especificidade de Hospedeiro , Humanos , Masculino , Pessoa de Meia-Idade , Filogenia , Fenômenos Fisiológicos Virais , Vírus/classificação , Vírus/genética , Adulto Jovem
10.
PLoS Negl Trop Dis ; 14(8): e0008381, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32804954

RESUMO

The world's most consequential pathogens occur in regions with the fewest diagnostic resources, leaving the true burden of these diseases largely under-represented. During a prospective observational study of sepsis in Takeo Province Cambodia, we enrolled 200 patients over an 18-month period. By coupling traditional diagnostic methods such as culture, serology, and PCR to Next Generation Sequencing (NGS) and advanced statistical analyses, we successfully identified a pathogenic cause in 46.5% of our cohort. In all, we detected 25 infectious agents in 93 patients, including severe threat pathogens such as Burkholderia pseudomallei and viral pathogens such as Dengue virus. Approximately half of our cohort remained undiagnosed; however, an independent panel of clinical adjudicators determined that 81% of those patients had infectious causes of their hospitalization, further underscoring the difficulty of diagnosing severe infections in resource-limited settings. We garnered greater insight as to the clinical features of severe infection in Cambodia through analysis of a robust set of clinical data.


Assuntos
Sepse/epidemiologia , Sepse/etiologia , Sepse/microbiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/classificação , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/epidemiologia , Camboja/epidemiologia , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , Estudos Prospectivos , Sepse/virologia , Análise de Sequência de RNA , Testes Sorológicos , Viroses/diagnóstico , Viroses/epidemiologia , Vírus/classificação
11.
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
12.
Nucleic Acids Res ; 48(16): 8883-8900, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32766782

RESUMO

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.


Assuntos
Bactérias/classificação , Microbioma Gastrointestinal , Genômica/métodos , Metabolômica/métodos , Software , Microbiologia do Solo , Vírus/classificação , Humanos , Metagenoma , Anotação de Sequência Molecular/métodos
13.
Arch Virol ; 165(11): 2733-2736, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32740831

RESUMO

Virus classification arranges viruses showing similar properties into groups and, even though this depends on choices of which specific properties have a value for classification, it does have certain important features. It aims to give a structured arrangement of viruses so that the human mind can comprehend them more easily. It helps with communication between virologists, and between virologists and non-virologists (e.g. regulators, advisers, other stakeholders etc.). It enables properties of new viruses to be predicted, and it could reveal possible evolutionary relationships. We need appropriate unambiguous names for virus species, which is the keystone taxon, howsoever these are defined. We react to the recent consultation paper [1] and suggest that, before deciding on a binomial (Latinized or non-Latinized) system for virus species names, the International Committee on Taxonomy of Viruses develops a 21st century virus classification system that handles the large numbers of new virus species expected from metagenomic studies. This system should be user-friendly for easy communication, especially between virologists and non-virologist stakeholders.


Assuntos
Classificação/métodos , Terminologia como Assunto , Vírus/classificação , Virologia/organização & administração , Vírus/isolamento & purificação
14.
Int J Infect Dis ; 98: 249-251, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32623079

RESUMO

OBJECTIVES: To metagenomically analyse blood units originating from the Brazilian Amazon and positive for parenterally transmitted infections (human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-lymphotropic virus (HTLV), Chagas disease or syphilis). METHODS: Twenty plasma samples (35% HBV-positive, 10% HIV-positive, 10% HCV-positive, 20% positive for syphilis, 20% for Chagas disease, and 5% for HTLV) assembled in pools were analysed by metagenomic next-generation sequencing. The obtained raw sequencing data were submitted to a bioinformatic pipeline set up for identification of emerging viruses. The viral reads of interest were phylogenetically analysed and confirmed by PCR in the individual samples. RESULTS: The metagenomic analysis identified contigs belonging to the emerging human Gemykibivirus-2 (HuGkV-2) in two pools. The HuGkV-1 phylogeny demonstrated that the Amazonian isolate formed a separate cluster with other HuGkV-2 strains obtained from human hosts. The PCR confirmation detected HuGkV-1 DNA in three individual samples (15%). CONCLUSIONS: HuGkV-2 is an emerging virus with unknown clinical impact. The detection of HuGkV-2 DNA in blood donations positive for parenterally transmitted infections showed that HuGkV-2 can be considered as an opportunistic viral agent with a hypothetic parenteral transmission route.


