Genome Center to sequence more local samples to verify if Omicron is dominant variant in the Philippines

The Philippine Genome Center (PGC) on Tuesday clarified Health Secretary Francisco Duque III’s statement that the Omicron is already the dominant variant in the country, saying such was just based on the last sequencing run and they have yet to sequence more local samples to verify this claim.

At the Laging Handa briefing, PGC Executive Director Dr. Cynthia Saloma said they still detected plenty of Delta variants in December 2021 but they have yet to determine their new data for January 2022.

“Ang data natin sa December, madami pa rin ang Delta doon except that when we did purposive sampling na mga ROFs (returning overseas Filipinos) natin ‘tsaka mga local samples with clusters sa National Capital Region (NCR), marami tayong nakitang Omicron,” she said.

(We still detected lots of Delta variant in our December data except when we did purposive sampling among the ROFs and local samples with clusters in NCR, we saw lots of Omicron too.)

This remark was made after Duque said on Monday night that the Omicron has surpassed Delta as the dominant variant in the country.

Duque noted that 60% of the samples sequenced during the latest run of whole genome sequencing tested positive for the Omicron variant.

“Base sa pinakahuling run of whole genome sequencing, 60% na po ng samples na nasequence ay positive na po for Omicron varaint so siya na po nagdo-dominate na variant whereas before it was the Delta,” he said during President Rodrigo Duterte's public address.

But Saloma clarified that this was only primarily based on their latest run where 48 samples were sequenced on January 2, 2022.

Of which, 29 cases were found to have the transmissible Omicron variant which brought the total confirmed cases to 43.

“Whether this is reflective of the fact that Omicron is already dominant in the country, we need to have further evidence,” she added.

Omicron cases

Saloma said that of 43 Omicron cases, which samples were collected from December 2 to 30, 2021, there were 21 local cases while 22 were international travelers.

She added that of these infections, 35 were asymptomatic, seven have symptoms, while the other one is unknown.

“So ‘yung mga active samples I think from the DOH data, kaunti na lang talaga kasi fully recovered naman na rin naman sila,” she said.

(Based on the DOH data, there are only a few active samples remaining as almost all of them have fully recovered.)

Saloma noted that the fast increase of COVID-19 cases in the country is a characteristic of the Omicron variant as experienced by other countries as well.

In fact, she said that several of the PGC personnel were also infected with the virus. She however assured that they have sufficient staff to continue conducting the whole genome sequencing analysis and RT-PCR testing.

“Pero totoo po ‘yan na compared to before, in early December, mas dumami ‘yung samples at tumaas talaga ang positivity rate,” she added.

(But it is true that compared to before, in early December, the samples have really increased and the positivity rate also rose.)

OCTA Research said Tuesday that the COVID-19 average daily attack rate in the NCR has increased to 89.42%, placing the region on "severe outbreak”.

Genome centers in Vis-Min

Further, Saloma noted that the PGC can currently run around 500 to 750 samples. They will also expand their genomic sequencing capacity in the Visayas and Mindanao that could accommodate 350 samples per week.

“Dumating na po ang ating machines doon sa Visayas at Mindanao and this week ini-install na sila tsaka tinetest. Hopefully, very very soon, sila po pwede nang mag-sequence doon,” she said.

(Our machines have arrived in the Visayas and Mindanao and these are being installed and tested this week. Hopefully, they can sequence on their own very soon.)

Earlier, Saloma said the Department of Budget and Management approved the funding of the genome sequencing equipment for the new genome centers that will be established in the Visayas and Mindanao.

She said that PGC also hired additional people in these new genome centers, with 10 people in each laboratory. These new hires are graduates from programs such as molecular biology and bioinformation. — RSJ, GMA News