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1.
J Virol ; 97(11): e0082923, 2023 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-37882520

RESUMO

IMPORTANCE: Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.


Assuntos
Alphacoronavirus , Carnívoros , Fezes , Saliva , Animais , Humanos , Alphacoronavirus/classificação , Alphacoronavirus/genética , Alphacoronavirus/isolamento & purificação , Animais Domésticos/virologia , Animais Selvagens/virologia , Carnívoros/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/veterinária , Fezes/virologia , Interações entre Hospedeiro e Microrganismos , New England/epidemiologia , Saliva/virologia , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Zoonoses Virais/transmissão , Zoonoses Virais/virologia
2.
Viruses ; 15(8)2023 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-37631969

RESUMO

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.


Assuntos
Doenças dos Cavalos , Reação em Cadeia da Polimerase em Tempo Real , Infecções por Rotavirus , Rotavirus , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Rotavirus/isolamento & purificação , Animais , Cavalos , Doenças dos Cavalos/virologia , Infecções por Rotavirus/veterinária , Fezes/virologia , Sensibilidade e Especificidade
3.
Arch Virol ; 168(9): 231, 2023 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-37584776

RESUMO

Noroviruses (NoVs) are a global concern, causing widespread outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Recent research has shed light on the emergence of novel recombinant strains of NoV in various countries. To delve deeper into this phenomenon, we extensively analyzed 1,175 stool samples collected from Japanese infants and children with AGE from six different prefectures in Japan over three years, from July 2018 to June 2021. Our investigation aimed to determine the prevalence and genetic characteristics of NoV associated with sporadic AGE while exploring the possibility of detecting NoV recombination events. Among the analyzed samples, we identified 355 cases positive for NoV, 11 cases attributed to GI genotypes, and 344 associated with GII genotypes. Notably, we discovered four distinct GI genotypes (GI.2, GI.3, GI.4, and GI.6) and seven diverse GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.14, and GII.17). The predominant genotypes were GII.4 (56.4%; 194 out of 344), followed by GII.2 and GII.3. Through dual genotyping based on sequencing of the ORF1/ORF2 junction region, we identified a total of 14 different RdRp/capsid genotypes. Of particular interest were the prevalent recombinant genotypes GII.4[P31] and GII.2[P16]. Notably, our study revealed a decrease in the number of children infected with NoV during and after the COVID-19 pandemic. These findings underscore the importance of continuous NoV surveillance efforts.


Assuntos
Infecções por Caliciviridae , Variação Genética , Norovirus , Criança , Pré-Escolar , Humanos , Lactente , Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , COVID-19 , Fezes/virologia , Genótipo , Japão/epidemiologia , Norovirus/classificação , Norovirus/genética , Filogenia , Prevalência , Adolescente , Proteínas do Capsídeo/genética
4.
Nature ; 617(7961): 581-591, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-37165188

RESUMO

The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.


Assuntos
Ácidos e Sais Biliares , Microbioma Gastrointestinal , Intestinos , Metaboloma , Proteoma , Humanos , Ácidos e Sais Biliares/metabolismo , Microbioma Gastrointestinal/fisiologia , Proteoma/metabolismo , Bactérias/classificação , Bactérias/isolamento & purificação , Bacteriófagos/isolamento & purificação , Bacteriófagos/fisiologia , Fezes/química , Fezes/microbiologia , Fezes/virologia , Intestinos/química , Intestinos/metabolismo , Intestinos/microbiologia , Intestinos/fisiologia , Intestinos/virologia , Digestão/fisiologia
5.
J Clin Virol ; 164: 105497, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37253299

RESUMO

BACKGROUND: Rotavirus group A (RVA) is a causative agent of acute gastroenteritis among young children worldwide, despite the global expansion of rotavirus vaccination. In Korea, although the prevalence of RVA has been reduced among young children owing to vaccination, nosocomial infections still occur among neonates. OBJECTIVES: The aim of this study was to investigate the molecular epidemiology of RVA strains associated with several neonatal outbreaks in Seoul from 2017 to 2020. STUDY DESIGN: Clinical and environmental samples were collected and screened for the presence of RVA using ELISA and PCR targeting VP6, respectively. RVA-positive strains were genotyped via RT-PCR and subsequent sequencing of VP4 and VP7 and were phylogenetically compared with RVA strains from other countries. RESULTS: During 2017-2020, a total of 15 RVA outbreaks occurred at neonatal facilities (six in hospital neonatal wards and nine in postpartum care centers) in Seoul, and only two RVA genotypes were detected: G4P[6] and G8P[6]. G8P[6] emerged in Seoul November 2018 and immediately became the predominant genotype among neonates, at least up to 2020. Phylogenetic analysis revealed that the G8P[6] genotype in this study was closely related to G8P[6] strains first identified in Korea in 2017, but differed from G8P[6] strains detected in Africa. CONCLUSIONS: A novel G8P[6] genotype of RVA strains has emerged and caused outbreaks among neonates in Seoul. Continued surveillance for circulating RVA genotypes is imperative to monitor genotype changes and their potential risks to public health.


