1. SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh.
- Author
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Kawser Z, Rahman S, Westeel E, Habib MT, Hossain M, Bulbul MRH, Mukta SA, Islam MZ, Hossain MZ, Afrad MH, Khan MH, Shirin T, Ahmed MS, Berland JL, Komurian-Pradel F, and Qadri F
- Subjects
- Bangladesh epidemiology, Humans, Female, Male, Mutation, Adult, High-Throughput Nucleotide Sequencing methods, Real-Time Polymerase Chain Reaction methods, Reverse Transcriptase Polymerase Chain Reaction methods, Middle Aged, Retrospective Studies, Whole Genome Sequencing methods, COVID-19 Nucleic Acid Testing methods, Spike Glycoprotein, Coronavirus genetics, Prospective Studies, SARS-CoV-2 genetics, SARS-CoV-2 isolation & purification, COVID-19 epidemiology, COVID-19 virology, COVID-19 diagnosis
- Abstract
Background: The widespread increase in multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) since 2020 is causing significant health concerns worldwide. While whole-genome sequencing (WGS) has played a leading role in surveillance programs, many local laboratories lack the expertise and resources. Thus, we aimed to investigate the circulating SARS-CoV-2 variants and evaluate the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) for screening and monitoring the emergence of new SARS-CoV-2 variants in Bangladesh., Methods: A total of 600 confirmed SARS-CoV-2-positive cases were enrolled either prospectively or retrospectively from two divisions of Bangladesh. The samples were screened by variant RT-PCR targeting five mutations of the spike gene (N501Y, P681R, L452R, E484K, E484Q). A subsample of the study population was also selected for third-generation sequencing (TGS) and the results were compared to the variant RT-PCR screening. An in-depth comparison was made between the two methods in terms of congruence and cost-benefit., Result: Seven variants were detected among samples, with similar distributions of the variants across both divisions. Variant RT-PCR for the targeted mutations lead to a 98.5% call rate; only nine samples failed to be determined. No association was found regarding the demographic features, clinical criteria, or routine RT-PCR Ct values across the variants. The clade diversity of the sequenced subpopulation (n = 99) exhibited similar distributions across the two study sites and other epidemiologic variables. Variant RT-PCR successfully distinguished variants of concern (VOCs) and variants of interest (VOIs); however, 8% discrepancy was observed for the closest lineages. Moreover, the variant RT-PCR represented an ideal balance of cost, time, and accuracy that outweigh their limitations., Conclusion: Based on the strong agreement of variant RT-PCR with TGS, such rapid, easily accessible approaches of rapid strain typing are essential in the context of pandemic responses to guide both treatment decisions and public health measures., Competing Interests: The authors declare no competing interest., (Copyright: © 2024 Kawser et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
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