Name: a small volume procedure for viral concentration from water
Uploaded: 2015-02-03T13:00:00.000+00:00
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Description: Watch this Scientific Journal Video about A Small Volume Procedure for Viral Concentration from Water at JoVE.com

We would like to thank Dr. Nicholas J. Ashbolt and Dr. G. Shay Fout for their review of the manuscript.

1. Preparación de Cristalería y alojamientos de los filtros <ol style="margin-left: 40px;"><li> A menos que se indique lo contrario, esterilizar todos los artículos de vidrio, soportes y soluciones de filtrado a 121 ° C durante 15 minutos. Para asegurar la esterilidad, cubrir todas las aberturas o las superficies expuestas, ya sea con papel de aluminio o papel cinta asegurado antes de la esterilización. </li><li> Montar aparato de filtración uniendo carcasa del filtro (47 mm de diámetro) a 1 L matraz Erlenmeyer de brazo lateral. Recoger filtros necesarios: filtros de disco electropositivos / electronegativo 47 mm de diámetro. </li><li> Preparar 1 L de extracto de carne 1,5% (floculación, produce partículas de flóculo cuando el pH de la solución se redujo a 3,5, o no floculante, lo que no hace agregada a pH 3,5), con 0,05 M de glicina, disolviendo 15 g de extracto de carne de vacuno en 1 L de agua desionizada y la adición de 3,75 g de glicina. NOTA: extractos de carne no floculantes requerirán la adición de celita antes de la concentración terciaria. </li><li> Añadir elución polyph sodio aditivoosphate al extracto de carne de vacuno en una concentración de 0,1%. </li><li> Añadir una solución de ácido clorhídrico 1 M, gota a gota, a la mezcla de extracto de carne, solución de pH a pH deseado. Extracto de carne Autoclave durante 15-30 minutos a 121 ° C. </li><li> Mide 0,1 g de fino, medio, o celita partícula grande (para usar con sólo el extracto de carne no floculantes). </li><li> Preparar vacío / aspiración uniendo tubos compatible con erlenmeyer brazo lateral ya la toma de vacío. </li></ol> 2. Preparación de Soluciones y virus Stock <ol style="margin-left: 40px;"><li> Preparar 1 L de HCl 1 M. </li><li> Preparar 1 l de 1 M NaOH. </li><li> Prepare la solución de PBS 1x (NaCl 137 mM, KCl 2,7 mM, 1,47 mM K 2 PO 4 y 4,3 mM NaH 2 PO 4). <ol><li> Ajustar el pH de 1x PBS a 9,0 utilizando 1 M NaOH. </li></ol></li><li> Preparar y diluir de virus a 10 4 -10 5 número más probable (NMP) ml -1 mezclando 1 ml de virus de reserva con 9 ml de PBS (pH7), como se describió previamente 8,13. Conservar a -80 ° C en alícuotas de 1 ml. <ol><li> Esterilizar virus de stock de filtrado jeringa (0,22 m de tamaño de poro) para eliminar los contaminantes potenciales. </li></ol></li><li> Sin cloro del agua corriente <ol><li> Medida 1 L de agua del grifo estéril usando un cilindro graduado estéril y verter en un vaso de precipitados de 2 l que contenía una barra de agitación magnética. </li><li> Añadir 0,7 g de tiosulfato de sodio y mezclar hasta que se disuelven los gránulos. Ajustar el pH del agua del grifo para 7-7,5 si es necesario el uso de HCl 1 M o solución de NaOH 1M. </li><li> Pico virus Deshielo (1 ml) y se añade todo el volumen de pico a 1 l de agua del grifo estéril sin cloro. Mezclar durante 10 min. </li><li> Preparar un blanco método (el agua del grifo sin cloro y sin adenovirus) con cada experimento y el proceso de la misma manera que la muestra de púas. </li></ol></li></ol> 3. Preparación de Millipore Filtro Aparato <ol style="margin-left: 40px;"><li> Retirar la cobertura estéril sobre la carcasa del filtro. Asegurarajuste adecuado entre la carcasa del filtro tazón superior y pantalla de filtro inferior para evitar fugas de la muestra durante la filtración. </li><li> Retirar la cobertura estéril de 1 frasco L Erlenmeyer. Asegúrese de que el corcho de la unidad de filtro se ajusta perfectamente en la abertura superior de erlenmeyer, creando un buen sello. </li><li> Retire el tazón superior de la unidad de filtro de malla del filtro inferior y colocar 47 mm disco de filtro electropositivo de lleno sobre la pantalla con pinzas estériles. Adjuntar filtro tazón vivienda a la pantalla inferior y ajustar en su lugar girando en sentido antihorario. </li></ol> 4. Pulse de filtración de agua (Concentración Primaria) <ol style="margin-left: 40px;"><li> Medir 100 ml de virus se dispararon el agua del grifo usando estéril probeta. </li><li> Vierta 100 ml de virus se dispararon el agua del grifo en la carcasa del filtro que contiene o bien un filtro de 47 mm de vidrio plisado / celulosa o un filtro de disco de fibra nano-alúmina / vidrio. </li><li> Deje que el agua pase lentamente a través del filtro. Aplicar vacío suave para eliminar los residuos restantes oagua del grifo f de la superficie del filtro. </li><li> Si se utiliza el tratamiento con tripsina, añadir 5 ml de tripsina al 0,25% para filtrar superficie e incubar durante 5 minutos. </li><li> Lavar la tripsina de la superficie del filtro utilizando 50 ml de agua desionizada estéril. </li></ol> 5. La elución Virus del filtro <ol style="margin-left: 40px;"><li> Retire la carcasa del filtro de 2 L frasco Erlenmeyer, y el lugar en frasco de 250 ml brazo lateral. </li><li> Medir 100 ml de extracto de carne utilizando cilindro graduado. Vierta lentamente 100 ml de extracto de carne en caja del filtro. </li><li> Permitir extracto de carne para verter a través del filtro, capturando extracto de carne en una pequeña (250 ml) matraz Erlenmeyer. Aplicar vacío para tirar a través de extracto de carne residual del filtro. </li></ol> 6. Celite Concentración Secundaria <ol style="margin-left: 40px;"><li> Frascos de transferencia que contiene los virus eluidas a una placa de agitación. Añadir estéril barra de agitación magnética y colocar en placa de agitación, mezcla para crear ligero vórtice. </li><li> Añadir 0,1 g de celitepolvo a 100 ml de extracto de carne y permitir de celite para dispersar. Coloque la sonda de pH estéril en extracto de carne. </li><li> Añadir gota a gota HCl 1 M de extracto de carne para alcanzar un pH de 4,0. Permita mezclar lentamente durante 10 min. </li><li> Coloque 47 mm pre-filtro en la carcasa del filtro (como se describió anteriormente) usando un matraz Erlenmeyer de 2 l. </li><li> Verter 100 ml de extracto de carne de vacuno / de la mezcla de celite sobre pre-filtro. Permita que el extracto de carne vierta a través. Aplicar ligero vacío para salir adelante extracto de carne residual del filtro. </li><li> Coloque el metal clip de tubo en el extremo del tubo de salida del filtro. Adjuntar estéril 15 ml tubo de recogida de polipropileno para clip de tubo de metal. Coloque la carcasa del filtro de nuevo en erlenmeyer. </li><li> Añadir 5 ml de tampón 1x PBS, pH 9,0 sobre celite recogida en pre-filtro. </li><li> Permita PBS gotee a través de pre-filtro. Aplicar ligero vacío para salir adelante PBS residual en 15 ml tubo de recogida. </li></ol> 7. Orgánica floculación Concentración Secundaria <ol style="margin-left: 40px;"><li>La transferencia de los vasos que contienen el virus se eluyó a una placa de agitación. Añadir una barra de agitación magnética estéril a 100 ml de extracto de carne y mezclar para crear ligero vórtice. </li><li> Coloque la sonda de pH estéril en extracto de carne. </li><li> Añadir 1 M de HCl gota a gota a extracto de carne y ajustar el pH a 3,5. Mezclar durante 30 min. </li><li> Verter el eluato en 250 ml tubos cónicos de centrífuga y centrifugar a 2500 xg durante 15 min a 4 ºC. </li><li> Verter el sobrenadante con cuidado de no de no perturbar el sedimento. Resuspender el precipitado en 5 ml de 1x PBS, pH 9. </li><li> Centrifugar la suspensión a 4.000 xg durante 10 min a 4 ºC. Verter el sobrenadante y desechar el sedimento. </li><li> Ajustar el pH a 7-7,5, esterilizar por filtración a través de filtro de jeringa de 0,22 micras y congelación a -80 ° C. </li></ol> 8. Viral Nucleic Acid Extracción <ol style="margin-left: 40px;"><li> Extraer ácidos nucleicos virales utilizando un kit comercial apropiado de acuerdo con las instrucciones del fabricante. </li></ol> &lt;p class = &quot;jove_title&quot;&gt; 9. AdV 40/41 qPCR <ol style="margin-left: 40px;"><li> Utilice cebadores y sondas, así como la mezcla de reacción y perfiles de ciclo térmico según lo publicado 8,13. NOTA: límite estimado de detección del ensayo es de aproximadamente 5 unidades qPCR por reacción. </li><li> Añadir componentes de las mezclas de amplificación de PCR en concentraciones como sigue: Tris 10 mM (pH 8,3), KCl 50 mM, 4,5 mM de MgCl 2, mM dNTPs 10, 10 mM cebadores y sonda 1 M y 0,5 l de polimerasa de manera que los volúmenes finales de 45 l se puede añadir al número apropiado de pozos dentro de una placa de 96 pocillos de reacción PCR. </li><li> Cargar 45 l de mezcla de amplificación PCR a cada pocillo apropiado de una de 96 pocillos, la placa de PCR reacción rápida. </li><li> Añadir 5 l de ADN extraído de la muestra a los pocillos apropiados de la placa de PCR. </li><li> Cubra la placa con junta de la tapa resistente al calor, girar la placa para mover cualquier gota a fondo de pozos de la placa de PCR. </li><li> Establecer ciclos de amplificación por PCR como follOWS: 95 ° C durante 10 min, seguido por 40 ciclos de 95 ° C durante 15 segundos y 60 ° C durante 1 min. </li></ol> 10. Análisis de datos <ol style="margin-left: 40px;"><li> Analizar mediciones por triplicado de las diluciones en serie de 5 veces de las muestras que abarcan 1: 5 a 1: 625 dilución gama con el fin de determinar el número más probable (MPN) de las partículas virales, como se describió previamente 8,13. </li><li> Analizar diluciones en serie de 5 veces de los picos experimentales de adenovirus que abarcan 1: 5 a 1: 15.625 rango de dilución para determinar el número más probable (MPN) de las partículas virales. </li><li> El uso de la calculadora EPA MPN (http://www.epa.gov/nerlcwww/online.html), ajustar la calculadora para tener en cuenta el tipo de dilución (1: 5 ó 1:10), el número de diluciones realizado, y el número de replicar muestras en serie de dilución. </li><li> Realizar log 10 transformación de los datos, seguido por la normalización a una unidad de volumen (por ejemplo, 1 ml, 100 ml, etc. </em&gt;). Calcular recuperaciones para experimento dado dividiendo la cantidad de partículas virales presentes en la muestra se concentra con el número de partículas virales presentes en los picos experimentales. </li><li> Evaluar el efecto de las diferentes variables experimentales (por ejemplo, diferentes tipos de celite, se rangos de pH, diferentes tipos de filtros y diferentes técnicas de concentración secundarios) sobre recuperaciones AdV mediante la realización de pruebas estadísticas paramétricas o no paramétricas (por ejemplo, prueba t pareada, uno o dos -Way ANOVA) dependiendo de la distribución de los datos y el diseño experimental. </li></ol>

