Philippines Reports Its First Set of SARS-CoV-2 Genome Sequences

The Philippines has reported its first set of SARS-CoV-2 (virus that causes the COVID-19 disease) genome sequences, which have been added to the global, open-source project tracking the trail of the COVID-19 pandemic, Nextstrain. 

On April 28, Nextstrain grouped the Philippines' first reported genome sequence in the same group as India, Brazil, Australia, and more. At the time, this clade was reportedly 71 percent from Oceania and 29 percent from Europe, meaning that this specific case most likely came from Australia or Europe, not directly from China, although China is still the ancestor to all the virus's genome sequences. 


But after more genome sequences from the Philippines were submitted, Nextstrain updated the Philippines' phylogeny to be in the same clade as Brazil, Taiwan, and Australia. The latest update suggests that the Philippine strain came straight from China (with 2 percent confidence), and has undergone a number of distinct but minimal mutations.

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However, it's important to note that Nextstrain data gathering is still in process, meaning that suggested origins are still inconclusive and subject to changes. 

Thanks to the nanopore sequencing efforts of the Research Institute of Tropic Medicine (RITM), more genome sequences have been submitted to Global Initiative for Sharing All Influenza Data (GISAID)

To clarify, the select samples represented on Nextstrain do not account for all patients/samples in the country. To trace the source of the Philippines’ COVID-19 outbreak, more genome sequencing is needed to determine how the virus spread into the country.

Why is Genome Sequencing Important?

All this science jargon can be confusing to most, so to lay it all down, this is what it means: genome sequencing is a tool that helps us track how a virus spreads and evolves. Think of the biologists who do the genome sequencing as COVID-19 detectives trying to find the virus’ trail.


This coronavirus reportedly mutates about twice a month, and these small changes give biologists clues as to how they evolved and where a specific genome is placed on phylogenies, a sort of family tree for genomes. 

Initial data from Nextstrain's first submitted Philippine genome sequence, as of April 28

What is Nextstrain?

Nextstrain is the open-source platform made by scientists from around the world collaborating to lay out the global trail of COVID-19. The interactive website has analyzed over 1,800 genome sequences, and it’s our best bet at understanding how COVID-19 reached every corner of the globe.

Originally built to stop future influenzas, it was eventually utilized to also track other outbreaks like Zika and Ebola. But then COVID-19 happened, and the biologists and data scientists behind Nextstrain recalibrated the website to track COVID-19 rapid spread.

Nextstrain sources its information from GISAID, which is where scientists have congregated to share the viral genome sequences found in their respective countries. And based on all the data laid out on Nextstrain, although China was the source, the SARS-CoV-2 quietly spread throughout Europe and the U.S. for months.

What Does This Mean for the Philippines?

It means we are one step closer to finding the Philippines’ patient zero, understanding how the virus entered our borders, and figuring out which strains later spread to those with no travel history whatsoever.


According to Darwin Bandoy, biological data scientist and PhD candidate at the University of California Davis, “One sequence is a start and we need to do more to create a more representative picture. If we sequence more viruses, we can identify clusters missed by contact tracing. This is a good start for science in the Philippines.”

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Anri Ichimura
Section Editor, Esquire Philippines
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