Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology
Abstract Background The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations. Methods Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-...
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| Veröffentlicht in: | Open Forum Infectious Diseases 2021-08, Vol.8 (8), p.ofab364-ofab364 |
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| container_issue | 8 |
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| container_title | Open Forum Infectious Diseases |
| container_volume | 8 |
| creator | Tierling, Sascha Kattler, Kathrin Vogelgesang, Markus Pfuhl, Thorsten Lohse, Stefan Lo Porto, Christina Schmitt, Beate Nastasja, Seiwert Salhab, Abdulrahman Smola, Sigrun Walter, Jörn |
| description | Abstract
Background
The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations.
Methods
Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions.
Results
The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours.
Conclusions
We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany. |
| doi_str_mv | 10.1093/ofid/ofab364 |
| format | Article |
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Background
The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations.
Methods
Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions.
Results
The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours.
Conclusions
We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.</description><identifier>ISSN: 2328-8957</identifier><identifier>EISSN: 2328-8957</identifier><identifier>DOI: 10.1093/ofid/ofab364</identifier><identifier>PMID: 34409122</identifier><language>eng</language><publisher>US: Oxford University Press</publisher><subject>Analysis ; Coronaviruses ; Health aspects ; High performance liquid chromatography ; Major ; Severe acute respiratory syndrome</subject><ispartof>Open Forum Infectious Diseases, 2021-08, Vol.8 (8), p.ofab364-ofab364</ispartof><rights>The Author(s) 2021. Published by Oxford University Press on behalf of Infectious Diseases Society of America. 2021</rights><rights>COPYRIGHT 2021 Oxford University Press</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4117-4b3c15b8a4200b1c3cf3005b6c20dfddfefc2d3ae9f609930bcdcd2a071f3d293</citedby><cites>FETCH-LOGICAL-c4117-4b3c15b8a4200b1c3cf3005b6c20dfddfefc2d3ae9f609930bcdcd2a071f3d293</cites><orcidid>0000-0003-0563-7417 ; 0000-0001-5488-6650</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364759/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364759/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids></links><search><creatorcontrib>Tierling, Sascha</creatorcontrib><creatorcontrib>Kattler, Kathrin</creatorcontrib><creatorcontrib>Vogelgesang, Markus</creatorcontrib><creatorcontrib>Pfuhl, Thorsten</creatorcontrib><creatorcontrib>Lohse, Stefan</creatorcontrib><creatorcontrib>Lo Porto, Christina</creatorcontrib><creatorcontrib>Schmitt, Beate</creatorcontrib><creatorcontrib>Nastasja, Seiwert</creatorcontrib><creatorcontrib>Salhab, Abdulrahman</creatorcontrib><creatorcontrib>Smola, Sigrun</creatorcontrib><creatorcontrib>Walter, Jörn</creatorcontrib><title>Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology</title><title>Open Forum Infectious Diseases</title><description>Abstract
Background
The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations.
Methods
Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions.
Results
The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours.