Assuntos
Infecção Hospitalar , Surtos de Doenças , Epidemiologia Molecular , Filogenia , Infecções por Rotavirus , Rotavirus , Feminino , Humanos , Recém-Nascido , Fezes/virologia , Genótipo , Rotavirus/genética , Infecções por Rotavirus/epidemiologia , Infecções por Rotavirus/virologia , Seul/epidemiologia , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/virologia , Proteínas do Capsídeo/genética , Microbiologia Ambiental , Masculino
6.
Sci Rep ; 13(1): 8410, 2023 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-37225865

RESUMO

Surveillance of influenza A viruses (IAVs) among migratory waterfowl is a first step in understanding the ecology, biology, and pathogenicity of IAVs. As part of the nationwide surveillance effort for IAVs in fowl in South Korea, we collected environmental fecal samples in different migratory bird stopover sites in South Korea during the winter seasons within November 2014 through January 2018. We collected a total of 6758 fecal samples, 75 of which were positive for IAV (1.11% positivity). Prevalence of IAVs varied per site and per year. Based on sequencing, the most prevalent hemagglutinin (HA) subtypes were H1, H6, and H5, and the most prevalent neuraminidase (NA) subtypes were N1, N3, and N2. Phylogenetic analyses showed that the genes we isolated clustered with reported isolates collected from other locations along the East Asian-Australasian Flyway. All the H5 and H7 isolates collected in this study were of low pathogenicity. None of the N1 and N2 genes carried amino acid markers of resistance against NA inhibitors. The winter 2016-2017 subset were primarily borne by migratory geese (Anser spp.). These results suggest that majority of the IAVs circulating among migratory wild fowl in South Korea in 2014-2018 were of low pathogenicity.


Assuntos
Anseriformes , Vírus da Influenza A , Influenza Aviária , Animais , Antivirais , Gansos/virologia , Vírus da Influenza A/genética , Vírus da Influenza A/patogenicidade , Filogenia , República da Coreia/epidemiologia , Influenza Aviária/diagnóstico , Influenza Aviária/epidemiologia , Influenza Aviária/genética , Influenza Aviária/virologia , Fezes/virologia , Anseriformes/virologia , Monitoramento Biológico
7.
Microbiol Spectr ; 11(3): e0434022, 2023 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-36995238

RESUMO

Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.


Assuntos
Bacteriófagos , Fezes , Lactobacillus plantarum , Humanos , Bacteriófagos/classificação , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Fezes/microbiologia , Fezes/virologia , Lactobacillus plantarum/virologia , Metagenômica , Técnicas de Cultura , Genoma Viral/genética , Biodiversidade
8.
PLoS One ; 18(1): e0278675, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36649247

RESUMO

BACKGROUND: HIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but data are limited about its impact on postpartum women and their infants. As such, we characterized SARS-CoV-2 infection among mother-infant pairs in Nairobi, Kenya. METHODS: We conducted a nested study of 62 HIV-uninfected and 64 healthy women living with HIV, as well as their HIV-exposed uninfected (N = 61) and HIV-unexposed (N = 64) infants, participating in a prospective cohort. SARS-CoV-2 serology was performed on plasma collected between May 1, 2020-February 1, 2022 to determine the incidence, risk factors, and symptoms of infection. SARS-CoV-2 RNA PCR and sequencing was also performed on available stool samples from seropositive participants. RESULTS: SARS-CoV-2 seropositivity was found in 66% of the 126 mothers and in 44% of the 125 infants. There was no significant association between SARS-CoV-2 infection and maternal HIV (Hazard Ratio [HR] = 0.810, 95% CI: 0.517-1.27) or infant HIV exposure (HR = 1.47, 95% CI: 0.859-2.53). Maternal SARS-CoV-2 was associated with a two-fold increased risk of infant infection (HR = 2.31, 95% CI: 1.08-4.94). Few participants (13% mothers, 33% infants) had symptoms; no participant experienced severe COVID-19 or death. Seroreversion occurred in about half of mothers and infants. SARS-CoV-2 sequences obtained from stool were related to contemporaneously circulating variants. CONCLUSIONS: These data indicate that postpartum Kenyan women and their infants were at high risk for SARS-CoV-2 infection and that antibody responses waned over an average of 8-10 months. However, most cases were asymptomatic and healthy women living with HIV did not have a substantially increased risk of infection or severe COVID-19.


