Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines

Coronavirus disease 2019 (COVID-19) is an infectious disease that has gained pandemic status from the World Health Organization, with millions of cases and deaths recorded worldwide. This global health crisis is caused by the virus referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the genus Betacoronavirus (Coronaviridae), together with the causative agents of the first SARS outbreak in 2003 and the Middle East respiratory syndrome (MERS) in 2012.

PGC SARS-CoV-2 Bulletin No. 7: Detection and characterization of a new SARS-CoV-2 lineage P.3, with spike protein mutations E484K, N501Y, P681H and LGV 141-143 deletion, from samples sequenced through the intensified UP-PGC, UP-NIH and DOH biosurveillance program

A close examination of the mutation profile of the P.3 viruses revealed that apart from E484K and N501Y, they also share other spike protein mutations that are likely to have functional significance (Figure 2). This includes the P681H mutation, also found in lineage B.1.1.7 viruses, as well as a three-amino acid deletion at positions 141 to 143 (LGV141_143del).

PGC SARS-CoV-2 Bulletin No. 6: First case of the new variant under Lineage B.1.1.7 detected in the Philippines

Through the biosurveillance efforts of the UP – Philippine Genome Center (PGC), in coordination with the Department of Health (DOH) – Epidemiology Bureau and the Inter-Agency Task Force (IATF) Task Force on COVID-19 Variants,  we report the first confirmed case of the SARS-CoV-2 B.1.1.7 lineage, more commonly known as the UK variant, in the Philippines. An announcement of this finding can be found in an official DOH press release dated January 13, 2021.

PGC SARS-CoV-2 Bulletin No. 5: New Variants from UK and South Africa NOT detected in 305 local viral samples

Recently, new SARS-CoV-2 variants were detected in the United Kingdom and South Africa with multiple spike protein mutations that may cause substantial changes in certain properties of the virus. These observations spurred biosurveillance efforts in different countries, with some countries outside of the UK and South Africa already reporting the presence of these new variants within their territories. The data presented in this report is part of our own continuing biosurveillance efforts to track the entry of these new variants in the country, as well as other viral mutations that may be of concern locally.

PGC SARS-CoV-2 Bulletin No. 4: Newly reported variant in the United Kingdom has yet to be observed locally

In a report posted at the Global Initiative for Sharing All Influenza Data (GISAID) website, the UK variant is said to harbor multiple spike protein mutations within a single sample, including a combination of the following: H69del, V70del(69), Y145del(143), N501Y, A570D, D614G, P681H(674), T716I, S982A, and D1118H (GISAID, 2020). While the discovery of this new UK variant appears to be concerning, the report cautions that the detailed effects of these mutations remain to be fully determined.

PGC SARS-CoV-2 Bulletin No. 3: 23 newly reported SARS-CoV-2 genome sequences from the Philippines support PGC’s previously hypothesized viral entry routes and waves of transmission

A group of researchers from the U.S. Army Medical Directorate–Armed Forces Research Institute of Medical Sciences, the University of the Philippines Manila, and the V. Luna Medical Center recently reported 23 new SARS-CoV-2 genome sequences from the Philippines, all of which were from cases of local transmission (Velasco et al., 2020). Among these samples, one was collected in early April while the rest were obtained in the months of June and July.

Updated rates for COVID-19 testing following the DOH & DTI JAO No. 2020-0001 starting Nov. 27, 2020

PGC’s Clinical Genomics Laboratory / COVID-19 lab releases updated rates for its swab testing services to reflect the base price of P3800.00 following the DOH & DTI Joint Administrative Order No. 2020-0001. The swabbing schedule runs from Mondays to Fridays, with the booth located at the Institute of Mathematics, National Science Complex, University of the Philippines, Diliman, Quezon City.

OnePGC Conference: PGC in Luzon, Visayas and Mindanao #ParaSaBayan

A virtual conference celebrating teamwork and Bayanihan to rise above the pandemic. Streaming from the PGC Headquarters, this online gathering gives thanks and recognition to the partners and stakeholders from Luzon, Visayas, and Mindanao who helped in the national call for increased capacity for COVID-19 testing in the country.