Rapid surveillance platforms for key SARS-CoV-2 mutations in Denmark

Abstract

Multiple mutations in SARS-CoV-2 variants of concern (VOCs) may increase, transmission, disease severity, immune evasion and facilitate zoonotic or anthoprozoonotic infections. Four such mutations, ΔH69/V70, L452R, E484K and N501Y, occur in the SARS-CoV-2 spike glycoprotein in combinations that allow detection of the most important VOCs. Here we present two flexible RT-qPCR platforms for small- and large-scale screening to detect these mutations, and schemes for adapting the platforms for future mutations. The large-scale RT-qPCR platform, was validated by pair-wise matching of RT-qPCR results with WGS consensus genomes, showing high specificity and sensitivity. Detection of mutations using this platform served as an important interventive measure for the Danish public health system to delay the emergence of VOCs and to gain time for vaccine administration. Both platforms are valuable tools for WGS-lean laboratories, as well for complementing WGS to support rapid control of local transmission chains worldwide.

Risk of hospitalisation associated with infection with SARS-CoV-2 omicron variant versus delta variant in Denmark: an observational cohort study

“…For the omicron variant, an RT-PCR test using the L452 marker (estimated specificity 99·99% based on retrospective analysis) was developed and implemented by the TCDK by Dec 1, 2021 (hereafter known as TCDK vPCR). 24 In eight of ten local CMDs (ie, the health-care track), similar omicron-specific vPCR solutions have been set up (hereafter CMD vPCR) and documented; the remaining two of ten local CMDs account for less than 7% of RT-PCR tests done by CMDs.…”

“…For the TCDK vPCR, we defined a confirmed omicron case as a case testing positive with RT-PCR targeting the wild type sequence L452, as described elsewhere. 24 The delta variant is detected by the 452R substitution and was the only predominant variant in Denmark (>99%) 25 in the period before occurrence of omicron; individuals testing positive for the 452R substitution were therefore considered to be infected with the delta VOC. 26 Similar descriptions for the CMD vPCR are not described in detail in this study, but are available on request.…”

Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021

“…An RT-PCR detecting the Omicron variant using the 452L marker (estimated specificity: 99.99% based on retrospective analysis) [5] was developed and implemented in the TCDK by 1 December. In the 10 local clinical microbiology departments, similar solutions have been set up.…”

Occurrence and significance of Omicron BA.1 infection followed by BA.2 reinfection

“…The Community track, TestCenter Denmark (TCDK) provides large scale testing for SARS-CoV-2 for all residents using RT-PCR through the free Danish universal health care system, providing easy access to testing facilities across the country. Since the end of 2021, surveillance of SARS-CoV-2 variants has been based on screening of ~15,000 positive samples per week using a variant-specific RT-PCR 9 and subsequent WGS as previously described 10 . Briefly, WGS was performed using Illumina technology using the ARTIC v3 amplicon sequencing panel (https://artic.network) with slight modifications.…”