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1.
J Med Microbiol ; 70(9)2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34516365

RESUMO

Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens: Shigella spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013-2018) included stool culture, microscopy and immunochromatography.Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013-2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested: Shigella spp./enteroinvasive Escherichia coli (EIEC) (P <0.05), Salmonella spp. (P <0.05) and Campylobacter spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.


Assuntos
Gastroenterite/diagnóstico , Reação em Cadeia da Polimerase Multiplex , Reação em Cadeia da Polimerase em Tempo Real , Adenoviridae/isolamento & purificação , Blastocystis hominis/isolamento & purificação , Campylobacter/isolamento & purificação , Cryptosporidium/isolamento & purificação , Dientamoeba/isolamento & purificação , Entamoeba histolytica/isolamento & purificação , Fezes/microbiologia , Fezes/parasitologia , Fezes/virologia , Gastroenterite/microbiologia , Gastroenterite/parasitologia , Giardia lamblia/isolamento & purificação , Humanos , Norovirus/isolamento & purificação , Rotavirus/isolamento & purificação , Salmonella/isolamento & purificação , Shigella/isolamento & purificação
2.
Virol J ; 18(1): 180, 2021 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-34482844

RESUMO

BACKGROUND: Covid-19 has the respiratory tract as the main target of infection, and patients present mainly dyspnea, pneumonia, dry cough, and fever. Nevertheless, organs outside the respiratory tract had been reported in recent studies, including the gastrointestinal tract and liver. The host innate immune system recognizes pathogen-associated molecular patterns (PAMPs) through their pattern recognition receptor (PRRs). Toll-like receptor 7 (TLR-7) is a pattern recognition receptor recognizing ssRNA (SARS-CoV-2 is an ssRNA). Polymorphisms are characterized by two or more alternative forms of a distinct phenotype in the same population. Polymorphisms in tlrs genes can negatively influence the immune response to infectious diseases. There are several references in the literature to non-synonymous single nucleotide (rs) polymorphisms related to several genes. Some of them are important for the innate immunity, as rs 179008 (tlr-7), rs3775291 (tlr3), rs8177374 (tir domain-containing adaptor protein, tirap), rs1024611 (monocyte chemoattractant protein-1, mcp-1) and rs61942233 (2'-5'-oligoadenylate synthase-3, oas-3). CASE PRESENTATION: We identified a 5-year-old-male child with gastrointestinal symptoms and fever presenting acholic stool and jaundice, who was positive for SARS-CoV-2 IgM, IgA, and IgG and presenting the Gln11Leu rs 179008 in tlr-7. The child presented high levels of aspartate aminotransferase, alanine aminotransferase, bilirubin, C-reactive protein, D-dimer, gamma-glutamyl transferase, alkaline phosphatase, and was negative for serological tests for hepatitis A, B, C, E, HIV 1 and 2, herpes virus, cytomegalovirus, Epstein-Barr virus, and negative for RTqPCR for Influenza A and B, RSV and SARS-CoV-2. We also investigated other SNPs in the tlr-3 (rs3775291), tirap (rs8177374), mcp-1 (rs1024611), and oas-3 (rs61942233) genes, and no mutation was detected. After an interview with the child's caregivers, any possible accidental ingestion of drugs or hepatotoxic substances was ruled out. CONCLUSION: To our knowledge, this is the first report of a SARS-CoV-2 caused hepatitis in a male child that has the tlr-7 Gln11Leu rs 179008, which could impair an efficient initial immune response. The knowledge of the patient's immune deficiency could improve the treatment to correct this deficiency with specific medications.