Conclusions
We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.</description><subject>Analysis</subject><subject>Coronaviruses</subject><subject>Health aspects</subject><subject>High performance liquid chromatography</subject><subject>Major</subject><subject>Severe acute respiratory syndrome</subject><issn>2328-8957</issn><issn>2328-8957</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNp9kc1u1DAUhSMEolXpjgfwDhak-CeJ4w3SEEFbqYgqmXZrOfb11Cixgz2p1B2PTtIZIdggS_b18XePrHuy7C3BFwQL9jFYZ5ZN9awqXmSnlNE6r0XJX_5Vn2TnKf3AGBOCS8zF6-yEFQUWhNLT7FerJmfQZ5Ug7ybQzjqNGjUMzu9QsKjbtF3ehPuconsVnfL7tMpN8BqiR3dp5Zow9s6DQe02v21a9A2G_bM-x0dAnY4Afr0rb1B33d5eoS3oBx-GsHt6k72yakhwfjzPsruvX7bNVX7z_fK62dzkuiCE50XPNCn7WhUU455opi3DuOwrTbGxxliwmhqmQNgKC8Fwr402VGFOLDNUsLPs08F3mvsRjAa_j2qQU3Sjik8yKCf_ffHuQe7Co6yX0fJyNXh_NIjh5wxpL0eXNAyD8hDmJGlZ0ZotU-cLenFAd2oA6bwNi6NeloHR6eDBukXfcF6xshC8XBo-HBp0DClFsH_-RbBcg5Zr0PIY9IK_O-Bhnv5P_gbMtqj7</recordid><startdate>20210801</startdate><enddate>20210801</enddate><creator>Tierling, Sascha</creator><creator>Kattler, Kathrin</creator><creator>Vogelgesang, Markus</creator><creator>Pfuhl, Thorsten</creator><creator>Lohse, Stefan</creator><creator>Lo Porto, Christina</creator><creator>Schmitt, Beate</creator><creator>Nastasja, Seiwert</creator><creator>Salhab, Abdulrahman</creator><creator>Smola, Sigrun</creator><creator>Walter, Jörn</creator><general>Oxford University Press</general><scope>TOX</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IAO</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0563-7417</orcidid><orcidid>https://orcid.org/0000-0001-5488-6650</orcidid></search><sort><creationdate>20210801</creationdate><title>Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology</title><author>Tierling, Sascha ; Kattler, Kathrin ; Vogelgesang, Markus ; Pfuhl, Thorsten ; Lohse, Stefan ; Lo Porto, Christina ; Schmitt, Beate ; Nastasja, Seiwert ; Salhab, Abdulrahman ; Smola, Sigrun ; Walter, Jörn</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4117-4b3c15b8a4200b1c3cf3005b6c20dfddfefc2d3ae9f609930bcdcd2a071f3d293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Coronaviruses</topic><topic>Health aspects</topic><topic>High performance liquid chromatography</topic><topic>Major</topic><topic>Severe acute respiratory syndrome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tierling, Sascha</creatorcontrib><creatorcontrib>Kattler, Kathrin</creatorcontrib><creatorcontrib>Vogelgesang, Markus</creatorcontrib><creatorcontrib>Pfuhl, Thorsten</creatorcontrib><creatorcontrib>Lohse, Stefan</creatorcontrib><creatorcontrib>Lo Porto, Christina</creatorcontrib><creatorcontrib>Schmitt, Beate</creatorcontrib><creatorcontrib>Nastasja, Seiwert</creatorcontrib><creatorcontrib>Salhab, Abdulrahman</creatorcontrib><creatorcontrib>Smola, Sigrun</creatorcontrib><creatorcontrib>Walter, Jörn</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>CrossRef</collection><collection>Gale Academic OneFile</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Open Forum Infectious Diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tierling, Sascha</au><au>Kattler, Kathrin</au><au>Vogelgesang, Markus</au><au>Pfuhl, Thorsten</au><au>Lohse, Stefan</au><au>Lo Porto, Christina</au><au>Schmitt, Beate</au><au>Nastasja, Seiwert</au><au>Salhab, Abdulrahman</au><au>Smola, Sigrun</au><au>Walter, Jörn</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology</atitle><jtitle>Open Forum Infectious Diseases</jtitle><date>2021-08-01</date><risdate>2021</risdate><volume>8</volume><issue>8</issue><spage>ofab364</spage><epage>ofab364</epage><pages>ofab364-ofab364</pages><issn>2328-8957</issn><eissn>2328-8957</eissn><abstract>Abstract
Background
The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations.
Methods
Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions.
Results
The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours.
Conclusions
We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.</abstract><cop>US</cop><pub>Oxford University Press</pub><pmid>34409122</pmid><doi>10.1093/ofid/ofab364</doi><orcidid>https://orcid.org/0000-0003-0563-7417</orcidid><orcidid>https://orcid.org/0000-0001-5488-6650</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central |
| subjects | Analysis Coronaviruses Health aspects High performance liquid chromatography Major Severe acute respiratory syndrome |
| title | Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology |
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