Comparison of SARS-CoV-2 Omicron nucleic acid test for COVID-19
infection with real-time RT-PCR using different nasopharyngeal swabs
Background: A new one SARS-CoV-2 Variant of Concern (VoC),
Omicron, was born in a world weary of COVID-19, which anger and
frustration with the pandemic was widespread, with wide-ranging negative
impacts on health, social and economic well-being. The Omicron variant,
which main types was BA5.2and BF.7 in China, in December 2022 to January
2023 leaded to off-target of the S and N genes, and the kits used were
not adequately and independently evaluated when these agents are studied
and developed. To ensure the accuracy of coronavirus test results,
performance verification of commercial Real-Time quantitative PCR
(RT-qPCR) was required. Objective: We performed a clinical
evaluation for two Real Time SARS-CoV-2 assay, and to verify them based
on different detection reagents and different clinical specimens.
Methods: We performed clinical evaluations of two existing
Chinese SARS-CoV-2 RT-qPCR kits COVID-19 nucleic acid detection kits
(e-Diagnostic Biomedical, Wuhan, China) and 2019-nCoV nucleic acid
diagnostic kits (Fosun Biotechnology, Shanghai, China) using BSD (
Bondson) (Guangzhou Bondson Biotechnology Co. Ltd.;batch number
2022101), quality controls provided by the inspection center and a large
number of clinically confirmed specimens. Overall, through the BDS
performance verification reference product kit, It was best used to
verify the performance of the reagent through a large number of clinical
specimens for further verification. Results: The coincidence
rate for Fosun and e-Diagnostic kits were individually 95% and 100%.
Verified that the detection limit for Fosun and e-Diagnostic kits was
300copies/mL. All were below the detection limit for Fosun reagent was
300copies/mL. e-Diagnostic was 500copies/mL. Fosun had the largest CV
for ORF1ab and N gene at the the detection limit
concentration(4.80%,3.49%), while e-Diagnostic had the smaller
(0.93%,1.10%). Negative results were tested in cross-reactivity.
During the verification of clinical samples, sequencing analyses had
shown that Fosun single gene miss rate was relatively high, especially
ORF1ab, followed by N gene miss rate. we survey that all N genes were
detected in clinical specimens, ,ORFab dropout (i.e., a negative/low
result) occurred in (10.8%) of 225 Omicron variant.
Conclusions: Our results endorse the use of these two
commercial kits for the diagnosis of SARS-CoV-2 in China, as their
clinical performance has been fully validated by a large number of
clinically confirmed cases.