PHL Genome Center stresses need to prevent spread of P.3 variant to other regions, other countries
(Courtesy UP-Pjilippine Genome Center)
(Eagle News) – The coronavirus variant P.3, which was first detected in the Philippines was the SARS-CoV2 mutation that was first observed in the Central Visayas region where there had been an observed spike in cases since January this year, according to the Philippine Genome Center (PGC).
The PGC said that most of the nearly 100 samples where the P.3 variant was found in the country came from Central Visayas.
Citing “potential public health implications of the mutations,” the country’s genome scientists stressed the need “strengthened measures to prevent the spread of P.3 to nearby islands of the archipelago and to other countries.”
“An emergent SARS-CoV-2 variant, now officially designated as Lineage P.3, has been detected in the Philippines with most of the samples coming from the Central Visayas Region,” the PGC said in a statement.
-Earliest case collected on Jan. 8, 2021-
“The P.3 cases were initially identified from a sequencing run on February 4, 2021 and have since been detected in all subsequent sequencing batches, with currently nearly a hundred cases under this new lineage. The earliest case was collected on January 8, 2021,” it said.
The PGC said that the “collection dates of the samples detected to be under this lineage coincide with a sharp increase in SARS-CoV-2 infections in Central Visayas.”
The P.3 variant carried “multiple mutations in the spike protein of the virus that are likely to have functional significance, including E484K, N501Y, and P681H that were previously associated with known SARS-CoV-2 variants of concern.”
The PGC said that these mutations in the P.3 variant had been “linked to possible increased transmissibility and immune escape in some studies.”
The genome scientists noted three amino acid deletions in the spike protein of the variant at positions 141 to 143.
The PGC said that the “combination of mutations observed” in the variant P.3 warranted further studies to “determine their collective effects on the transmissibility (rate of infection), pathogenicity (severity of the disease), and immunogenicity (impact on vaccine efficacy) of the virus.”
The Medrxiv, which distributes unpublished eprints about health science which have yet to be peer reviewed, already carried a post describing in detail the detection and genomic analysis of the first 33 cases of P.3 viruses initially identified in the country.
In this pre-print of the article which was authored and prepared by at least 30 Philippine doctors and scientists including those from the UP-PGC, the Department of Health, and the Inter-Agency Task Force on Emerging Infectious Diseases, it described the “13-lineage defining mutations” of the P.3 variant found mainly in Central Visayas.
“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,” it said in the abstract.
-Public health implications-
“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,” it said.
It said that the “mutation profile of this new virus variant warrants closer investigation due to its potential public health implications.”
-“The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country,” it added.
It was the University of the Philippines – Philippine Genome Center and National Institutes of Health in coordination with the DOH and the Philippine Genomic Biosurveillance Network, that detected the SARS-CoV-2 cases initially classified to be under lineage B.1.1.28, but with the co-occurrence of the E484K and N501Y spike protein mutations.
-P.3 variant associated with UK, South African and Brazilian variants-
Philippine genome scientists said that these mutations had been previously associated with the UK variant (B.1.1.7), the South African variant (B.1.351) and the Brazilian variant (P.1).
All these three variants of concern had been linked to high transmissibility of the COVID-19 virus, SARS-CoV-2. These had also been noted for their so-called “viral immune escape” or the ability to resist the host’s immune response.
The PGC said that P.3 variant found in the Philippines has a “shared ancestry with the B.1.1.28 viruses that also gave rise to the P.1 variant of concern” or the so-called Brazilian variant.
“The first P.3 virus isolates were identified from a sequencing run last February 04, 2021, and have been detected in all of the subsequent sequencing batches since then,” the PGC said.
“To date, a total of 98 sequenced samples can be classified under this lineage, majority of which were collected from Central Visayas. The recorded collection dates of these samples coincide with a sharp increase in the number of SARS-CoV-2 infections registered in the said region,” it noted.
The PGC also analyzed the “geographic distribution of the first 33 detected P.3 cases (unofficially designated as PHL-B.1.1.28)” which were mostly in the Central Visayas region.
The country’s scientists will also conduct further studies if the current batch of vaccines would be effective against this P.3 variant
“Deletions in this region of the spike protein have been implicated in possible immune escape mechanisms,” the PGC noted referring to the three-amino acid deletion at positions 141 to 143 of the P.3 variant.
(Eagle News Service)
