Name: swab sampling method for the detection of human norovirus on surfaces
Uploaded: 2017-02-06T10:45:00.000+00:00
Duration: 10 min 3 s
Description: Watch this Scientific Journal Video about Swab Sampling Method for the Detection of Human Norovirus on Surfaces at JoVE.com

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1. Swab Probenahme im Feld <ol><li> Tragen Sie ein sauberes Paar Handschuhe. </li><li> Messen Sie die Größe des Beprobungsfläche ohne Berührung der Oberfläche mit einem Maßband oder Lineal. Versuchen Sie, den Bereich so genau wie möglich zu ermitteln und füllen Sie ein Berichtsformular (Supplementary Tabelle 1). </li><li> Überprüfen Sie den Tupfer-Kit für mögliche Leckagen und Etikettenprobentransporttaschen und Tupfer-Kits. </li><li> Bewegen des Tupfers über die Flächenabtastung folgendermaßen: einen Hub in horizontaler Richtung, einen Hub in vertikaler Richtung und einem Hub in einer diagonalen Richtung. Seien Sie nicht eine Fläche größer als 700 cm 2 Tupfer. </li><li> Legen Sie jedes Tupfer in ein Röhrchen und ziehen Sie die Kappe. </li></ol> 2. Lagerung und Transport von Putzlappen zum Labor <ol><li> Halten Tupfer bei 4 ° C für bis zu 48 h. Falls eine Lagerung für einen längeren Zeitraum erforderlich ist, lagern die Abstriche bei -20 ° C (oder -70 ° C). </li><li> Halten Sie die Röhrchen bei 0-4 ° C (dh. verwenden, Kältepackungen) in einem isolierten Behälter während des Transports zum Labor und werden innerhalb von 24 bis 48 h der Sammlung. </li></ol> 3. Viruskonzentration, Viral RNA Extraktion und Reinigung HINWEIS: Alle Zentrifugationsschritte verwenden, um eine Tischzentrifuge bei 5.000 × g für 5 Minuten bei Raumtemperatur, sofern nicht anders angegeben. Seien Sie besonders vorsichtig, wenn Sie mit der universellen Nukleinsäure-Extraktion (UNEX) Puffer arbeiten. Schutzbrille oder Gesichtsschutz. <ol><li> Beschriften Sie ein 15 ml-Röhrchen und einer RNA-Midi-Säule für jede Probe. Fügen Sie eine negative Extraktionskontrolle in jedem Experiment. </li><li> Die Lyse-Lösung für 10 Tupfer vorzubereiten, mit 25 ml PBST (PBS, pH 7,2, enthaltend 0,02% Tween-80) 25 ml UNEX Puffer mischen. </li><li> Je 50 ul der Coliphage MS2 - Suspension (10 &amp; sup6 ; PFU / &amp; mgr; l) zu 50 ml Lysis - Lösung. </li><li> Legen Sie einen Tupfer in einem 15 ml-Röhrchen und mit 5 ml Lyselösung. Mischen und Inkubation für 10 min bei Raumtemperatur. </li><li>5 ml 100% Ethanol zu jedem Röhrchen und Vortex für 10 s. </li><li> Vorsichtig den Tupfer aus dem 15 ml-Röhrchen zu entfernen (es enthält UNEX Puffer) es leicht gegen die Seite des Schlauchpress überschüssige Flüssigkeit zu entfernen und dann den Tupfer verwerfen. Die restlichen Mengen sollten zwischen 9-10 ml sein. </li></ol> 4. Midi Säule viralen Nukleinsäureextraktion <ol><li> Transfer vorsichtig 4,5 ml UNEX / Ethanol-Mischung aus Schritt 3.6 auf einem Midi-Säule, Zentrifuge und Filtrat verwerfen. </li><li> Legen Sie eine andere 4,5 ml aus der gleichen Mischung auf die gleiche Säule, Zentrifuge und verwerfen Sie das Filtrat. </li><li> Für die erste Wäsche, fügen Sie 3,5 ml 70% Ethanol auf die Midi-Säule, Zentrifuge und das Filtrat verwerfen. </li><li> Für die zweite Wäsche, weitere 3,5 ml 70% Ethanol auf die Midi-Spalte hinzufügen. Zentrifuge und Filtrat verwerfen. </li><li> Für die Trockenschleuder Zentrifugation der Midi Spalten alle Spuren von Ethanol zu entfernen (was sich negativ auf Ihre virale RNA-Gewinnung beeinflussen können). </li><li>Legen Sie die Midi-Spalte in einer neuen 15 ml Zentrifugenröhrchen. In 250 ul Elutionspuffer auf die Midi-Säule; 1 min warten, bevor das Zentrifugieren der höchsten viralen RNA-Gewinnung