Abstract
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.
Highlights
22 complete and near-complete genome sequences of SARS-CoV-2 strains detected in Malaysia were generated (Table 1)
All SARS-CoV-2 complete genome sequences (16 out of 22) in this study possessed a similar genome structure with the reference sequence, Wuhan-Hu-1 with no insertion or deletion detected within the positions that ranged from nucleotide 26 to 29,847
While the other ten SARS-CoV-2 strains were detected from Sabah and Selangor, representing a subset of circulating strains detected during the initial phase of the third COVID-19 epidemic wave
Summary
The etiologic agent causing the pandemic is a novel beta coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which was initially named as the 2019 novel coronavirus (2019-nCoV)[3] It is a single-stranded positive-sense RNA virus, with a genome of 29.9 kb in length[4]. The operation of all educational institutions, government agencies, and non-essential businesses temporarily ceased These strict control strategies successfully contained the spread of SARS-CoV-2 and flattened the COVID-19 epidemic curve[21] and Malaysia entered the recovery MCO (RMCO) phase on 10th Jun 2 02022. With limited available full genome sequences, the study’s findings allowed us to resolve the relationship between isolates detected from the different states and times It provides a better insight into the epidemiological link and elucidated the possible link of the actively circulating strains/clusters in the community.
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