tetano
Editor, Senior Moderator
Int J Infect Dis
. 2022 Nov 3;S1201-9712(22)00582-3.
doi: 10.1016/j.ijid.2022.10.044. Online ahead of print.
SARS-CoV-2 genomic surveillance in Malaysia: Displacement of B.1.617.2 with AY lineages as dominant Delta variants and the introduction of Omicron during the fourth epidemic wave
Nor Azila Muhammad Azami[SUP] 1 [/SUP], David Perera[SUP] 2 [/SUP], Ravindran Thayan[SUP] 3 [/SUP], Sazaly Abu Bakar[SUP] 4 [/SUP], I-Ching Sam[SUP] 5 [/SUP], Mohd Zaki Salleh[SUP] 6 [/SUP], Mohd Noor Mat Isa[SUP] 7 [/SUP], Nurul Syakima Ab Mutalib[SUP] 1 [/SUP], Wong Kiing Aik[SUP] 2 [/SUP], Jeyanthi Suppiah[SUP] 3 [/SUP], Kim-Kee Tan[SUP] 4 [/SUP], Yoke Fun Chan[SUP] 8 [/SUP], Lay Kek Teh[SUP] 6 [/SUP], Ghows Azzam[SUP] 9 [/SUP], Zahirrah Begam Mohamed Rasheed[SUP] 1 [/SUP], Jonathan Chia Jui Chan[SUP] 2 [/SUP], Khayri Azizi Kamel[SUP] 3 [/SUP], Jia-Yi Tan[SUP] 4 [/SUP], Omar Khalilur Rahman[SUP] 8 [/SUP], Wai Feng Lim[SUP] 6 [/SUP], Nor Azfa Johari[SUP] 7 [/SUP], Muhiddin Ishak[SUP] 1 [/SUP], Ryia Illani Mohd Yunos[SUP] 1 [/SUP], Mohd Ishtiaq Anasir[SUP] 3 [/SUP], Jo-Ern Wong[SUP] 4 [/SUP], Jolene Yin Ling Fu[SUP] 8 [/SUP], Mohd Nur Fakhruzzaman Noorizhab[SUP] 6 [/SUP], Irni Suhayu Sapian[SUP] 7 [/SUP], Mira Farzana Mohamad Mokhtar[SUP] 1 [/SUP], Nur Alyaa Afifah Md Shahri[SUP] 1 [/SUP], Khairun Nur Abdul Ghafar[SUP] 1 [/SUP], Siti Nur Hasanah Mohd Yusuf[SUP] 1 [/SUP], Yusuf Muhammad Noor[SUP] 7 [/SUP], Rahman Jamal[SUP] 10 [/SUP], Malaysia COVID-19 Genomics Surveillance Consortium
Affiliations
Abstract
Objective: This study reported severe respiratory syndrome coronavirus-2 (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: Coronavirus disease 2019 (COVID-19) samples that tested positive by reverse transcription polymerase chain reaction and with CT 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 (GISAID) database.
Results: From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern (VOC) 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 VOC) 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: COVID-19; Delta; Genome surveillance; Malaysia; Omicron; SARS-CoV-2; genomic profile; whole genome sequencing.
. 2022 Nov 3;S1201-9712(22)00582-3.
doi: 10.1016/j.ijid.2022.10.044. Online ahead of print.
SARS-CoV-2 genomic surveillance in Malaysia: Displacement of B.1.617.2 with AY lineages as dominant Delta variants and the introduction of Omicron during the fourth epidemic wave
Nor Azila Muhammad Azami[SUP] 1 [/SUP], David Perera[SUP] 2 [/SUP], Ravindran Thayan[SUP] 3 [/SUP], Sazaly Abu Bakar[SUP] 4 [/SUP], I-Ching Sam[SUP] 5 [/SUP], Mohd Zaki Salleh[SUP] 6 [/SUP], Mohd Noor Mat Isa[SUP] 7 [/SUP], Nurul Syakima Ab Mutalib[SUP] 1 [/SUP], Wong Kiing Aik[SUP] 2 [/SUP], Jeyanthi Suppiah[SUP] 3 [/SUP], Kim-Kee Tan[SUP] 4 [/SUP], Yoke Fun Chan[SUP] 8 [/SUP], Lay Kek Teh[SUP] 6 [/SUP], Ghows Azzam[SUP] 9 [/SUP], Zahirrah Begam Mohamed Rasheed[SUP] 1 [/SUP], Jonathan Chia Jui Chan[SUP] 2 [/SUP], Khayri Azizi Kamel[SUP] 3 [/SUP], Jia-Yi Tan[SUP] 4 [/SUP], Omar Khalilur Rahman[SUP] 8 [/SUP], Wai Feng Lim[SUP] 6 [/SUP], Nor Azfa Johari[SUP] 7 [/SUP], Muhiddin Ishak[SUP] 1 [/SUP], Ryia Illani Mohd Yunos[SUP] 1 [/SUP], Mohd Ishtiaq Anasir[SUP] 3 [/SUP], Jo-Ern Wong[SUP] 4 [/SUP], Jolene Yin Ling Fu[SUP] 8 [/SUP], Mohd Nur Fakhruzzaman Noorizhab[SUP] 6 [/SUP], Irni Suhayu Sapian[SUP] 7 [/SUP], Mira Farzana Mohamad Mokhtar[SUP] 1 [/SUP], Nur Alyaa Afifah Md Shahri[SUP] 1 [/SUP], Khairun Nur Abdul Ghafar[SUP] 1 [/SUP], Siti Nur Hasanah Mohd Yusuf[SUP] 1 [/SUP], Yusuf Muhammad Noor[SUP] 7 [/SUP], Rahman Jamal[SUP] 10 [/SUP], Malaysia COVID-19 Genomics Surveillance Consortium
Affiliations
- PMID: 36336246
- DOI: 10.1016/j.ijid.2022.10.044
Abstract
Objective: This study reported severe respiratory syndrome coronavirus-2 (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: Coronavirus disease 2019 (COVID-19) samples that tested positive by reverse transcription polymerase chain reaction and with CT 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 (GISAID) database.
Results: From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern (VOC) 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 VOC) 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: COVID-19; Delta; Genome surveillance; Malaysia; Omicron; SARS-CoV-2; genomic profile; whole genome sequencing.