scholarly journals Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)

2020 ◽  
Vol 8 (3) ◽  
pp. 458 ◽  
Author(s):  
Cristina Santiso-Bellón ◽  
Walter Randazzo ◽  
Alba Pérez-Cataluña ◽  
Susana Vila-Vicent ◽  
Roberto Gozalbo-Rovira ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Epidemiological Surveillance ◽  
Rt Pcr ◽  
Viral Loads ◽  
Norovirus Gii ◽  
One Year ◽  
The City

The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology.

scholarly journals ACUTE GASTROENTERITIS ASSOCIATED WITH NOROVIRUS GII.4 VARIANTS

2018 ◽  
Vol 55 (3) ◽  
pp. 264-266 ◽  
Author(s):  
Fabiana Lopes de PAULA ◽  
Silvia Inês SARDI ◽  
Dellane Martins TIGRE ◽  
Flora Maria de Campos FERNANDES ◽  
Gúbio Soares CAMPOS
Keyword(s):  
Molecular Epidemiology ◽  
New Orleans ◽  
Acute Gastroenteritis ◽  
Etiologic Agent ◽  
Rt Pcr ◽  
Stool Samples ◽  
Sequences Analysis ◽  
Norovirus Gii ◽  
The City ◽  
Children Under 5

ABSTRACT BACKGROUND: Norovirus (NoV) is an important etiologic agent of acute gastroenteritis and infects individuals of all ages, especially children in Brazil and worldwide. NoV GII.4 was the most prevalent genotype worldwide because of your extensive genetic diversity. In Brazil, especially in the Northeast, few studies have been developed for identify and molecularly characterize NoV. OBJECTIVE: The present study aimed to detect and describe the molecular epidemiology of NoV associated with acute gastroenteritis. METHODS: The viral RNA extracted from stool samples were subjected to Nested RT-PCR and the genotypes were determined by nucleotide sequences analysis. In total, 278 stool samples assisted at Aliança Hospital in the city of Salvador, with acute gastroenteritis were examined, between March 2009 and July 2012. RESULTS: A high NoV rate (54.2%) was identified in children under 5 years of age. We detected the circulation of different NoV GII.4 variants in Salvador, during the study period as Den Haag 2006b, New Orleans 2009 and Sydney 2012. CONCLUSION: These findings reinforce the need to study the molecular epidemiology of NoV infections in acute gastroenteritis.

scholarly journals Multiple-serotype models of dengue virus transmission: simulation study and perspectives for the application of inference in epidemiological surveillance

2019 ◽  
Author(s):  
Caetano Souto-Maior
Keyword(s):  
Dengue Virus ◽  
Rio De Janeiro ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Simulated Data ◽  
Epidemiological Surveillance ◽  
Model Parameters ◽  
The City

AbstractWith around 3 billion people at risk, dengue virus is endemic to many parts of the world. In the Brazilian city of Rio de Janeiro, surveillance measures require notification of new dengue virus cases, and are supplemented by serum collection from patients and sequencing of viral RNA. Phylogenetic analyses have been performed for all serotypes circulating in the country to identify viral genotypes, potentially identify new introductions, and compare viruses presently circulating in the country with those in the past, and of other countries. As a separate type of analysis, a number of mathematical models have been developed to describe dengue virus transmission – particularly qualitative incidence or prevalence patterns – although few have been tested. In this chapter, I show how different mathematical formulations could represent transmission of dengue virus by mosquitoes to humans, how the different model structures entail assumptions about the process, and how these affect outputs qualitatively. Inference from simulated data is used as proof of principle that the kind of data available could be used to accurately estimate all model parameters; however, it is shown that stochasticity may severely hamper efforts to test the models quantitatively. I further implement inference from sequence data for the different models, and compare the performance to that of time series. The methods are applied to the data available for the city of Rio de Janeiro.

