Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings.

Area of Science:

• Virology
• Epidemiology
• Molecular Diagnostics

Background:

• COVID-19 pandemic caused by SARS-CoV-2 led to significant global morbidity and mortality.
• Rapid evolution of SARS-CoV-2 resulted in Variants of Concern (VOC) with increased transmissibility.
• Genomic surveillance gaps existed in low-middle income countries (LMIC), hindering effective public health responses.

Purpose of the Study:

• To demonstrate a specific mutation RT-PCR based approach for identifying SARS-CoV-2 VOC in Pakistan.
• To track the prevalence of different VOC during pandemic waves.
• To evaluate the utility of RT-PCR assays as a rapid, low-cost adjunct to Next-Generation Sequencing (NGS).

Main Methods:

• Selection of 2150 SARS-CoV-2 PCR positive respiratory specimens from April 2021 to February 2022.
• Utilized commercially available RT-PCR assays targeting key spike protein mutations (N501Y, A570D, E484K, K417N, L452R, P681R, deletion69_70).
• Identified Alpha, Beta, Gamma, Delta, and Omicron variants based on specific mutation profiles.

Main Results:

• VOC were identified in 81.7% of screened samples, predominantly Delta (37.2%), Alpha (29.8%), and Omicron (17.1%).
• Observed distinct pandemic waves: Alpha (April-May 2021), Delta (July-November 2021), and Omicron (December 2021-February 2022).
• Significantly higher CT values were observed for Alpha, Beta, Gamma, and Delta variants compared to Omicron (p<0.0001).

Conclusions:

• Spike mutation-specific RT-PCR assays effectively identified VOC throughout pandemic waves in Pakistan.
• This RT-PCR approach is rapid, low-cost, and adaptable, serving as a valuable adjunct to NGS for public health.
• Linking VOC identification with CT values provides insights into viral load, transmission, and potential disease severity.