Genome center exec: Delta community transmission present in Philippines

MANILA, Philippines — With the linkages of COVID-19 cases no longer traceable, the Philippine Genome Center (PGC) confirmed yesterday that there is already community transmission of the highly contagious Delta variant in the country.

According to PGC executive director Cynthia Saloma, the Delta variant is “associated with the very sudden rise in cases” based on the results of their genome sequencing of swab samples collected from COVID-19 patients in June and July.

“For me, professionally, based on the view of PGC, we do our analysis and we try to link the cases based on the phylogenetic tree that we have been doing, it’s really community transmission,” she said in an interview with dzBB.

A phylogenetic tree, or phylogeny, is a diagram that shows relationship among organisms or genes from a common source.

Saloma noted the “branches” of the phylogenetic tree is now “long” and they could no longer trace where these branches came from. This is “very suggestive of community transmission.”

Health Undersecretary Maria Rosario Vergeire said at a public briefing “it seems that community transmission is there” but that more evidence is needed for this to be officially declared.

“As I always say right from the start, we treat it already as a community transmission and our actions have been going towards that direction. We just need enough evidence to officially declare this,” she added.

But Saloma, who is a member of the Department of Health’s Technical Working Group on the New Variants, revealed that in the National Capital Region and in the country in general, there has been an increase in Delta variant detected in positive swab samples sequenced in June and July.

She said that nationally, five percent of the samples sequenced in June yielded Delta variant. The following month, the figure rose to 48 percent.

Delta variant was also detected in five percent of the samples collected from the NCR in June and this increased to 68 percent in July.

“It was so fast. From five percent and then it went to 68 percent of sequenced samples,” she pointed out.

Asked if NCR is the epicenter of the Delta variant, Saloma maintained that many other regions are having spikes in cases, citing Ilocos region, Cagayan Valley, Central Luzon, Calabarzon,Western Visayas, Central Visayas and Northern Mindanao. “Before it was NCR but now it is multiple areas,” she added.

Based on the last sequencing report of PGC, the number of Lambda variant cases detected in the country remains at one.

Data showed that PGC had already sequenced some 11,000 samples, representing only less than one percent of the overall COVID-19 cases in the country.

Meanwhile, Interior Secretary Eduardo Año said local government units (LGUs) should take appropriate measures and immediately locate close contacts of COVID-19 patients instead of waiting for results of genome sequencing performed to determine which variant infected them.

“Contact tracing shall be done upon the confirmation of any COVID-19 case regardless of variant,” Año said in a memorandum circular dated Aug. 18.

“The LGU must not wait for the results of genome sequencing before commencing the tracing of close contacts,” the department chief added.

Some local officials have lamented delays in PGC’s release of genome sequencing results.

There were cases of LGUs receiving the results of genome sequencing only after the patient has recovered from what turned out to be Delta variant.

Citing a recommendation from the DOH, Año said the contact tracing shall be done up to the third generation of close contacts.

For the first generation of close contacts, contact tracing must be completed within 24 hours upon the confirmation of the COVID-19 cases.

Año also ordered local chief executives to hire more contact tracers or seek volunteers.

The department chief has directed LGUs to activate their respective coordinate operations to defeat epidemic or CODE teams to detect and isolate COVID-19 cases in communities. – Emmanuel Tupas