Real-time molecular beacon NASBA for rapid and sensitive detection of norovirus GII in clinical samples

2009 ◽  
Vol 55 (12) ◽  
pp. 1375-1380 ◽  
Author(s):  
Safaa Lamhoujeb ◽  
Hugues Charest ◽  
Ismail Fliss ◽  
Solange Ngazoa ◽  
Julie Jean
Keyword(s):  
Real Time ◽  
Molecular Beacon ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Reading Frame ◽  
Viral Loads ◽  
Reverse Transcription Pcr ◽  
Highly Sensitive ◽  
Nasba Assay ◽  
Norovirus Gii

To improve the sensitivity and efficiency of the real-time nucleic acid sequence based amplification (NASBA) assay targeting the open reading frame 1–2 (ORF1–ORF2) junction of the norovirus (NoV) genome, a selection of clinical samples were analyzed. The assay results were compared with those of TaqMan and conventional reverse transcription PCR (RT-PCR) and a commercial enzyme-linked immunoassay (ELISA) for the specific detection of GII NoV in 96 fecal samples. Based on end-point dilution, the two real-time assays had similar sensitivities (0.01 particle detectable units), two log10cycles greater than that of conventional RT-PCR. GII NoV was detected in 88.54% of the samples by real-time NASBA, in 86.46% by TaqMan RT-PCR, in 81.25% by conventional RT-PCR, and in 65.7% by ELISA. The two real-time assays were in agreement for 88.5% of the samples. These results demonstrate that real-time NASBA with a molecular beacon probe is highly sensitive, accurate, and specific for NoV detection in clinical samples. Applying this technique to samples with complex matrix and low viral loads, such as food and environmental samples, could be useful for the detection of NoVs and will improve the prevention of NoV outbreaks.

scholarly journals Molecular Epidemiology of Human Norovirus in Korea in 2013

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Jae-Seok Kim ◽  
Hyun Soo Kim ◽  
Jungwon Hyun ◽  
Han-Sung Kim ◽  
Wonkeun Song
Keyword(s):  
Molecular Epidemiology ◽  
Acute Gastroenteritis ◽  
Antigen Test ◽  
Rt Pcr ◽  
Human Norovirus ◽  
Norovirus Gii

Norovirus is a major cause of acute gastroenteritis. The molecular epidemiology of norovirus exhibits temporal and geographical fluctuations, and new variants of the GII.4 genotype emerge every 2-3 years to cause global epidemics of acute gastroenteritis. We investigated GI and GII genotypes of human norovirus strains isolated from patients with acute gastroenteritis in Korea in 2013. Norovirus antigen test was performed on 2,980 fecal specimens from January to December 2013. RNA was extracted from norovirus antigen-positive fecal suspensions, and the norovirus capsid (VP1) and polymerase (RdRp) genes were characterized by RT-PCR and sequencing. Of the 230 genotyped strains, GII.4 (77.3%) was the most frequently observed capsid genotype, followed by GII.3 (6.1%) and GII.13 (3.9%). A norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the most frequently found polymerase/capsid genotype (65.7%), followed by GII.P17/GII.17 (2.1%) and GII.P21/GII.3 (2.1%). Phylogenetic, similarity, and capsid epitope analyses of GII.Pe/GII.4 Sydney 2012 strains were performed. We concluded that the norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the main cause of norovirus-related gastroenteritis in Korea in 2013.

L’absence chez Michel Butor. L’Emploi du temps et Degrés

2012 ◽  
pp. 66-80
Author(s):  
Michał Mrozowicki
Keyword(s):  
Human Memory ◽  
Point Of View ◽  
Narrative Discourse ◽  
The Novel ◽  
Michel Butor ◽  
Starting Point ◽  
One Year ◽  
The Moment ◽  
Narrative Mode ◽  
The City

