Fu, Jolene Yin Ling and Chong, Yoong Min and Sam, I-Ching and Chan, Yoke Fun (2022) SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. Journal of Virological Methods, 301. ISSN 0166-0934, DOI https://doi.org/10.1016/j.jviromet.2022.114462.
Full text not available from this repository.Abstract
Emerging SARS-CoV-2 variants of concern (VOC) have been associated with enhanced transmissibility and immune escape. Next-generation sequencing (NGS) of the whole genome is the gold standard for variant identification for surveillance but is time-consuming and costly. Rapid and cost-effective assays that detect SARS-CoV2 variants are needed. We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021. Spike variants were detected in 78/248 (31.5 %), comprising 60 VOC B.1.351 (beta) and 18 B.1.1.7 (alpha). With NGS as reference for 115 samples, the sensitivity for detecting the spike mutations was 98.7 % with the Master Assay and 100 % with the Variants I Assay. The emergence of beta variants correlated with increasing COVID-19 infections in Malaysia. The prevalence of alpha VOC and lineage B.1.466.2 was low. These assays detect mutations present in alpha, beta and gamma VOCs. Of the VOCs which have subsequently emerged, the assays should detect omicron (B.1.1.529) but not B.1.617.2 (delta). In conclusion, spike variant PCR assays can be used to rapidly monitor selected SARS-CoV-2 VOCs in resource-limited settings, but require updates as new variants emerge.
| Item Type: | Article |
|---|---|
| Funders: | Seegene Inc, South Korea [Grant No: IF050-2021], Fundamental Research Grant Scheme from the Ministry of Education Malaysia [Grant No: FRGS/1/2020/SKK0/UM/02/5] |
| Uncontrolled Keywords: | COVID-19; SARS-CoV-2; Next-generation sequencing; RT-qPCR; Variants of concern; Malaysia |
| Subjects: | Q Science > QR Microbiology Q Science > QR Microbiology > QR355 Virology |
| Divisions: | Faculty of Medicine |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 05 Aug 2022 06:04 |
| Last Modified: | 05 Aug 2022 06:04 |
| URI: | http://eprints.um.edu.my/id/eprint/32760 |
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