COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang

Abstract

SARS-CoV-2 is a very transmissible and pathogenic coronavirus which detected in Malaysia in January 2020. Nevertheless, the sample from Malaysia is still under-sequenced. Hence lacking clarity of the circulating strain in Malaysia leads to a deadlock in understanding the virus infectivity. This study aimed to investigate the genome identity of circulating COVID-19 strains in Pahang and understand disease epidemiology during the pandemic. This study leveraged high-throughput sequencing analysis for the whole genome sequencing and implemented bioinformatic technique for the analysis. Here we reported that the virus with D614G mutation in Spike protein circulates in a few Malaysia states before the Sivagangga cluster announced in Kedah in July 2020. This mutated virus includes our virus sample isolated in April 2020 from an asymptomatic patient in Pahang. Based on the phylogenetic analysis, we discovered the origin of our sample Pahang/IIUM91 was not related to Sivagangga cluster. Here, we have generated 3D structure model of Pahang/IIUM91 Spike protein. D614G mutation in Pahang/IIUM91 Spike protein increases viral stability and flexibility, hence render higher infectivity. Collectively, our results suggest for the establishment of a complete SARS-CoV-2 genome database in Malaysia. Hence, more research should be established to learn the behaviour of this virus.

COVID-19: Malaysia's fight against this deadly virus

“…As the outbreak progressed and more confirmed cases were reported, different variants of the coronavirus were isolated in Malaysia. For instance, in Pahang, SARS-CoV-2 with D614G mutation was found in an asymptomatic patient and this mutation resulted in higher infectivity of the coronavirus [47] . Other variants of concern (VOC ) strains include the SARS-CoV-2 lineage B.1.351 (South African), B.117 (United Kingdom), and B.1.617.1 (Indian).…”

Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

“…The current pandemic of coronavirus disease 19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which belongs to the viral family Coronaviridae and genus Betacoronavirus ( 1 ). The COVID-19 D614G mutation was associated with higher risk of infection ( 2 ). Here, we report nine nearly complete genome sequences of variants of concern (VOC) from the Beta B.1.351 lineage and several unassigned variants that belong to local lineages ( 3 ).…”

The D614G virus mutation enhances anosmia in COVID-19 patients: Evidence from a systematic review and meta-analysis of studies from South Asia

“…17,18,[20][21][22]25,30 Such regional differences were caused by travel routes as well as regional spreader events, e.g., in Delhi. 17 Indians and Bangladeshis were exposed primarily to the D614 virus in March through June or July of 2020 in some regions outside the Indian subcontinent, e.g., Kuwait, 37 Malaysia, 38,39 and Singapore, 14,23 while South Asians in Oman were mostly exposed to the G614 virus in March and April of 2020. 37,40 The temporospatial distribution of the D614 virus vs G614 virus in South Asia is summarized in Fig.…”