zu erhalten. </li><li> Die extrahierten Nukleinsäure bei -70 ° C oder sofort zu Schritt 5. </li></ol> 5. Die Konzentration der viralen Nukleinsäure Verwendung von RNA-Clean and Concentrator Kits <ol><li> In 500 &amp; mgr; l RNA Binding Buffer zu 250 &amp; mgr; l in Schritt eluierte RNA 4.7 oben und Vortex für 10 s. </li><li> In 750 &amp; mgr; l 100% Ethanol und Vortex für 10 s. </li><li> Beschriften Sie eine Spin-Säule für jede Probe. Laden Sie die 750 &amp; mgr; l Probe auf eine Spin-Säule. </li><li> Zentrifugieren Sie die Spin-Säulen bei 12.000 × g für 1 min. Verwerfen Sie den Durchfluss durch. </li><li> Legen Sie die restlichen 750 &amp; mgr; l auf eine Spin-Säule und Zentrifuge bei 12.000 g für 1 min. </li><li> Für die Vorwäsche, werden 400 &amp; mgr; l RNA Prep Puffer zu jeder Spin-Säule und Zentrifuge bei 12.000 g für 1 min. Verwerfen Sie den Durchfluss durch. </li><li> Für die erste Wäsche, fügen 800 &amp; mgr; l RNA Waschpuffer in jede Spin-Säule und Zentrifuge bei 12.000 g für 1 min. Verwerfen Sie den Durchfluss durch. </li><li> Für das zweite Waschen werden 400 &amp; mgr; l RNA Waschpuffer Säule und Zentrifuge bei 12.000 g für 1 min zu spinnen. Verwerfen Sie den Durchfluss durch. </li><li> Für die Trockenschleuder Zentrifugation der Spin-Säule alle Spuren von Waschpuffer für 2 min bei 12.000 xg zu entfernen. </li><li> Transfer vorsichtig Spin-Säule in ein sauberes 1,5 ml Mikrozentrifugenröhrchen. </li><li> Zugeben von 25 &amp; mgr; l Elutionspuffer auf die spin-Säule und Inkubation für 1 min bei Raumtemperatur. Dadurch wird die Rückgewinnung von viraler RNA aus der Säule zu erhöhen. </li><li> Sammeln RNA durch die Spin-Säule bei 10.000 × g für 1 min zentrifugiert. </li><li> Entweder gehen Sie direkt auf RT-qPCR (Schritt 6) oder Speicher-RNA bei -70 ° C. </li></ol> 6. Mutiplex RT-qPCR Nachweis von Genogruppe I und II Noroviren und Coliphage MS 2 (Supplementary Tabelle 2) <ol><li> Saubere Arbeitsflächen, pipettes und Zentrifugen mit RNase Dekontaminationslösung auf eine mögliche Kontamination zu reduzieren. </li><li> Auftauen RT-qPCR-Reagenzien auf Eis. Thaw RNA auf Eis (in einem separaten Bereich / Zimmer). </li><li> Bestimmen Sie die Anzahl der Reaktionen und fügen Sie mindestens 10% mehr von ihnen (zB wenn 10 Reaktionen benötigt werden, machen Master - Mix für 11). </li><li> Vortex einzelnen Master-Mix-Komponenten, mit Ausnahme von 25x RT-qPCR Enzym, für 5 s. durch Ausklopfen der Röhre mit einem Finger vorsichtig das Enzym mischen. </li><li> Kurz Zentrifuge Master-Mix-Komponenten für 5 s. </li><li> Bereiten Sie den Master - Mix für die Echtzeit - RT-PCR - Nachweis von Noroviren GI und GII gemäß dem Kit - Anweisungen und Norovirus-spezifischen Oligonukleotid - Primer und Sonden in einem 1,5 ml Mikrozentrifugenröhrchen (Supplementary Tabelle 3) hinzuzufügen. </li><li> Mischen Sie den Master-Mix durch Pipettieren von 5-10 mal nach oben und unten (Verwirbelung wird nicht empfohlen). Aliquot 22 ul des Master-Mix in jeder Vertiefung der Echtzeit-PCR-96-Well-Platte. </li><li> Vortex Probe RNA5 Sekunden, und sammeln Sie durch kurzes (5 s) Zentrifugation. </li><li> In 3 ul der Probe RNA und GI und GII positive Kontrollen an den RT-qPCR Platte (folgen Vorlage aus Tabelle 2). In 3 ul Nuklease-Freewater in den No-Template-Steuerung (NTC) Brunnen. </li><li> Verschließen Sie die Echtzeit-Platte mit optischen Klebefilm. </li><li> Zentrifuge vorsichtig die Echtzeit-Platte bei 1300 × g für 1 min alle Luftblasen oder Flüssigkeitstropfen zu entfernen, die in den Vertiefungen vorhanden sein können. </li><li> Stellen Sie eine Echtzeit-PCR-Instrument und Set-up folgende Thermozyklisierung Bedingungen: 