Assuntos
COVID-19/genética , COVID-19/virologia , Hepatite Viral Humana/genética , Hepatite Viral Humana/virologia , Receptor 7 Toll-Like/genética , Anticorpos Antivirais/sangue , COVID-19/imunologia , Pré-Escolar , Infecções por Vírus Epstein-Barr/genética , Infecções por Vírus Epstein-Barr/virologia , Fezes/virologia , Hepatite Viral Humana/imunologia , Herpesvirus Humano 4/isolamento & purificação , Humanos , Imunidade Inata , Influenza Humana , Masculino , Polimorfismo de Nucleotídeo Único , SARS-CoV-2/isolamento & purificação
3.
BMC Microbiol ; 21(1): 242, 2021 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-34488633

RESUMO

BACKGROUND: SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. However, robust and reliable methods are needed to estimate the prevalence and persistence of SARS-CoV-2 in the gut and to ensure the safety of microbiome-based procedures such as faecal microbiota transplant (FMT). The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples. RESULTS: Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Viral particles were concentrated by ultrafiltration, RNA was extracted, and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. The RNA extraction procedure we used allowed for the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool. CONCLUSIONS: Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as FMT.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19 , Fezes/virologia , RNA Viral/isolamento & purificação , SARS-CoV-2/isolamento & purificação , COVID-19/diagnóstico , COVID-19/virologia , Humanos , Limite de Detecção
4.
Viruses ; 13(7)2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34372536

RESUMO

Equine rotavirus group A (ERVA) is one of the most common causes of foal diarrhea. Starting in February 2021, there was an increase in the frequency of severe watery to hemorrhagic diarrhea cases in neonatal foals in Central Kentucky. Diagnostic investigation of fecal samples failed to detect evidence of diarrhea-causing pathogens including ERVA. Based on Illumina-based metagenomic sequencing, we identified a novel equine rotavirus group B (ERVB) in fecal specimens from the affected foals in the absence of any other known enteric pathogens. Interestingly, the protein sequence of all 11 segments had greater than 96% identity with group B rotaviruses previously found in ruminants. Furthermore, phylogenetic analysis demonstrated clustering of the ERVB with group B rotaviruses of caprine and bovine strains from the USA. Subsequent analysis of 33 foal diarrheic samples by RT-qPCR identified 23 rotavirus B-positive cases (69.69%). These observations suggest that the ERVB originated from ruminants and was associated with outbreaks of neonatal foal diarrhea in the 2021 foaling season in Kentucky. Emergence of the ruminant-like group B rotavirus in foals clearly warrants further investigation due to the significant impact of the disease in neonatal foals and its economic impact on the equine industry.


Assuntos
Doenças dos Cavalos/virologia , Cavalos/virologia , Rotavirus/patogenicidade , Animais , Proteínas do Capsídeo/genética , Diarreia/etiologia , Diarreia/virologia , Surtos de Doenças/veterinária , Fezes/virologia , Kentucky , Filogenia , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Rotavirus/classificação , Infecções por Rotavirus/veterinária
5.
Viruses ; 13(7)2021 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-34372544

RESUMO

Porcine deltacoronavirus (PDCoV), a highly transmissible intestinal pathogen, causes mild to severe clinical symptoms, such as anorexia, vomiting and watery diarrhea, in piglets and/or sows. Since the first report of PDCoV infection in Hong Kong in 2012, the virus has readily disseminated to North America and several countries in Asia. However, to date, no unified phylogenetic classification system has been developed. To fill this gap, we classified historical PDCoV reference strains into two major genogroups (G-I and G-II) and three subgroups (G-II-a, G-II-b and G-II-c). In addition, no genetic research on the whole PDCoV genome or spike gene has been conducted on isolates from Taiwan so far. To delineate the genetic characteristics of Taiwanese PDCoV, we performed whole-genome sequencing to decode the viral sequence. The PDCoV/104-553/TW-2015 strain is closely related to the G-II-b group, which is mainly composed of PDCoV variants from China. Additionally, various mutations in the Taiwanese PDCoV (104-553/TW-2015) strain might be linked to the probability of recombination with other genogroups of PDCoVs or other porcine coronaviruses. These results represent a pioneering phylogenetic characterization of the whole genome of a PDCoV strain isolated in Taiwan in 2015 and will potentially facilitate the development of applicable preventive strategies against this problematic virus.


