Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia

Baiba Niedre-Otomere; Inara Kampenusa; Julija Trofimova; Jevgenijs Bodrenko; Reinis Vangravs; Girts Skenders; Sergejs Nikisins; Oksana Savicka

doi:10.3390/diagnostics13223467

Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia

Diagnostics (Basel). 2023 Nov 17;13(22):3467. doi: 10.3390/diagnostics13223467.

Authors

Baiba Niedre-Otomere¹, Inara Kampenusa¹, Julija Trofimova¹, Jevgenijs Bodrenko¹, Reinis Vangravs¹, Girts Skenders¹, Sergejs Nikisins¹, Oksana Savicka¹

Affiliation

¹ National Microbiology Reference Laboratory of Latvia, Laboratory "Latvian Centre of Infectious Diseases", Laboratory Service, Riga East University Hospital, Linezera Street 3, LV-1006 Riga, Latvia.

Abstract

At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain's quality threshold for "good". We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2.

Keywords: E484A; N501Y; SARS-CoV-2 Omicron variant of concern; SARS-CoV-2 signature mutations: ΔH69/V70; multiplexed RT-qPCR; whole-genome sequencing.

Grants and funding

This retrospective research received no external funding. Data generation in this study was supported by ECDC grant received under contract No. ECDC/HERA/2021/014 ECD.12229 for action “Enhancing Whole Genome Sequencing (WGS) and/or Reverse Transcription Polymerase Chain Reaction (RT-PCR) national infrastructures and capacities to respond to the COVID-19 pandemic in the European Union and European Economic Area”.