Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian...

Area of Science:

• Virology
• Genomics
• Public Health

Background:

• SARS-CoV-2 rapidly evolves, producing variants of concern (VOCs) with increased transmissibility and immune evasion.
• Whole genome sequencing (WGS) is the gold standard for variant identification but resource-intensive.
• Genomic surveillance in Bolivia faces challenges due to limited infrastructure and resources.

Purpose of the Study:

• To develop and validate an RT-qPCR-based strategy for detecting key mutations of SARS-CoV-2 VOCs and variants of interest (VOIs) in Bolivia.
• To address limitations in genomic surveillance capacity in resource-constrained settings.

Main Methods:

• Utilized multiplex RT-qPCR commercial kits (Allplex Master and Variants I, ValuPanel) to target specific mutations (HV69/70del, E484K, N501Y, P681H, K417N/T).
• These mutations are characteristic of Alpha, Beta, Gamma, Omicron, Mu, and Zeta variants.
• Evaluated 157 samples from Cochabamba, Bolivia, between January and November 2021.

Main Results:

• Identified 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron variant samples.
• Validated the RT-qPCR strategy against whole genome sequencing (WGS) data using Oxford Nanopore technology.
• Achieved a high concordance rate of 0.96 between the RT-qPCR strategy and WGS.

Conclusions:

• The RT-qPCR strategy is effective for rapid, cost-efficient detection of known SARS-CoV-2 variants in resource-limited settings.
• This approach enhances genomic surveillance by guiding the selection of samples for WGS, enabling broader variant detection.
• The strategy supports public health efforts in controlling COVID-19 by facilitating timely identification of emerging variants.