Assuntos
Deltacoronavirus/classificação , Deltacoronavirus/genética , Suínos/virologia , Animais , Coronavirus/genética , Infecções por Coronavirus/virologia , Diarreia/genética , Diarreia/virologia , Fezes/virologia , Filogenia , Doenças dos Suínos/virologia , Taiwan , Sequenciamento Completo do Genoma/métodos
6.
J Gen Virol ; 102(8)2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34424158

RESUMO

Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.


Assuntos
Infecções por Astroviridae , Doenças dos Bovinos , Coinfecção , Diarreia , Animais , Animais Recém-Nascidos/virologia , Infecções por Astroviridae/epidemiologia , Infecções por Astroviridae/veterinária , Infecções por Astroviridae/virologia , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/virologia , China/epidemiologia , Coinfecção/epidemiologia , Coinfecção/veterinária , Coinfecção/virologia , Diarreia/epidemiologia , Diarreia/veterinária , Diarreia/virologia , Fezes/virologia , Prevalência
7.
Sci Rep ; 11(1): 16131, 2021 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-34373501

RESUMO

SARS-CoV-2 has posed an unprecedented challenge to the world. Pandemics have been caused previously by viruses of this family like Middle East Respiratory Corona Virus (MERS CoV), Severe Acute Respiratory Syndrome Corona Virus (SARS CoV). Although these viruses are primarily respiratory viruses, but they have been isolated from non-respiratory samples as well. Presently, the detection rate of SARS-CoV-2 RNA from different clinical specimens using Real Time Reverse Transcriptase Polymerized Chain Reaction (qRT-PCR) after onset of symptoms is not yet well established. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2, MERS CoV, SARS CoV from different types of clinical specimens other than the respiratory using a standard diagnostic test (qRT-PCR). A total of 3429 non-respiratory specimens were recorded: SARS CoV (total sample-802), MERS CoV (total sample-155), SARS CoV-2 (total sample-2347). Out of all the samples studied high positive rate was seen for saliva with 96.7% (14/14; 95% CI 87.6-100.0%) for SARS CoV and 57.5% (58/250; 95% CI - 1.2 to 116.2%) for SARS CoV-2, while low detection rate in urine samples for SARS CoV-2 with 2.2% (8/318; 95% CI 0.6-3.7%) and 9.6% (12/61; 95% CI - 0.9 to 20.1%) for SARS CoV but there was relatively higher positivity in urine samples for MERS CoV with detection rate of 32.4% (2/38; 95% CI - 37.3 to 102.1%). In Stool sample positivity was 54.9% (396/779; 95% CI 41.0-68.8%), 45.2% (180/430; 95% CI 28.1-62.3%) and 34.7% (4/38; 95% CI - 29.5 to 98.9%) for SARS CoV-2, MERS CoV, and SARS CoV, respectively. In blood sample the positivity was 33.3% (7/21; 95% CI 13.2-53.5%), 23.7% (42/277; 95% CI 10.5-36.9%) and 2.5% (2/81; 95% CI 0.00-5.8%) for MERS CoV, SARS CoV-2 and SARS CoV respectively. SARS-CoV-2 along with previous two pandemic causing viruses from this family, were highly detected stool and saliva. A low positive rate was recorded in blood samples. Viruses were also detected in fluids along with unusual samples like semen and vaginal secretions thus highlighting unique pathogenic potential of SARS-CoV-2.


Assuntos
Coronavírus da Síndrome Respiratória do Oriente Médio/genética , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Vírus da SARS/genética , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , COVID-19/virologia , Fezes/virologia , Humanos , Pandemias , SARS-CoV-2/fisiologia , Saliva/virologia
8.
Int J Mol Sci ; 22(16)2021 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-34445529

