SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

Objectives This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. Methods COVID-19 samples that tested positive by reverse transcription polymerase chain reactio...

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Main Authors: Nor Azila, Muhammad Azami, David, Perera, Ravindran, Thayan, Sazaly, AbuBakar, I-Ching, Sam, Mohd Zaki, Salleh, Mohd Noor, Mat Isa, Nurul Syakima, Ab Mutalib, Kiing Aik, Wong, Jeyanthi, Suppiah, Kim-Kee, Tan, Yoke Fun, Chan, Lay Kek, Teh, Ghows, Azzam, Zahirrah Begum, Mohammed Rasheed, Jonathan Chia Jui, Chan, Khayri Azizi, Kamel, Jia -Yi, Tan, Omar Khalilur, Rahman, Wai Feng, Lim, Nor Azfa, Johari, Muhiddin, Ishak, Ryia Illani, Mohd Yunos, Mohd Ishtiaq, Anasir, Jo-Ern, Wong, Jolene Yin Ling, Fu, Mohd Nur Fakhruzzaman, Noorizhab, Irni Suhayu, Sapian, Mira Farzana, Mohamad Mokhtar, Nur Alyaa Afifah, Md Shahri, Khairun, Ghafar, Siti Nur Hasanah, Mohd Yusuf, Yusuf, Muhammad Noor, Rahman, Jamal
Format: Article
Language:en
Published: Elsevier 2022
Subjects:
Q Science (General)
QR355 Virology
Online Access:http://ir.unimas.my/id/eprint/40570/3/SARS-CoV-2%20genomic%20-%20Copy.pdf
http://ir.unimas.my/id/eprint/40570/
https://www.sciencedirect.com/science/article/pii/S1201971222005823?via%3Dihub
https://doi.org/10.1016/j.ijid.2022.10.044
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Summary:Objectives This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. Methods COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values <30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database. Results From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country. Conclusion The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness.

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