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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

Azami NAM 1 , Perera D 2 , Thayan R 3 , AbuBakar S 4 , Sam IC 5 , Salleh MZ 6 Show all authors , Isa MNM 7 , Ab Mutalib NS 1 , Aik WK 2 , Suppiah J 3 , Tan KK 4 , Chan YF 8 , Teh LK 6 , Azzam G 9 , Rasheed ZBM 1 , Chan JCJ 2 , Kamel KA 3 , Tan JY 4 , Khalilur Rahman O 10 , Lim WF 6 , Johari NA 7 , Ishak M 1 , Yunos RIM 1 , Anasir MI 3 , Wong JE 4 , Fu JYL 8 , Noorizhab MNF 6 , Sapian IS 7 , Mokhtar MFM 1 , Md Shahri NAA 1 , Ghafar K 1 , Yusuf SNHM 1 , Noor YM 7 , Jamal R 11 , Malaysia COVID-19 Genomics Surveillance Consortium

Affiliations 

  • 1 UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
  • 2 Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
  • 3 Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
  • 4 Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia
  • 5 Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia
  • 6 Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
  • 7 Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
  • 8 Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
  • 9 Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
  • 10 Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia
  • 11 UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia. Electronic address: rahmanj@ppukm.ukm.edu.my
Int J Infect Dis, 2022 Dec;125:216-226.
PMID: 36336246 DOI: 10.1016/j.ijid.2022.10.044

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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