RESUMO

The circulation of the H9N2 virus results in significant economic losses in the poultry industry, and its zoonotic transmission highlights the need for a highly sensitive and rapid diagnostic and detection system for this virus. In this study, the performance of lateral flow test strips for a fluorescent immunochromatographic test (FICT) was optimized for the diagnosis of H9N2 virus-infected animal samples. The novel monoclonal antibodies (McAbs) against influenza A H9 viruses were developed, and two categories of McAbs with linear and conformational epitopes were compared for the performance of rapid diagnostic performance in the presence of feces sample at different time points (2, 4, and 6 days) post-infection (dpi). The limit of detection (LOD) of FICT and Kd values were comparable between linear and conformational epitope McAbs. However, superior performance of linear epitope McAbs pairs were confirmed by two animal studies, showing the better diagnostic performance showing 100% relative sensitivity in fecal samples at 6 dpi although it showed less than 80% sensitivity in early infection. Our results imply that the comparable performance of the linear epitope McAbs can potentially improve the diagnostic performance of FICT for H9N2 detection in feces samples. This highly sensitive rapid diagnostic method can be utilized in field studies of broiler poultry and wild birds.


Assuntos
Fezes/virologia , Fluorescência , Vírus da Influenza A Subtipo H9N2/isolamento & purificação , Influenza Aviária/diagnóstico , Infecções por Orthomyxoviridae/diagnóstico , Doenças das Aves Domésticas/diagnóstico , Animais , Galinhas , Testes Diagnósticos de Rotina , Feminino , Vírus da Influenza A Subtipo H9N2/imunologia , Influenza Aviária/virologia , Limite de Detecção , Camundongos , Camundongos Endogâmicos BALB C , Infecções por Orthomyxoviridae/virologia , Doenças das Aves Domésticas/virologia
9.
Viruses ; 13(7)2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34372580

RESUMO

Most of the defective/non-infectious enteric phages and viruses that end up in wastewater originate in human feces. Some of the causes of this high level of inactivity at the host stage are unknown. There is a significant gap between how enteric phages are environmentally transmitted and how we might design molecular tools that would only detect infectious ones. Thus, there is a need to explain the low proportion of infectious viral particles once replicated. By analyzing lysis plaque content, we were able to confirm that, under aerobic conditions, Escherichia coli produce low numbers of infectious MS2 phages (I) than the total number of phages indicated by the genome copies (G) with an I/G ratio of around 2%. Anaerobic conditions of replication and ROS inhibition increase the I/G ratio to 8 and 25%, respectively. These data cannot only be explained by variations in the total numbers of MS2 phages produced or in the metabolism of E. coli. We therefore suggest that oxidative damage impacts the molecular replication and assembly of MS2 phages.


Assuntos
Anaerobiose/fisiologia , Levivirus/metabolismo , Replicação Viral/fisiologia , Aerobiose/fisiologia , Colífagos/genética , Escherichia coli/metabolismo , Escherichia coli/virologia , Proteínas de Escherichia coli/metabolismo , Fezes/virologia , Humanos , Levivirus/patogenicidade , Espécies Reativas de Oxigênio/metabolismo , Virulência
10.
J Clin Lab Anal ; 35(9): e23923, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34390043

RESUMO

BACKGROUND: The dynamic alteration and comparative study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding pattern during treatment are limited. This study explores the potential risk factors influencing prolonged viral shedding in COVID-19. METHODS: A total of 126 COVID-19 patients were enrolled in this retrospective longitudinal study. A multivariate logistic regression analysis was carried out to estimate the potential risk factors. RESULTS: 38.1% (48/126) cases presented prolonged respiratory tract viral shedding, and 30 (23.8%) cases presented prolonged rectal swab viral shedding. Obesity (OR, 3.31; 95% CI, 1.08-10.09), positive rectal swab (OR, 3.43; 95% CI, 1.53-7.7), treatment by lopinavir/ritonavir with chloroquine phosphate (OR, 2.5; 95% CI, 1.04-6.03), the interval from onset to antiviral treatment more than 7 days (OR, 2.26; 95% CI, 1.04-4.93), lower CD4+ T cell (OR, 0.92; 95% CI, 0.86-0.99) and higher NK cells (OR, 1.11; 95% CI, 1.02-1.20) were significantly associated with prolonged respiratory tract viral shedding. CD3-CD56+ NK cells (OR, 0.87; 95% CI, 0.76-0.99) were related with prolonged fecal shedding. CONCLUSIONS: Obesity, delayed antiviral treatment, and positive SARS-CoV-2 for stool were independent risk factors for prolonged SARS-CoV-2 RNA shedding of the respiratory tract. A combination of LPV/r and abidol as the initial antiviral regimen was effective in shortening the duration of viral shedding compared with LPV/r combined with chloroquine phosphate. CD4+ T cell and NK cells were significantly associated with prolonged viral shedding, and further studies are to be warranted to determine the mechanism of immunomodulatory response in virus clearance.


