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SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021

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...

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Main Authors: Fu, Jolene Yin Ling, Chong, Yoong Min, Sam, I-Ching, Chan, Yoke Fun
Format: Article
Published: Elsevier 2022
Subjects:
QR Microbiology
QR355 Virology
Online Access:http://eprints.um.edu.my/32760/
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spelling my.um.eprints.327602022-08-05T06:04:25Z http://eprints.um.edu.my/32760/ SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021 Fu, Jolene Yin Ling Chong, Yoong Min Sam, I-Ching Chan, Yoke Fun QR Microbiology QR355 Virology 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. Elsevier 2022-03 Article PeerReviewed 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 <https://doi.org/10.1016/j.jviromet.2022.114462>. 10.1016/j.jviromet.2022.114462
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic QR Microbiology
QR355 Virology
spellingShingle QR Microbiology
QR355 Virology
Fu, Jolene Yin Ling
Chong, Yoong Min
Sam, I-Ching
Chan, Yoke Fun
SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
description 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.
format Article
author Fu, Jolene Yin Ling
Chong, Yoong Min
Sam, I-Ching
Chan, Yoke Fun
author_facet Fu, Jolene Yin Ling
Chong, Yoong Min
Sam, I-Ching
Chan, Yoke Fun
author_sort Fu, Jolene Yin Ling
title SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
title_short SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
title_full SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
title_fullStr SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
title_full_unstemmed SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021
title_sort sars-cov-2 multiplex rt-pcr to detect variants of concern (vocs) in malaysia, between january to may 2021
publisher Elsevier
publishDate 2022
url http://eprints.um.edu.my/32760/
_version_ 1740826020742692864
score 13.211869

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