Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia
Abstract Background In a year-long pneumonia etiology study conducted June 2017 to May 2018 in Sarawak, Malaysia, 599 patients’ nasopharyngeal swab specimens were studied with real-time polymerase chain reaction (rPCR)/ reverse-transcription (rRT-PCR) assays for respiratory pathogens known to contri...
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ftdoajarticles:oai:doaj.org/article:8654e22a628240cbb2102bc8065dc160 2023-05-15T15:11:43+02:00 Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia Jane K. Fieldhouse Emily S. Bailey Teck-Hock Toh King-Ching Hii Kerry A. Mallinson Jakie Ting John A. Lednicky Antoinette Berita Tham Thi Nguyen Diego Galan Son T. Than See-Chang Wong Toh-Mee Wong Patrick J. Blair Gregory C. Gray 2020-08-01T00:00:00Z https://doi.org/10.1186/s40794-020-00114-2 https://doaj.org/article/8654e22a628240cbb2102bc8065dc160 EN eng BMC http://link.springer.com/article/10.1186/s40794-020-00114-2 https://doaj.org/toc/2055-0936 doi:10.1186/s40794-020-00114-2 2055-0936 https://doaj.org/article/8654e22a628240cbb2102bc8065dc160 Tropical Diseases, Travel Medicine and Vaccines, Vol 6, Iss 1, Pp 1-8 (2020) Pneumonia Respiratory viruses Molecular assay Panspecies Malaysia Arctic medicine. Tropical medicine RC955-962 article 2020 ftdoajarticles https://doi.org/10.1186/s40794-020-00114-2 2022-12-31T02:15:49Z Abstract Background In a year-long pneumonia etiology study conducted June 2017 to May 2018 in Sarawak, Malaysia, 599 patients’ nasopharyngeal swab specimens were studied with real-time polymerase chain reaction (rPCR)/ reverse-transcription (rRT-PCR) assays for respiratory pathogens known to contribute to the high burden of lower respiratory tract infections. The study team sought to compare real-time assay results with panspecies conventional molecular diagnostics to compare sensitivities and learn if novel viruses had been missed. Methods Specimens were studied for evidence of adenovirus (AdV), enterovirus (EV) and coronavirus (CoV) with panspecies gel-based nested PCR/RT-PCR assays. Gene sequences of specimens positive by panspecies assays were sequenced and studied with the NCBI Basic Local Alignment Search Tool software. Results There was considerable discordance between real-time and conventional molecular methods. The real-time AdV assay found a positivity of 10.4%; however, the AdV panspecies assay detected a positivity of 12.4% and the conventional AdV-Hexon assay detected a positivity of 19.6%. The CoV and EV panspecies assays similarly detected more positive specimens than the real-time assays, with a positivity of 7.8% by the CoV panspecies assay versus 4.2% by rRT-PCR, and 8.0% by the EV panspecies assay versus 1.0% by rRT-PCR. We were not able to ascertain virus viability in this setting. While most discordance was likely due to assay sensitivity for previously described human viruses, two novel, possible zoonotic AdV were detected. Conclusions The observed differences in the two modes of amplification suggest that where a problem with sensitivity is suspected, real-time assay results might be supplemented with panspecies conventional PCR/RT-PCR assays. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Tropical Diseases, Travel Medicine and Vaccines 6 1 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
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Pneumonia Respiratory viruses Molecular assay Panspecies Malaysia Arctic medicine. Tropical medicine RC955-962 |
spellingShingle |
Pneumonia Respiratory viruses Molecular assay Panspecies Malaysia Arctic medicine. Tropical medicine RC955-962 Jane K. Fieldhouse Emily S. Bailey Teck-Hock Toh King-Ching Hii Kerry A. Mallinson Jakie Ting John A. Lednicky Antoinette Berita Tham Thi Nguyen Diego Galan Son T. Than See-Chang Wong Toh-Mee Wong Patrick J. Blair Gregory C. Gray Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
topic_facet |
Pneumonia Respiratory viruses Molecular assay Panspecies Malaysia Arctic medicine. Tropical medicine RC955-962 |
description |
Abstract Background In a year-long pneumonia etiology study conducted June 2017 to May 2018 in Sarawak, Malaysia, 599 patients’ nasopharyngeal swab specimens were studied with real-time polymerase chain reaction (rPCR)/ reverse-transcription (rRT-PCR) assays for respiratory pathogens known to contribute to the high burden of lower respiratory tract infections. The study team sought to compare real-time assay results with panspecies conventional molecular diagnostics to compare sensitivities and learn if novel viruses had been missed. Methods Specimens were studied for evidence of adenovirus (AdV), enterovirus (EV) and coronavirus (CoV) with panspecies gel-based nested PCR/RT-PCR assays. Gene sequences of specimens positive by panspecies assays were sequenced and studied with the NCBI Basic Local Alignment Search Tool software. Results There was considerable discordance between real-time and conventional molecular methods. The real-time AdV assay found a positivity of 10.4%; however, the AdV panspecies assay detected a positivity of 12.4% and the conventional AdV-Hexon assay detected a positivity of 19.6%. The CoV and EV panspecies assays similarly detected more positive specimens than the real-time assays, with a positivity of 7.8% by the CoV panspecies assay versus 4.2% by rRT-PCR, and 8.0% by the EV panspecies assay versus 1.0% by rRT-PCR. We were not able to ascertain virus viability in this setting. While most discordance was likely due to assay sensitivity for previously described human viruses, two novel, possible zoonotic AdV were detected. Conclusions The observed differences in the two modes of amplification suggest that where a problem with sensitivity is suspected, real-time assay results might be supplemented with panspecies conventional PCR/RT-PCR assays. |
format |
Article in Journal/Newspaper |
author |
Jane K. Fieldhouse Emily S. Bailey Teck-Hock Toh King-Ching Hii Kerry A. Mallinson Jakie Ting John A. Lednicky Antoinette Berita Tham Thi Nguyen Diego Galan Son T. Than See-Chang Wong Toh-Mee Wong Patrick J. Blair Gregory C. Gray |
author_facet |
Jane K. Fieldhouse Emily S. Bailey Teck-Hock Toh King-Ching Hii Kerry A. Mallinson Jakie Ting John A. Lednicky Antoinette Berita Tham Thi Nguyen Diego Galan Son T. Than See-Chang Wong Toh-Mee Wong Patrick J. Blair Gregory C. Gray |
author_sort |
Jane K. Fieldhouse |
title |
Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
title_short |
Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
title_full |
Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
title_fullStr |
Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
title_full_unstemmed |
Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia |
title_sort |
panspecies molecular assays detect viral pathogens missed by real-time pcr/reverse-transcriptase pcr among pneumonia patients, sarawak, malaysia |
publisher |
BMC |
publishDate |
2020 |
url |
https://doi.org/10.1186/s40794-020-00114-2 https://doaj.org/article/8654e22a628240cbb2102bc8065dc160 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Tropical Diseases, Travel Medicine and Vaccines, Vol 6, Iss 1, Pp 1-8 (2020) |
op_relation |
http://link.springer.com/article/10.1186/s40794-020-00114-2 https://doaj.org/toc/2055-0936 doi:10.1186/s40794-020-00114-2 2055-0936 https://doaj.org/article/8654e22a628240cbb2102bc8065dc160 |
op_doi |
https://doi.org/10.1186/s40794-020-00114-2 |
container_title |
Tropical Diseases, Travel Medicine and Vaccines |
container_volume |
6 |
container_issue |
1 |
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1766342527456116736 |