Assuntos
Doadores de Sangue/estatística & dados numéricos , Sangue/virologia , Viroses/virologia , Vírus/genética , Vírus/isolamento & purificação , Adulto , Brasil/epidemiologia , Feminino , Humanos , Masculino , Metagenômica , Pessoa de Meia-Idade , Filogenia , Viroses/sangue , Viroses/epidemiologia , Vírus/classificação , Adulto Jovem
15.
RNA ; 26(11): 1509-1518, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32699064

RESUMO

Viruses have evolved in tandem with the organisms that they infect. Afflictions of the plant and animal kingdoms with viral infections have forced the host organism to evolve new or exploit existing systems to develop the countermeasures needed to offset viral insults. As one example, nonsense-mediated mRNA decay, a cellular quality-control mechanism ensuring the translational fidelity of mRNA transcripts, has been used to restrict virus replication in both plants and animals. In response, viruses have developed a slew of means to disrupt or become insensitive to NMD, providing researchers with potential new reagents that can be used to more fully understand the NMD mechanism.


Assuntos
Interações Hospedeiro-Patógeno , Degradação do RNAm Mediada por Códon sem Sentido , Vírus/metabolismo , Animais , Humanos , Plantas/virologia , Biossíntese de Proteínas , Estabilidade de RNA , RNA Mensageiro/metabolismo , Proteínas Virais/genética , Fenômenos Fisiológicos Virais , Vírus/classificação , Vírus/genética , Vírus/crescimento & desenvolvimento
16.
J Appl Lab Med ; 5(5): 897-907, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32674131

RESUMO

BACKGROUND: Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management. METHODS: We evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test. RESULTS: Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results. CONCLUSIONS: Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.


Assuntos
Vírus da Influenza A , Vírus da Influenza B , Influenza Humana , Técnicas de Amplificação de Ácido Nucleico/métodos , Infecções por Vírus de RNA , Infecções Respiratórias , Diagnóstico Diferencial , Humanos , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Vírus da Influenza B/genética , Vírus da Influenza B/isolamento & purificação , Influenza Humana/diagnóstico , Influenza Humana/virologia , Reação em Cadeia da Polimerase Multiplex/métodos , Utilização de Procedimentos e Técnicas , Infecções por Vírus de RNA/diagnóstico , Infecções por Vírus de RNA/virologia , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Vírus/classificação , Vírus/isolamento & purificação
17.
Influenza Other Respir Viruses ; 14(6): 739-746, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32567818

RESUMO

BACKGROUND: Acute respiratory illnesses are a leading cause of global morbidity and mortality in children. Coinfection with multiple respiratory viruses is common. Although the effects of each virus have been studied individually, the impacts of coinfection on disease severity are less understood. METHODS: A secondary analysis was performed of a maternal influenza vaccine trial conducted between 2011 and 2014 in Nepal. Prospective weekly household-based active surveillance of infants was conducted from birth to 180 days of age. Mid-nasal swabs were collected and tested for respiratory syncytial virus (RSV), rhinovirus, influenza, human metapneumovirus (HMPV), coronavirus, parainfluenza (HPIV), and bocavirus by RT-PCR. Coinfection was defined as the presence of two or more respiratory viruses detected as part of the same illness episode. RESULTS: Of 1730 infants with a respiratory illness, 327 (19%) had at least two respiratory viruses detected in their primary illness episode. Of 113 infants with influenza, 23 (20%) had coinfection. Of 214 infants with RSV, 87 (41%) had coinfection. The cohort of infants with coinfection had increased occurrence of fever lasting ≥ 4 days (OR 1.4, 95% CI: 1.1, 2.0), and so did the subset of coinfected infants with influenza (OR 5.8, 95% CI: 1.8, 18.7). Coinfection was not associated with seeking further care (OR 1.1, 95% CI: 0.8, 1.5) or pneumonia (OR 1.2, 95% CI: 0.96, 1.6). CONCLUSION: A high proportion of infants had multiple viruses detected. Coinfection was associated with greater odds of fever lasting for four or more days, but not with increased illness severity by other measures.


Assuntos
Coinfecção/epidemiologia , Coinfecção/virologia , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Coinfecção/patologia , Febre/epidemiologia , Febre/patologia , Febre/virologia , Humanos , Lactente , Recém-Nascido , Nepal/epidemiologia , Razão de Chances , Estudos Prospectivos , Infecções Respiratórias/patologia , População Rural , Viroses/epidemiologia , Viroses/patologia , Viroses/virologia , Vírus/classificação , Vírus/isolamento & purificação
18.
Forensic Sci Med Pathol ; 16(3): 457-462, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32578131

