Duplex RTqPCRs for detection and relative quantification of SARS-CoV-2 variants of concern (VOC) Article Swipe
Albert Carcereny
,
David García-Pedemonte
,
Albert Bosch
,
Rosa M Pintó
,
Susana Guix
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.pex-1688/v4
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.pex-1688/v4
During the evolution of the SARS-CoV-2 pandemic, new variants of the virus have emerged and spread worldwide. The increased transmissibility and proclivity of some of these variants to cause more serious disease threatens public health responses against the virus, thus being its monitoring relevant. While Next-Generation-Sequencing (NGS) is the gold standard to identify variants, it cannot always be rapidly implemented in some settings to provide information as an early warning tool. Duplex quantitative real time RTqPCR assays offer a sensitive and easy-to-use tool to detect, discriminate, and estimate relative proportions of SARS-CoV-2 variants containing signature mutations from variants lacking it, using allelic discrimination probes. We developed ten multiplexed RTqPCR assays that can detect Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron (B.1.1.529), Omicron BA.1 (B.1.1.529.1), Omicron BA.2 (B.1.1.529.2), Omicron FLip (XBB.1.5-like + L455F + F456L), Omicron BA.2.86 (B.1.1.529.2.86) and Omicron DeFLiRT (JN.1 + delS31) variants by targeting 21765_21770DelTACATG, 22281_22289DelCTTTACTTG, 28262_28263InsAACA, 22029_22034DelAGTTCA, 28362_28370DelGAGAACGCA, 22121InsGAGCCAGAA, 21633_21641DelTACCCCCTG, G22927T, T22928C and T22930A (L455F and F456L SNVs), ins21610ATGCCGCTGTTT and 21654_21656DelCTT deletions, insertions and SNVs in their genomes. Alpha, Beta, Delta, Omicron BA.1, Omicron BA.2, Omicron Flip, Omicron BA.2.86 and Omicron DeFLiRT markers are mapped to the S gene (residues 69/70, 241/243, 157/158, 214, 25/27, 455/456, 16 and 31 respectively), Gamma insertion is located between the end of ORF8 and the beginning of N gene, and Omicron (B.1.1.529) deletion is mapped to the N gene (residues 31/33). The duplex RTqPCR assay targeting 21765-21770DelTACATG mutation affecting residues HV69/70 has been previously used to estimate the relative proportion of Alpha VOC (Carcereny et al., 2021), and is also suitable to estimate the proportions of Omicron BA.4 and BA.5. All duplex RTqPCR assays targeting signature mutations may be used as a complementary tool to NGS for rapid variant tracking and surveillance in wastewater-based epidemiology.
Related Topics
Concepts
Duplex (building)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Coronavirus disease 2019 (COVID-19)
2019-20 coronavirus outbreak
Virology
Medicine
Biology
Infectious disease (medical specialty)
Genetics
Disease
Internal medicine
Outbreak
DNA
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.pex-1688/v4
- https://www.researchsquare.com/article/pex-1688/latest.pdf
- OA Status
- gold
- References
- 1
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4399242579
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4399242579Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.pex-1688/v4Digital Object Identifier
- Title
-
Duplex RTqPCRs for detection and relative quantification of SARS-CoV-2 variants of concern (VOC)Work title
- Type
-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-05-31Full publication date if available
- Authors
-
Albert Carcereny, David García-Pedemonte, Albert Bosch, Rosa M Pintó, Susana GuixList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.pex-1688/v4Publisher landing page
- PDF URL
-
https://www.researchsquare.com/article/pex-1688/latest.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.researchsquare.com/article/pex-1688/latest.pdfDirect OA link when available
