To date, the Institute for Medical Research (IMR), National Institutes of Health (NIH), MOH Malaysia has conducted analysis on more than 120 SARS-CoV-2 full genome sequences from clinical samples encompassing the first wave till the recent third wave of COVID-19 cases in Malaysia. The analysis has focused on timely monitoring of all gene mutations particularly in the spike protein which plays a key role in the receptor recognition and cell membrane fusion process.

Apart from the most prominent spike mutation D614G, we are now seeing another form of variant, A701V, which was first detected in the Benteng Lahad Datu (Benteng LD) cluster and subsequently spread to almost all clusters including in Peninsular Malaysia and Sabah (post Benteng LD clusters).

A701V mutation; Highlights of the A701V variant
The A701V variant has substitution of amino acid Alanine to Valine at codon position 701 in the spike protein. This mutation was first found among 22 SARS-CoV-2 sequences from the Benteng LD clusters and subsequently passed on to the vast majority of third wave clusters in Peninsular Malaysia and Sabah.
Among the third wave clusters that have been sequenced are Teratai, Benteng LD third generation, Damanlela Construction Site, Perigi, Selasih, Saguking, Tenaga, Kasih, Bah Ketil, Bukit and Kaya clusters.

The prevalence of A701V among cases in the third wave is 85% (51/60), whereas D614G is 100%.
The A701V is now co-circulating with D614G in conjunction with the tremendous increase of cases during the third wave. Globally, South Africa, Australia, Netherlands and England also reported A701V at about the same time as Malaysia. In GISAID, the prevalence of this mutation is found to be about 0.18%. The role of this mutation is yet to be determined. As most clusters have this mutation, the presence of mutation A701V may have given the virus an added advantage in becoming the dominant strain, suggesting better transmissibility.

VUI 202012/01 mutation the new variant from UK;
At this point, we are informed about the emergence of a new variant of SARS-CoV-2 in the United Kingdom i.e. SARS-CoV-2 VUI-202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) where they have observed 70% increase of transmissibility rate and 3-fold increase in cases in the 14-days notification period. The new variant has new mutations in the spike protein, including amino acid changes as well as 3 amino acid deletions.

Currently the SARS-CoV-2 VUI 202012-01 is not found in Malaysia. IMR will continuously perform whole genome sequencing to monitor the presence of this variant as well as other variants.
MOH Malaysia will continue our vigilance with various measures put in place to prevent spill-over of the new variant into Malaysia.

Rujuk : FB Ketua Pengarah Kesihatan KKM