Assuntos
COVID-19 , Infecções por HIV , Feminino , Humanos , Lactente , COVID-19/epidemiologia , COVID-19/complicações , Infecções por HIV/epidemiologia , Infecções por HIV/complicações , Quênia/epidemiologia , Período Pós-Parto , Estudos Prospectivos , RNA Viral/análise , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Estudos de Casos e Controles , Fezes/virologia , Reação em Cadeia da Polimerase
9.
J Virol ; 96(18): e0103422, 2022 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-36040179

RESUMO

The duration of SARS-CoV-2 genomic RNA shedding is much longer than that of infectious SARS-CoV-2 in most COVID-19 patients. It is very important to determine the relationship between test results and infectivity for efficient isolation, contact tracing, and post-isolation. We characterized the duration of viable SARS-CoV-2, viral genomic and subgenomic RNA (gRNA and sgRNA), and rapid antigen test positivity in nasal washes, oropharyngeal swabs, and feces of experimentally infected Syrian hamsters. The duration of viral genomic RNA shedding is longer than that of viral subgenomic RNA, and far longer than those of rapid antigen test (RAgT) and viral culture positivity. The rapid antigen test results were strongly correlated with the viral culture results. The trend of subgenomic RNA is similar to that of genomic RNA, and furthermore, the subgenomic RNA load is highly correlated with the genomic RNA load. IMPORTANCE Our findings highlight the high correlation between rapid antigen test and virus culture results. The rapid antigen test would be an important supplement to real-time reverse transcription-RCR (RT-PCR) in early COVID-19 screening and in shortening the isolation period of COVID-19 patients. Because the subgenomic RNA load can be predicted from the genomic RNA load, measuring sgRNA does not add more benefit to determining infectivity than a threshold determined for gRNA based on viral culture.


Assuntos
COVID-19 , RNA Viral , SARS-CoV-2 , Animais , COVID-19/diagnóstico , COVID-19/virologia , Cricetinae , Fezes/virologia , Genômica , Humanos , Mesocricetus , RNA Viral/análise , RNA Viral/genética , SARS-CoV-2/genética , Eliminação de Partículas Virais
10.
Nature ; 607(7918): 345-350, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35768512

RESUMO

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


Assuntos
Saliva , Glândulas Salivares , Viroses , Vírus , Astroviridae , Aleitamento Materno , Células Cultivadas , Fezes/virologia , Feminino , Humanos , Imunoglobulina A/imunologia , Lactente , Norovirus , Rotavirus , Saliva/virologia , Glândulas Salivares/virologia , Esferoides Celulares/virologia , Viroses/transmissão , Viroses/virologia , Vírus/crescimento & desenvolvimento
12.
BMC Vet Res ; 18(1): 195, 2022 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-35606875

RESUMO

BACKGROUND: Feline parvovirus (FPV) is a member of the family Parvoviridae, which is a major enteric pathogen of cats worldwide. This study aimed to investigate the prevalence of feline parvovirus in Beijing of China and analyze the genetic features of detected viruses. RESULTS: In this study, a total of 60 (8.5%) parvovirus-positive samples were detected from 702 cat fecal samples using parvovirus-specific PCR. The complete VP2 genes were amplified from all these samples. Among them, 55 (91.7%) sequences were characterized as FPV, and the other five (8.3%) were typed as canine parvovirus type 2 (CPV-2) variants, comprised of four CPV-2c and a new CPV-2b strain. In order to investigate the origin of CPV-2 variants in cats, we amplified full-length VP2 genes from seven fecal samples of dogs infected with CPV-2, which were further classified as CPV-2c. The sequences of new CPV-2b/MT270586 and CPV-2c/MT270587 detected from feline samples shared 100% identity with previous canine isolates KT156833 and MF467242 respectively, suggesting the CPV-2 variants circulating in cats might be derived from dogs. Sequence analysis indicated new mutations, Ala91Ser and Ser192Phe, in the FPV sequences, while obtained CPV-2c carried mutations reported in Asian CPV variants, showing they share a common evolutionary pattern with the Asian 2c strains. Interestingly, the FPV sequence (MT270571), displaying four CPV-specific residues, was found to be a putative recombinant sequence between CPV-2c and FPV. Phylogenetic analysis of the VP2 gene showed that amino acid and nucleotide mutations promoted the evolution of FPV and CPV lineages. CONCLUSIONS: Our findings will be helpful to further understand the circulation and evolution of feline and canine parvovirus in Beijing.