- Concepts
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Duplex (building), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronavirus disease 2019 (COVID-19), 2019-20 coronavirus outbreak, Virology, Medicine, Biology, Infectious disease (medical specialty), Genetics, Disease, Internal medicine, Outbreak, DNATop concepts (fields/topics) attached by OpenAlex
- Cited by
-
0Total citation count in OpenAlex
- References (count)
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1Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.(NGS) | 47 |
| abstract_inverted_index.Alpha | 114, 253 |
| abstract_inverted_index.BA.1, | 178 |
| abstract_inverted_index.BA.2, | 180 |
| abstract_inverted_index.BA.5. | 271 |
| abstract_inverted_index.Beta, | 175 |
| abstract_inverted_index.Delta | 120 |
| abstract_inverted_index.F456L | 162 |
| abstract_inverted_index.Flip, | 182 |
| abstract_inverted_index.Gamma | 118, 206 |
| abstract_inverted_index.L455F | 134 |
| abstract_inverted_index.While | 45 |
| abstract_inverted_index.assay | 236 |
| abstract_inverted_index.being | 41 |
| abstract_inverted_index.cause | 29 |
| abstract_inverted_index.early | 69 |
| abstract_inverted_index.gene, | 220 |
| abstract_inverted_index.offer | 78 |
| abstract_inverted_index.rapid | 289 |
| abstract_inverted_index.their | 172 |
| abstract_inverted_index.these | 26 |
| abstract_inverted_index.tool. | 71 |
| abstract_inverted_index.using | 101 |
| abstract_inverted_index.virus | 12 |
| abstract_inverted_index.(L455F | 160 |
| abstract_inverted_index.(P.1), | 119 |
| abstract_inverted_index.2021), | 258 |
| abstract_inverted_index.25/27, | 200 |
| abstract_inverted_index.69/70, | 196 |
| abstract_inverted_index.Alpha, | 174 |
| abstract_inverted_index.Delta, | 176 |
| abstract_inverted_index.Duplex | 72 |
| abstract_inverted_index.During | 1 |
| abstract_inverted_index.RTqPCR | 76, 109, 235, 274 |
| abstract_inverted_index.SNVs), | 163 |
| abstract_inverted_index.always | 57 |
| abstract_inverted_index.assays | 77, 110, 275 |
| abstract_inverted_index.cannot | 56 |
| abstract_inverted_index.detect | 113 |
| abstract_inverted_index.duplex | 234, 273 |
| abstract_inverted_index.health | 35 |
| abstract_inverted_index.mapped | 190, 226 |
| abstract_inverted_index.public | 34 |
| abstract_inverted_index.spread | 16 |
| abstract_inverted_index.virus, | 39 |
| abstract_inverted_index.31/33). | 232 |
| abstract_inverted_index.BA.2.86 | 138, 184 |
| abstract_inverted_index.DeFLiRT | 142, 187 |
| abstract_inverted_index.F456L), | 136 |
| abstract_inverted_index.HV69/70 | 242 |
| abstract_inverted_index.Omicron | 122, 124, 127, 130, 137, 141, 177, 179, 181, 183, 186, 222, 268 |
| abstract_inverted_index.T22928C | 157 |
| abstract_inverted_index.T22930A | 159 |
| abstract_inverted_index.against | 37 |
| abstract_inverted_index.allelic | 102 |
| abstract_inverted_index.between | 210 |
| abstract_inverted_index.delS31) | 145 |
| abstract_inverted_index.detect, | 85 |
| abstract_inverted_index.disease | 32 |
| abstract_inverted_index.emerged | 14 |
| abstract_inverted_index.lacking | 99 |
| abstract_inverted_index.located | 209 |
| abstract_inverted_index.markers | 188 |
| abstract_inverted_index.probes. | 104 |
| abstract_inverted_index.provide | 65 |
| abstract_inverted_index.rapidly | 59 |
| abstract_inverted_index.serious | 31 |
| abstract_inverted_index.variant | 290 |
| abstract_inverted_index.warning | 70 |
| abstract_inverted_index.157/158, | 198 |
| abstract_inverted_index.241/243, | 197 |
| abstract_inverted_index.455/456, | 201 |
| abstract_inverted_index.G22927T, | 156 |
| abstract_inverted_index.deletion | 224 |
| abstract_inverted_index.estimate | 88, 248, 264 |
| abstract_inverted_index.genomes. | 173 |
