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Confirmed Delta cases are only by the hundreds due to limited sequencing capacity

By AYIE LICSI Published Aug 10, 2021 6:25 pm

With the highly virulent Delta variant of COVID-19 now found in 13 out of 17 regions in the Philippines, the Department of Health (DOH) classified the country’s status as "high risk."

Despite this and the rising number of cases—now averaging over 8,000 daily infections—only a limited number of samples are being tested for the Delta strain, making it likely that the numbers are underreported or delayed.

OCTA Research has previously said that cases with the more contagious variant could be at around the 2,000-mark, which is a lot higher than the confirmed cases currently.

“This is not the actual number of the Delta variant but what we know is the limited genome sequencing that we have accounts for just 100 samples per day out of around 8,000 cases that we have now, so that is less than two percent of the total number of cases,” said OCTA Research fellow Guido David.

At the Philippine Genome Center (PGC), only 750 samples are tested weekly for the Delta variant. With the limited sequencing capacity, they focus on testing samples from areas with a high increase in cases and hospitals reporting more severe types of COVID-19.

"Limited sequencing will only make us see a few cases every batch," said University of the Philippines School of Statistics associate professor and UP COVID-19 Response Team’s Peter Cayton.

"The best way to look at the sequencing reports is by the percent of variant cases per batch. With 25-30% of batches reported as Delta by PGC, it is possible that the same percentages may be seen in our daily reported cases, though this is an assumption with the limited data we have."

The confirmed numbers

During a press briefing on Monday, DOH Usec. Rosette Vergiere announced that there are 450 confirmed Delta infections in the country. Of these cases, 35 individuals are fully vaccinated, 17 are first-dose vaccinated, 83 are unvaccinated, and 315 are for verification.

In analyzing the figures that the DOH has presented so far, Cayton said details are still too few to make an analysis on the impact of vaccines on the Delta variant in the country.

"Our detection of Delta is limited with respect to the sampling the PGC is doing, so any analysis will have some unmeasurable bias," he told PhilStar L!fe. "Note the large number of cases for verification, of which could alter our analysis later on."

He hypothesized that the 315 unverified Delta cases are unvaccinated individuals, noting the limited sampling for the Delta strain as a source of bias. "Please complete your vaccination program if you still need a second dose," he said on the matter.

Studies suggest that the more contagious variant might cause more severe illness in unvaccinated persons than those vaccinated. Experts have also said that vaccines are still effective against the Delta strain.

Areas like Metro Manila are recording high daily attack rates and positive growth rates. 85% of healthcare facilities in the region are also at a critical level.

Cayton added that people should be concerned about "reproduction number in terms of transmission statistics, and also the percentage of samples from PGC reported as Delta. Most recent data suggest that 25-30% of recent batches were detected as Delta cases."

With the DOH expecting the number of cases to rise within the next days, Cayton said the lockdown will help lower infections in the short term.

"Typically, it takes about two weeks, depends on how much mobility has been reduced. However, if there is no sufficient tracing, testing, isolation and healthcare infrastructure, and vaccinations after lifting the lockdown, the risk of another surge will still be present."

Although the DOH has yet to declare a community transmission for the variant, the agency said that it is treating the current situation as such.

"We do not know what scale DOH would use to indicate community transmission of Delta variant COVID," Cayton commented. "In DOH's pronouncements in the past, so long as they can trace Delta variant transmissions, they would only say definite local transmission."