Assuntos
Doenças do Gato , Vírus da Panleucopenia Felina , Infecções por Parvoviridae , Animais , Pequim , Doenças do Gato/epidemiologia , Doenças do Gato/genética , Doenças do Gato/virologia , Gatos/virologia , Doenças do Cão/epidemiologia , Doenças do Cão/genética , Doenças do Cão/virologia , Cães , Fezes/virologia , Vírus da Panleucopenia Felina/genética , Vírus da Panleucopenia Felina/isolamento & purificação , Infecções por Parvoviridae/epidemiologia , Infecções por Parvoviridae/genética , Infecções por Parvoviridae/veterinária , Infecções por Parvoviridae/virologia , Parvovirus Canino/genética , Parvovirus Canino/isolamento & purificação , Filogenia
13.
PLoS One ; 17(3): e0265426, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35298520

RESUMO

BACKGROUND: Faecal microbiota transplantation (FMT) is an efficacious treatment for patients with recurrent Clostridioides difficile infections (rCDI). Stool banks facilitate FMT by providing screened faecal suspensions from highly selected healthy donors. Due to the ongoing coronavirus disease 2019 (COVID-19) pandemic and the potential risk of SARS coronavirus-2 (SARS-CoV-2) transmission via FMT, many stool banks were forced to temporarily halt and adjust donor activities. GOAL: The evaluation of a strategy to effectively continue stool banking activities during the ongoing COVID-19 pandemic. STUDY: To restart our stool banking activities after an initial halt, we implemented periodic SARS-CoV-2 screening in donor faeces and serum, and frequent donor assessment for COVID-19 related symptoms. FMT donor and recipient data obtained before (2016-2019) and during the COVID-19 pandemic (March 2020-August 2021) were compared to assess stool banking efficacy. RESULTS: Two out of ten donors developed COVID-19. No differences during versus before the COVID-19 pandemic were observed in the number of approved faeces donations (14 vs 22/month, p = 0.06), FMT requests for rCDI (3.9 vs 4.3/month, p = 0.6); rCDI patients eligible for FMT (80.6% vs 73.3%, p = 0.2); rCDI cure rate (90.3% vs 89.2%, p = 0.9); CDI-free survival (p = 0.7); the number of non-rCDI patients treated with FMT (0.5/month vs 0.4/month), and the number of possibly FMT related adverse events (9.5% vs 7.8%, p = 0.7). Two FMTs for rCDI were delayed due to COVID-19. CONCLUSIONS: There is a continued need for FMT treatment of rCDI during the COVID-19 pandemic. Appropriate donor screening and SARS-CoV-2 infection prevention measures can be implemented in existing protocols without increasing the burden for donors, and allow safe, effective and efficient FMT during the ongoing COVID-19 pandemic. Stool banks should evaluate their SARS-CoV-2 donor screening protocols for long-term sustainability and efficacy, and share their experiences to help the utilisation, standardisation and improvement of stool banks worldwide.


Assuntos
COVID-19/prevenção & controle , Transplante de Microbiota Fecal/métodos , Fezes/virologia , Bancos de Tecidos , Idoso , COVID-19/epidemiologia , COVID-19/transmissão , Infecções por Clostridium/terapia , Feminino , Humanos , Masculino , Países Baixos/epidemiologia , Estudos Retrospectivos , SARS-CoV-2
14.
Science ; 375(6585): 1100-1104, 2022 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-35271341
15.
Sci Rep ; 12(1): 1824, 2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35115615

RESUMO

The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.


