Rapid detection of the SARS-CoV-2 omicron variants based on high-resolution melting curve analysis.

Publication date: Nov 15, 2024

With the continuous spread of the SARS-CoV-2 globally, viral mutations have accumulated. As a result, SARS-CoV-2 became more contagious, and has a higher risk of immune escape and reinfection. To identify variants and have an awareness of the prevalence of these variants, this study selected four segments containing mutations on the S gene of the SARS-CoV-2. Then a rapid and convenient variants detection method was established using high-resolution melting(HRM) analysis combined with nested polymerase chain reaction(PCR). The total detection process takes about 5 h. Through comprehensive analysis of the results from the four reaction systems, the identification of seven important Omicron variants(BA. 2, BA. 2.75, BA. 5.2, BF. 7, BQ. 1, XBB. 1 and XBB. 2) can be achieved, with significant differentiation in the melting curves of each variant group. The method established in this study was used to genotype positive specimens in COVID-19 nucleic acid testing, the overall concordance rate compared to whole genome sequencing results was 88. 9%, and the positive concordance rate of each sublineage was greater than 80% and the negative concordance rate was greater than 94. 4%. The detection of clinical specimens has demonstrated that the HRM analysis established in this study is an effective, rapid and convenient variant identification method, which can be used for monitoring SARS-CoV-2 variants and has important value in addressing public health issues caused by the ongoing mutations of the SARS-CoV-2.

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Concepts Keywords
Contagious COVID-19
Genome HRM Analysis
Reinfection Humans
Viral Mutation
Omicron
Polymerase Chain Reaction
RNA, Viral
RNA, Viral
SARS-CoV-2
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Spike Glycoprotein, Coronavirus
Variant detection

Semantics

Type Source Name
disease MESH reinfection
disease IDO process
disease MESH COVID-19
disease IDO nucleic acid
disease IDO infectivity
drug DRUGBANK Coenzyme M
disease IDO host
pathway REACTOME Methylation
drug DRUGBANK Platinum
drug DRUGBANK Water
drug DRUGBANK Flunarizine
disease MESH respiratory tract infections
disease MESH influenza
disease MESH parainfluenza
disease IDO protein
disease IDO assay
disease IDO virulence
disease MESH mutation rate
drug DRUGBANK Amino acids
disease MESH death
disease MESH infection
disease MESH Cyclopia
disease MESH AIDS
drug DRUGBANK Meticillin
disease MESH colorectal neoplasms
disease MESH coronavirus infection
disease IDO cell
pathway REACTOME Reproduction

Original Article

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