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Filtros electropositivos son útiles en la concentración de virus del agua; sin embargo, estos filtros pueden diferir en su estructura y composición, que a su vez podría alterar su eficacia. Para agravar este problema, las estructuras de la cápside y cargos varían entre las cepas de virus que requieren ser adaptados técnicas de concentración para asegurar una recuperación óptima 15. A través de simples modificaciones de las técnicas de concentración existentes (por ejemplo, los filtros el...

Virus entéricos humanos son agentes causantes importantes de enfermedades de origen hídrico 1-3, pero generalmente están presentes en números bajos en aguas ambientales contaminadas, por lo que su detección difícil sin concentración. Los procedimientos utilizados para concentrar virus incluyen típicamente una etapa de filtración, seguido de elución de filtro, y la concentración secundaria del eluato filtro. Un procedimiento de filtración común se basa en la utilización de membranas cargadas tales como filtros electropositivos (recientemente revisado en 4,5). Estos filtros se basan en la captura de los virus en suspensión en el agua utilizando interacciones electrostáticas entre la superficie del filtro (con carga positiva) y partículas de virus específicos (con carga negativa). Dos filtros electropositivos que están disponibles comercialmente se basan en esta tecnología, los filtros de vidrio / celulosa y fibra nano-alúmina / vidrio. Los costes de filtro de vidrio / celulosa son hasta 10 veces mayor que la de la fibra nano-alúmina / vidrio, que limitan el uso del vidrio / cefiltros llulose para la vigilancia del virus de rutina. Estudios recientes han concluido diferencias son nominales entre estos dos filtros en la recuperación de los enterovirus desde 6,7 del agua ambiente, lo que justifica el uso de una alternativa de filtro más barato. Otras opciones de filtro, como los filtros electronegativos y de lana de vidrio se han estudiado, sin embargo, o bien requieren el tratamiento previo de las fuentes de agua (filtros electronegativos) o no están disponibles en el mercado (filtros de lana de vidrio). El desarrollo de procedimientos de concentración de virus se ha centrado principalmente en la optimización de las técnicas de concentración primaria (filtros) con el fin de mejorar la recuperación de virus de agua. Sin embargo, los procedimientos de concentración secundarios, que reducen el volumen de eluyente típicamente de 1 L a mililitro volúmenes, también pueden tener un impacto significativo en las recuperaciones de virus 8. Concentración secundaria de virus entéricos típicamente se basa en un agente floculante, tales como algunos tipos de extracto de carne (floccu orgánicamento) o floculación de la leche desnatada 9-12 para eliminar las partículas de virus de las superficies del filtro. Recientemente, otro procedimiento de concentración secundaria utilizando extracto de carne junto con la adición de celita (partículas finas) ha mostrado ser prometedor para la recuperación de adenovirus, enterovirus y norovirus 8,13,14. Obras de concentración Celite bajo principios similares a la del método de floculación orgánica en que las partículas de virus se unen a y se liberan de partículas (floc o de celite) alterando el pH de la solución en suspensión. Las comparaciones entre estas dos técnicas de concentración secundarias han sido evaluadas en la recuperación de adenovirus (ADV) de pinchos tipos 40 y 41 8. Este estudio concluyó que las dos técnicas de concentración secundarias fueron estadísticamente