Assuntos
COVID-19/virologia , Fezes/virologia , SARS-CoV-2/fisiologia , Eliminação de Partículas Virais/fisiologia , Adulto , Animais , Antivirais/administração & dosagem , Contagem de Linfócito CD4 , COVID-19/epidemiologia , Cloroquina/administração & dosagem , Cloroquina/efeitos adversos , Cloroquina/análogos & derivados , Feminino , Humanos , Células Matadoras Naturais , Estudos Longitudinais , Lopinavir/administração & dosagem , Lynx , Masculino , Obesidade/epidemiologia , Sistema Respiratório/virologia , Estudos Retrospectivos , Fatores de Risco , Ritonavir/administração & dosagem , Fatores de Tempo , Eliminação de Partículas Virais/efeitos dos fármacos
11.
Viruses ; 13(7)2021 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-34372557

RESUMO

Human coronaviruses, including SARS-CoV-2, are known to spread mainly via close contact and respiratory droplets. However, other potential means of transmission may be present. Fomite-mediated transmission occurs when viruses are deposited onto a surface and then transfer to a subsequent individual. Surfaces can become contaminated directly from respiratory droplets or from a contaminated hand. Due to mask mandates in many countries around the world, the former is less likely. Hands can become contaminated if respiratory droplets are deposited on them (i.e., coughing or sneezing) or through contact with fecal material where human coronaviruses (HCoVs) can be shed. The focus of this paper is on whether human coronaviruses can transfer efficiently from contaminated hands to food or food contact surfaces. The surfaces chosen were: stainless steel, plastic, cucumber and apple. Transfer was first tested with cellular maintenance media and three viruses: two human coronaviruses, 229E and OC43, and murine norovirus-1, as a surrogate for human norovirus. There was no transfer for either of the human coronaviruses to any of the surfaces. Murine norovirus-1 did transfer to stainless steel, cucumber and apple, with transfer efficiencies of 9.19%, 5.95% and 0.329%, respectively. Human coronavirus OC43 transfer was then tested in the presence of fecal material, and transfer was observed for stainless steel (0.52%), cucumber (19.82%) and apple (15.51%) but not plastic. This study indicates that human coronaviruses do not transfer effectively from contaminated hands to contact surfaces without the presence of fecal material.


Assuntos
COVID-19/transmissão , Infecções por Coronavirus/transmissão , Microbiologia de Alimentos , SARS-CoV-2/fisiologia , COVID-19/virologia , Linhagem Celular , Resfriado Comum/transmissão , Coronavirus/isolamento & purificação , Coronavirus Humano 229E/isolamento & purificação , Coronavirus Humano OC43/isolamento & purificação , Contaminação de Equipamentos , Fezes/virologia , Fômites , Doenças Transmitidas por Alimentos/virologia , Humanos , Norovirus/isolamento & purificação , Aço Inoxidável
12.
Arch Virol ; 166(9): 2461-2468, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34212242

RESUMO

Bovine coronavirus (BCoV) can be spread by animal activity. Although cattle farming is widespread in Turkey, there are few studies of BCoV. The aim of this study was to evaluate the current situation regarding BCoV in Turkey. This is the first study reporting the full-length nucleotide sequences of BCoV spike (S) genes in Turkey. Samples were collected from 119 cattle with clinical signs of respiratory (n = 78) or digestive tract (n = 41) infection on different farms located across widely separated provinces in Turkey. The samples were screened for BCoV using RT-nested PCR targeting the N gene, which identified BCoV in 35 samples (9 faeces and 26 nasal discharge). RT-PCR analysis of the S gene produced partial/full-length S gene sequences from 11 samples (8 faeces and 3 nasal discharge samples). A phylogenetic tree of the S gene sequences was made to analyze the genetic relationships among BCoVs from Turkey and other countries. The results showed that the local strains present in faeces and nasal discharge samples had many different amino acid changes. Some of these changes were shown in previous studies to be critical for tropism. This study provides new data on BCoV in Turkey that will be valuable in designing effective vaccine approaches and control strategies.


