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Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.

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Zika virus (ZIKV) infection is associated with the Guillain-Barré syndrome, and when non-vector congenital transmission occurs, fetal brain abnormalities are expected. After ZIKV infection, the blood, breast milk, and other body fluids contain low viral loads. Their detection is challenging as it requires the processing of larger input volumes of the clinical samples. Pre-enrichment is a valuable strategy to increase the analyte concentration. Therefore, the authors propose the use of a hierarchal composite polyaniline-(electrospun nanofiber) hydrogel mat (ENM) for the simultaneous enrichment and impedimetric sensing of ZIKV viral particles. The electrospinning conditions of polyvinyl alcohol and alginate, including blend formulation, were optimized through a factorial design. Disintegration and gelatinization were controlled via cross-linking to improve the hydrogel properties. Hierarchization was achieved by in situ chemical deposition of conductive polyaniline. The carboxyl groups of the ENM were used for the covalent immobilization of anti-ZIKV polyclonal antibodies used in the specific recognition of ZIKV within the medium of Vero cell culture. The specific capture and desorption of virions were studied at different pHs. ENMs were characterized by scanning electron microscopy and FTIR. Atomic force microscopy along with UV-vis and electrochemical impedance spectroscopies was used to monitor the antibody immobilization, ZIKV capture, and elution processes. Our results show that 14.2 mg (0.25 cm3) of ENM can capture 38.7 ± 2.5 µg of ZIKV with a desorption rate of 99.97% (38.29 ± 2.7 µg ZIKV), which is reusable for at least three times. Therefore, the capture capacity (micrograms of ZIKV captured per milligram of ENM) of polyaniline-hierarchized mats was 2.72 µg ZIKV/mg. The impedance LOD value was determined to be 2.76 µg of ZIKV particles (approximately 6.6 × 103 PFU/mL). As a result, we present a fast small-scale purification system that can simultaneously monitor ZIKV electrochemically and optically.

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The new coronavirus that was first identified in December 2019 in Wuhan China, now called SARS-CoV-2, which causes the disease called COVID-19, has spread from China to the entire world in a few months. Due to its contagious potential (R0: 5.7) and because there is still no effective treatment to stop the infection, and a vaccine for prevention it is not yet available to the general population, COVID-19 is currently considered a global health problem. The need to implement sensitive methods for the identification of individuals with COVID-19 has led to the development of different molecular and immunological tests. The importance of a timely and accurate diagnosis is essential to determine the course of the pandemic. The interpretation of the results obtained by each test as well as the factors that affect these results have not been fully described. In this review, we describe and analyze the different SARS-CoV-2 detection methods that have been performed in Mexico and are available worldwide, outlining their strengths and weaknesses. Further, a broader perspective of the correct use and interpretation of the results obtained with these diagnostic tools is proposed to improve the containment strategy and identify the true impact of the pandemic.

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Biosensors are measurement devices that can sense several biomolecules, and are widely used for the detection of relevant clinical pathogens such as bacteria and viruses, showing outstanding results. Because of the latent existing risk of facing another pandemic like the one we are living through due to COVID-19, researchers are constantly looking forward to developing new technologies for diagnosis and treatment of infections caused by different bacteria and viruses. Regarding that, nanotechnology has improved biosensors' design and performance through the development of materials and nanoparticles that enhance their affinity, selectivity, and efficacy in detecting these pathogens, such as employing nanoparticles, graphene quantum dots, and electrospun nanofibers. Therefore, this work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.

