tetano
Editor, Senior Moderator
PLoS One
. 2024 Oct 17;19(10):e0311993.
doi: 10.1371/journal.pone.0311993. eCollection 2024. SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh
Zannat Kawser[SUP] 1 [/SUP], Saikt Rahman[SUP] 1 [/SUP], Emilie Westeel[SUP] 2 [/SUP], Mohammad Tanbir Habib[SUP] 1 [/SUP], Mohabbat Hossain[SUP] 1 3 [/SUP], Md Rakibul Hassan Bulbul[SUP] 1 4 [/SUP], Sharmin Aktar Mukta[SUP] 1 [/SUP], Md Zahirul Islam[SUP] 1 4 [/SUP], Md Zakir Hossain[SUP] 4 [/SUP], Mokibul Hassan Afrad[SUP] 5 [/SUP], Manjur Hossain Khan[SUP] 6 [/SUP], Tahmina Shirin[SUP] 6 [/SUP], Md Shakeel Ahmed[SUP] 4 [/SUP], Jean-Luc Berland[SUP] 2 [/SUP], Florence Komurian-Pradel[SUP] 2 [/SUP], Firdausi Qadri[SUP] 1 5 [/SUP]
Affiliations
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.
. 2024 Oct 17;19(10):e0311993.
doi: 10.1371/journal.pone.0311993. eCollection 2024. SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh
Zannat Kawser[SUP] 1 [/SUP], Saikt Rahman[SUP] 1 [/SUP], Emilie Westeel[SUP] 2 [/SUP], Mohammad Tanbir Habib[SUP] 1 [/SUP], Mohabbat Hossain[SUP] 1 3 [/SUP], Md Rakibul Hassan Bulbul[SUP] 1 4 [/SUP], Sharmin Aktar Mukta[SUP] 1 [/SUP], Md Zahirul Islam[SUP] 1 4 [/SUP], Md Zakir Hossain[SUP] 4 [/SUP], Mokibul Hassan Afrad[SUP] 5 [/SUP], Manjur Hossain Khan[SUP] 6 [/SUP], Tahmina Shirin[SUP] 6 [/SUP], Md Shakeel Ahmed[SUP] 4 [/SUP], Jean-Luc Berland[SUP] 2 [/SUP], Florence Komurian-Pradel[SUP] 2 [/SUP], Firdausi Qadri[SUP] 1 5 [/SUP]
Affiliations
- PMID: 39418288
- DOI: 10.1371/journal.pone.0311993
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.