similares en la recuperación de adenovirus. Sin embargo, el método de floculación orgánica requiere una 30 min. de incubación a pH 3,5, mientras que la técnica de celite requiere una incubación más corto (10 min) a pH 4,0. El flocculat orgánicaion también requiere el uso de equipo de laboratorio caro (centrifugadoras) para recoger las partículas de flóculos durante la concentración terciaria, la técnica de celite en contraste utiliza sólo el equipo de laboratorio básico (filtración a vacío) para separar partículas de Celite de la suspensión. Ciertas combinaciones de filtros y técnicas de elución secundarias también pueden afectar a las recuperaciones de virus. Un estudio concluyó que ciertas combinaciones de (filtros electropositivos) primarias y secundarias técnicas de concentración (Celite o floculación orgánica) tuvieron un impacto significativo de la recuperación del adenovirus 13. Estos hallazgos sugieren que se requiere la optimización a fin de recuperar de manera óptima virus diana a partir de una matriz de agua dado al utilizar estas técnicas. La optimización es una pérdida de tiempo y arduo proceso de muchos investigadores evitan activamente desde numerosas variables serán evaluados (tipo de filtro / marca, solución de elución de pH, celita / floculación orgánica). Para este study, se desarrolló un procedimiento para identificar las condiciones óptimas para la concentración de virus a partir de agua usando cepas de adenovirus humano de púas 40 y 41. Presumiblemente, ya que cada tipo virus muestra una morfología de la cápside único y carga específica de la cápside, pueden necesitar ser optimizado para cada virus protocolos de concentración apuntar a fin de alcanzar la recuperación viral óptima. Este estudio proporciona un enfoque para AdV 40 y 41 de concentración por: 1) la evaluación de la recuperación de virus en el agua del grifo, usando discos de filtro electropositivos seguido por 2) evaluación de un método de floculación orgánica establecido frente a la técnica de celite como una concentración secundaria, y 3) evaluación de tampones de elución para la concentración terciaria.

<table><tbody><tr><td>Adenovirus 40 stock</td><td>ATCC</td><td>VR-931</td><td></td></tr><tr><td>Adenovirus 41 stock</td><td>ATCC</td><td>VR-930</td><td></td></tr><tr><td>Sodium Thiosulfate</td><td>Fluka Chemical Co.</td><td>72051</td><td></td></tr><tr><td>Celites #577</td><td>Fluka Chemical Co.</td><td>22142</td><td></td></tr><tr><td>NanoCeram 47 mm</td><td>Argonide</td><td>N/A</td><td></td></tr><tr><td>1MDS 47 mm</td><td>3M</td><td>6408502</td><td></td></tr><tr><td>AP-20 Prefilter 47 mm</td><td>Millipore Corp.</td><td>AP2004700</td><td></td></tr><tr><td>Glycine&amp;nbsp;</td><td>Sigma</td><td>50046-1KG</td><td></td></tr><tr><td>Sodium Polyphosphate</td><td>Acros Organics</td><td>390930010</td><td></td></tr><tr><td>Trypsin</td><td>Gibco</td><td>25200</td><td></td></tr><tr><td>PBS</td><td>Sigma</td><td>P5368</td><td></td></tr><tr><td>Hydrochloric Acid</td><td>Fisher</td><td>A481-212</td><td></td></tr><tr><td>BBL Beef Extract</td><td>BD Biosciences</td><td>212303</td><td></td></tr><tr><td>Difco Beef Extract</td><td>BD Biosciences</td><td>211520</td><td></td></tr><tr><td>ABI 7900 Real-time PCR system</td><td>ABI</td><td>N/A</td><td></td></tr><tr><td>Stainless Steel Filter Housing</td><td>Millipore Corp.</td><td>XX2004720</td><td></td></tr><tr><td>Blood DNA Extraction Kit</td><td>Qiagen&amp;nbsp;</td><td>51104</td><td></td></tr><tr><td>EPA MPN Calculator</td><td></td><td></td><td>http://www.epa.gov/nerlcwww/online.html</td></tr></tbody></table>