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O objetivo do estudo foi produzir anticorpos policlonais para vírus bovino e testar a reatividade em imunoensaios como imunofluorescência, imunoperoxidase e slot blot. Como imunógeno utilizou-se cepas e/ou isolados dos herpesvírus bovino tipo 1, 2 e 5 (BoHV-1, BoHV-2 e BoHV-5), vírus da diarreia viral bovina (BVDV), vírus respiratório sincicial bovino (BRSV), vírus da língua azul (BTV) e vírus vaccina (VACV) amplificados em cultivo celular. Os coelhos foram imunizados em intervalos regulares e o soro hiperimune produzido foi utilizado como anticorpo primário nos imunoensaios. A diluição de trabalho para cada antissoro foi determinada por diluição seriada limitante e variaram entre 1:800 e 1:51.200. As maiores diluições foram observadas para imunoperoxidase, quando comparadas com a imunofluorescência e slot blot. Diluições menores que 1:800 foram associadas com aumento de reações inespecíficas. Os antissoros anti-BoHV-1, -BoHV-5, -BVDV e -BRSV reagiram frente a isolados heterólogos em ensaios de imunofluorescência e imunoperoxidase. Conclui-se que os antissoros produzidos possuem elevadas concentrações de anticorpos específicos para os vírus e é uma alternativa para a utilização em imunoensaios.(AU)

The objective of the study was to produce polyclonal antibodies to bovine viruses and to test the reactivity in immunoassays such as immunofluorescence, immunoperoxidase and slot blot. Bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1, 2 and 5 (BoHV-1, BoHV-2 and BoHV-5) blue tongue virus (BTV) and vaccinia virus (VACV) were amplified in cell culture and used to immunize rabbits. Animals were immunized at regular intervals and the hyper immune serum produced was used as primary antibody in the immunoassays. The working dilution for each antiserum was determined by limiting serial dilution and varied from 1: 800 to 1: 51,200. The highest dilutions were observed for immunoperoxidase, when compared with immunofluorescence and slot blot. Dilutions lower than 1:800 were associated with the presence of nonspecific reactions. Anti-BoHV-1, -BoHV-5, -BVDV and -BRSV antisera reacted against heterologous isolates in immunofluorescence and immunoperoxidase assays. It is concluded that the produced polyclonal antibodies have high concentrations of virus-specific antibodies and are an alternative for use in immunoassays.(AU)

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Non-melanoma skin cancers (NMSC) share similar risk factors with other virus-related cancers, despite the lack of proved causal association between viral infection and NMSC development. We investigated the presence of Merkel cell polyomavirus (MCPyV), Epstein-Barr virus (EBV), and human papillomavirus (HPV) DNA in 83 NMSC fresh-frozen and 16 non-cancerous skin biopsies and evaluated viral infection according to demographical data, histopathological diagnosis, and ultraviolet exposure. Our results showed that 75% of NMSC biopsies were positive for at least one out of three viruses, whereas only 38% of non-cancerous skin biopsies were positive (p = 0.02). Notably, HPV detection was frequent in NMSC (43%) and nearly absent (one sample, 6.7%) in non-cancerous biopsies (p = 0.007). MCPyV was associated with sites of higher exposure to ultraviolet radiation (p = 0.010), while EBV was associated with a compromised immune system (p = 0.032). Our study showed that HPV was strongly associated with NMSC while EBV and MCPyV with other risk factors. Though further studies are required to elucidate the role of viral infection in NMSC development and management, this study supports the possible role of oncogenic viruses in skin cancers, especially HPV.

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O objetivo do estudo foi produzir anticorpos policlonais para vírus bovino e testar a reatividade em imunoensaios como imunofluorescência, imunoperoxidase e slot blot. Como imunógeno utilizou-se cepas e/ou isolados dos herpesvírus bovino tipo 1, 2 e 5 (BoHV-1, BoHV-2 e BoHV-5), vírus da diarreia viral bovina (BVDV), vírus respiratório sincicial bovino (BRSV), vírus da língua azul (BTV) e vírus vaccina (VACV) amplificados em cultivo celular. Os coelhos foram imunizados em intervalos regulares e o soro hiperimune produzido foi utilizado como anticorpo primário nos imunoensaios. A diluição de trabalho para cada antissoro foi determinada por diluição seriada limitante e variaram entre 1:800 e 1:51.200. As maiores diluições foram observadas para imunoperoxidase, quando comparadas com a imunofluorescência e slot blot. Diluições menores que 1:800 foram associadas com aumento de reações inespecíficas. Os antissoros anti-BoHV-1, -BoHV-5, -BVDV e -BRSV reagiram frente a isolados heterólogos em ensaios de imunofluorescência e imunoperoxidase. Conclui-se que os antissoros produzidos possuem elevadas concentrações de anticorpos específicos para os vírus e é uma alternativa para a utilização em imunoensaios.

