Expert flags PH’s ‘very low’ sampling for COVID-19 genome sequencing

FILE PHOTO: A computer image created by Nexu Science Communication together with Trinity College in Dublin, shows a model structurally representative of a betacoronavirus which is the type of virus linked to COVID-19, better known as the coronavirus linked to the Wuhan outbreak, shared with Reuters on February 18, 2020. NEXU Science Communication/via REUTERS

MANILA, Philippines — The number of COVID-19 samples being subjected to genome sequencing is “very low,” an infectious disease expert said Thursday as he noted that it will take time to determine if there is already community transmission of the SARS-CoV-2 variants of concern in the country.

“This is just my thought. ‘Yung sampling natin [Our sampling] is really very low,” Dr. Rontgene Solante, head of the Adult Infectious Diseases and Tropical Medicine unit at the San Lazaro Hospital and member of the country’s Vaccine Expert Panel said in an online media forum.

Latest data from the Department of Health (DOH) as of May 3, showed that there are only a total of 7,167 COVID-19 positive samples that have been sequenced nationwide.

Solante said the Philippine Genome Center (PGC) primarily tasked to conduct genome sequencing to identify if select COVID-19 samples are positive of the variants should collaborate with more laboratories to increase output. At present, the PGC is only able to sequence over 700 samples in one batch.

LOOK: Breakdown of cases per variant according to the latest report from the Philippine Genome Center. @inquirerdotnet pic.twitter.com/7ARz6AAU6Q

— Cathrine Gonzales (@cgonzalesINQ) May 4, 2021

“Sa UK [In the United Kingdom], it took them sampling 10 percent of the total population. Doon pa lang sila nagdeclare sa dalawang cities na nagiging community transmission, because the majority of the samples, 70 to 80 percent, are positive of the variant,” Solante said.

(In the UK, it took them sampling 10 percent of the population before declaring community transmission in two cities, because majority of the samples, about 70 to 80 percent, are positive of the variant.)

“So it will take time for us if this is the trend of the number of samples we are testing. It will really take time,” he added.

The University of the Philippines-National Institutes of Health and Research Institute for Tropical Medicine have also been involved in detecting SARS-CoV-2 variants in the country.

The DOH earlier said it is conducting a “purposive sampling” for genome sequencing to ensure a higher likelihood of detecting these variants. This means that more samples are taken from areas, clusters, and groups of people that are likely to have the variants.

The country has so far reported a total of 1,075 B.1351 variant cases (first detected in South Africa), 948 B.1.1.7 variant cases (first detected in UK), 157 P.3 variant cases (first detected in the Philippines), and 2 P.1 variant cases (first detected in Brazil) as of May 3.

However, the health department said the detection of these variants does not mean that these are now dominant in the country.

The variants, first detected in the UK, South Africa, and Brazil, are called variants of concern, while the variant reported in the Philippines is considered a variant under investigation.

Health Undersecretary Maria Rosario Vergeire said the World Health Organization (WHO) has yet to confirm if there is already community transmission of the variants in the country, citing the need for further study.

The DOH said that based on WHO’s guidelines, community transmission can be confirmed if there is an appearance of a large number of cases, occurrence of case clusters in multiple areas, and inability to link cases to known sources of infection.

JPV