Michel Butor, born in 1926, one of the leaders of the French New Novel movement, has written only four novels between 1954 and 1960. The most famous of them is La Modification (Second thoughts), published in 1957. The author of the paper analyzes two other Butor’s novels: L’Emploi du temps (Passing time) – 1956, and Degrés (Degrees) – 1960. The theme of absence is crucial in both of them. In the former, the novel, presented as the diary of Jacques Revel, a young Frenchman spending a year in Bleston (a fictitious English city vaguely similar to Manchester), describes the narrator’s struggle to survive in a double – spatial and temporal – labyrinth. The first of them, formed by Bleston’s streets, squares and parks, is symbolized by the City plan. During his one year sojourn in the city, using its plan, Revel learns patiently how to move in its different districts, and in its strange labyrinth – strange because devoid any centre – that at the end stops annoying him. The other, the temporal one, symbolized by the diary itself, the labyrinth of the human memory, discovered by the narrator rather lately, somewhere in the middle of the year passed in Bleston, becomes, by contrast, more and more dense and complex, which is reflected by an increasinly complex narration used to describe the past. However, at the moment Revel is leaving the city, he is still unable to recall and to describe the events of the 29th of February 1952. This gap, this absence, symbolizes his defeat as the narrator, and, in the same time, the human memory’s limits. In Degrees temporal and spatial structures are also very important. This time round, however, the problems of the narration itself, become predominant. Considered from this point of view, the novel announces Gerard Genette’s work Narrative Discourse and his theoretical discussion of two narratological categories: narrative voice and narrative mode. Having transgressed his narrative competences, Pierre Vernier, the narrator of the first and the second parts of the novel, who, taking as a starting point, a complete account of one hour at school, tries to describe the whole world and various aspects of the human civilization for the benefit of his nephew, Pierre Eller, must fail and disappear, as the narrator, from the third part, which is narrated by another narrator, less audacious and more credible.

Perfil da Linguagem em Pacientes com Acidente Vascular Encefálico Atendidos pelo Serviço Assistencial Domiciliar Multidisciplinar em Porto Velho – Rondônia

REVISTA FIMCA ◽  
2018 ◽  
Vol 5 (1) ◽  
pp. 34-42
Author(s):  
Amanda Leite Silva Cabral ◽  
Flávia Peres Lima ◽  
Jéssica Iara Costa Bessa Paraguassú
Keyword(s):  
Communication Skills ◽  
Oral Language ◽  
Care Service ◽  
Oral Communication ◽  
Etiologic Factor ◽  
Test Protocol ◽  
Cross Sectional ◽  
One Year ◽  
The City ◽  
Porto Velho

Introdução: A afasia é uma das sequelas mais importantes que ocorrem após lesão cerebral de acidente vascular encefálico (AVE). Objetivos: Identificar o perfil da linguagem oral de pacientes com AVE, atendidos pelo Serviço Assistencial Multidisciplinar Domiciliar (SAMD) na cidade de Porto Velho – RO. Materiais e Métodos: Trata-se de um estudo transversal e quantitativo, realizado na residência dos pacientes que estavam sendo atendidos pelo SAMD. Onde foi utilizado o protocolo de Teste de Reabilitação das Afasias composto inicialmente de um questionário que foi aplicados com os familiares dos pacientes para coletar dados quanto ao AVE e os Testes de Comunicação Oral para avaliar dos pacientes. Resultados: Foram avaliados 11 sujeitos com AVE e oito sujeitos apresentaram afasia emissiva do tipo Broca (100%) com presença de agramatismo e anomia (87,5%), e déficit na organização da comunicação e na memória (100%). Referente à etiologia do AVE, verificou-se que 62,5% dos sujeitos apresentaram etiologia decorrente de hipertensão, com tempo de sequelas com tempo entre um ano menos e a três anos (37,5%). Todos os sujeitos (100%) eram muito falantes antes do AVE, porem 50% continuaram muito falantes após o AVE e os outros 50% se tornaram pouco falantes. Conclusão: Os resultados evidenciam que a maioria dos sujeitos apresentaram afasia emissiva do tipo Broca, em decorrência de Acidente Vascular Encefálico Isquêmico tendo como fator etiológico a hipertensão. Desencadeando alterações de linguagem como anomia e agramatismo, afetando ainda suas habilidades de comunicação como a memória e a organização da linguagem. Introduction: Aphasia is one of the most important sequels that occur after brain injury from stroke. Objectives: To identify the oral language profile of patients with stroke, assisted by the Multidisciplinary Home Care Service (SAMD) in the city of Porto Velho - RO. Materials and Methods: This was a cross-sectional and quantitative study carried out at the residence of the patients who were being treated by the SAMD. Where the Aphasia Rehabilitation Test protocol was used, composed initially of a questionnaire that was applied with the relatives of the patients to collect data regarding the AVE and the Oral Communication Tests to evaluate the patients. Results: Eleven subjects with EVA were evaluated, and eight subjects presented Embryonic Emphasis of Broca type (100%) with presence of agramatism and anomia (87.5%), and deficits in the organization of communication and memory (100%). Regarding the etiology of the AVE, 62.5% of the subjects presented etiology due to hypertension, with sequelae time between one year less and three years (37.5%). All subjects (100%) were very talented before the AVE, but 50% remained very talented after the AVE and the other 50% became less talkative. Conclusion: The results show that most of the subjects presented Embryonic Emphasis of the Broca type, due to Ischemic Stroke, having as etiologic factor hypertension. Unleashing language changes such as anomie and agramatism, still affecting his communication skills as memory and the organization of language.

