Genome study on samples from late March shows COVID-19 in Manila was community-acquired

Published April 30, 2020, 12:00 AM

by manilabulletin_admin

By Ellalyn De Vera-Ruiz

A study by the Philippine Genome Center (PGC) revealed on Thursday that coronavirus infections in Metro Manila between March 22 and 28 were community-acquired but cluster closely with samples collected from Japan, Australia, and China.

Through its Core Facility for Bioinformatics, the PGC deposited six genome sequence samples of the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), the virus that causes COVID-19, in the Global Initiative on Sharing All Influenza Data (GISAID) database.

GISAID is a global databank for the sharing of genomic information of all influenza data by researchers around the world.

A team of physicians and epidemiologists from the University of the Philippines (UP) National Institutes of Health and the Philippine General Hospital collected the specimens as part of the Department of Science and Technology-Philippine Council for Health Research and Development-sponsored field validation of the UP-developed GenAmplify COVID-19 detection kit led by PGC Deputy Executive Director Raul Destura.

PGC found that the cases from March 22 to 28 had no travel history outside the Philippines.

“Two of the sequences reveal that the community-acquired infections cluster closely with samples collected from Japan and Australia from February 15 to March 14, 2020, while four cluster closely with a sample collected from Shanghai, China on February 4, 2020,” the experts said.

“The six viral sequences range from 29,869 to 29,981 bases in length similar to the complete SARS-CoV-2 sequences now deposited at the GISAID database,” they added.

The team has also been tracking sequence variations from the local cases of coronavirus as part of its surveillance of regions targeted by the test kits, and to see if regions where various vaccines are targeted are mutating or not in local COVID-19 samples.

PGC clarified, however, that to provide a broader view regarding the sources, spread, and evolution of SARS-CoV-2 locally, it is important to conduct sequencing of more samples aside from the released six genome sequences.