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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, Nor Azila Muhammad; Perera, David; Thayan, Ravindran; AbuBakar, Sazaly; Sam, I-Ching; Salleh, Mohd Zaki; Isa, Mohd Noor Mat; Ab Mutalib, Nurul Syakima; Aik, Wong Kiing; Suppiah, Jeyanthi; Tan, Kim-Kee; Chan, Yoke Fun; Teh, Lay Kek; Azzam, Ghows; Rasheed, Zahirrah Begam Mohamed; Chan, Jonathan Chia Jui; Kamel, Khayri Azizi; Tan, Jia-Yi; Khalilur Rahman, Omar; Lim, Wai Feng; Johari, Nor Azfa; Ishak, Muhiddin; Yunos, Ryia Illani Mohd; Anasir, Mohd Ishtiaq; Wong, Jo-Ern; Fu, Jolene Yin Ling; Noorizhab, Mohd Nur Fakhruzzaman; Sapian, Irni Suhayu; Mokhtar, Mira Farzana Mohamad; Md Shahri, Nur Alyaa Afifah; Ghafar, Khairun; Yusuf, Siti Nur Hasanah Mohd; Noor, Yusuf Muhammad; Jamal, Rahman.
  • Azami NAM; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Perera D; Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia.
  • Thayan R; Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia.
  • AbuBakar S; Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia.
  • Sam IC; Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
  • Salleh MZ; Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
  • Isa MNM; Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia.
  • Ab Mutalib NS; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Aik WK; Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia.
  • Suppiah J; Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia.
  • Tan KK; Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia.
  • Chan YF; Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
  • Teh LK; Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
  • Azzam G; Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia.
  • Rasheed ZBM; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Chan JCJ; Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia.
  • Kamel KA; Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia.
  • Tan JY; Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia.
  • Khalilur Rahman O; Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
  • Lim WF; Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
  • Johari NA; Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia.
  • Ishak M; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Yunos RIM; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Anasir MI; Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia.
  • Wong JE; Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia.
  • Fu JYL; Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
  • Noorizhab MNF; Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
  • Sapian IS; Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia.
  • Mokhtar MFM; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Md Shahri NAA; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Ghafar K; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Yusuf SNHM; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
  • Noor YM; Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia.
  • Jamal R; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia. Electronic address: rahmanj@ppukm.ukm.edu.my.
Int J Infect Dis ; 125: 216-226, 2022 Nov 03.
Article in English | MEDLINE | ID: covidwho-2095477
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.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Int J Infect Dis Journal subject: Communicable Diseases Year: 2022 Document Type: Article Affiliation country: J.ijid.2022.10.044

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Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Int J Infect Dis Journal subject: Communicable Diseases Year: 2022 Document Type: Article Affiliation country: J.ijid.2022.10.044