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Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing

Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmatio...

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Autores principales: Temte, Jonathan L., Bell, Cristalyne, Goss, Maureen D., Reisdorf, Erik, Tamerius, John, Reddy, Sushruth, Griesser, Richard, Barlow, Shari, Temte, Emily, Wedig, Mary, Shult, Peter A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208452/
https://www.ncbi.nlm.nih.gov/pubmed/37224148
http://dx.doi.org/10.1371/journal.pgph.0001422
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author Temte, Jonathan L.
Bell, Cristalyne
Goss, Maureen D.
Reisdorf, Erik
Tamerius, John
Reddy, Sushruth
Griesser, Richard
Barlow, Shari
Temte, Emily
Wedig, Mary
Shult, Peter A.
author_facet Temte, Jonathan L.
Bell, Cristalyne
Goss, Maureen D.
Reisdorf, Erik
Tamerius, John
Reddy, Sushruth
Griesser, Richard
Barlow, Shari
Temte, Emily
Wedig, Mary
Shult, Peter A.
author_sort Temte, Jonathan L.
collection PubMed
description Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014–2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.
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spelling pubmed-102084522023-05-25 Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing Temte, Jonathan L. Bell, Cristalyne Goss, Maureen D. Reisdorf, Erik Tamerius, John Reddy, Sushruth Griesser, Richard Barlow, Shari Temte, Emily Wedig, Mary Shult, Peter A. PLOS Glob Public Health Research Article Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014–2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results. Public Library of Science 2023-05-24 /pmc/articles/PMC10208452/ /pubmed/37224148 http://dx.doi.org/10.1371/journal.pgph.0001422 Text en © 2023 Temte et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Temte, Jonathan L.
Bell, Cristalyne
Goss, Maureen D.
Reisdorf, Erik
Tamerius, John
Reddy, Sushruth
Griesser, Richard
Barlow, Shari
Temte, Emily
Wedig, Mary
Shult, Peter A.
Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title_full Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title_fullStr Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title_full_unstemmed Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title_short Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
title_sort adequacy of using a single nasal swab for rapid influenza diagnostic testing, pcr, and whole genome sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208452/
https://www.ncbi.nlm.nih.gov/pubmed/37224148
http://dx.doi.org/10.1371/journal.pgph.0001422
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