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Tierling S, Kattler K, Vogelgesang M, Pfuhl T, Lohse S, Lo Porto C, Schmitt B, Nastasja S, Salhab A, Smola S, Walter J. Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology. Open Forum Infect Dis 2021; 8:ofab364. [PMID: 34409122 PMCID: PMC8364759 DOI: 10.1093/ofid/ofab364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
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.
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Affiliation(s)
- Sascha Tierling
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Markus Vogelgesang
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Thorsten Pfuhl
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Stefan Lohse
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Christina Lo Porto
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Beate Schmitt
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Seiwert Nastasja
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Abdulrahman Salhab
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
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Rupf S, Laczny CC, Galata V, Backes C, Keller A, Umanskaya N, Erol A, Tierling S, Lo Porto C, Walter J, Kirsch J, Hannig M, Hannig C. Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model. Sci Rep 2018; 8:14010. [PMID: 30228377 PMCID: PMC6143549 DOI: 10.1038/s41598-018-32361-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023] Open
Abstract
Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of ~0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals.
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Affiliation(s)
- Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany.
| | - Cedric C Laczny
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Natalia Umanskaya
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Arzu Erol
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Sascha Tierling
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Christina Lo Porto
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jasmin Kirsch
- Policlinic of Operative and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Christian Hannig
- Policlinic of Operative and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
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