An ARMS-Multiplex PCR Targeting SARS-CoV-2 Omicron Sub-Variants

Area of Science:

• Virology
• Molecular Biology
• Genetics

Background:

• The SARS-CoV-2 Omicron variant emerged in November 2021, rapidly replacing the Delta variant.
• Omicron has since evolved into numerous strains, primarily categorized into five sub-variants: BA.1, BA.2, BA.3, BA.4, and BA.5.

Purpose of the Study:

• To develop a rapid and specific multiplex polymerase chain reaction (PCR) assay.
• To differentiate between the main Omicron sub-variants (BA.1, BA.2, BA.4, BA.5).

Main Methods:

• Retrieved full genome sequences of high-frequency Omicron strains from public databases (NCBI Virus, ENA).
• Identified single nucleotide polymorphisms (SNPs) characteristic of each sub-variant.
• Designed specific primers using the Amplification Refractory Mutation System (ARMS) for multiplex PCR conditions.

Main Results:

• Developed ARMS-multiplex PCR primers targeting characteristic polymorphisms.
• The assay successfully distinguished between the targeted Omicron sub-variants (BA.1, BA.2, BA.4, BA.5).
• The method demonstrated specificity in differentiating Omicron sub-variants from each other and potentially from previous SARS-CoV-2 variants.

Conclusions:

• The developed ARMS-multiplex PCR assay is a valuable tool for rapid and accurate identification of SARS-CoV-2 Omicron sub-variants.
• This method can aid in epidemiological surveillance and understanding the evolution of the Omicron variant.