RESUMO

Death due to respiratory infection is commonly encountered at autopsy. With only one opportunity to obtain samples for identification of a causative agent, it is important to ensure that sampling regimes are optimized to provide the greatest detection, without the expense and redundancy that can arise from over-sampling. This study was performed retrospectively using data from Coronial autopsies over the period 2012-2019 from which swabs from the nasopharyngeal region, trachea and lung parenchyma, in addition to samples of lung tissue, had been submitted for multiplex PCR detection of respiratory pathogens. From 97 cases with all four samples, there were 24 with at least one positive result for viral infection. Some cases had multiple positive results and a total of 27 respiratory tract viruses were identified, of which rhinovirus, influenza A virus and respiratory syncytial virus were the most common. Seventeen of the 27 viral infections (63%) were identified in all four samples. However, in nearly all cases (96%) the nasopharyngeal swab detected the infective agent when the multiplex PCR panel had detected infection in any of the four sample types. A nasopharyngeal swab is considered to be an optimal sample for detection of respiratory tract viral infection. As the samples analyzed were acquired before the appearance of the COVID-19 virus, the applicability of this finding for COVID-19 screening is not established.


Assuntos
DNA Viral/isolamento & purificação , Pulmão/virologia , Reação em Cadeia da Polimerase Multiplex , Nasofaringe/virologia , Infecções Respiratórias/diagnóstico , Manejo de Espécimes , Virologia , Viroses/diagnóstico , Vírus/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Autopsia , Causas de Morte , DNA Viral/classificação , DNA Viral/genética , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Reprodutibilidade dos Testes , Infecções Respiratórias/virologia , Estudos Retrospectivos , Viroses/virologia , Vírus/classificação , Vírus/genética
19.
Int J Infect Dis ; 98: 21-32, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32562851

RESUMO

BACKGROUND: Acute respiratory infections (ARIs) remain a significant public threat with high morbidity and mortality worldwide; viruses are significant pathogens that cause ARIs. This study was conducted to better understand the epidemiological characteristics of respiratory viruses circulating in southern China. METHODS: We collected 22,680 respiratory samples from ARI patients in 18 hospitals in southern China during 2009-2018; seven common respiratory viruses including Flu, RSV, PIV, hMPV, ADV, HCoV, and HBoV were screened using in-house real-time PCR. RESULTS: Of all samples, 9760 ARI cases (9760/22680, 43.03%) tested positive for the seven common respiratory viruses. The most detected virus was Flu (14.15%), followed by RSV (10.33%) and PIV (5.43%); Flu-A, PIV3, and HCoV-OC43 were the predominant subtypes. Although most of the viruses were detected in male inpatients, Flu was more likely detected in female outpatients. Flu infection was more likely to cause URTI (upper respiratory tract infection), whereas RSV infection was more likely to cause pneumonia and bronchitis. The prevalence of Flu was particularly high in 2009. The epidemic level was found notably high in 2014-2018 for RSV, in 2016-2018 for PIV, in the summer of 2018 for ADV, in the summer of 2016 and winter of 2018 for HCoV, and in the summer of 2011 and autumn of 2018 for HBoV. The co-detection rate of the seven viruses was 4.70%; RSV, PIV, and Flu were the most commonly co-detected viruses. CONCLUSIONS: This work demonstrates the epidemiological characteristics of seven common respiratory viruses in ARI patients in southern China.


Assuntos
Infecções Respiratórias/virologia , Vírus/isolamento & purificação , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , China/epidemiologia , Feminino , Hospitais/estatística & dados numéricos , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Pacientes Ambulatoriais/estatística & dados numéricos , Prevalência , Infecções por Vírus Respiratório Sincicial/epidemiologia , Infecções Respiratórias/epidemiologia , Estações do Ano , Vírus/classificação , Vírus/genética , Adulto Jovem
20.
Immunity ; 52(6): 905-909, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32497522

RESUMO

Respiratory viruses affect us throughout our lives, from infancy to old age, causing illnesses ranging from a common cold to severe pneumonia. They belong to several virus families, and although many features of infection with these diverse viruses are shared, some have unique characteristics. Here we explain what happens when we are infected by respiratory viruses, including SARS-CoV-2, which causes COVID-19.


Assuntos
Infecções por Coronavirus/fisiopatologia , Pneumonia Viral/fisiopatologia , Sistema Respiratório/fisiopatologia , Imunidade Adaptativa , Betacoronavirus/fisiologia , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/terapia , Infecções por Coronavirus/virologia , Humanos , Imunidade Inata , Pandemias , Pneumonia Viral/imunologia , Pneumonia Viral/terapia , Pneumonia Viral/virologia , Sistema Respiratório/imunologia , Sistema Respiratório/virologia , Fenômenos Fisiológicos Virais , Vírus/classificação
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