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