SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Diagnostics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4418/12/9/2056 |
| _version_ | 1797489565021241344 |
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| author | Kym Lowry Claire Wang Amanda Bordin Cameron Buckley Steven Badman Patrick Harris Ian Mackay David Whiley |
| author_facet | Kym Lowry Claire Wang Amanda Bordin Cameron Buckley Steven Badman Patrick Harris Ian Mackay David Whiley |
| author_sort | Kym Lowry |
| collection | DOAJ |
| description | The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance. |
| first_indexed | 2024-03-10T00:18:25Z |
| format | Article |
| id | doaj.art-ed5b77db26624145ae9abfea8c52e35f |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-10T00:18:25Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-ed5b77db26624145ae9abfea8c52e35f2023-11-23T15:48:00ZengMDPI AGDiagnostics2075-44182022-08-01129205610.3390/diagnostics12092056SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of ConcernKym Lowry0Claire Wang1Amanda Bordin2Cameron Buckley3Steven Badman4Patrick Harris5Ian Mackay6David Whiley7The Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, AustraliaThe Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, AustraliaThe Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, AustraliaInfectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, AustraliaKirby Institute for Infection and Immunity in Society, University of New South Wales (UNSW) Medicine, UNSW Sydney, Kensington, Sydney, NSW 2052, AustraliaThe University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, AustraliaInfectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, AustraliaThe Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, AustraliaThe continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance.https://www.mdpi.com/2075-4418/12/9/2056SARS-CoV-2RT-PCRvariant assayvariant of concernDeltawhole genome sequencing |
| spellingShingle | Kym Lowry Claire Wang Amanda Bordin Cameron Buckley Steven Badman Patrick Harris Ian Mackay David Whiley SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern Diagnostics SARS-CoV-2 RT-PCR variant assay variant of concern Delta whole genome sequencing |
| title | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern |
| title_full | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern |
| title_fullStr | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern |
| title_full_unstemmed | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern |
| title_short | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern |
| title_sort | sars cov 2 rt pcr to screen for b 1 617 2 delta variant of concern |
| topic | SARS-CoV-2 RT-PCR variant assay variant of concern Delta whole genome sequencing |
| url | https://www.mdpi.com/2075-4418/12/9/2056 |
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