Your browser doesn't support javascript.
Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene.
Hale, Richard S; Green, Ashleigh; Cunningham, Emma; Paul, Joel.
  • Hale RS; AusDiagnostics UK Limited, Unit 3 Anglo Business Park, Asheridge Road, Chesham, Bucks, HP5 2QA, United Kingdom.
  • Green A; AusDiagnostics UK Limited, Unit 3 Anglo Business Park, Asheridge Road, Chesham, Bucks, HP5 2QA, United Kingdom.
  • Cunningham E; Viapath, Infection Sciences - Virology, St. Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, United Kingdom.
  • Paul J; Department of Microbiology, The Royal Oldham Hospital, Rochdale Road, OL1 2JH, United Kingdom.
J Clin Virol Plus ; 1(3): 100025, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1253163
ABSTRACT
A new variant of SARS-CoV-2 (Lineage B.1.1.7) was identified in the UK in December 2020 which was associated with higher transmissibility of COVID-19. The AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay is used at sixteen UK hospitals and detects part of the ORF8 gene (together with a segment from the ORF1a gene). The objective of this study was to determine if the recently identified mutation in ORF8 (G28048T) in the B.1.1.7. lineage could be used to identify the new variant quickly in clinical cases with PCR positive results. The melt data from SARS-CoV-2 positives from two hospitals (October through December 2020) were reviewed, and distribution over time and location was evaluated. A low melt variant of the ORF8 amplicon started to appear in samples from Guy's and St. Thomas' NHS Trust, London, at the start of November, and grew as a proportion of the total positives during the subsequent two months. These low melt variants were very rare during the same period at the Northern Care Alliance, Greater Manchester, North West of UK. It was confirmed that these carried the G28048T mutation. The geographic and temporal distribution of the low melt amplicons makes it very likely that these are lineage B.1.1.7 strains. The melt temperature of this amplicon could be used to discriminate between the original and new variants in advance of the full sequencing of the isolate. However, the appearance of other mutations in the same amplicon means that this approach would be of diminishing value over time.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Variants Language: English Journal: J Clin Virol Plus Year: 2021 Document Type: Article Affiliation country: J.jcvp.2021.100025

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Variants Language: English Journal: J Clin Virol Plus Year: 2021 Document Type: Article Affiliation country: J.jcvp.2021.100025