Samples from 3 COVID labs sent to PGC Mindanao for variant detection

DAVAO CITY (MindaNews / 23 June) – A total of 23 sample specimens from three coronavirus disease (COVID-19) laboratories in Mindanao have been submitted to the Philippine Genome Center (PGC) Mindanao as its on-site sequencing facility that can detect new variants of SARS-CoV-2, the virus that causes the infection, begins operations.

The Philippine Genome Center – Mindanao (PGC-Mindanao) at the University of the Philippines Mindanao campus in Davao City. MindaNews file photo by MANMAN DEJETO

Dr. Lyre Anni Murao, a professor of virology at the University of Philippines-Mindanao and director of the Philippine Genome Center (PGC) Mindanao, told MindaNews in an email that the laboratories that have submitted specimens are COVID-19 laboratories of Cotabato Regional and Medical Center in Cotabato City, Davao de Oro Provincial Hospital in Montevista, and the Department of Health (DOH) in Northern Mindanao.

She said the genome sequencing at the PGC Mindanao is a pilot project in collaboration with Accessible Genomics, Research Institute for Tropical Medicine (RITM) and University of Glasgow.

She said the project is not yet part of the biosurveillance program of the DOH, which is being undertaken by the PGC in Diliman.

Murao said the DOH-Davao currently sends samples to Metro Manila because of the existing memorandum of agreement that had been entered into between PGC in Diliman and DOH for the biosurveillance of SARS-CoV-2.

Dr. Rachel Joy Pasion, head of the DOH-Davao’s Regional Epidemiology Surveillance Unit, told a press briefing on Monday that she received a letter regarding the MOA between the Davao City-based Southern Philippines Medical Center (SPMC) and UP Mindanao “because UP Mindanao has vouched that they can really do the whole genome sequencing.”

“Can we allow them? I am still in coordination with the Epidemiology Bureau – headed by Dr. Thea (Dr. Alethea de Guzman, OIC Director of the DOH central office’s Epidemiology Bureau) – regarding how to go about the MOA and how to go about the sending of specimens since it entails assessments and funding. So we will update everyone regarding this one. But for now, what we do would be really send specimens to UP PGC (in Diliman) and UP PGC sends us feedback on what are the results of our specimens na sent to them,” she added.

Murao said the collaborative project with RITM and the University of Glasgow “aims to operationalize genomic surveillance and inform responses across the Philippines. The report will serve as a baseline data in Mindanao for SARS-CoV2 variants.”

She added that the RITM “will be responsible to relay all information that we get from the study to DOH, and then DOH will be the one to take care of the release of this information.”

She said the PGC in Diliman uses “Next Generation Sequencing” to sequence the genome of SARS-CoV-2.

PGC Mindanao will use a handheld MinION sequencer with Oxford Nanopore Technology, donated by Project Accessible Genomics through funding from JOGL or Just One Giant Lab.

Murao said the PGC Mindanao targets to gather samples from all six regions of Mindanao.

Michael Bacus, University Research Associate of PGC Mindanao, said the time needed to complete the processing takes one to two weeks from the day of submission of samples to PGC Mindanao.

“This is an estimated range of all processing time, including the data analysis,” he said.

Previous reports on the presence of variants in Mindanao took a month from the sending of the samples to UP-PGC in Diliman, Quezon City.

Through genome sequencing, Murao said new variants circulating in different communities will be determined to enable an efficient monitoring of the mutated viruses of SARS-CoV-2 if they are more transmissible, cause more severe diseases, or lessen the efficacy of the vaccines.

She added that the sequencing can also provide a more accurate and efficient analysis on how the virus spreads than the data provided in the contact-tracing, which suffers from some lapses.

“Contact-tracing allows us to indicate the people who have been infected due to one person, but there are gaps in contact tracing because the information that is given to contact tracers may not be accurate or some of them may not be true. But the beauty of sequencing is that we can also do similar kind of analysis but sequences don’t lie. So, the information that we can get from sequences are accurate,” Murao added.

As of June 22, DOH-Davao reported 38,108 cases with 8,780 active, 28,011 recoveries, and 1,317 deaths.

Out of the total cases, Davao City, the epicenter of the COVID-19 pandemic in Mindanao, logged 22,151 cases with 4,701 active, 16,616 recoveries and 834 deaths.

Davao del Norte recorded 7,201cases; Davao del Sur 2,926; Davao de Oro, 2,861; Davao Oriental 2,439; and Davao Occidental 520. (Antonio L. Colina IV / MindaNews)