Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave.

The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5'UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.

Tan KK ，Tan JY ，Wong JE ，Teoh BT ，Tiong V ，Abd-Jamil J ，Nor'e SS ，Khor CS ，Johari J ，Yaacob CN ，Zulkifli MM ，CheMatSeri A ，Mahfodz NH ，Azizan NS ，AbuBakar S ... -  《Scientific Reports》

Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021.

Malaysia has experienced three waves of coronavirus disease 2019 (COVID-19) as of March 31, 2021. We studied the associated molecular epidemiology and SARS-CoV-2 seroprevalence during the third wave. We obtained 60 whole-genome SARS-CoV-2 sequences between October 2020 and January 2021 in Kuala Lumpur/Selangor and analyzed 989 available Malaysian sequences. We tested 653 residual serum samples collected between December 2020 to April 2021 for anti-SARS-CoV-2 total antibodies, as a proxy for population immunity. The first wave (January 2020) comprised sporadic imported cases from China of early Pango lineages A and B. The second wave (March-June 2020) was associated with lineage B.6. The ongoing third wave (from September 2020) was propagated by a state election in Sabah. It is due to lineage B.1.524 viruses containing spike mutations D614G and A701V. Lineages B.1.459, B.1.470, and B.1.466.2 were likely imported from the region and confined to Sarawak state. Direct age-standardized seroprevalence in Kuala Lumpur/Selangor was 3.0%. The second and third waves were driven by super-spreading events and different circulating lineages. Malaysia is highly susceptible to further waves, especially as alpha (B.1.1.7) and beta (B.1.351) variants of concern were first detected in December 2020/January 2021. Increased genomic surveillance is critical.

Sam IC ，Chong YM ，Abdullah A ，Fu JYL ，Hasan MS ，Jamaluddin FH ，Kamarulzaman A ，Lim KK ，Mohd Nor MA ，Pang YK ，Ponnampalavanar S ，Shahib MF ，Syed Omar SF ，Chan JCJ ，Perera D ，Chan YF ... -  《-》

Phylogenomic analysis of SARS-CoV-2 from third wave clusters in Malaysia reveals dominant local lineage B.1.524 and persistent spike mutation A701V.

Suppiah J ，Kamel KA ，Mohd-Zawawi Z ，Afizan MA ，Yahya H ，Md-Hanif SA ，Thayan R ... -  《-》

SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia.

Chong YM ，Sam IC ，Chong J ，Kahar Bador M ，Ponnampalavanar S ，Syed Omar SF ，Kamarulzaman A ，Munusamy V ，Wong CK ，Jamaluddin FH ，Chan YF ... -  《PLoS Neglected Tropical Diseases》

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.

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. 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. 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. 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.

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