1) RT-Schritt 10 min. bei 45 ° C (2) Aktivierung der Taq-Polymerase, 10 min. bei 95 ° C und (3) 45 Zyklen von 15 s bei 95 ° C und 60 s bei 60 ° C. </li></ol> 7. Quantifizierung von Norovirus in Tupferproben <ol><li> Überprüfen Sie die Ergebnisse der positiven und negativen Kontrollen RT-qPCR Ergebnisse (Ergänzende Tabelle 3) zu validieren. </li><li> Bestimmen Sie, ob jede Standardkurve erfüllt dieakzeptable Werte in Ergänzungs Tabelle 2 und berechnen die Gesamtstandardabweichung für die Standardkurve unter Verwendung von Gleichung 1 gegeben. (Gleichung 1)% Wirkungsgrad = 100 x 10 (Durchschnitt CT - Werte-Intercept) / Slope. </li><li> Wenn die PCR - Thermocycler - Software wird die Steigung nicht für jede Standardkurve zu berechnen, bestimmen Steigung und R 2 Werte , die durch Regression Statistik - Software (zB Excel, SPSS oder SAS). Darüber hinaus berechnen für Standardkurven folgende Gleichung I die% Wirkungsgrad </li><li> Notieren Sie sich die RNA - Kopienzahl von Thermocycler - Software berechnet für alle Testproben auf der Basis von Standardkurven, die den Kriterien in Ergänzende Tabelle 4 erfüllen. Rerun alle Proben mit Standard - t Hut Kurven erfüllen nicht die Kriterien oder haben falsch-positive Kontrollen. Überprüfen Ct-Werte von Coliphage MS2, die als interne Kontrolle zur Überwachung PCR Hemmung aufgenommen. </li><li> Bestimmen Sie die Gesamtzahl der RNA-Kopien per Probe durch die in Schritt 7.2 berechnet, um die RNA-Kopienzahl multipliziert mit dem Verhältnis des Volumens (25 bis 50 &amp; mgr; l) der gesamten RNA Eluent derjenigen der RNA (3 bis 5 &amp; mgr; l), die für die RT-qPCR-Reaktion. Alternativ berechnen die RNA - Dichte durch die Gesamt - RNA - Kopienzahl durch die Objektfläche (cm 2) analysiert geteilt wird . </li></ol> 8. Genotypisierung von Echtzeit-RT-PCR-positiven Proben von Hemi Nested Herkömmliche PCR-Amplifikation <ol><li> Bereiten Sie die erste Runde des Master - Mix für jeden Primersatz der RT-PCR - Assays (Supplementary Tabellen 2 und 5). </li><li> In 5 ul Norovirus positive RNA zu 20 &amp; mgr; l Master-Mix. </li><li> Führen Sie die RT-PCR unter den folgenden Bedingungen: (1) RT-Schritt 30 min bei 42 ° C (2) Aktivierung der Taq-Polymerase, 15 min bei 95 ° C, und (3) 40 Zyklen von 30 s bei 95 ° C , 30 s bei 50 ° C und 60 sec bei 72 ° C. Nach 40 Zyklen bei 72 ° C für weitere 10 min inkubiert. </li><li>Bereiten Sie die zweite Runde der mater - Mix für jeden Primersatz der RT-PCR - Assays (Supplementary Tabellen 2 und 5). </li><li> In 23 &amp; mgr; l Master-Mix und mit 2 &amp; mgr; l der ersten Runde RT-PCR-Produkte (von der ersten Runde) zu jedem Röhrchen (idealerweise der ersten Runde Produkt 1/10 in RNase-freiem Wasser verdünnt werden sollte). </li><li> Wiederholen Sie Schritt 8.3. </li><li> Vorbereiten eines 2% igen Agarose-Gel in 100 ml 1x Tris-Acetat-EDTA (40 mM Tris, 20 mM Essigsäure und 1 mM EDTA bei pH 8,3). Nach dem Auflösen von Agarose, indem die Mischung in einem Mikrowellenofen erhitzt wird, 10 ul Nukleinsäurefarbstoff pro 100 ml der vorbereiteten Gel hinzu, nachdem die Mischung auf 60-70 ° C abgekühlt, um das Gel gießen und die Kämme einzufügen. Lassen Sie das Gel für mindestens 30 min absetzen. </li><li> Mischen Sie 15 ul jeder RT-PCR-Produkt mit 3 &amp; mgr; l 6-fachem Beladungs ​​Farbstoff. Last 15 ul jeder Probe und dem Agarosegel elektrophoretisch bei 100 V für 1 h. </li><li> Excise Ziel RT-PCR-Fragmente von geeigneter Größe (330 bp für GI und 341 bp für GII) aus dem Gel eind RNA unter Verwendung eines kommerziellen Gel-Extraktions-Kits reinigen. Das gereinigte PCR-Produkt kann jetzt Sanger-Sequenzierung verwendet werden. </li></ol>

