On the trail of the virus in the Philippines: What SARS-CoV-2 whole genome sequences tell us


  • Cynthia Palmes-Saloma ⋅ PH Philippine Genome Center and National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman


The COVID-19 pandemic that was first reported in Wuhan, China since December 2019, has now spread to more than 227 countries and territories around the world. The SARS-CoV-2 virus infection was first reported in the Philippines in late January 2020 from Chinese tourists who came from Wuhan. Fears of a potential pandemic led our government and others to restrict and eventually ban the entry of tourists and travelers coming from areas with reported cases. This culminated in the total closure of our airports and seaports in the entire island of Luzon from March 17 to May 31. By this time, however, community infection for COVID-19 in the country first reported on March 7, has taken root with the first 100 cases reported by the middle of March 2020.

The repatriation of overseas Filipino workers (OFWs) with a large contingent coming from the shipping and cruise ship industries hard hit with outbreaks of COVID-19 infections on board, provided an avenue for the entry of the virus into the country circumventing the hard lock down imposed in the island of Luzon. This has been the revealed by the data we obtained when we utilized next generation sequencing and viral metagenomics to analyze more than 75 COVID-19 positive cases collected between 22-28 March 2020 as part of the field validation study of the UP NIH-Manila HealthTek GenAmplify nCov RT-PCR test. Based on phylogenetic analysis 1,335 SARS-CoV-2 virus sequences including the 23 local submissions to the Global Initiative for Sharing All Influenza Data (GISAID) database as of August, the local isolates can be divided into eight (8) clades that form three groups associated with possible sources of entry or routes of infection into the country: (i) foreign visitors from China with the January cases being closely related to the original isolates from Wuhan, the epicenter of the pandemic at that time; (ii) repatriated seafarers from the M/V Diamond Princess COVID-19 outbreak in Yokohama, Japan with the March cases being primarily community transmissions linked to the M/V Diamond Princess cruise ship cluster of cases; and (iii) European sources with samples from June primarily clustering with European clades, possibly from repatriated OFWs and tourists returning in May from Europe and the Middle East.

We also report the detection of the D614G variant of SARS-CoV-2 that seems to predominate in Europe and the Americas. Efforts are underway to do further genomic biosurveillance of circulating strains of the virus in the country to provide our policy makers, our epidemiologists and health care specialists a better picture of the evolutionary trajectory and genetic landscape of SARS-CoV-2 in the Philippines.

About the Speaker

Cynthia Palmes-Saloma, Philippine Genome Center and National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman

Cynthia Palmes-Saloma is presently a Professor of Molecular Biology and Biotechnology and Principal Investigator at the Laboratory of Molecular and Cell Biology (LMCB) in the National Institute of Molecular Biology and Biotechnology in the University of the Philippines (UP) Diliman. She currently serves as the Executive Director of the Philippine Genome Center (PGC), University of the Philippines System.

Dr. Palmes-Saloma received her Ph.D. in Physiology in 1998 and her MS in Medical Science in 1995 from Osaka University, Japan. She holds two Bachelor's degrees, one in Molecular Biology from Nagoya University (1993) and the other in Fisheries from UP Visayas, where she finished her course in three and a half years graduating with magna cum laude honors in October 1987. She was a recipient of the Monbusho scholarship as an undergraduate and MS student and became a research fellow of the Japan Society for the Promotion of Science (JSPS) while pursuing her PhD degree. She joined NIMBB in 1998 and started the Neurobiology Research Group, which has now evolved into the Laboratory of Molecular and Cell Biology (LMCB). For her contributions in teaching, she was awarded the UP Diliman Centennial Gawad Chancellor para sa Natatanging Guro Award in 2008.

Dr. Palmes-Saloma served as past President of the Philippine Society for Biochemisty and Molecular Biology, the Philippine Society for Cell Biology as well as the Outstanding Young Scientists' Inc.–Philippine Academy of Young Scientists. She started the PGC DNA Sequencing Core Laboratory in 2012 and was appointed as PGC Executive Director in 2017. Since April 2020, the Philippine Genome Center Clinical Genomics Laboratory has been licensed by the DOH as a COVID-19 RT-PCR testing laboratory. Their PGC team, together with the NIMBB UP Diliman and NIH UP Manila, has been helping the DOH in training medical technologists around the country to expand local capacity in COVID-19 testing by RT-PCR.



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How to Cite

C Palmes-Saloma, On the trail of the virus in the Philippines: What SARS-CoV-2 whole genome sequences tell us, Proceedings of the Samahang Pisika ng Pilipinas 38, SPP-2020-INV-1B-01 (2020). URL: https://proceedings.spp-online.org/article/view/SPP-2020-INV-1B-01.