Genomic Variant Surveillance of SARS-CoV-2 Positive Specimens Using a Direct PCR Product Sequencing Surveillance...

Area of Science:

• Virology
• Genomic Surveillance
• Molecular Diagnostics

Background:

• The COVID-19 pandemic, caused by SARS-CoV-2, has been marked by the emergence of multiple Variants of Concern (VOCs).
• Accurate and timely detection of these viral variants is crucial for effective public health responses.
• Omicron has emerged as the most prevalent SARS-CoV-2 variant globally.

Purpose of the Study:

• To evaluate the feasibility of an in-house genomic surveillance method for detecting SARS-CoV-2 variants.
• To assess the utility of in silico designed primers for variant identification.

Main Methods:

• Design of specific oligonucleotide primers targeting conserved regions of SARS-CoV-2 genes.
• RNA extraction from nasopharyngeal samples followed by RT-PCR amplification.
• Sequencing of amplicons and subsequent sequence alignment for variant identification.

Main Results:

• The in-house method successfully amplified conserved viral sequences (spike, envelope, membrane, ORF1ab).
• The majority of samples were identified as the Omicron variant, with key mutations like K417N, S477N, and P681H detected.
• The method also identified an unclassified lineage (B.1.448), demonstrating potential for detecting novel variants.

Conclusions:

• The developed in-house direct PCR product sequencing surveillance (DPPSS) method offers an accessible and affordable alternative for SARS-CoV-2 variant analysis.
• This approach complements conventional diagnostic and whole-genome sequencing methods.
• Further optimization of primers could enhance the direct PCR-based detection of emerging COVID-19 variants.