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