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Authors have no conflicting interest. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

Noroviren haben eine 50% human infektiöse Dosis zwischen 18 und 10 drei Viruspartikel 20. Deshalb, auch Low-Level-Kontamination von Oberflächen kann eine Gefahr für die Gesundheit darstellen. Verschiedene Aspekte der Tupfer Probenahmeprotokoll wurden einschließlich ausgewertet: 1) verschiedene Tupfer Materialien, 2) Lagerbedingungen Tupfer während des Transports, 3) Virus-RNA-Konzentration und 4) Coliphage MS2 als interne Extraktionskontrolle. Bis vor ...

<html> Menschliche Noroviren sind eine führende Ursache für Epidemie und sporadischen akuten Gastroenteritis weltweit 1, 2, 3. Das Virus ist sehr ansteckend und Übertragung erfolgt durch direkten Mensch zu Mensch Interaktion oder indirekt durch Kontakt mit kontaminierten Lebensmitteln, Wasser oder Umwelt-Oberflächen. Noroviren können für längere Zeit vergossen werden und verlängert das Überleben des Virus auf Umwelt Oberflächen hat 1 dokumentiert, 2, 3. Während der Spitzenabwurf, Milliarden von Viruspartikeln pro Gramm Faeces freigesetzt werden, und Erbrochenem enthält auch eine ausreichende Anzahl von Viruspartikeln 4 Infektion zu verursachen, 5, 6, 7, 8,ef &quot;&gt; 9, 10. Darüber hinaus wird die Übertragung des Virus zwischen leblosen Oberflächen und die menschliche Haut kann leicht 2, 11, 12. Daher Überwachung der Umweltverschmutzung in Ausbruchsuntersuchungen auftreten unterstützen können und in der Wirksamkeit der Clean-up - Bewertung und Desinfektionsverfahren. Mehrere Umweltprobenahme Protokolle zum Nachweis von Rotavirus, Coliphage MS2, feline Calicivirus (FCV) und Bakteriophagen P22 13, 14, 15, 16 beschrieben worden. Jedoch sind die Validierungsbedingungen in diesen Studien beschrieben, einschließlich der schnellen Austrocknung (&lt;1 h) und kleine Oberflächenbereiche (25 x 100 cm 2), möglicherweise nicht ausreichend Feldeinstellungen repräsentieren. Darüber hinaus ist die geringe Belastung von Enviro erwartetnmental Oberflächen erfordern Protokolle, die der Lage sind, sehr wenige Viruspartikel zu detektieren. Wir entwickelten eine Makroschaum-basierte Oberfläche Probenahmeverfahren zum Nachweis und zur Typisierung von Norovirus. Dieses Verfahren wurde bei mehreren Norovirusausbrüchen validiert. Das Protokoll enthält 1), wie Tupferproben von Umwelt Oberflächen (2), wie die Integrität der Proben während der Entnahme und Versand an das Labor, und 3) Labortests und Typisierung von Norovirus am besten halten zu sammeln.

<table><tbody><tr><td>&lt;strong&gt;Generic name for kits&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>&lt;strong&gt;Macrofoam swab&lt;/strong&gt;</td><td>Premoistened EnviroMax Swab kit&amp;nbsp;</td><td>Puritan</td><td>2588060PFUW</td></tr><tr><td>&lt;strong&gt;RNA Lysis buffer&amp;nbsp;&lt;/strong&gt;</td><td>CDC UNEX buffer</td><td>Microbiologics</td><td>Cat No MR0501</td></tr><tr><td>&lt;strong&gt;RNA extraction spin column&lt;/strong&gt;</td><td>Midi column</td><td>Omega Biotek</td><td>Cat No R6664-02</td></tr><tr><td>&lt;strong&gt;RNA purification spin column&lt;/strong&gt;</td><td>Zymol RNA Clean and Concentrator kit&amp;nbsp;</td><td>Zymo Research</td><td>Cat No R1016</td></tr><tr><td>&lt;strong&gt;Real time RT-PCR kit&lt;/strong&gt;</td><td>AgPath kit One-Step RT-PCR Kit</td><td>Life Technologies</td><td>Cat No 4387391</td></tr><tr><td>&lt;strong&gt;Conventional RT-PCR kit&lt;/strong&gt;</td><td>Qiagen one step RT-PCR kit</td><td>Qiagen kit</td><td>Cat No 210212</td></tr><tr><td>&lt;strong&gt;Gel extraction kit&lt;/strong&gt;</td><td>Qiagen QIAquick gel extraction kit</td><td>Qiagen kit</td><td>Cat No 28704 or 28706</td></tr><tr><td></td><td>Coliphage MS2</td><td>ATCC</td><td>Cat No 15597-B1</td></tr><tr><td></td><td>RNA run-off transcripts</td><td></td><td></td></tr><tr><td></td><td>Realtime PCR platform</td><td>Applied Biosystems</td><td>Model ABI 7500</td></tr><tr><td></td><td>Optical 96-well reaction plate</td><td>Thermo Scientific</td><td>Cat No 4316813</td></tr><tr><td></td><td>&lt;a href=&quot;http://www.thermofisher.com/order/catalog/en/US/adirect/%20https:/www.thermofisher.com/order/catalog/en/US/adirect/lt?cmd=catProductDetail&amp;amp;showAddButton=true&amp;amp;productID=4306311&amp;amp;_bcs_=H4sIAAAAAAAAAI1RTWvDMAz9Nb4srDg2yXpNW3rZVyHbuRhHSQx2HWwnJf9%2BUkO6scMYGEmWnqX3%0A5Mec8e0p%2BGbUKWZMlFkNYTIa4h%2F5PqWByYqJI57r9bpJPQTnWxPRb7R3mB4jGrig6b0DdD40WOyT%0As9iBCUmHb1MYge78iYi06ZznPEd0exacF6LkD5h%2BNTr4yg1II0DH5C6rmh6imSA7GuuInsIq5TUy%0AjD6Yf%2FKU1Zav3NBrlZT13cr8s0ajGhNAJ4xsYvKoXcPkAYEHEwer5jrNFuWVdF1ieajNpbPwAhPY%0AvUrQ%2BTAjAt88w4zlm8Ly%2FYRha2yiyeUSUJM35ajHt%2BZiUS0KuWNityrHkLSjuyHUDbkgfuxgbfwx%0AD9Q0vydo9rrs4te675%2FTKhvpd74AhB0C9yUCAAA%3D&amp;amp;returnURL=http%3A%2F%2Fwww.thermofisher.com%3A80%2Forder%2Fcatalog%2Fen%2FUS%2Fadirect%2Flt%3Fcmd%3DcatDisplayStyle%26catKey%3D101%26filterType%3D1%26OP%3Dfilter%26filter%3Dft_1101%252Ff_2005260*&quot;&gt;MicroAmp Clear Adhesive Film&amp;nbsp;&lt;/a&gt;</td><td>Thermo Scientific</td><td>Cat No 4306311</td></tr></tbody></table>