a small volume procedure for viral concentration from water

Small-scale concentration of viruses (sample volumes 1-10 L, here simulated with spiked 100 ml water samples) is an efficient, cost-effective way to identify optimal parameters for virus concentration. Viruses can be concentrated from water using filtration (electropositive, electronegative, glass wool or size exclusion), followed by secondary concentration with beef extract to release viruses from filter surfaces, and finally tertiary concentration resulting in a 5-30 ml volume virus concentrate. In order to identify optimal concentration procedures, two different electropositive filters were evaluated (a glass/cellulose filter [1MDS] and a nano-alumina/glass filter [NanoCeram]), as well as different secondary concentration techniques; the celite technique where three different celite particle sizes were evaluated (fine, medium and large) followed by comparing this technique with that of the established organic flocculation method. Various elution additives were also evaluated for their ability to enhance the release of adenovirus (AdV) particles from filter surfaces. Fine particle celite recovered similar levels of AdV40 and 41 to that of the established organic flocculation method when viral spikes were added during secondary concentration. The glass/cellulose filter recovered higher levels of both, AdV40 and 41, compared to that of a nano-alumina/glass fiber filter. Although not statistically significant, the addition of 0.1% sodium polyphosphate amended beef extract eluant recovered 10% more AdV particles compared to unamended beef extract.

<html> Selección de Celite Tres tipos diferentes de celita fueron probados antes de la selección de la mejor variante de realización. Celites con bien a las partículas de tamaño mediano producen los más altos recuperaciones de adenovirus. El uso de celites más grandes resultó en menores recuperaciones tanto para AdV40 y 41 (rango de 32% -100%) (Figura 1). Promedio de recuperaciones de adenovirus 40 eran 144% ± 52% (muy bien), 115% ± 28% (medio) y 82% ± 53% celites ...

Watch this Scientific Journal Video about A Small Volume Procedure for Viral Concentration from Water at JoVE.com

A Small Volume Procedure for Viral Concentration from Water

An approach was developed for identifying optimal viral concentration conditions for small volume water samples using spikes of human adenovirus. The techniques described here are used to identify concentration parameters for other viral targets, and applied to large-scale viral concentration experimentation.

Un procedimiento de volumen pequeño para la concentración viral del Agua

Small-scale concentration of viruses (sample volumes 1-10 L, here simulated with spiked 100 ml water samples) is an efficient, cost-effective way to ...

a-small-volume-procedure-for-viral-concentration-from-water

Universidad de Cartagena UDEC

Research

JoVE Journal

Environment

10.0K vistas.  U.S. EPA. An approach was developed for identifying optimal viral concentration conditions for small volume water samples using spikes of human adenovirus. The techniques described here are used to identify concentration parameters for other viral targets, and applied to large-scale viral concentration experimentation. 

Video: A Small Volume Procedure for Viral Concentration from Water

Estimating Virus Production Rates in Aquatic Systems

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative estimates of this process is critical as we can then develop better models of microbial community structure and function as well as advance our understanding of how viruses work to alter aquatic biogeochemical cycles. The virus reduction technique allows researchers to estimate the rate at which virus particles are released from the endemic microbial community. In brief, the abundance of free (extracellular) viruses is reduced in a sample while the microbial community is maintained at near ambient concentration. The microbial community is then incubated in the absence of free viruses and the rate at which viruses reoccur in the sample (through the lysis of already infected members of the community) can be quantified by epifluorescence microscopy or, in the case of specific viruses, quantitative PCR. These rates can then be used to estimate the rate of microbial mortality due to virus-mediated cell lysis.

The turnover rate of viruses in marine and freshwater systems can be estimated by a reduction and reoccurrence technique. The data allow researchers to infer rates of virus-mediated microbial mortality in aquatic systems.

Estimación de las tasas de producción de virus en los sistemas acuáticos

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative ...

Investigación

Inmunología e Infección

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

Here we introduce a series of thoroughly tested and well standardized research protocols adapted for use in remote marine environments. The sampling protocols include the assessment of resources available to the microbial community (dissolved organic carbon, particulate organic matter, inorganic nutrients), and a comprehensive description of the viral and bacterial communities (via direct viral and microbial counts, enumeration of autofluorescent microbes, and construction of viral and microbial metagenomes). We use a combination of methods, which represent a dispersed field of scientific disciplines comprising already established protocols and some of the most recent techniques developed. Especially metagenomic sequencing techniques used for viral and bacterial community characterization, have been established only in recent years, and are thus still subjected to constant improvement. This has led to a variety of sampling and sample processing procedures currently in use. The set of methods presented here provides an up to date approach to collect and process environmental samples. Parameters addressed with these protocols yield the minimum on information essential to characterize and understand the underlying mechanisms of viral and microbial community dynamics. It gives easy to follow guidelines to conduct comprehensive surveys and discusses critical steps and potential caveats pertinent to each technique.

Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.

Desentrañar los jugadores invisibles en el Océano - Guía de Campo a la química del agua y Microbiología Marina

Here we introduce a series of thoroughly tested and well standardized research protocols adapted for use in remote marine environments. The sampling ...

