Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.

PURPOSE: In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains. METHODS: Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model's performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model's generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison. RESULTS: DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research. CONCLUSION: DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool's ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains.

Betacoronavirus Infection Outbreak, São Paulo, Brazil, Fall 2023.

We report a human coronavirus OC43 infection outbreak in hospitalized patients and healthcare workers in São Paulo, Brazil, occurring after SARS-CoV-2 cases disappeared. Infection was associated with healthcare workers in 5 (29.4%) patients. Routine surveillance including a respiratory virus panel can improve coronavirus detection in both healthcare professionals and patients.

[Clinical symptoms and signs in hamsters during experimental infection with the SARS-CoV-2 virus (Coronaviridae: Betacoronavirus)].

INTRODUCTION: At the beginning of December 2019, humanity has faced a new problem caused by coronavirus. In Hubei province of central China, epidemic events associated with severe primary viral pneumonia in humans began to develop. The isolated etiological agent was identified as a representative of Coronaviridae family. The global pandemic associated with the new coronavirus infection, acute respiratory syndrome type 2 (Severe acute respiratory syndrome 2, SARS-CoV-2), has become a challenge for humanity. OBJECTIVE: In our work, we assessed the replicative ability and pathogenesis of the SARS-CoV-2 virus in hamsters. MATERIALS AND METHODS: Syrian hamsters (n=16) randomly divided into two groups were used in experiment. The first group was infected intranasally with the SARS-CoV-2 virus, strain SARS-CoV-2/human/KAZ/KZ_Almaty/2020 deposited in GenBank under number MZ379258.1. The second group remained as a control group. Clinical manifestations of the disease in hamsters were observed within 14 days. Samples were collected on days 3, 5, 7, 9, 12, and 14 postinfection. The obtained samples were tested for viral isolation in cell culture, histological examination and analysis of viral RNA by RT-PCR. RESULTS: SARS-CoV-2 virus isolates showed efficient replication in the lungs of hamsters, causing pathological lung lesions in animals infected intranasally. Clinical manifestations of the disease in hamsters infected with this virus were characterized by a decrease in temperature and body weight, wetness and ruffled fur, and frequent stroking of the nasal planum. High virus titers were observed following the virus isolation in cell cultures from nasal, oral swabs and lungs of animals infected intranasally. Pathological autopsy demonstrated pathological changes in the lungs. Moreover, transmission by airborne droplets has been established when a healthy hamster was kept together with animals infected using the intranasal method. CONCLUSION: In conclusion, our study showed that the Syrian hamster model is a useful tool for studying the SARS-CoV-2 pathogenesis, as well as testing vaccine candidates against acute respiratory syndrome type 2.

Valor pronóstico de los marcadores bioquímicos en pacientes con COVID-19 / Prognostic value of biochemical markers in patients with COVID-19

Resumen El SARS-CoV-2 es un virus de la familia Coronaviridae, subfamilia coronavirus (CoV) y género β. Este se ha convertido en una amenaza inminente para toda la humanidad por ser el agente causal de la pandemia COVID-19, la cual llevó, por un lado, a la declaratoria de emergencia sanitaria a nivel mundial por parte de la Organización Mundial de la Salud (OMS) y, por otro, a instituir estrictas medidas de control para prevenir su contagio por parte de muchos gobiernos. En cuanto a la fisiopatología presentada en esta entidad, aunque las lesiones pulmonares han sido consideradas como las principales consecuencias de esta infección, a medida que avanza el conocimiento sobre el virus se han identificado también lesiones a nivel cardiaco, hepático y renal, que potencian la severidad de la infección y generan un mayor deterioro de los pacientes, su ingreso a las Unidades de Cuidados Intensivos y un mayor riesgo de mortalidad. Con base en esto, diversas investigaciones se han encaminado a determinar aquellos hallazgos clínicos y paraclínicos que puedan ser relevantes frente al pronóstico de los pacientes. Por lo anterior, la presente revisión aborda literatura disponible sobre los principales biomarcadores bioquímicos reportados por su asociación a daños cardiaco, hepático y renal, los cuales presentan mayor significancia para evaluar el curso, severidad, manejo y pronóstico de la infección, y cuya alteración conlleva finalmente a un mayor riesgo de mortalidad en pacientes hospitalizados que presentan COVID-19.

Abstract SARS-CoV-2 is a virus from the coronaviridae family, coronavirus (CoV) subfamily and genus β, it has become an imminent threat to all humanity as it is the causal agent of the COVID-19 pandemic, which led to On the one hand, the World Health Organization (WHO) declares a worldwide health emergency, and on the other, to institute strict control measures to prevent its spread by many governments. Regarding the pathophysiology presented in this entity, although lung lesions have been considered the main consequences of this infection, as knowledge about the virus progresses, cardiac, hepatic, and renal lesions have also been identified that enhance severity of the infection generating greater deterioration of the patients, their admission to the Intensive Care Units and a higher risk of mortality; Based on this, various investigations have aimed to determine those clinical and paraclinical findings that may be relevant to the prognosis of the patients. Therefore, this review addresses available literature on the main biochemical biomarkers reported for their association with cardiac, liver and kidney damage, which are more significant in evaluating the course, severity, management and prognosis of the infection and whose alteration ultimately leads to an increased risk of mortality in hospitalized patients presenting with COVID-19.