Assuntos
Microbioma Gastrointestinal/genética , Genoma Viral , Povos Indígenas , Vírus/genética , Fezes/virologia , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Malásia , Metagenômica/métodos , Filogenia , Viroma/genética , Vírus/classificação
16.
Sci Rep ; 12(1): 2842, 2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35181717

RESUMO

In neonates, rotavirus (RV) infection is generally nosocomial. The control of rotaviral infection within hospital settings is challenging due to prolonged shedding of the virus and contamination of the surrounding environment. There are few studies that have reported asymptomatic infection within neonates. In this study, neonates were screened for RV infection and possible clinical manifestations that may play a role in RV acquisition were analysed. Stool samples were collected from 523 hospitalized neonates admitted for > 48 h in a low-cost and higher-cost tertiary centre. RV antigen was screened using ELISA and the samples which tested positive were confirmed by semi-nested RT-PCR. RV was detected in 34% of participants and genotypes identified included G12P[11] (44.4%), G10 P[11] (42.6%), G10G12P[11] (10.1%) and G3P[8] (2.9%). ICU admissions were associated with higher viral shedding (p < 0.05). Hospitalization in the low-cost facility ICU was associated with higher RV acquisition risk (p < 0.05). RV was detected in higher rates (36.9%) among neonates with gastrointestinal manifestations. G10P[11] was the predominant genotype for several years (1988-2016) among neonates within India. The preponderance of an emerging G12P[11] genotype and heterotypic distribution was documented. RV surveillance is important to identify emerging strains and establish the road ahead in managing RV infection.


Assuntos
Gastroenterite/diagnóstico , Infecções por Rotavirus/diagnóstico , Rotavirus/isolamento & purificação , Ensaio de Imunoadsorção Enzimática , Fezes/virologia , Feminino , Gastroenterite/genética , Gastroenterite/virologia , Genótipo , Hospitalização , Humanos , Índia/epidemiologia , Lactente , Recém-Nascido , Masculino , Reação em Cadeia da Polimerase , Rotavirus/genética , Rotavirus/patogenicidade , Infecções por Rotavirus/genética , Infecções por Rotavirus/virologia
17.
J Gen Virol ; 103(2)2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-35138239

RESUMO

A novel picornavirus was isolated from the faeces of a diarrhoeic cow using MA-104 cells at the third blind passage. This virus, named Den1/2021/JPN, was completely sequenced using total RNA from the cell culture supernatant by deep sequencing. The genome of Den1/2021/JPN had a standard picornavirus genome organisation with conserved picornaviral motifs. The 5' untranslated region harboured a type-II internal ribosomal entry site. Den1/2021/JPN was most closely related to a bovine parechovirus (Bo_ParV) named cow/2018/4, which has been recently identified in publicly available databases. Phylogenetic analyses and pairwise sequence comparison revealed that Den1/2021/JPN and Bo_ParV cow/2018/4 clustered with parechoviruses and were most closely related to Parechovirus E identified in birds of prey, exhibiting nucleotide sequence similarity of 64.2-64.5 %, 58.6-59.7 % and 66.3-66.4 % in the polyprotein, P1 and 2C+3 CD coding regions, respectively. This study presents the first report on the isolation of Bo_ParV. Den1/2021/JPN and Bo_ParV cow/2018/4, which are candidates for a novel species in the genus Parechovirus.


Assuntos
Fezes/virologia , Genoma Viral , Parechovirus/isolamento & purificação , Infecções por Picornaviridae , RNA Viral , Animais , Bovinos , Japão , Infecções por Picornaviridae/veterinária , Infecções por Picornaviridae/virologia
18.
Viruses ; 14(2)2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-35215766

RESUMO

Few studies have shown the presence of norovirus (NoV) RNA in blood circulation but there is no data on norovirus antigenemia. We examined both antigenemia and RNAemia from the sera of children with NoV infections and studied whether norovirus antigenemia is correlated with the levels of norovirus-specific antibodies and clinical severity of gastroenteritis. Both stool and serum samples were collected from 63 children admitted to Mie National Hospital with acute NoV gastroenteritis. Norovirus antigen and RNA were detected in sera by ELISA and real-time RT-PCR, respectively. NoV antigenemia was found in 54.8% (34/62) and RNAemia in 14.3% (9/63) of sera samples. Antigenemia was more common in the younger age group (0-2 years) than in the older age groups, and most patients were male. There was no correlation between stool viral load and norovirus antigen (NoV-Ag) levels (rs = -0.063; Cl -0.3150 to 0.1967; p = 0.6251). Higher levels of acute norovirus-specific IgG serum antibodies resulted in a lower antigenemia OD value (n = 61; r = -0.4258; CI -0.62 to -0.19; p = 0.0006). Norovirus antigenemia occurred more commonly in children under 2 years of age with NoV-associated acute gastroenteritis. The occurrence of antigenemia was not correlated with stool viral load or disease severity.