Medio ambiente

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay

A standardized method is required when national studies on virus occurrence in environmental and drinking waters utilize multiple analytical laboratories. The U.S Environmental Protection Agency&#8217;s (USEPA) Method 1615 was developed with the goal of providing such a standard for measuring Enterovirus and Norovirus in these waters. Virus is concentrated from water using an electropositive filter, eluted from the filter surface with beef extract, and then concentrated further using organic flocculation. Herein we present the protocol from Method 1615 for filter elution, secondary concentration, and measurement of total culturable viruses. A portion of the concentrated eluate from each sample is inoculated onto ten replicate flasks of Buffalo Green Monkey kidney cells. The number of flasks demonstrating cytopathic effects is used to quantify the most probable number (MPN) of infectious units per liter. The method uses a number of quality controls to increase data quality and to reduce interlaboratory and intralaboratory variation. Laboratories must meet defined performance standards. Method 1615 was evaluated by examining virus recovery from reagent-grade and ground waters seeded with Sabin poliovirus type 3. Mean poliovirus recoveries with the total culturable assay were 111% in reagent grade water and 58% in groundwaters.

Here we present a procedure to measure total culturable viruses using the Buffalo Green Monkey kidney cell line. The procedure provides a standardized tool for measuring the occurrence of infectious viruses in environmental and drinking waters.

Método EPA 1615. La medición de enterovirus y la aparición norovirus en agua por cultura y RT-qPCR. II. Ensayo Virus Culturable total

A standardized method is required when national studies on virus occurrence in environmental and drinking waters utilize multiple analytical laboratories. ...

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

EPA Method 1615 measures enteroviruses and noroviruses present in environmental and drinking waters. This method was developed with the goal of having a standardized method for use in multiple analytical laboratories during monitoring period 3 of the Unregulated Contaminant Monitoring Rule. Herein we present the protocol for extraction of viral ribonucleic acid (RNA) from water sample concentrates and for quantitatively measuring enterovirus and norovirus concentrations using reverse transcription-quantitative PCR (RT-qPCR). Virus concentrations for the molecular assay are calculated in terms of genomic copies of viral RNA per liter based upon a standard curve. The method uses a number of quality controls to increase data quality and to reduce interlaboratory and intralaboratory variation. The method has been evaluated by examining virus recovery from ground and reagent grade waters seeded with poliovirus type 3 and murine norovirus as a surrogate for human noroviruses. Mean poliovirus recoveries were 20% in groundwaters and 44% in reagent grade water. Mean murine norovirus recoveries with the RT-qPCR assay were 30% in groundwaters and 4% in reagent grade water.

Here we present a procedure to quantify enterovirus and norovirus in environmental and drinking waters using reverse transcription-quantitative PCR. Mean virus recovery from groundwater with this standardized procedure from EPA Method 1615 was 20% for poliovirus and 30% for murine norovirus.

Método EPA 1615. La medición de enterovirus y norovirus Ocurrencia en agua por cultura y RT-qPCR. Parte III. Detección de virus por RT-qPCR

EPA Method 1615 measures enteroviruses and noroviruses present in environmental and drinking waters. This method was developed with the goal of having a ...

Cost-effective Method for Microbial Source Tracking Using Specific Human and Animal Viruses

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant limitations, viruses are more resistant to many inactivation processes and standard fecal indicators do not inform on the source of contamination. The development of cost-effective methods for the concentration of viruses from water and molecular assays facilitates the applicability of viruses as indicators of fecal contamination and as microbial source tracking (MST) tools. Adenoviruses and polyomaviruses are DNA viruses infecting specific vertebrate species including humans and are persistently excreted in feces and/or urine in all geographical areas studied. In previous studies, we suggested the quantification of human adenoviruses (HAdV) and JC polyomaviruses (JCPyV) by quantitative PCR (qPCR) as an index of human fecal contamination. Recently, we have developed qPCR assays for the specific quantification of porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) as animal fecal markers of contamination with sensitivities of 1-10 genome copies per test tube. In this study, we present the procedure to be followed to identify the source of contamination in water samples using these tools. As example of representative results, analysis of viruses in ground water presenting high levels of nitrates is shown.
Detection of viruses in low or moderately polluted waters requires the concentration of the viruses from at least several liters of water into a much smaller volume, a procedure that usually includes two concentration steps in series. This somewhat cumbersome procedure and the variability observed in viral recoveries significantly hamper the simultaneous processing of a large number of water samples.
In order to eliminate the bottleneck caused by the two-step procedures we have applied a one-step protocol developed in previous studies and applicable to a diversity of water matrices. The procedure includes: acidification of ten-liter water samples, flocculation by skimmed milk, gravity sedimentation of the flocculated materials, collection of the precipitate and centrifugation, resuspension of the precipitate in 10 ml phosphate buffer. The viral concentrate is used for the extraction of viral nucleic acids and the specific adenoviruses and polyomaviruses of interest are quantified by qPCR. High number of samples may be simultaneously analyzed using this low-cost concentration method.
The procedure has been applied to the analysis of bathing waters, seawater and river water and in this study, we present results analyzing groundwater samples. This high-throughput quantitative method is reliable, straightforward, and cost-effective.

