Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced.
Medrxiv paper Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines
On Thursday, the Department of Health (DoH) in Central Visayas (The Philippines) confirmed that they have detected two mutations with “potential clinical significance” of SARS-CoV-2 that cause the disease.
The two mutations were identified as E484K and N501Y and they were detected from samples from Central Visayas.
The 484K mutation – which differs from its genetic sequence – is found in the South African variant of SARS-CoV-2, while the N501Y mutation is found in the UK coronavirus variant and is said to have a higher chance of infection.