Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights
ABSTRACT The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2021-10-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/Spectrum.00197-21 |
| _version_ | 1830210872575787008 |
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| author | Dorottya Nagy-Szakal Mara Couto-Rodriguez Heather L. Wells Joseph E. Barrows Marilyne Debieu Kristin Butcher Siyuan Chen Agnes Berki Courteny Hager Robert J. Boorstein Mariah K. Taylor Colleen B. Jonsson Christopher E. Mason Niamh B. O’Hara |
| author_facet | Dorottya Nagy-Szakal Mara Couto-Rodriguez Heather L. Wells Joseph E. Barrows Marilyne Debieu Kristin Butcher Siyuan Chen Agnes Berki Courteny Hager Robert J. Boorstein Mariah K. Taylor Colleen B. Jonsson Christopher E. Mason Niamh B. O’Hara |
| author_sort | Dorottya Nagy-Szakal |
| collection | DOAJ |
| description | ABSTRACT The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates. IMPORTANCE This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks. Better understanding of the continuously evolving SARS-CoV-2 viral genome and the impact of genetic variants may provide individual risk stratification, precision therapeutic options, improved molecular diagnostics, and population-based therapeutic solutions. |
| first_indexed | 2024-12-18T05:33:23Z |
| format | Article |
| id | doaj.art-5bf722a718e44fe8899653dbabfb2536 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-12-18T05:33:23Z |
| publishDate | 2021-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-5bf722a718e44fe8899653dbabfb25362022-12-21T21:19:22ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972021-10-019210.1128/Spectrum.00197-21Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome InsightsDorottya Nagy-Szakal0Mara Couto-Rodriguez1Heather L. Wells2Joseph E. Barrows3Marilyne Debieu4Kristin Butcher5Siyuan Chen6Agnes Berki7Courteny Hager8Robert J. Boorstein9Mariah K. Taylor10Colleen B. Jonsson11Christopher E. Mason12Niamh B. O’Hara13Biotia, Inc., New York, New York, USABiotia, Inc., New York, New York, USABiotia, Inc., New York, New York, USABiotia, Inc., New York, New York, USABiotia, Inc., New York, New York, USATwist Bioscience, South San Francisco, California, USATwist Bioscience, South San Francisco, California, USASchool of Natural Sciences, College of Natural, Behavioral and Health Sciences, Caldwell University, Caldwell, New Jersey, USABiotia, Inc., New York, New York, USALenco Diagnostic Laboratories, Inc., New York, New York, USAThe University of Tennessee Health Science Center, Memphis, Tennessee, USAThe University of Tennessee Health Science Center, Memphis, Tennessee, USABiotia, Inc., New York, New York, USABiotia, Inc., New York, New York, USAABSTRACT The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates. IMPORTANCE This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks. Better understanding of the continuously evolving SARS-CoV-2 viral genome and the impact of genetic variants may provide individual risk stratification, precision therapeutic options, improved molecular diagnostics, and population-based therapeutic solutions.https://journals.asm.org/doi/10.1128/Spectrum.00197-21COVID-19SARS-CoV-2infectious diseasemicrobiomenext-generation sequencingviral genomics |
| spellingShingle | Dorottya Nagy-Szakal Mara Couto-Rodriguez Heather L. Wells Joseph E. Barrows Marilyne Debieu Kristin Butcher Siyuan Chen Agnes Berki Courteny Hager Robert J. Boorstein Mariah K. Taylor Colleen B. Jonsson Christopher E. Mason Niamh B. O’Hara Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights Microbiology Spectrum COVID-19 SARS-CoV-2 infectious disease microbiome next-generation sequencing viral genomics |
| title | Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights |
| title_full | Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights |
| title_fullStr | Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights |
| title_full_unstemmed | Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights |
| title_short | Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights |
| title_sort | targeted hybridization capture of sars cov 2 and metagenomics enables genetic variant discovery and nasal microbiome insights |
| topic | COVID-19 SARS-CoV-2 infectious disease microbiome next-generation sequencing viral genomics |
| url | https://journals.asm.org/doi/10.1128/Spectrum.00197-21 |
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