“On 9 March, PHE noted a report of 33 cases of a new variant reported by the Philippines. The variant includes a number of notable mutations including E484K and N501Y, which are found in several other Variants of Concern. PHE has identified 2 cases of this variant in England. One of the cases is linked with international travel and the other is currently under investigation. All appropriate public health interventions are being undertaken.
This variant has been designated VUI-21MAR-02 (P.3). PHE and international partners continue to monitor the situation closely.”
See also: Other reports on the Philippines variant
The Philippines now has all three variants of the coronavirus that have been fuelling record-breaking spikes in infections across the globe, and a Philippine variant (PHL-B.1.1.28) that has the same lineage as the infectious Brazilian variant.
There are currently 177 cases of the British variant and 90 cases of the South African variety in the Philippines.
A fourth variant (PHL-B.1.1.28) that originated in the Philippines itself is also spreading. It was first identified in a Filipino who travelled to Japan. This so-called Philippine variant has the same lineage as the Brazilian strain.
Over 90 cases of this local strain are now being monitored.
See also [HERE]: Japan identifies a B.1.1.28 #coronavirus strain with E484K and N501Y mutations from a traveller from the Philippines
See also [HERE]: New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28
The National Institute of Infectious Diseases, Japan, identified a B.1.1.28 strain with E484K and N501Y mutations from a SARS-CoV-2-positive sample collected on February 25, 2020 at a point of entry to Japan from a traveller from the Philippines（virus name : hCoV-19/Japan/IC-0824/2021, GISAID Accession ID: EPI_ISL_1198832) (1).
These mutations are found in known VOCs (501Y.V2, 501Y.V3). This variant isolate also has the P681H mutation in the spike protein as with B.1.1.7 lineage (VOC-202012/01) which is suggested to be associated with increased transmissibility.
34 draft genome sequences of B.1.1.28 lineage with E484K/N501Y mutations have been uploaded to GISAID from the Philippines (1 sequence on February 26, 33 sequences on March 3) .
The Department of Health, Republic of Philippines, published that they found 34 cases with E484K and N501Y mutations on March 2 (1).
This variant isolate does not meet the criteria of VOC as we do not know how widely this variant strain is spreading within the Philippines and whether this variant strain is associated with the recent increase in reported cases in the Philippines. However, this variant strain may be circulating in the Philippines at a certain level as the similar strain has been reported domestically and identified from travelers.
The potential public health impact from this variant strain shall be considered to be equivalent to those from known VOCs as this variant strain shares the same mutations of concern with VOCs
See also: New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28
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.