swab sampling method for the detection of human norovirus on surfaces

Menschliche Noroviren sind eine führende Ursache für Epidemie und sporadische Gastroenteritis weltweit. Da die meisten Infektionen entweder direkt über die Person-to-Person Route oder indirekt durch Umwelt Oberflächen oder Lebensmittel übertragen werden, kontaminierte fomites und leblose Oberflächen sind wichtige Vehikel für die Verbreitung des Virus während Norovirusausbrüchen. Wir entwickelt und evaluiert ein Protokoll Makroschaums Tupfer zum Nachweis und zur Typisierung von humanen Noroviren von harten Oberflächen verwendet wird. Im Vergleich zu faser bestückte Tupfer oder antistatische Wischtücher ermöglichen Makroschaum Tupfer Virus Recovery (Bereich 1,2 bis 33,6%) von Toilettensitzflächen von bis zu 700 cm 2. Das Protokoll enthält die Schritte zur Extraktion des Virus aus den Tupfer und eine weitere Konzentration der viralen RNA unter Verwendung von Spin-Säulen. Insgesamt 127 (58,5%) von 217 Tupferproben, die von den Oberflächen auf Kreuzfahrtschiffen und Langzeitpflegeeinrichtungen, wo Norovirus-Gastroenteritis war gesammelt worden warenpositiv getestet GII Norovirus durch RT-qPCR berichtet. Von diesen 29 (22,8%) erfolgreich genotypisiert werden konnte. Abschließend Nachweis von Noroviren auf Umgebungsoberflächen unter Verwendung des Protokolls wir bei der Bestimmung des Grades der Umweltverschmutzung während der Ausbrüche sowie Nachweis von Virus kann helfen entwickelt, wenn klinische Proben nicht zur Verfügung stehen; es kann auch die Überwachung der Wirksamkeit von Sanierungsstrategien erleichtern.

Abbildung 1 zeigt ein Flussdiagramm des Tupferprobenahmeprotokoll. Dieses Protokoll besteht aus vier Hauptschritten; 1) Probenentnahme, 2) Probenlagerung und Transport, 3) die virale RNA-Reinigung und Konzentration und 4) RT-qPCR-Assay und die Genotypisierung. <img alt="Abbildung 1" src="/files/ftp_upload/55205/55205fig1.jpg" /> Abbildung 1: Ablaufdiagramm des endgültigen Protokolls für Umweltob...

Watch this Scientific Journal Video about Swab Sampling Method for the Detection of Human Norovirus on Surfaces at JoVE.com

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

A macrofoam based sampling methodology was developed and evaluated for the detection and quantification of norovirus on environmental hard surfaces.

Swab Sampling Verfahren zum Nachweis von humanem Norovirus auf Oberflächen

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the ...

swab-sampling-method-for-the-detection-of-human-norovirus-on-surfaces

Research

JoVE Journal

Immunology and Infection

19.5K Aufrufe.  Centers for Disease Control and Prevention. A macrofoam based sampling methodology was developed and evaluated for the detection and quantification of norovirus on environmental hard surfaces. 

Serie: Swab Sampling Method for the Detection of Human Norovirus on Surfaces

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. The standardized sampling component of the method concentrates viruses that may be present in water by passage of a minimum specified volume of water through an electropositive cartridge filter. The minimum specified volumes for surface and finished/ground water are 300 L and 1,500 L, respectively. A major method limitation is the tendency for the filters to clog before meeting the sample volume requirement. Studies using two different, but equivalent, cartridge filter options showed that filter clogging was a problem with 10% of the samples with one of the filter types compared to 6% with the other filter type. Clogging tends to increase with turbidity, but cannot be predicted based on turbidity measurements only. From a cost standpoint one of the filter options is preferable over the other, but the water quality and experience with the water system to be sampled should be taken into consideration in making filter selections.

