Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification.
J Clin Virol
; 162: 105444, 2023 05.
Article
in English
| MEDLINE | ID: covidwho-2304003
ABSTRACT
BACKGROUND:
SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts.METHODS:
This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern.RESULTS:
Initial valid results were obtained from 95.8% [95% confidence interval (CI) 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5.CONCLUSIONS:
This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
COVID-19
Type of study:
Diagnostic study
/
Experimental Studies
/
Qualitative research
Topics:
Vaccines
/
Variants
Limits:
Humans
Language:
English
Journal:
J Clin Virol
Journal subject:
Virology
Year:
2023
Document Type:
Article
Affiliation country:
J.jcv.2023.105444
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