The objective of the study was to produce polyclonal antibodies to bovine viruses and to test the reactivity in immunoassays such as immunofluorescence, immunoperoxidase and slot blot. Bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1, 2 and 5 (BoHV-1, BoHV-2 and BoHV-5) blue tongue virus (BTV) and vaccinia virus (VACV) were amplified in cell culture and used to immunize rabbits. Animals were immunized at regular intervals and the hyper immune serum produced was used as primary antibody in the immunoassays. The working dilution for each antiserum was determined by limiting serial dilution and varied from 1: 800 to 1: 51,200. The highest dilutions were observed for immunoperoxidase, when compared with immunofluorescence and slot blot. Dilutions lower than 1:800 were associated with the presence of nonspecific reactions. Anti-BoHV-1, -BoHV-5, -BVDV and -BRSV antisera reacted against heterologous isolates in immunofluorescence and immunoperoxidase assays. It is concluded that the produced polyclonal antibodies have high concentrations of virus-specific antibodies and are an alternative for use in immunoassays.

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Introduction Rabies is an important zoonosis that occurs in mammals, with bats acting as Lyssavirus reservoirs in urban, rural and natural areas. Rabies cases in bats have been recorded primarily in urban areas in Northwestern State of São Paulo since 1998. This study investigated the circulation of rabies virus by seeking to identify the virus in the brain in several species of bats in this region and by measuring rabies-virus neutralizing antibody levels in the hematophagous bat Desmodus rotundus. Methods From 2008 to 2012, 1,490 bat brain samples were sent to the Universidade Estadual Paulista (UNESP) Rabies Laboratory in Araçatuba, and 125 serum samples from vampire bats that were captured in this geographical region were analyzed. Results Rabies virus was detected in the brains of 26 (2%) of 1,314 non-hematophagous bats using the fluorescent antibody test (FAT) and the mouse inoculation test (MIT). None of the 176 hematophagous bat samples were positive for rabies virus when a virus detection test was utilized. Out of 125 vampire bat serum samples, 9 (7%) had levels of rabies virus neutralization antibodies (RVNAs) that were higher than 0.5IU/mL; 65% (81/125) had titers between 0.10IU/mL and 0.5IU/mL; and 28% (35/125) were negative for RVNAs using the simplified fluorescent inhibition ...

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Introducción: en el diagnóstico de dengue es importante la determinación del serotipo viral. A pesar de existir otros métodos, el aislamiento viral en cultivos de células y la identificación por la técnica de inmunofluorescencia siguen siendo muy utilizados. Por lo tanto, la búsqueda de sistemas celulares más sensibles ha sido un tema reiterado durante muchos años para el virus dengue y otros agentes. Objetivo: obtener una sublínea celular a partir del clon CLA-1 (Aedes pseudoscutellaris) que crece a 28 ºC, capaz de multiplicarse a 33ºC (CLA-HT) y evaluar su utilidad para el aislamiento y la identificación de los virus del dengue. Métodos: a partir del clono CLA-1 de la línea celular AP-61(Aedes pseudoscutellaris) se obtuvo por selección una cepa o sublínea celular CLA-HT capaz de crecer a 33 °C. Se estudió su sensibilidad para la multiplicación de los 4 serotipos del virus del dengue y su eficiencia para el aislamiento directo de sueros de pacientes en fase aguda de la enfermedad, ambos comparativamente con la línea C6/36HT (A. albopictus). Resultados: la sublínea CLA-HT permitió el crecimiento de los 4 serotipos del virus dengue aunque para algunos requirió más tiempo que la C6/36 HT. Para el aislamiento a partir de muestras de sueros colectadas de individuos en fase aguda, la sublínea CLA-HT detectó el virus en el 40 por ciento de las muestras, mientras que C6/36 detectó el virus en el 50 por ciento. Discusión: CLA-HT es capaz de detectar todos los serotipos del virus dengue a partir de las 96 horas pos inoculación, por lo que es útil para la investigación como sistema alternativo y su eficiencia de aislamiento directo es buena para aplicar en grandes brotes. Además, la principal ventaja es que es posible utilizarla para proporcionar una respuesta rápida a situaciones emergentes en laboratorios de escasos recursos, ya que no precisa de condiciones de incubación con CO2. Conclusiones: se obtuvo una sublínea CLA-HT a partir de la línea CLA-1 capaz de crecer a 33ºC, la cual detecta los 4 serotipos del virus dengue. Su eficiencia de aislamiento es ligeramente menor que la sublínea C6/36 HT, pero se puede utilizar como sistema alternativo para el aislamiento de los virus dengue sobre todo en laboratorios con bajos recursos que no cuenten con condiciones óptimas de incubación(AU)

Introduction: the identification of viral serotypes is an important issue for dengue diagnosis. Despite the existence of other identification methods, the viral isolation in cell cultures and determination by immunofluorescent technique remain as the most used. Therefore the search for more sensitive cellular systems has been a repeated topic during many years for dengue virus and other agents. Objective: to obtain a cell subline from CLA-1 clone (Aedes pseudoscutellaris), that grows at 28 °C, capable of multiplying at 33 °C (CLA-HT)and to evaluate its usefulness for Dengue virus isolation and identification. Methods: by using a CLA-1 clone of the AP-61(Aedes pseudoscutellaris) cell line, it was possible to obtain a strain or cell subline CLA-HT capable of growing at 33 oC (CLA-HT) through a temperature selection method. Its sensitivity for the multiplication of the 4 dengue virus serotypes and its efficiency for direct virus isolation from acutely ill patients' sera were studied in comparison to C6/36 HT cell line (A. albopictus). Results: four dengue virus serotypes grew in CLA-HT cell subline but some serotypes were detected later in CLA-HT than in C6/36 HT. For dengue isolation from serum samples taken in acutely ill patients, the CLA-HT subline detected 40 percent positive samples whereas C6/36 HT did 50 percent. Discussion: CLA-HT is able to detect all dengue virus serotypes from 96 hours on post inoculation. It makes the new cell line useful for research as an alternative system and the direct isolation efficiency is good to be applied in large outbreaks. The most important advantage of CLA-HT is the possibility of giving rapid answer in emergency situations in low resource laboratories since it does not require special incubation conditions with CO2. Conclusions: a CLA-HT subline was obtained from CLA-1 line and it grows at 33 oC and capable of detecting 4 dengue virus serotypes. Its isolation efficiency is slightly lower than that of C6/36 HT subline, but it may be used as an alternative system for dengue virus isolation, mainly in resource-poor laboratories that do not have the optimal conditions for incubation(AU)

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Objective: real time PCR analysis for the detection of seven bovine pathogenic viruses: Bovine Adenovirus (BAdV), Bovine Viral Diarrhea Virus Types 1 and 2 (BVDV-1 and BVDV-2), Bovine Respiratory Syncytial Virus (BRSV), Vesicular Stomatitis Virus (VSV), Bovine Parainfluenza Virus 3 (BPIV-3), Bovine Herpes Virus-1 (BoHV-1), and Mycoplasma was conducted using fetal bovine serum (FBS, MICROGEN®) obtained in Colombia, aiming to include it as part of the serum quality control. Methods: bovine derived MDBK and human derived HEp-2 cell lines were cultured with the test serum for 21 days, collecting supernatant and cellular samples every 7-days. Once DNA and RNA were extracted, the later was converted into cDNA and both samples were subjected to real time PCR using specific primers and Resolight® (DNA-binding fluorescent dye). Standard curves were generated using serial dilutions of cloned specific viral sequences. Accurate amplification and high efficiency was demonstrated in these reactions. Results: realtime PCR amplification did not show a persistent increase of viral counts in cultures during the 21-day follow-up. However, for vesicular stomatitis virus, a transient increase was observed at 7 and 14 days in both cell lines, but considered as not conclusive for viral presence. Conclusions: real time PCR analysis showed to be a suitable method for viral detection in fetal bovine serum samples and through this method no consistent viral or mycoplasma presence was detected in the MICROGEN® fetal bovine serum.