EPA Method 1615 uses an electropositive filter to concentrate enteroviruses and noroviruses in environmental and drinking waters. This manuscript describes the procedure for collecting samples for Method 1615 analyses.

EPA-Methode 1615 Messung der Enterovirus und Norovirus Vorkommen in Wasser von Kultur und RT-qPCR. I. Sammlung von Virenproben

EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. ...

Forschung

Umwelt

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in situ hybridization (FISH) for rapid culture-independent detection of Salmonella spp. Cell-charged tapes can also be placed face-down on selective agar for solid-phase enrichment prior to detection. Alternatively, low-volume liquid enrichments (liquid surface miniculture) can be performed on the surface of the tape in non-selective broth, followed by FISH and analysis via flow cytometry. To begin, sterile adhesive tape is brought into contact with fresh produce, gentle pressure is applied, and the tape is removed, physically extracting microbes present on these surfaces. Tapes are mounted sticky-side up onto glass microscope slides and the sampled cells are fixed with 10% formalin (30 min) and dehydrated using a graded ethanol series (50, 80, and 95%; 3 min each concentration). Next, cell-charged tapes are spotted with buffer containing a Salmonella-targeted DNA probe cocktail and hybridized for 15 - 30 min at 55&deg;C, followed by a brief rinse in a washing buffer to remove unbound probe. Adherent, FISH-labeled cells are then counterstained with the DNA dye 4',6-diamidino-2-phenylindole (DAPI) and results are viewed using fluorescence microscopy. For solid-phase enrichment, cell-charged tapes are placed face-down on a suitable selective agar surface and incubated to allow in situ growth of Salmonella microcolonies, followed by FISH and microscopy as described above. For liquid surface miniculture, cell-charged tapes are placed sticky side up and a silicone perfusion chamber is applied so that the tape and microscope slide form the bottom of a water-tight chamber into which a small volume (&le; 500 &mu;L) of Trypticase Soy Broth (TSB) is introduced. The inlet ports are sealed and the chambers are incubated at 35 - 37&deg;C, allowing growth-based amplification of tape-extracted microbes. Following incubation, inlet ports are unsealed, cells are detached and mixed with vigorous back and forth pipetting, harvested via centrifugation and fixed in 10% neutral buffered formalin. Finally, samples are hybridized and examined via flow cytometry to reveal the presence of Salmonella spp. As described here, our "tape-FISH" approach can provide simple and rapid sampling and detection of Salmonella on tomato surfaces. We have also used this approach for sampling other types of fresh produce, including spinach and jalape&ntilde;o peppers.

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).

Kombination von Klebstoff-tape-basierten Sampling und Fluoreszenz In situ Hybridisierung zum schnellen Nachweis von Salmonellen On Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in ...

Immunologie und Infektion

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.

EPA-Methode 1615 Messung von Enterovirus und Norovirus Vorkommen in Wasser durch Kultur und RT-qPCR. II. Insgesamt kultivierbaren Virus Assay

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.

EPA-Methode 1615 Messung der Enterovirus und Norovirus Vorkommen in Wasser, Kultur und RT-qPCR. Teil III. Virenerkennung durch 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 ...

Finger-stick Blood Sampling Methodology for the Determination of Exercise-induced Lymphocyte Apoptosis

Exercise is a physiological stimulus capable of inducing apoptosis in immune cells. To date, various limitations have been identified with the measurement of this phenomenon, particularly relating to the amount of time required to isolate and treat a blood sample prior to the assessment of cell death. Because of this, it is difficult to determine whether reported increases in immune cell apoptosis can be contributed to the actual effect of exercise on the system, or are a reflection of the time and processing necessary to eventually obtain this measurement. In this article we demonstrate a rapid and minimally invasive procedure for the analysis of exercise-induced lymphocyte apoptosis. Unlike other techniques, whole blood is added to an antibody panel immediately upon obtaining a sample. Following the incubation period, red blood cells are lysed and samples are ready to be analyzed. The use of a finger-stick sampling procedure reduces the volume of blood required, and minimizes the discomfort to subjects.

Exercise is capable of inducing apoptosis in immune cells. There are various measurement limitations, particularly relating to the amount of time required to isolate and treat a blood sample prior to the assessment. Demonstrated is a rapid and minimally invasive procedure for the analysis of exercise-induced lymphocyte apoptosis.

Finger-Stick Blutprobenentnahme Methodik zur Bestimmung der Übung-induzierte Lymphozyten Apoptose

Exercise is a physiological stimulus capable of inducing apoptosis in immune cells. To date, various limitations have been identified with the measurement ...