scholarly journals Molecular Epidemiology and Phylogenetic Analyses of Influenza B Virus in Thailand during 2010 to 2014

PLoS ONE ◽  
2015 ◽  
Vol 10 (1) ◽  
pp. e0116302 ◽  
Author(s):  
Nipaporn Tewawong ◽  
Kamol Suwannakarn ◽  
Slinporn Prachayangprecha ◽  
Sumeth Korkong ◽  
Preeyaporn Vichiwattana ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Influenza B Virus ◽  
Influenza B ◽  
B Virus

scholarly journals Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study

2021 ◽  
Vol 9 (4) ◽  
pp. 798
Author(s):  
Giorgia Caruana ◽  
Antony Croxatto ◽  
Eleftheria Kampouri ◽  
Antonios Kritikos ◽  
Onya Opota ◽  
...  
Keyword(s):  
Immunoglobulin A ◽  
University Hospital ◽  
Lower Sensitivity ◽  
Clinical Settings ◽  
Rt Pcr ◽  
Emergency Ward ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Asymptomatic Subjects ◽  
Antigen Testing

Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for patients’ cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q®, PanbioTM and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q®, PanbioTM and BD Veritor™, respectively, for viral loads above 105 copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/mL and 100% for viral loads above 107 copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.

scholarly journals COVID-19 among the inhabitants of the slums in the city of Buenos Aires: a population-based study

BMJ Open ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. e044592
Author(s):  
Alejandro Macchia ◽  
Daniel Ferrante ◽  
Gabriel Battistella ◽  
Javier Mariani ◽  
Fernán González Bernaldo de Quirós
Keyword(s):  
Incidence Rate ◽  
Buenos Aires ◽  
Reporting System ◽  
Incidence Rates ◽  
Health Reporting ◽  
Rt Pcr ◽  
Slum Dwellers ◽  
Integrated Health ◽  
The Impact ◽  
The City

ObjectiveTo summarise the unfolding of the COVID-19 epidemic among slum dwellers and different social strata in the city of Buenos Aires during the first 20 weeks after the first reported case.DesignObservational study using a time-series analysis. Natural experiment in a big city.SettingPopulation of the city of Buenos Aires and the integrated health reporting system records of positive RT-PCR for COVID-19 tests.ParticipantsRecords from the Argentine Integrated Health Reporting System for all persons with suspected and RT-PCR-confirmed diagnosis of COVID-19 between 31 January and 14 July 2020.OutcomesTo estimate the effects of living in a slum on the standardised incidence rate of COVID-19, corrected Poisson regression models were used. Additionally, the impact of socioeconomic status was performed using an ecological analysis at the community level.ResultsA total of 114 052 people were tested for symptoms related with COVID-19. Of these, 39 039 (34.2%) were RT-PCR positive. The incidence rates for COVID-19 towards the end of the 20th week were 160 (155 to 165) per 100 000 people among the inhabitants who did not reside in the slums (n=2 841 997) and 708 (674 to 642) among slums dwellers (n=233 749). Compared with the better-off socioeconomic quintile (1.00), there was a linear gradient on incidence rates: 1.36 (1.25 to 1.46), 1.61 (1.49 to 1.74), 1.86 (1.72 to 2.01), 2.94 (2.74 to 3.16) from Q2 to Q5, respectively. Slum dwellers were associated with an incidence rate of 14.3 (13.4 to 15.4).ConclusionsThe distribution of the epidemic is socially conditioned. Slum dwellers are at a much higher risk than the rest of the community. Slum dwellers should not be considered just another risk category but an entirely different reality that requires policies tailored to their needs.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

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