Objetivos: se empleó el método de PCR en tiempo real para detectar los virus patógenos bovinos: Adenovirus bovino (BAdV), virus de la diarrea Viral Bovina tipos 1 y 2 (BVDV-1 y BVDV-2), Virus Respiratorio Sincitial Bovino (BRSV), Virus de la Estomatitis Vesicular (VSV), Virus de la Parainfluenza Bovina tipo 3 (BPIV-3), Herpesvirus Bovino-1 (BoHV-1) y Mycoplasma, en suero fetal bovino (FBS, MICROGEN ®)obtenido en Colombia, con el objetivo de incluir estos análisis en el control de calidad del FBS. Metodos: las líneas celulares MDBK de origen bovino y HEp-2 de origen humano se cultivaron con el FBS MICROGEN® por 21 días, tomando muestras de cultivos y sobrenadantes cada 7 días. Una ves extraido el DNA y RNA, a partir de este último se sintetizó cDNA, y en los dos tipos de muestras se analizó la presencia de los agentes patógenos mencionados por PCR en tiempo real empleando iniciadores específicos para cada uno y Resolight® (colorante fluorescente de unión a DNA). Se generaron curvas estándar con diluciones seriadas de secuencias virales específicas clonadas en plásmidos, que mostraron amplificación específica y altas eficiencias. Resultados: el análisis de los cultivos mantenidos con el FBS en estudio no mostró aumento del número de copias virales detectadas a lo largo del periodo de 21 días de seguimiento, excepto para el virus de la estomatitis vesicular, que mostró un incremento transitorio en los sobrenadantes de los cultivos de las dos líneas celulares a los 7 y 14 días de cultivo, que no se consideró concluyente para la presencia del virus. Conclusiones: el método de PCR en tiempo real mostró utilidad para la detección de virus patógenos y mycoplasma en FBS, y mediante este método no se obtuvieron resultados que permitan concluir que los patógenos virales o los mycoplasmas están presentes en los cultivos mantenidos con el suero fetal bovino MICROGEN®.

Objetivo: Foi utilizado o método de PCR em tempo real para detectar os vírus patogénicos bovinos: Adenovírus Bovino (BAdV), Vírus da Diarreia Viral (BVDV-1 e BVDV-2), Vírus Respiratório Sincicial Bovino (BRSV ), Vírus da Estomatite Vesicular (VSV), Vírus da Parainfluenza Bovina tipo 3 (BPIV- 3), Herpesvírus Bovino-1 (BoHV-1) e Mycoplasma, em soro fetal bovino (FBS, Microgen®) obtido na Colômbia, de modo a incluir esta análise no controle de qualidade FBS. Métodos: as linhas celulares de MDBK de origem bovina e HEp-2 de origem humana foram cultivadas com FBS Microgen® durante 21 dias, tomando amostras de cultura e sobrenadantes cada 7 dias. Uma vez retirado o DNA e RNA, foi sintetizado o cDNA a partir do RNA. Nos dois tipos de amostras foram analisadas para determinar a presença de patógenos mencionados por PCR em tempo real usando primers específicos para cada um e Resolight®(corante fluorescente de união à DNA). As curvas padrão foram geradas com diluições em série de sequências virais específicas, clonadas em Resultados: plasmídeos, que mostram amplificação específica e altas eficiências. a análise das culturas mantidas em FBS em estudo, não mostraram aumento no número de cópias virais detectadas ao longo do período de 21 dias de seguimento, exceto para o vírus da estomatite vesicular, que mostrou um aumento transitório nos sobrenadantes das culturas de duas linhas celulares aos 7 e 14 dias de cultura, que não foi considerado conclusivo para a presença do vírus. Conclusões: O método de PCR em tempo real foi útil para a detecção de vírus patogênicos e mycoplasma em FBS, e por este método foram obtidos resultados que demonstram que patógenos virais ou mycoplasmas estão presentes nas culturas mantidas com soro fetal bovino Microgen®.