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VERA FILES FACT SHEET: How the Philippines is detecting new SARS-CoV-2 variants

The Philippines welcomed the second quarter of 2021 with record-high numbers of coronavirus disease 2019 (COVID-19) cases. Currently at over 864,000, a research group has predicted that the nationwide count for local coronavirus infections will reach one million by the end of the month.

Cynthia Saloma, executive director of the Philippine Genome Center (PGC) at the University of the Philippines (UP), said on April 6 that one factor for the surge may have been the emergence of variants of concern, reported to be “50% more transmissible” than earlier versions of the virus behind COVID-19.

Variants of concern are mutated versions of a virus observed to be more transmissible, increase disease severity, or negatively affect treatment and vaccines.

How exactly does the Philippines detect these new variants? Here are four things you need to know:

1. What is genome sequencing?

Variants are detected through a process called genome sequencing, which looks into the entire genetic makeup of an organism and compares it with other virus samples.

A genome is a set of genetic instructions found in a cell. Sequencing detects mutations or errors and “misspellings” in the genome’s spike protein, which is used by the virus to attach to human cells. (See: Mutations and misunderstandings: Are we now dealing with a supercharged COVID-19?)

At present, only the PGC does weekly genome sequencing, the center’s DNA Sequencing Core Facility head Benedict Maralit told VERA Files Fact Check in an email. The UP National Institutes of Health and the Research Institute for Tropical Medicine under the Department of Health are also tasked to perform the analysis.

“The sequencing program would like to get a general idea of the evolution and spread of SARS-CoV-2 in the Philippines to inform and guide public health policy,” he added.

To detect variants of SARS-CoV-2 (the virus causing COVID-19), the PGC uses a technology called Next Generation Sequencing, which analyzes hundreds to millions of DNA fragments across many samples, said Maralit, program leader of a SARS-CoV-2 genomic biosurveillance project funded by the Department of Science and Technology’s Philippine Council for Health Research and Development (DOST-PCHRD).

In this process, DNA and RNAーwhich make up genomesーare broken down into several pieces. After a specialized adapter is added to these fragments to differentiate them, they become part of a library that is analyzed in a sequencer.

Currently, PGC sequences 750 samples a week and it also has a smaller machine that can sequence 48 samples.

“We have to sequence deeply… kumbaga, ‘yung isang genome na ‘yan ise-sequence natin 2,000 times para makita natin ‘yung mga minute changes (as in, we have to sequence a genome 2,000 times so that we can see the minute changes),” PGC’s Saloma said in a media forum on Dec. 27, 2020.

2. What are the SARS-CoV-2 variants detected in the Philippines so far?

When a group of coronaviruses inherits the same set of distinctive mutations, it is considered a variant. Some mutations have “little or no impact on how a virus works,” according to experts from the Digital Health Lab of global nonprofit Meedan.

Others, however, may change how easily the virus spreads, impact how ill someone may become when infected, or reduce effectiveness of treatments and vaccines—in which case, it will be classified as a variant of interest, of concern, or of high consequence.

In the Philippines, the following variants of concern have been identified:

Saloma of the PGC said on April 6 that only 9.9% of over 4,000 samples tested since January carried these variants of concern.

“If the highly transmissible virus is not contained,” daily cases could reach 17,000 to 18,000 by mid-April, the OCTA Research Group has forecasted. The highest count so far of COVID-19 infections reported in a day is 15,310 cases on April 2.

3. How long does it usually take to sequence the variants?

The whole process of SARS-CoV-2 viral genome sequencing — particularly for a large sample set like 750 in a single sequencing run — is “very tedious,” according to PGC.

The process of isolating and extracting DNA and RNA from swab samples to the actual loading, generation of sequence data, and releasing useful information from it can take three to seven days, Maralit told VERA Files Fact Check.

“It (the whole genome sequencing) requires a specialized skill set and long training hours and a very experienced team of molecular biologists and laboratory personnel,” he added.

The PGC has three teams: Clinical Genomics with 20 members, Sequencing with 12, and Bioinformatics with 11.

Maralit added that there are many bottlenecks in the sequencing process, including the timely sendout of samples from regions.

Health Undersecretary Maria Rosario Vergeire said in a forum last month that these include Regions V (Bicol), VIII (Eastern Visayas), IX (Zamboanga Peninsula), and the Bangsamoro Administrative Region in Muslim Mindanao (BARMM), which face problems in transportation and lack of laboratories.

Maralit also said some regions do not have easy sources of dry ice, which is needed to prevent cross-contamination or degradation of samples.

As of April 11, the PGC has sequenced over 5,000 samples nationwide.

The Philippines has tested only 9% (or about 9.8 million) of its 110 million population.

4. How does genome sequencing affect the government’s pandemic response?

In a report on genomic sequencing of SARS-CoV-2, the World Health Organization said virus genome sequences can be used “to investigate the outbreak dynamics.”

By looking at changes in the size of the epidemic over time, its spread in a given time and space, and its transmission routes, national and local authorities can “better understand SARS-CoV-2 transmission and monitor for the emergence of variants,” the report said.

The Philippines began to “strengthen and widen” its genome sequencing capacity towards the start of January, Vergeire told reporters on March 11.

British Prime Minister Boris Johnson announced the detection of the B.1.1.7 variant on Dec. 19, 2020.

Maralit said the PGC aims to “provide information that will support policies” such as determining which places need enhanced protocols for recommendation to local governments for localized lockdowns and other similar transmission management strategies.

The national government has recently downgraded the enhanced community quarantine (ECQ) imposed in the National Capital Region (NCR) Plus — which consists of Metro Manila, Bulacan, Cavite, Laguna, and Rizal — from March 29 to April 11 in response to the surge in COVID-19 cases, to a modified ECQ starting April 12 until the end of the month.



Department of Health, COVID-19 Tracker

OCTA Research Group: Philippines could reach 1 million COVID-19 cases by end-April

Presidential Communications Operations Office, #LagingHanda Public Briefing, April 6, 2021

Whole Genome Sequencing:

Mutations of Concern Infographic:

Variants of Concern:





Department of Health, DOH Presser: New SARS-CoV-2 variant, Dec. 27, 2020

Department of Health, Beat COVID-19 Media Forum, Feb. 19, 2021

Department of Health, Beat COVID-19 Media Forum, March 12, 2021

Department of Health, Media Solusyon Forum, March 17, 2021

Department of Health, Beat COVID-19 Media Forum, March 24, 2021

People’s Television Network, #LagingHanda Public Briefing, March 10, 2021

Department of Health, PH Genome Center Biosurveillance Report Batch 12-14, April 11, 2021

Inter-Agency Task Force on Emerging Infectious Diseases, Resolution No. 92, Jan. 5, 2021

World Health Organization, Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health, 8 January 2021, Jan. 8, 2021

Presidential Communications Operations Office, NCR Plus placed under MECQ until end of April, April 11, 2021

Presidential Communications Operations Office, Memorandum from the Executive Secretary: Imposition of Enhanced Community Quarantine (ECQ) in Bulacan, Cavite, Laguna, Rizal, and the National Capital Region, March 27, 2021

Presidential Communications Operations Office, NCR Plus remains ECQ for one week, April 3, 2021


(Guided by the code of principles of the International Fact-Checking Network at Poynter, VERA Files tracks the false claims, flip-flops, misleading statements of public officials and figures, and debunks them with factual evidence. Find out more about this initiative and our methodology.)