Assuntos
Doenças dos Bovinos/epidemiologia , Infecções por Coronavirus/veterinária , Coronavirus Bovino/genética , Diarreia/veterinária , RNA Viral/genética , Infecções Respiratórias/veterinária , Glicoproteína da Espícula de Coronavírus/genética , Agricultura , Substituição de Aminoácidos , Animais , Bovinos , Doenças dos Bovinos/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Coronavirus Bovino/classificação , Diarreia/epidemiologia , Diarreia/virologia , Monitoramento Epidemiológico/veterinária , Evolução Molecular , Fezes/virologia , Humanos , Mutação , Cavidade Nasal/virologia , Filogenia , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de DNA , Turquia/epidemiologia
13.
Arch Virol ; 166(9): 2623-2625, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34244860

RESUMO

Here, using viral metagenomics combined with conventional PCR, the complete genome sequence of a novel anellovirus (named anel-ch-zj and GenBank no. MT157223) from nasopharynx secretion specimens from hospitalized neonates was determined, and the deduced amino acid sequence of its ODF1 protein was found to be only 33.19%-39.33% identical to those of related anelloviruses with sequences available in the GenBank database, suggesting that it represents a putative new genus within the family Anelloviridae. PCR screening of 135 samples (including 45 nasopharynx secretion, 45 blood, and 45 fecal specimens collected from 45 individual hospitalized neonates) indicated that two nasopharynx secretion, two blood, and four fecal samples were positive for anel-ch-zj. Further PCR screening of 50 blood samples, 115 fecal samples, and 396 nasopharynx secretions collected from hospitalized children 1-5 years old did not yield any positive results. Whether this novel anellovirus detected in neonates is associated with specific diseases needs future investigation.


Assuntos
Anelloviridae/classificação , Anelloviridae/isolamento & purificação , Criança Hospitalizada , Filogenia , Anelloviridae/genética , DNA Viral/genética , Fezes/virologia , Humanos , Recém-Nascido , Metagenômica , Nasofaringe/virologia , Reação em Cadeia da Polimerase , Sequenciamento Completo do Genoma
14.
Arch Virol ; 166(9): 2591-2596, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34244861

RESUMO

Between 2016 and 2018, the prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in Korean wild boars (n = 845) was 28.0% and 10.7%, respectively. Coinfection by both viruses was detected in 5.1% of boars. Phylogenetic analysis revealed that 134 PKoV isolates belonged to diverse lineages within the species Aichivirus C; however, one strain (WKoV16CN-8627) clustered with bovine kobuvirus (Aichivirus B). Forty-seven PAstVs belonged to lineage PAstV4, and only one strain (WAst17JN-10931) was a novel addition to lineage PAstV2. The two viruses were more prevalent in boars weighing ≤ 60 kg than in boars weighing > 61 kg.


Assuntos
Kobuvirus/classificação , Kobuvirus/isolamento & purificação , Mamastrovirus/classificação , Mamastrovirus/isolamento & purificação , Filogenia , Sus scrofa/virologia , Animais , Infecções por Astroviridae/epidemiologia , Infecções por Astroviridae/virologia , Bovinos , DNA Viral , Diarreia/virologia , Fezes/virologia , Genótipo , Kobuvirus/genética , Mamastrovirus/genética , Prevalência , República da Coreia/epidemiologia , Análise de Sequência de DNA , Suínos , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/virologia
15.
Viruses ; 13(6)2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34199933

