The Philippine Genome Center is ready to verify the presence of 2019-nCoV through whole genome sequencing. With the use of Next Generation DNA/RNA Sequencing equipment (NGS) available at the Philippine Genome Center (PGC) in the University of the Philippines Diliman Campus, the team of the DNA Sequencing Core Facility (DCSF) is ready to assist RITM and the DOH in confirming suspected cases of 2019-Novel Coronavirus (2019-nCoV) in the country.
Due to the recent declaration of the Metro Manila-wide community quarantine and with the DNA Sequencing Core Facility currently assisting in the UP NIH Kit validation and field testing (COVID-19), PGC management has decided to temporarily halt accepting all samples and requests for services starting March 16, 2020 until further notice.
SEE THE ANNOUNCEMENT AND LIST OF PGC SERVICES HERE
The Philippine Genome Center of the University of the Philippines was tasked to handle the sequencing of COVID-19 samples in coordination with the health workers from UP Manila National Institutes of Health, to provide our scientists with crucial scientific information to mitigate the spread of the disease.
In our effort to continually protect the PGC skeletal workforce during this national health emergency, we are accepting Personal Protective Equipment (PPE) donations.
Contact Ms. Katie Raymundo via 09190006087 (Smart) or send an email to [email protected] for inquiries and to coordinate donations.
Gamit ang mga halaw na salita ni Prof. Eilene Narvaez mula sa College of Arts and Letters, University of the Philippines Diliman, ginawang ng Philippine Genome Center ng mga illustrations ang mga terminolohiyang may kinalaman sa COVID-19.
PGC thanks its skeletal force involved in the validation and field testing of the UP NIH and Manila HealthTek developed kits as well as in sequencing COVID-19 samples. The genome center extends its appreciation and support to all front liners and health workers in general.
Major steps in in using the local rRT-PCR Detection Kit, general requirements in terms of equipment and supplies, as well as a step-by-step guide about testing.
Upon completing and passing the Research Institute for Tropical Medicine’s (RITM) proficiency testing for SARS-CoV-2 detection by Real-Time PCR, the Clinical Genomics Laboratory (CGL) of the Philippine Genome Center is now certified to perform independent testing for COVID-19.
READ THE ANNOUNCEMENT HERE
PGC’s Core Facility for Bioinformatics releases to the global community through the GISAID database six (6) viral genome sequences of the SARS-CoV-2 from COVID-19 cases between March 22-28, 2020 in Metro Manila. All the cases had no travel history outside the Philippines. Two of the sequences reveal that the community-acquired infections cluster closely with samples collected from Japan and Australia from February 15 to March 14, 2020 while four cluster closely with a sample collected from Shanghai, China on February 4, 2020.
The DNA Sequencing Core Facility will resume its services on July 1, 2020 (Wed) and will be accepting sample submissions following the schedule below:
PGC GF lobby, reception
Tues to Fri, 09:00 am – 02:00 pm
*Walk-ins will not be accommodated. Please email the lab and arrange drop-off appointment within the provided schedule and wait for confirmation prior bringing your samples to PGC.
The Office of the Vice President for Public Affairs Give to UP channel supports the Philippine Genome Center’s call for donations campaign: PGC Para sa Bayan—the call for donations aims to provide support for PGC’s COVID-19 Testing Laboratory (Clinical Genomics Laboratory) and will facilitate the procurement of essential lab supplies, additional equipment, and/or other necessary costs related to testing.
For inquiries regarding official receipts/certificate of donation and for other queries, please contact the Office of the Vice President for Public Affairs (OVPPA) through the following channels:
Mobile: 0917 571 8886
Email: [email protected] | [email protected]
The Philippine Genome Center’s Clinical Genomics Laboratory is certified to conduct testing for COVID-19 (SARS-CoV-2) by Real-Time PCR. PGC’s COVID-19 laboratory is a non-hospital based facility (NHB) that accepts samples for testing from hospitals/healthcare centers and does not perform swab collection.
In contrast to the coronavirus collected in March, we now report the detection of the D614 variant among nine (9) randomly selected COVID-19 positive samples collected in Quezon City in July. In the month of June, both the D614 as well as the G614 have been detected in a small sample of positive cases. Although this information confirms the presence of G614 in the Philippines, we note that all the samples tested were from Quezon City and may not represent the mutational landscape for the whole country.
Majority of the Philippine submissions (18 of 23) were collected in the month of March, wherein except for one sample which clustered with isolates from Shanghai, China, all others were observed to group into clades linked to the outbreak in the cruise ship, M/V Diamond Princess, moored in Yokohama, Japan in early February 2020. Later that month, passengers and crew members of this cruise ship representing various nationalities including Filipinos, Indians, and Australians were repatriated to their home countries.
The Philippine Genome Center’s COVID-19 Lab (Clinical Genomics Laboratory) developed a Contact Exposure Algorithm designed following the latest community guidelines of the WHO and CDC. The chart is intended to help inform the UP System Community with regard to conducting one self in the event of potential exposure.
This algorithm may serve as reference for other communities, institutions, and/or offices with confirmed cases and for staff who have had potential exposure.
In addition to its mandated COVID-19 testing (RT-PCR) for PhilHealth covered patients, the Philippine Genome Center’s Clinical Genomics Laboratory (CGL) / COVID-19 Testing Lab will open its Drive-thru & On-foot Swabbing Operations on October 12, 2020, Monday. The drive-thru and on-foot service will cater to private testing requests for elective cases. Elective swabbing applies to individuals without symptoms or those requiring testing as part of routine clearance. It will include clearance purposes such as for work, travel, and/or medical clearance (i.e. dental, surgical, etc.).
In PGC’s past SARS-CoV-2 bulletins, we reported the detection of the D614G variant in samples from June and July (PGC SARS-CoV-2 Bulletin No. 1) and also inferred the possible sources of infection in the country (PGC SARS-CoV-2 Bulletin No. 2). We earlier hypothesized at least three major waves of viral entry and transmission: (i) January samples linked to foreign visitors from China, (ii) March samples mainly associated with the M/V Diamond Princess Cruise Ship outbreak, and (iii) samples from June onwards that are closely related with European isolates. Here, we report that the analysis results incorporating the 23 newly published Philippine SARS-CoV-2 genome sequences further corroborate our previous observations and hypothesis.
The United Kingdom health ministry has reported a new SARS-CoV-2 variant characterized by multiple mutations in the spike protein region of the virus (Kozlov, 2020). In response to this report, we analyzed Philippine SARS-CoV-2 samples with publicly available genome sequences from the GISAID and NCBI GenBank databases, as well as from internal samples recently collected in Metro Manila as part of the Philippine Genome Center’s biosurveillance efforts. In this bulletin, we present relevant information on the genetic changes found in the UK variant, as well as the results of our latest analysis focusing on locally observed spike protein mutations.
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.