Assuntos
Antígenos Virais/sangue , Infecções por Caliciviridae/epidemiologia , Gastroenterite/epidemiologia , Norovirus/imunologia , Adolescente , Infecções por Caliciviridae/virologia , Pré-Escolar , Reações Cruzadas , Ensaio de Imunoadsorção Enzimática , Fezes/virologia , Feminino , Gastroenterite/virologia , Humanos , Lactente , Cinética , Masculino , Epidemiologia Molecular , Norovirus/genética , Filogenia , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real , Carga Viral
19.
Viruses ; 14(2)2022 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-35215796

RESUMO

Bats are widespread mammals of the order Chiroptera. They are key for ecosystem functioning, participating in crucial processes. Their unique ability amongst mammals to fly long distances, their frequently large population sizes, and their longevity favor infectious agent persistence and spread. This includes a large variety of viruses, encompassing many important zoonotic ones that cause severe diseases in humans and domestic animals. Despite this, the understanding of the viral ecological diversity residing in bat populations remains unclear, which complicates the determination of the origins of zoonotic viruses. To gain knowledge on the viral community of a widely distributed insectivorous bat species, we characterized the guano virome of a native Chilean bat species (Myotis chiloensis (Waterhouse, 1840)). By applying a novel enrichment strategy, we were able to secure a consequent percentage of viral reads, providing unprecedented resolution for a bat virome. This in turn enabled us to identify and assemble a new bat alphacoronavirus from Chilean bats closely related to PEDV, an important viral pathogen with high mortality rates in suckling piglets. This study highlights the importance of applying and improving high-resolution virome studies in this vital order to ultimately enhance epidemiological surveillance for potentially zoonotic pathogens.


Assuntos
Alphacoronavirus/genética , Quirópteros/virologia , Genoma Viral/genética , Viroma , Alphacoronavirus/classificação , Alphacoronavirus/isolamento & purificação , Animais , Chile , Fezes/virologia , Filogenia , RNA Viral/genética , Viroma/genética
20.
Viruses ; 14(2)2022 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-35215886

RESUMO

Rat hepatitis E virus (rat HEV) was first identified in wild rats and was classified as the species Orthohepevirus C in the genera Orthohepevirus, which is genetically different from the genotypes HEV-1 to HEV-8, which are classified as the species Orthohepevirus A. Although recent reports suggest that rat HEV transmits to humans and causes hepatitis, the infectivity of rat HEV to non-human primates such as cynomolgus and rhesus monkeys remains controversial. To investigate whether rat HEV infects non-human primates, we inoculated one cynomolgus monkey and five rhesus monkeys with a V-105 strain of rat HEV via an intravenous injection. Although no significant elevation of alanine aminotransferase (ALT) was observed, rat HEV RNA was detected in fecal specimens, and seroconversion was observed in all six monkeys. The partial nucleotide sequences of the rat HEV recovered from the rat HEV-infected monkeys were identical to those of the V-105 strain, indicating that the infection was caused by the rat HEV. The rat HEV recovered from the cynomolgus and rhesus monkeys successfully infected both nude and Sprague-Dawley rats. The entire rat HEV genome recovered from nude rats was identical to that of the V-105 strain, suggesting that the rat HEV replicates in monkeys and infectious viruses were released into the fecal specimens. These results demonstrated that cynomolgus and rhesus monkeys are susceptible to rat HEV, and they indicate the possibility of a zoonotic infection of rat HEV. Cynomolgus and rhesus monkeys might be useful as animal models for vaccine development.


Assuntos
Hepatite Viral Animal/transmissão , Hepevirus/fisiologia , Infecções por Vírus de RNA/veterinária , Zoonoses Virais/transmissão , Alanina Transaminase/sangue , Animais , Anticorpos Antivirais/sangue , Fezes/virologia , Feminino , Hepatite Viral Animal/virologia , Macaca fascicularis , Macaca mulatta , Masculino , Infecções por Vírus de RNA/transmissão , Infecções por Vírus de RNA/virologia , RNA Viral/análise , Ratos , Zoonoses Virais/virologia , Replicação Viral
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