Estudo preliminar para avaliação de sintomas e medicamentos prevalentes do "gênio epidêmico" da pandemia de COVID-19 no Brasil / Preliminary study to assess symptoms and prevalent drugs of the "epidemic genius" of the COVID-19 pandemic in Brazil

Estamos no meio da pandemia do Covid-19, em franco desenvolvimento no Brasil. No momento há perspectivas terapêuticas medicamentosa sem fases iniciais de teste, especialmente para o tratamento dos casos graves, aqueles que implicam em internação ou encaminhamento para Unidades de Terapia Intensiva. Pouco tem sido abordado sobre tentativas de tratamento de pacientes com síndrome respiratória leve. Não há escolha terapêutica efetiva para o início do quadro e, desta forma, a doença cursa de acordo com a resposta imune ou suscetibilidade individual do acometido, e há muito pouco de efetivo e específico que altere a história natural dessa enfermidade. (AU)

Hora de analizar la evidencia de izquierda a derecha / It is time to analyze the evidence from left to right

En este artículo, el autor reflexiona sobre las expectativas de los profesionales de la salud acerca de la evidencia para recomendar tratamiento farmacológico a los pacientes con COVID-19. (AU)

In this article, the author reflects on the expectations of health professionals regarding the evidence to recommend pharmacological treatment to patients with COVID-19. (AU)

Human virome in nasopharynx and tracheal secretion samples

BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

A simple and rapid identification method for newly emerged porcine Deltacoronavirus with loop-mediated isothermal amplification

BACKGROUND: Porcine Deltacoronavirus (PDCoV) is a newly emerged enteropathogenic coronavirus that causes diarrhea and mortality in neonatal piglets. PDCoV has spread to many countries around the world, leading to significant economic losses in the pork industry. Therefore, a rapid and sensitive method for detection of PDCoV in clinical samples is urgently needed. RESULTS: In this study, we developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay specific for nucleocapsid gene to diagnose and monitor PDCoV infections. The detection limit of RT-LAMP assay was 1 × 101 copies of PDCoV, which was approximately 100-fold more sensitive than gel-based one-step reverse transcription polymerase chain reaction (RT-PCR). This assay could specifically amplify PDCoV and had no cross amplification with porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine kobuvirus (PKoV), porcine astrovirus (PAstV), porcine reproductive and respiratory syndrome virus (PRRSV), classic swine fever virus (CSFV), and porcine circovirus type 2 (PCV2). By screening a panel of clinical specimens (N = 192), this method presented a similar sensitivity with nested RT-PCR and was 1-2 log more sensitive than conventional RT-PCR in detection of PDCoV. CONCLUSIONS: The RT-LAMP assay established in this study is a potentially valuable tool, especially in low-resource laboratories and filed settings, for a rapid diagnosis, surveillance, and molecular epidemiology investigation of PDCoV infections. To the best of our knowledge, this is the first work for detection of newly emerged PDCoV with LAMP technology.

Tracking viral particles in the intestinal contents of the American bullfrog, Lithobates catesbeianus, by Transmission Electron Microscopy / Pesquisa de partículas virais em conteúdo intestinal de rãs-touro americanas, Lithobates catesbeianus, por meio da microscopia eletrônica de transmissão

Feces are an important viral agent elimination route for infected carrier animals and in aquatic organisms these pathogenic agents can very rapidly propagate due to the habitation environment. The objective of this work is to track viral particles in the intestinal contents of bullfrogs (Lithobates catesbeianus) from five commercial frog farms in the region of Vale do Paraíba, in the State of São Paulo, Brazil, using negative contrast transmission electron microscopy (TEM). The Coronaviridae, Paramyxoviridae, Parvoviridae and Herpesviridae families were observed and photographed in specimens. This work emphasizes the importance of adopting sanitary measures in commercial farms and confirms that observing feces by TEM is an efficient and rapid diagnostic tool for detecting viral agents...

Sabendo-se que as fezes são uma importante via de eliminação de agentes virais pelos animais portadores e que, por estarem na água, os agentes patogênicos podem se propagar mais rapidamente, objetivou-se a pesquisa de vírus em conteúdo intestinal de rãs-touro (Lithobates catesbeianus) de cinco ranários comerciais na região do Vale do Paraíba, no estado de São Paulo, pela técnica de microscopia eletrônica de transmissão. As famílias Coronaviridae, Paramixoviridae, Parvoviridae e Herpesviridae foram observadas e fotografadas. Este trabalho ressalta a importância da adoção de medidas sanitárias nas criações, além da confirmação de que a observação de fezes pela microscopia eletrônica de transmissão é uma eficiente ferramenta de diagnóstico rápido para agentes virais...

Etiología de las enfermedades diarreicas agudas. I: agentes virales / Etiology of acute diarrheal disease I: viral agents

Se hace una revisión actualizada de los diferentes agentes virales causantes de diarrea tanto en el niño como en el adulto. Se describen las manifestaciones clínicas de los mismos y se hace énfasis en los rotavirus, agente de Norwalk y adenovirus, así como también en los diferentes métodos para su diagnóstico. Se destaca la importancia de la fisiopatología de las diarreas virales, particularmente la concerniente a los rotavirus

Nonfatal demyelinating encephalomyelitis induced by coronavirus (JHM strain) infection in mice

C3H mice infected intravenously with the JHM strain of coronavirus showed high incidence of demyelination (44.8%) and low incidence of encephalitis-induced mortality (6.9%). High titers of virus were detectable in the brain and liver of mice only during the first 3 to 12 days of infection (10 and 10 PFU/g, respectively). Most of the animals recovered from the first phase of disease and some (1.1%) came down with paralysis 6 to 7 weeks after the infection, with no histological changes or virus detectable in their tissues