The study describes a cost-effective method for the identification of the source of fecal/urine contamination or contamination by nitrates in water using qPCR for the specific quantification of human/porcine/bovine DNA viruses, adenoviruses and polyomaviruses, proposed as MST tools.

Método rentable para el Rastreo de uso microbiana específica virus humanos y animales

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant ...

Preparation of Viral DNA from Nucleocapsids

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. Several downstream applications require large quantities of pure viral DNA, which is provided by this protocol. These applications include viral genome sequencing, where the removal of host DNA is crucial to optimize data output for viral sequences, and the production of new viral recombinant strains, where co-transfection of purified plasmid and linear viral DNA facilitates recombination.1,2,3 
This procedure utilizes a combination of extractions and density-based centrifugation to isolate purified linear herpesvirus nucleocapsid DNA from infected cells.4,5 The initial purification steps aim to isolate purified viral capsids, which contain and protect the viral DNA during the extractions and centrifugation steps that remove cellular proteins and DNA. Lysis of nucleocapsids then releases viral DNA, and two final phenol-chloroform steps remove remaining proteins. The final DNA captured from solution is highly concentrated and pure, with an average OD260/280 of 1.90. Depending on the quantity of infected cells used, yields of viral DNA range from 150-800 &mu;g or more. The purity of this DNA makes it stable during long-term storage at 4C. This DNA is thus ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections. 
Prior to beginning the protocol, it is important to know the average number of cells per dish (e.g. an average of 8 x 106 PK-15 cells in a confluent 15 cm dish), and the titer of the viral stock to be used (e.g. 1 x 108 plaque-forming units per ml). These are necessary to calculate the appropriate multiplicity of infection (MOI) for the protocol.6 For instance, to infect one 15 cm dish of PK-15 cells with the above viral stock, at an MOI of 5, you would use 400 &mu;l of viral stock and dilute it with 3.6 ml of medium (total inoculation volume of 4 ml for one 15 cm plate).
Multiple viral DNA preparations can be prepared at the same time. The number of simultaneous preparations is limited only by the number of tubes held by the ultracentrifuge rotor (one per virus; see step 3.9 below). Here we describe the procedure as though being done for one virus.

We describe the process of isolating high purity herpesvirus nucleocapsid DNA from infected cells. The final DNA captured from solution is of high concentration and purity, making it ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections to produce new viral recombinants.

Preparación de ADN viral de nucleocápside

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. ...

Glass Wool Filters for Concentrating Waterborne Viruses and Agricultural Zoonotic Pathogens

The key first step in evaluating pathogen levels in suspected contaminated water is concentration. Concentration methods tend to be specific for a particular pathogen group, for example US Environmental Protection Agency Method 1623 for Giardia and Cryptosporidium1, which means multiple methods are required if the sampling program is targeting more than one pathogen group. Another drawback of current methods is the equipment can be complicated and expensive, for example the VIRADEL method with the 1MDS cartridge filter for concentrating viruses2. In this article we describe how to construct glass wool filters for concentrating waterborne pathogens. After filter elution, the concentrate is amenable to a second concentration step, such as centrifugation, followed by pathogen detection and enumeration by cultural or molecular methods. The filters have several advantages. Construction is easy and the filters can be built to any size for meeting specific sampling requirements. The filter parts are inexpensive, making it possible to collect a large number of samples without severely impacting a project budget. Large sample volumes (100s to 1,000s L) can be concentrated depending on the rate of clogging from sample turbidity. The filters are highly portable and with minimal equipment, such as a pump and flow meter, they can be implemented in the field for sampling finished drinking water, surface water, groundwater, and agricultural runoff. Lastly, glass wool filtration is effective for concentrating a variety of pathogen types so only one method is necessary. Here we report on filter effectiveness in concentrating waterborne human enterovirus, Salmonella enterica, Cryptosporidium parvum, and avian influenza virus.

Glass wool filters have been used to concentrate waterborne viruses by a number of research groups around the world. Here we show a simple approach for constructing glass wool filters and demonstrate the filters are also effective in concentrating waterborne viral, bacterial and protozoan pathogens.

Los filtros de lana de vidrio para la concentración de virus transmitidas por el agua y la agricultura patógenos zoonóticos

The key first step in evaluating pathogen levels in suspected contaminated water is concentration.  Concentration methods tend to be specific for a ...

