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

Nor Azila, Muhammad Azami and David, Perera and Ravindran, Thayan and Sazaly, AbuBakar and I-Ching, Sam and Mohd Zaki, Salleh and Mohd Noor, Mat Isa and Nurul Syakima, Ab Mutalib and Kiing Aik, Wong and Jeyanthi, Suppiah and Kim-Kee, Tan and Yoke Fun, Chan and Lay Kek, Teh and Ghows, Azzam and Zahirrah Begum, Mohammed Rasheed and Jonathan Chia Jui, Chan and Khayri Azizi, Kamel and Jia -Yi, Tan and Omar Khalilur, Rahman and Wai Feng, Lim and Nor Azfa, Johari and Muhiddin, Ishak and Ryia Illani, Mohd Yunos and Mohd Ishtiaq, Anasir and Jo-Ern, Wong and Jolene Yin Ling, Fu and Mohd Nur Fakhruzzaman, Noorizhab and Irni Suhayu, Sapian and Mira Farzana, Mohamad Mokhtar and Nur Alyaa Afifah, Md Shahri and Khairun, Ghafar and Siti Nur Hasanah, Mohd Yusuf and Yusuf, Muhammad Noor and Rahman, Jamal (2022) 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. International Journal of Infectious Diseases, 125. pp. 216-226. ISSN 1201-9712

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Abstract

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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