Detection and Genogrouping of Noroviruses from Children's Stools By Taqman One-step RT-PCR

Noroviruses (NoVs) are the leading cause of outbreaks of sporadic acute gastroenteritis worldwide in humans of all ages. They are important cause of hospitalizations in children with a public health impact similar to that of Rotavirus. NoVs are RNA viruses of great genetic diversity and there is a continuous appearance of new strains. Five genogroups are recognized; GI and GII with their many genotypes and subtypes being the most important for human infection. However, the diagnosis of these two genotypes remains problematic, delaying diagnosis and treatment. 1, 2, 3
For RNA extraction from stool specimens the most commonly used method is the QIAmp Viral RNA commercial kit from Qiagen. This method combines the binding properties of a silica gel membrane, buffers that control RNases and provide optimum binding of the RNA to the column together with the speed of microspin. This method is simple, fast and reliable and is carried out in a few steps that are detailed in the description provided by the manufacturer. 
 Norovirus is second only to rotavirus as the most common cause of diarrhea. Norovirus diagnosis should be available in all studies on pathogenesis of diarrhea as well as in outbreaks or individual diarrhea cases. At present however norovirus diagnosis is restricted to only a few centers due to the lack of simple methods of diagnosis. This delays diagnosis and treatment 1, 2, 3. In addition, due to costs and regulated transportation of corrosive buffers within and between countries use of these manufactured kits poses logistical problems. As a result, in this protocol we describe an alternative, economic, in-house method which is based on the original Boom et al. method4 which uses the nucleic acid binding properties of silica particles together with the anti-nuclease properties of guanidinium thiocyanate.
For the detection and genogrouping (GI and GII) of NoVs isolates from stool specimens, several RT-PCR protocols utilizing different targets have been developed. The consensus is that an RT-PCR using TaqMan chemistry would be the best molecular technique for diagnosis, because it combines high sensitivity, specificity and reproducibility with high throughput and ease of use. Here we describe an assay targeting the open reading frame 1 (ORF1)-ORF2 junction region; the most conserved region of the NoV genome and hence most suitable for diagnosis. For further genetic analysis a conventional RT-PCR that targets the highly variable N-terminal-shell from the major protein of the capsid (Region C) using primers originally described by Kojima et al. 5 is detailed. Sequencing of the PCR product from the conventional PCR enables the differentiation of genotypes belonging to the GI and GII genogroups.

A One-Step RT-PCR assay for detection and genogroup identification of Norovirus isolates from children&#x2019;s stools, that utilizes primers and TaqMan probes specific to the open reading frame 1 (ORF1)-ORF2 junction region, the most conserved region of the Norovirus genome is described. A non-commercial, cost-effective RNA extraction method is detailed.

Erkennung und Genogrouping von Noroviren aus Kinder-Hocker mit der TaqMan One-Step RT-PCR

Noroviruses (NoVs) are the leading cause of outbreaks of sporadic acute gastroenteritis worldwide in humans of all ages. They are important cause of ...

Medizin

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine detection of the virus. The current detection and quantification techniques, which rely primarily on nucleic acid amplification, do not discriminate infectious from non-infectious viral particles. The purpose of this article is to present specific details on recent advances in techniques used together in order to acquire further information on the infectivity status of viral particles. One technique involves assessing binding of a norovirus ssDNA aptamer to capsids. Aptamers have the advantage of being easily synthesized and modified, and are inexpensive and stable. Another technique, dynamic light scattering (DLS), has the advantage of observing capsid behavior in solution. Electron microscopy allows for visualization of the structural integrity of the viral capsids. Although promising, there are some drawbacks to each technique, such as non-specific aptamer binding to positively-charged molecules from sample matrices, requirement of purified capsid for DLS, and poor sensitivity for electron microscopy. Nonetheless, when these techniques are used in combination, the body of data produced provides more comprehensive information on norovirus capsid integrity that can be used to infer infectivity, information which is essential for accurate evaluation of inactivation methods or interpretation of virus detection. This article provides protocols for using these methods to discriminate infectious human norovirus particles.

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Routine detection methods utilizing viral genome amplification are limited by their inability to discriminate infectious from non-infectious particles. The purpose of this article is to provide detailed protocols for alternative methods to aid in discrimination of infectious norovirus particles using aptamer binding, dynamic light scattering, and transmission electron microscopy.

Alternative In-vitro- Methoden zur Bestimmung der viralen Kapsid strukturelle Integrität

Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine ...

Quantifying Human Norovirus Virus-like Particles Binding to Commensal Bacteria Using Flow Cytometry

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is responsible for altering infection for many of these viruses. Thus, characterizing the nature of virus-bacteria binding is a foundational step needed for elucidating the mechanism(s) by which bacteria alter viral infection. For human norovirus, commensal bacteria enhance B cell infection. The virus directly binds to these bacteria, indicating that this direct interaction is involved in the mechanism of infection enhancement. A variety of techniques can be used to quantify interactions between bacteria and viruses including scintillation counting of radiolabeled viruses and polymerase chain reaction (PCR). Both methods require the use of live virus, which may need to be generated in the laboratory. Currently, none of the established in vitro culture systems available for human norovirus are robust enough to allow for generation of highly concentrated viral stocks. In lieu of live virus, virus-like particles (VLPs) have been used to characterize the interactions between norovirus and bacteria. Herein a flow cytometry method is described with uses virus specific antibodies to quantify VLP binding to gram-negative and gram-positive bacteria. Inclusion of both bacteria only and isotype controls allowed for optimization of the assay to reduce background antibody binding and accurate quantification of VLP attachment to the bacteria tested. High VLP:bacterium ratios result in VLPs binding to large percentages of the bacterial population. However, when VLP quantities are decreased, the percent of bacteria bound also decreases. Ultimately, this method can be employed in future experiments elucidating the specific conditions and structural components that regulate norovirus:bacterial interactions.