Concentration of Virus Particles from Environmental Water and Wastewater Samples Using Skimmed Milk Flocculation and Ultrafiltration

Water and wastewater-based epidemiology have emerged as alternative methods to monitor and predict the course of outbreaks in communities.&#160;The recovery of microbial fractions, including viruses, bacteria, and microeukaryotes from wastewater and environmental water samples&#160;is one of the challenging steps in these approaches. In this study, we focused on the recovery efficiency of sequential ultrafiltration and skimmed milk flocculation (SMF) methods using Armored RNA as a test virus, which is also used as a control by some other studies. Prefiltration with 0.45 &#181;m and 0.2 &#181;m membrane disc filters were applied to eliminate solid particles before ultrafiltration to prevent the clogging of ultrafiltration devices. Test samples, processed with the sequential ultrafiltration method, were centrifuged at two different speeds. An increased speed resulted in lower recovery and positivity rates of Armored RNA.&#160;On the other hand, SMF resulted in relatively consistent recovery and positivity rates of Armored RNA. Additional tests conducted with environmental water samples demonstrated the utility of SMF to concentrate other microbial fractions. The partitioning of viruses into solid particles might have an impact on the overall recovery rates, considering the prefiltration step applied before the ultrafiltration of wastewater samples. SMF with prefiltration performed better when applied to environmental water samples&#160;due to lower solid concentrations in the samples and thus lower partitioning rates to solids. In the present study, the idea of using a sequential ultrafiltration method arose from the necessity to decrease the final volume of the viral concentrates during the COVID-19 pandemic, when the supply of the commonly used ultrafiltration devices was limited, and there was a need for the development of alternative viral concentration methods.

Virus concentration from environmental water and wastewater samples is a challenging task, carried out primarily for the identification and quantification of viruses. While several virus concentration methods have been developed and tested, we demonstrate here the effectiveness of ultrafiltration and skimmed milk flocculation for RNA viruses with different sample types.

Concentración de partículas de virus de muestras ambientales de agua y aguas residuales mediante floculación y ultrafiltración de leche desnatada

Water and wastewater-based epidemiology have emerged as alternative methods to monitor and predict the course of outbreaks in communities.&#160;The ...

Lentivirus Production

RNA interference (RNAi) is a system of gene silencing in living cells. In RNAi, genes homologous in sequence to short interfering RNAs (siRNA) are silenced at the post-transcriptional state. Short hairpin RNAs, precursors to siRNA, can be expressed using lentivirus, allowing for RNAi in a variety of cell types. Lentiviruses, such as the Human Immunodeficiency Virus, are capable to infecting both dividing and non-dividing cells. We will describe a procedure which to package lentiviruses. Packaging refers to the preparation of competent virus from DNA vectors. Lentiviral vector production systems are based on a 'split' system, where the natural viral genome has been split into individual helper plasmid constructs. This splitting of the different viral elements into four separate vectors diminishes the risk of creating a replication-capable virus by adventitious recombination of the lentiviral genome. Here, a vector containing the shRNA of interest and three packaging vectors (p-VSVG, pRSV, pMDL) are transiently transfected into human 293 cells. After at least a 48-hour incubation period, the virus containing supernatant is harvested and concentrated. Finally, virus titer is determined by reporter (fluorescent) expression with a flow cytometer.

To make lentiviruses, DNA vectors are transfected into human 293 cells. After harvest and concentrating the supernatant, virus titer is determined by fluorescence expression with a flow cytometer.

Lentivirus de producción

RNA interference (RNAi) is a system of gene silencing in living cells. In RNAi, genes homologous in sequence to short interfering RNAs (siRNA) are ...

Biología

A Rapid Strategy for the Isolation of New Faustoviruses from Environmental Samples Using Vermamoeba vermiformis

The isolation of giant viruses is of great interest in this new era of virology, especially since these giant viruses are related to protists. Giant viruses may be potentially pathogenic for many species of protists. They belong to the recently described order of Megavirales. The new lineage Faustovirus that has been isolated from sewage samples is distantly related to the mammalian pathogen African swine fever virus. This virus is also specific to its amoebal host, Vermamoeba vermiformis, a protist common in health care water systems. It is crucial to continue isolating new Faustovirus genotypes in order to enlarge its genotype collection and study its pan-genome. We developed new strategies for the isolation of additional strains by improving the use of antibiotic and antifungal combinations in order to avoid bacterial and fungal contaminations of the amoeba co-culture and favoring the virus multiplication. We also implemented a new starvation medium to maintain V. vermiformis in optimal conditions for viruses co-culture. Finally, we used flow cytometry rather than microscopic observation, which is time-consuming, to detect the cytopathogenic effect. We obtained two isolates from sewage samples, proving the efficiency of this method and thus widening the collection of Faustoviruses, to better understand their environment, host specificity and genetic content.

A Rapid Strategy for the Isolation of New Faustoviruses from Environmental Samples Using Vermamoeba vermiformis

We describe here the latest advances in viral isolation for the characterization of new genotypes of Faustovirus, a new asfarvirus-related lineage of giant viruses. This protocol can be applied to the high throughput isolation of viruses, especially giant viruses infecting amoeba.

Una estrategia rápida para el aislamiento de nuevos Faustoviruses de muestras ambientales Uso<em&gt; vermiformis Vermamoeba</em

The isolation of giant viruses is of great interest in this new era of virology, especially since these giant viruses are related to protists. Giant ...