RESUMO

Bovine coronavirus (BCoV) is the causative agent of winter dysentery (WD). In adult dairy cattle, WD is characterized by hemorrhagic diarrhea and a reduction in milk production. Therefore, WD leads to significant economic losses in dairy farms. In this study, we aimed to isolate and characterize local BCoV strains. BCoV positive samples, collected during 2017-2021, were used to amplify and sequence the S1 domain of S glycoprotein and the full hemagglutinin esterase gene. Based on our molecular analysis, local strains belong to different genetic variants circulating in dairy farms in Israel. Phylogenetic analysis revealed that all local strains clustered together and in proximity to other BCoV circulating in the area. Additionally, we found that local strains are genetically distant from the reference enteric strain Mebus. To our knowledge, this is the first report providing molecular data on BCoV circulating in Israel.


Assuntos
Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/veterinária , Coronavirus Bovino/genética , Disenteria/veterinária , Filogenia , Animais , Antígenos Virais/genética , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/virologia , Coronavirus Bovino/classificação , Coronavirus Bovino/isolamento & purificação , Indústria de Laticínios , Disenteria/virologia , Fezes/virologia , Feminino , Variação Genética , Israel/epidemiologia , Análise de Sequência de DNA
16.
Virol J ; 18(1): 134, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210325

RESUMO

BACKGROUND: The persistence of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) RNA in the body fluids of patients with the novel coronavirus disease 2019 (COVID-19) may increase the potential risk of viral transmission. There is still uncertainty on whether the recommended quarantine duration is sufficient to reduce the risk of transmission. This study aimed to investigate the persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19. METHODS: In this hospital-based longitudinal study, 100 confirmed cases of COVID-19 were recruited between March 2020 and August 2020 in Guilan Province, north of Iran. Nasopharyngeal, blood, urine, and stool samples were obtained from each participant at the time of hospital admission, upon discharge, 1 week after discharge, and every 2 weeks until all samples were negative for SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) assay. A survival analysis was also performed to identify the duration of viral persistence. RESULTS: The median duration of viral RNA persistence in the nasopharyngeal samples was 8 days from the first positive RT-PCR result upon admission (95% CI 6.91-9.09); the maximum duration of viral shedding was 25 days from admission. Positive blood, urine, and stool RT-PCR results were detected in 24%, 7%, and 6% of the patients, respectively. The median duration of viral persistence in the blood, urine, and stool samples was 7 days (95% CI 6.07-7.93), 6 days (95% CI 4.16-8.41), and 13 days (95% CI 6.96-19.4), respectively. Also, the maximum duration of viral persistence in the blood, urine, and stool samples was 17, 11, and 42 days from admission, respectively. CONCLUSION: According to the present results, immediately after the hospitalized patients were discharged, no evidence of viral genetic materials was found. Therefore, appropriate treatments were selected for the patients at this hospital. However, we recommend further investigations on a larger sample size in multi-center and prospective randomized controlled trials (RCTs) to evaluate the effects of different drugs on the shedding of the virus through body secretions.


Assuntos
Fezes/virologia , Hospitalização/estatística & dados numéricos , Nasofaringe/virologia , RNA Viral/sangue , RNA Viral/urina , SARS-CoV-2/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/mortalidade , COVID-19/transmissão , COVID-19/virologia , Teste de Ácido Nucleico para COVID-19 , Feminino , Humanos , Irã (Geográfico) , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , RNA Viral/análise , Análise de Sobrevida , Eliminação de Partículas Virais
17.
Arch Virol ; 166(10): 2683-2692, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34268639

