Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR
The occurrence of highly pathogenic (HP) avian influenza (AI) H5N1 in Asia and its spread to Africa and Europe prompted costly monitoring programs of wild birds and domestic poultry. AI virus excretion is tested by examining avian swab samples by real-time reverse transcription PCR (RT-qPCR). In this study, pools of swab samples and a reagents volume reduction per RT-qPCR were evaluated as measures of economization. Viral transport medium and faecal matrices were spiked with different low pathogenic AI virus strains and tested for loss of target RNA during all processing steps as individual rayon swabs or in sample pools of 5, 10 and 15 swabs. Fresh faeces from Mallard ducks and other aquatic bird species as sample matrix resulted in loss of AIV RNA of about 90% compared to transport medium. Due to sample RNA dilution in pools the likelihood of detection of single positive samples is decreasing with increasing size of sample pools. However, pools of five samples containing only one positive sample consistently gave positive results. Similarly, no differences in detection rates were obtained when analyzing 1030 wild bird swab samples either individually or in pools of five. Reducing the reaction volume of influenza A virus generic as well as of subtype-specific RT-qPCRs to 12.5 ?l (2.5 ?l template) instead of 25 ?l did not adversely affect the limit of detection of these RT-qPCRs. A significant economic benefit without impeding detection efficacy can be achieved when sample pools of five samples are analyzed by RT-qPCR using a reduction of the reaction mix to the half of the original volume.
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Format: | article biblioteca |
Language: | eng |
Subjects: | L73 - Maladies des animaux, Influenzavirus aviaire, surveillance épidémiologique, technique analytique, échantillonnage, excrétion, oiseau, animal sauvage, coût, http://aims.fao.org/aos/agrovoc/c_9017, http://aims.fao.org/aos/agrovoc/c_16411, http://aims.fao.org/aos/agrovoc/c_1513, http://aims.fao.org/aos/agrovoc/c_6774, http://aims.fao.org/aos/agrovoc/c_2750, http://aims.fao.org/aos/agrovoc/c_935, http://aims.fao.org/aos/agrovoc/c_24103, http://aims.fao.org/aos/agrovoc/c_1922, http://aims.fao.org/aos/agrovoc/c_3245, http://aims.fao.org/aos/agrovoc/c_3081, |
Online Access: | http://agritrop.cirad.fr/565660/ http://agritrop.cirad.fr/565660/1/document_565660.pdf |
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dig-cirad-fr-5656602024-01-28T20:45:39Z http://agritrop.cirad.fr/565660/ http://agritrop.cirad.fr/565660/ Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR. Fereidouni Sasan R., Harder Timm C., Gaidet Nicolas, Ziller Mario, Hoffmann Bernd, Hammoumi Saliha, Globig Anja, Starick Elke. 2012. Journal of Virological Methods, 186 (1-2) : 119-125.https://doi.org/10.1016/j.jviromet.2012.08.002 <https://doi.org/10.1016/j.jviromet.2012.08.002> Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR Fereidouni, Sasan R. Harder, Timm C. Gaidet, Nicolas Ziller, Mario Hoffmann, Bernd Hammoumi, Saliha Globig, Anja Starick, Elke eng 2012 Journal of Virological Methods L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 Allemagne France http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 The occurrence of highly pathogenic (HP) avian influenza (AI) H5N1 in Asia and its spread to Africa and Europe prompted costly monitoring programs of wild birds and domestic poultry. AI virus excretion is tested by examining avian swab samples by real-time reverse transcription PCR (RT-qPCR). In this study, pools of swab samples and a reagents volume reduction per RT-qPCR were evaluated as measures of economization. Viral transport medium and faecal matrices were spiked with different low pathogenic AI virus strains and tested for loss of target RNA during all processing steps as individual rayon swabs or in sample pools of 5, 10 and 15 swabs. Fresh faeces from Mallard ducks and other aquatic bird species as sample matrix resulted in loss of AIV RNA of about 90% compared to transport medium. Due to sample RNA dilution in pools the likelihood of detection of single positive samples is decreasing with increasing size of sample pools. However, pools of five samples containing only one positive sample consistently gave positive results. Similarly, no differences in detection rates were obtained when analyzing 1030 wild bird swab samples either individually or in pools of five. Reducing the reaction volume of influenza A virus generic as well as of subtype-specific RT-qPCRs to 12.5 ?l (2.5 ?l template) instead of 25 ?l did not adversely affect the limit of detection of these RT-qPCRs. A significant economic benefit without impeding detection efficacy can be achieved when sample pools of five samples are analyzed by RT-qPCR using a reduction of the reaction mix to the half of the original volume. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/565660/1/document_565660.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1016/j.jviromet.2012.08.002 10.1016/j.jviromet.2012.08.002 http://catalogue-bibliotheques.cirad.fr/cgi-bin/koha/opac-detail.pl?biblionumber=203386 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jviromet.2012.08.002 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1016/j.jviromet.2012.08.002 |
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L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 |
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L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 Fereidouni, Sasan R. Harder, Timm C. Gaidet, Nicolas Ziller, Mario Hoffmann, Bernd Hammoumi, Saliha Globig, Anja Starick, Elke Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
description |
The occurrence of highly pathogenic (HP) avian influenza (AI) H5N1 in Asia and its spread to Africa and Europe prompted costly monitoring programs of wild birds and domestic poultry. AI virus excretion is tested by examining avian swab samples by real-time reverse transcription PCR (RT-qPCR). In this study, pools of swab samples and a reagents volume reduction per RT-qPCR were evaluated as measures of economization. Viral transport medium and faecal matrices were spiked with different low pathogenic AI virus strains and tested for loss of target RNA during all processing steps as individual rayon swabs or in sample pools of 5, 10 and 15 swabs. Fresh faeces from Mallard ducks and other aquatic bird species as sample matrix resulted in loss of AIV RNA of about 90% compared to transport medium. Due to sample RNA dilution in pools the likelihood of detection of single positive samples is decreasing with increasing size of sample pools. However, pools of five samples containing only one positive sample consistently gave positive results. Similarly, no differences in detection rates were obtained when analyzing 1030 wild bird swab samples either individually or in pools of five. Reducing the reaction volume of influenza A virus generic as well as of subtype-specific RT-qPCRs to 12.5 ?l (2.5 ?l template) instead of 25 ?l did not adversely affect the limit of detection of these RT-qPCRs. A significant economic benefit without impeding detection efficacy can be achieved when sample pools of five samples are analyzed by RT-qPCR using a reduction of the reaction mix to the half of the original volume. |
format |
article |
topic_facet |
L73 - Maladies des animaux Influenzavirus aviaire surveillance épidémiologique technique analytique échantillonnage excrétion oiseau animal sauvage coût http://aims.fao.org/aos/agrovoc/c_9017 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_1513 http://aims.fao.org/aos/agrovoc/c_6774 http://aims.fao.org/aos/agrovoc/c_2750 http://aims.fao.org/aos/agrovoc/c_935 http://aims.fao.org/aos/agrovoc/c_24103 http://aims.fao.org/aos/agrovoc/c_1922 http://aims.fao.org/aos/agrovoc/c_3245 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Fereidouni, Sasan R. Harder, Timm C. Gaidet, Nicolas Ziller, Mario Hoffmann, Bernd Hammoumi, Saliha Globig, Anja Starick, Elke |
author_facet |
Fereidouni, Sasan R. Harder, Timm C. Gaidet, Nicolas Ziller, Mario Hoffmann, Bernd Hammoumi, Saliha Globig, Anja Starick, Elke |
author_sort |
Fereidouni, Sasan R. |
title |
Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
title_short |
Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
title_full |
Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
title_fullStr |
Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
title_full_unstemmed |
Saving resources: Avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR |
title_sort |
saving resources: avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time rt-pcr |
url |
http://agritrop.cirad.fr/565660/ http://agritrop.cirad.fr/565660/1/document_565660.pdf |
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