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 reaction a...

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Published in:International Journal of Infectious Diseases
Main Author: Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
Format: Article
Language:English
Published: Elsevier B.V. 2022
Online Access:https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142135931&doi=10.1016%2fj.ijid.2022.10.044&partnerID=40&md5=e848a3937099020359e2eb5d0b2fd3c3
id 2-s2.0-85142135931
spelling 2-s2.0-85142135931
Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
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
2022
International Journal of Infectious Diseases
125

10.1016/j.ijid.2022.10.044
https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142135931&doi=10.1016%2fj.ijid.2022.10.044&partnerID=40&md5=e848a3937099020359e2eb5d0b2fd3c3
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. © 2022 The Authors
Elsevier B.V.
12019712
English
Article
All Open Access; Gold Open Access
author Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
spellingShingle Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
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
author_facet Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
author_sort Azami N.A.M.; Perera D.; Thayan R.; AbuBakar S.; Sam I.-C.; Salleh M.Z.; Isa M.N.M.; Ab Mutalib N.S.; Aik W.K.; Suppiah J.; Tan K.-K.; Chan Y.F.; Teh L.K.; Azzam G.; Rasheed Z.B.M.; Chan J.C.J.; Kamel K.A.; Tan J.-Y.; Khalilur Rahman O.; Lim W.F.; Johari N.A.; Ishak M.; Yunos R.I.M.; Anasir M.I.; Wong J.-E.; Fu J.Y.L.; Noorizhab M.N.F.; Sapian I.S.; Mokhtar M.F.M.; Md Shahri N.A.A.; Ghafar K.; Yusuf S.N.H.M.; Noor Y.M.; Jamal R.
title 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
title_short 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_sort 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
publishDate 2022
container_title International Journal of Infectious Diseases
container_volume 125
container_issue
doi_str_mv 10.1016/j.ijid.2022.10.044
url https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142135931&doi=10.1016%2fj.ijid.2022.10.044&partnerID=40&md5=e848a3937099020359e2eb5d0b2fd3c3
description 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. © 2022 The Authors
publisher Elsevier B.V.
issn 12019712
language English
format Article
accesstype All Open Access; Gold Open Access
record_format scopus
collection Scopus
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