RESUMO

Porcine sapelovirus (PSV) infections have been associated with a wide spectrum of symptoms, ranging from asymptomatic infection to clinical signs including diarrhoea, pneumonia, reproductive disorders, and polioencephalomyelitis. Although it has a global distribution, there have been relatively few studies on PSV in domestic animals. We isolated a PSV strain, SHCM2019, from faecal specimens from swine, using PK-15 cells. To investigate its molecular characteristics and pathogenicity, the genomic sequence of strain SHCM2019 was analysed, and clinical manifestations and pathological changes occurring after inoculation of neonatal piglets were observed. The virus isolated using PK-15 cells was identified as PSV using RT-PCR, transmission electron microscopy (TEM), and immunofluorescence assay (IFA). Sequencing results showed that the full-length genome of the SHCM2019 strain was 7,567 nucleotides (nt) in length, including a 27-nucleotide poly(A) tail. Phylogenetic analysis demonstrated that this virus was a PSV isolate belonging to the Chinese strain cluster. Recombination analysis indicated that there might be a recombination breakpoint upstream of the 3D region of the genome. Pathogenicity experiments demonstrated that the virus isolate could cause diarrhoea and pneumonia in piglets. In breif, a recombinant PSV strain, SHCM2019, was isolated and shown to be pathogenic. Our results may provide a reference for future research on the pathogenic mechanism and evolutionary characteristics of PSV.


Assuntos
Infecções por Enterovirus/veterinária , Enterovirus Suínos/genética , Enterovirus Suínos/isolamento & purificação , Doenças dos Suínos/virologia , Animais , Linhagem Celular , China , Infecções por Enterovirus/patologia , Infecções por Enterovirus/virologia , Enterovirus Suínos/classificação , Enterovirus Suínos/patogenicidade , Fezes/virologia , Genoma Viral/genética , Filogenia , Recombinação Genética , Suínos , Doenças dos Suínos/patologia , Virulência
18.
Arch Virol ; 166(9): 2627-2632, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34255185

RESUMO

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.


Assuntos
Ictaluridae/virologia , Percas/virologia , Filogenia , Infecções por Picornaviridae/veterinária , Infecções por Picornaviridae/virologia , Picornaviridae/classificação , Picornaviridae/isolamento & purificação , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência de Aminoácidos , Animais , Fezes/virologia , Água Doce , Genoma Viral , Hungria , Picornaviridae/genética , RNA Viral/genética , Análise de Sequência , Proteínas Virais/genética
19.
Viruses ; 13(6)2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34199948

RESUMO

Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.


Assuntos
Alphacoronavirus/genética , Astroviridae/genética , Quirópteros/virologia , Genoma Viral , Sequenciamento Completo do Genoma , Alphacoronavirus/classificação , Alphacoronavirus/isolamento & purificação , Animais , Astroviridae/classificação , Astroviridae/isolamento & purificação , Dinamarca , Fezes/virologia , Genômica/métodos , Fases de Leitura Aberta , Filogenia
20.
Vet Ital ; 57(1): 19-27, 2021 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-34313095

RESUMO

Individual faecal samples were collected from adult animals in 275 cattle farms previously positive for Mycobacterium avium subsp. paratuberculosis (MAP). In addition, boot swab samples were collected in 30 randomly chosen farms. Faecal samples were tested for MAP by a combination of bacterial culture and PCR. A logistic regression and the Pearson Correlation were used to calculate the relation between the number of MAP­positive cows and boot swab results. In 66.9% of all previously tested herds, no positive individual faecal sample was detected, indicating possible fadeout of the infection. In 9 (30.0%) of the 30 selected farms, at least one MAP­shedding animal was detected in faecal samples individually collected, while only 5 (16.7%) of these farms were found positive when the boot sampling method was used. The sensitivity of the boot swab sampling increased up to 92% (95% CI: 41%­99%), if at least 12 animals were faecal MAP­shedders in a herd. The current study shows possible fadeout of JD in a substantial percentage of previously infected herds. Furthermore, in small herds, a relatively high within­herd prevalence of MAP­shedding animals is needed to assure reliable positive boot swab results.


Assuntos
Doenças dos Bovinos/epidemiologia , Mycobacterium avium subsp. paratuberculosis/isolamento & purificação , Paratuberculose/epidemiologia , Animais , Áustria/epidemiologia , Bovinos , Doenças dos Bovinos/etiologia , Indústria de Laticínios , Fezes/virologia , Feminino , Paratuberculose/etiologia , Prevalência , Sensibilidade e Especificidade , Sapatos , Manejo de Espécimes
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