The goal of this protocol is to quantify binding of the eukaryotic pathogen human norovirus to bacteria. After performing an initial virus-bacterium attachment assay, flow cytometry is used to detect virally-bound bacteria within the population.

Quantifizierung der menschlichen Norovirus-Virus-ähnlichen Partikelbindung an commensale Bakterien mittels Durchflusszytometrie

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is ...

Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs

To control community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the 2020 global pandemic, most countries implemented strategies based on direct human testing, face covering, and surface disinfection. Under the assumption that the main route of transmission includes aerosols and respiratory droplets, efforts to detect SARS-CoV-2 in fomites have focused on locations suspected of high prevalence (e.g., hospital wards, cruise ships, and mass transportation systems). To investigate the presence of SARS-CoV-2 on surfaces in the urban environment that are rarely cleaned and&#160;seldomly disinfected, 350 citizens were enlisted from the greater San Diego County. In total, these citizen scientists collected 4,080 samples. An online platform was developed to monitor sampling kit delivery and pickup, as well as to collect sample data. The sampling kits were mostly built from supplies available in pandemic-stressed stores. Samples were processed using reagents that were easy to access despite the recurrent supply shortage. The methods used were highly sensitive and resistant to inhibitors that are commonly present in environmental samples. The proposed experimental design and processing methods were successful at engaging numerous citizen scientists who effectively gathered samples from diverse surface areas. The workflow and methods described here are relevant to survey the urban environment for other viruses, which are of public health concern and pose a threat for&#160;future pandemics.

A citizen science project was designed to recruit San Diego residents to collect environmental samples for SARS-CoV-2. A multilingual web-based platform was created for data submission using a user-friendly mobile device interface. A laboratory information management system facilitated the collection of thousands of geographically diverse samples with real-time outcome tracking.

Swabbing the Urban Environment - Eine Pipeline zur Probenahme und zum Nachweis von SARS-CoV-2 aus Umweltreservoirs

To control community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the 2020 global pandemic, most countries ...

Biologie

An Assay to Quantify the Binding of Human Norovirus VLPs to Intestinal Bacteria

After preparing the reagents, antibodies, and bacteria as described in the manuscript, assemble all the materials in a BSL II biosafety cabinet.
Virus-like particles for human norovirus are listed as BSL II pathogens, and all work performed using VLPs should be conducted in a certified biosafety cabinet.
Add 10 micrograms of human norovirus VLPs to each tube of bacteria, and mix thoroughly by pipetting. Incubate the tubes for 1 hour at 37 degrees Celsius with constant rotation. After incubation, centrifuge the tubes at 10,000 times g for 5 minutes.
Aspirate and discard the supernatant and resuspend the bacterial pellet in 1 milliliter of PBS. After repeating the wash steps once, centrifuge the tubes again at 10,000 times g for 5 minutes. Discard the supernatant and resuspend the VLP bacteria pellet in 150 microliters of 5% blocking buffer.
A common error that occurs is that tubes are swapped and the wrong treatment is added. To prevent this, arrange all tubes in lines that correspond to the correct treatment, and add one treatment all at once to the tubes.
For each bacterial sample, prepare 50 microliters of diluted human norovirus G2 antibody. Using 5% blocking buffer, dilute the antibody 1 to 125 for E. coli case samples. Prepare 50 microliters of diluted isotype antibody for each bacterial sample using the same dilution ratios. Divide each attachment assay sample into 350-microliter aliquots by transferring them into clean 1.5-milliliter centrifuge tubes.
To create unstained controls, add 50 microliters of blocking buffer to the first aliquot from each bacterial sample. For the stained samples, add 50 microliters of the G2 antibody dilution to the second set of aliquots. Create the isotype controls by adding 50 microliters of the diluted isotype antibody to the third set of aliquots.
Incubate all the samples on ice and in the dark for 30 minutes. Then, centrifuge all the samples at 10,000 times g for 5 minutes. Discard the supernatants and resuspend each sample in 150 microliters of FCSB. Again, centrifuge all the samples at 10,000 times g for 5 minutes. Again, discard the supernatants and resuspend the samples in 100 microliters of FCSB.
After centrifuging the samples one final time and discarding the supernatant, resuspend the samples in 150 microliters of FCSB. Transfer each sample to a tube containing 400 microliters of FCSB for a total volume of 550 microliters. Store the samples at 4 degrees Celsius until they are analyzed by flow cytometry.