| abstract_inverted_index.identify | 53 |
| abstract_inverted_index.mutation | 239 |
| abstract_inverted_index.relative | 89, 250 |
| abstract_inverted_index.residues | 241 |
| abstract_inverted_index.settings | 63 |
| abstract_inverted_index.standard | 51 |
| abstract_inverted_index.suitable | 262 |
| abstract_inverted_index.tracking | 291 |
| abstract_inverted_index.variants | 9, 27, 93, 98, 146 |
| abstract_inverted_index.(residues | 195, 231 |
| abstract_inverted_index.affecting | 240 |
| abstract_inverted_index.beginning | 217 |
| abstract_inverted_index.developed | 106 |
| abstract_inverted_index.evolution | 3 |
| abstract_inverted_index.increased | 19 |
| abstract_inverted_index.insertion | 207 |
| abstract_inverted_index.mutations | 96, 278 |
| abstract_inverted_index.pandemic, | 7 |
| abstract_inverted_index.relevant. | 44 |
| abstract_inverted_index.responses | 36 |
| abstract_inverted_index.sensitive | 80 |
| abstract_inverted_index.signature | 95, 277 |
| abstract_inverted_index.targeting | 148, 237, 276 |
| abstract_inverted_index.threatens | 33 |
| abstract_inverted_index.variants, | 54 |
| abstract_inverted_index.(B.1.1.7), | 115 |
| abstract_inverted_index.(B.1.351), | 117 |
| abstract_inverted_index.(Carcereny | 255 |
| abstract_inverted_index.SARS-CoV-2 | 6, 92 |
| abstract_inverted_index.containing | 94 |
| abstract_inverted_index.deletions, | 167 |
| abstract_inverted_index.insertions | 168 |
| abstract_inverted_index.monitoring | 43 |
| abstract_inverted_index.previously | 245 |
| abstract_inverted_index.proclivity | 22 |
| abstract_inverted_index.proportion | 251 |
| abstract_inverted_index.worldwide. | 17 |
| abstract_inverted_index.(B.1.1.529) | 223 |
| abstract_inverted_index.easy-to-use | 82 |
| abstract_inverted_index.implemented | 60 |
| abstract_inverted_index.information | 66 |
| abstract_inverted_index.multiplexed | 108 |
| abstract_inverted_index.proportions | 90, 266 |
| abstract_inverted_index.(B.1.1.529), | 123 |
| abstract_inverted_index.(B.1.617.2), | 121 |
| abstract_inverted_index.quantitative | 73 |
| abstract_inverted_index.surveillance | 293 |
| abstract_inverted_index.(XBB.1.5-like | 132 |
| abstract_inverted_index.complementary | 284 |
| abstract_inverted_index.discriminate, | 86 |
| abstract_inverted_index.epidemiology. | 296 |
| abstract_inverted_index.(B.1.1.529.1), | 126 |
| abstract_inverted_index.(B.1.1.529.2), | 129 |
| abstract_inverted_index.discrimination | 103 |
| abstract_inverted_index.respectively), | 205 |
| abstract_inverted_index.(B.1.1.529.2.86) | 139 |
| abstract_inverted_index.transmissibility | 20 |
| abstract_inverted_index.wastewater-based | 295 |
| abstract_inverted_index.21654_21656DelCTT | 166 |
| abstract_inverted_index.22121InsGAGCCAGAA, | 154 |
| abstract_inverted_index.28262_28263InsAACA, | 151 |
| abstract_inverted_index.21765-21770DelTACATG | 238 |
| abstract_inverted_index.ins21610ATGCCGCTGTTT | 164 |
| abstract_inverted_index.21765_21770DelTACATG, | 149 |
| abstract_inverted_index.22029_22034DelAGTTCA, | 152 |
| abstract_inverted_index.<title>Abstract</title> | 0 |
| abstract_inverted_index.21633_21641DelTACCCCCTG, | 155 |
| abstract_inverted_index.22281_22289DelCTTTACTTG, | 150 |
| abstract_inverted_index.28362_28370DelGAGAACGCA, | 153 |
| abstract_inverted_index.Next-Generation-Sequencing | 46 |
| cited_by_percentile_year | |
| countries_distinct_count | 1 |
| institutions_distinct_count | 5 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/10 |
| sustainable_development_goals[0].score | 0.5799999833106995 |
| sustainable_development_goals[0].display_name | Reduced inequalities |
| citation_normalized_percentile.value | 0.09964499 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |