PH Genome Center to release more sequencing data by end of week: chief

Gillan Ropero, ABS-CBN News

Posted at Jan 11 2022 01:04 PM | Updated as of Jan 11 2022 08:58 PM

Researchers work in a laboratory at the Philippine Genome Center on March 12, 2020. Mark Demayo, ABS-CBN News
Researchers work in a laboratory at the Philippine Genome Center on March 12, 2020. Mark Demayo, ABS-CBN News

MANILA (UPDATE) - The Philippine Genome Center will have more whole genome sequencing data on the country's COVID-19 cases by end of the week, its chief said Tuesday.

The nation has so far tallied 43 omicron variant cases, of which 21 were local cases and 22 were international travelers, said PGC executive director Dr. Cynthia Saloma.

"Today, ongoing po ang ating sequencing. It’s a bigger run. Hopefully, before the end of the week, mailabas na po natin so we can have a bigger picture of January," she said during a virtual public briefing.

(Today, our sequencing is ongoing. It’s a bigger run. Hopefully, before the end of the week, we can release it so we can have a bigger picture of January.)

"We will have more sequencing data towards the end of this week.
Nitong tumaas na naman ang cases, we have been encouraging labs to send to us cases... Today, yung ating nira-run is good for 750. We are sequencing between 500 to 700 today na samples po."

(When cases increased anew, we have been encouraging labs to send to us cases... Today, what we're running is good for 750 samples. We are sequencing between 500 to 700 samples today.)

Health Secretary Francisco Duque's remark that the omicron was now the predominant variant in the country was "based on the last sequencing run," Saloma said.

"Siguro, yung sinabi sa'tin ni Secretary should be interpreted in context. It was based on the last sequencing run. Marami pa ring delta nung December," she said.

(We should interpret what the Secretary said in context. It was based on the last sequencing run. There were still many delta cases last December.)

"In the last sequencing run, we tried to focus on ROFs (returning overseas Filipinos) and NCR (National Capital Region)... Nakita natin na marami tayong nailabas na omicron results. We need to have further evidence po. Ang ating DOH ay gumagawa ng sampling."

(We saw many omicron results. We need to have further evidence. The DOH is doing the sampling.)

Saloma said there was a "possibility" that a 40-year-old seafarer from Kenya, who landed in Cebu and later in Iloilo, got infected with the omicron variant here in the Philippines.

"The possibility is there na pwede siyang (that it could be) locally acquired," she said.

"There is a big possibility. Kung bumaba siya ng (barko sa) Kenya ng Dec. 12, umalis sa Kenya ng Dec. 15, by the time we sequenced Dec. 27 na, there’s possibility na yung kaniyang case ay 'di galing sa Kenya but somewhere here. The signature of omicron is, normally, within 3-6 days, nakikita mo na ang positive value."

(There is a big possibility. If he left his ship in Kenya on Dec. 12, and he left Kenya on Dec. 15, by the time we sequenced last Dec. 27, there’s possibility that his case was not from Kenya but somewhere here. The signature of omicron is, normally, within 3-6 days, you can see the positive value.)

Machines for whole genome sequencing have also arrived in the Visayas and Mindanao, Saloma said.

"Hopefully, very, very soon, sila po ay pwede nang mag-sequence doon (they will be able to conduct sequencing there), about a week or 3 days," she said.

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Other variants?

Authorities are monitoring the presence of new variants, Saloma said, following reports of the IHU variant and deltacron/delmicron.

The IHU variant was detected by a medical institute in France in 19 cases and it does not seem to be "expanding so much" there, according to Saloma.

"The entire world community, binabantayan natin ang mga bagong variants na lumalabas. So far, ang pinaka-on the watchout natin is really the omicron variant," she said.

(The entire world community is monitoring new variants. So far, what we really watch out for is really the omicron variant.)

"Just because a laboratory has detected a variant with a lot of mutations, it doesn’t necessarily translate na magiging transmissible siya or magiging severe siya...So 'yung IHU, 'di nga siya variant of interest or concern, pero binabantayan po siya."

(Just because a laboratory has detected a variant with a lot of mutations, it doesn’t necessarily translate it will be very transmissible or it will become severe... The IHU is not a variant of interest or concern, although we're monitoring it.)

The parent of the IHU variant is B.1.640, a variant under monitoring by the World Health Organization, according to Dr. Edsel Salvaña, member of the DOH-technical advisory group.

"Lower tier po siya (It's lower tier) and they've been looking at this since November. They're monitoring it, but no this is not a variant of concern, it's not even a variant under investigation," he told reporters.

As for the deltacron or delmicron reported in Cyprus, Salvana said the sequencing might have been contaminated.

"Ang sabi ng isang taga-WHO, mukhang contaminated yung sequencing na ginawa dun sa Cyprus, na na-contaminate ng omicron yung sinisequence nilang delta," he said.

(One member of the WHO said it seems the sequencing done in Cyprus was contaminated, the omicron variant contaminated a delta variant sequencing sample.)

"Again, this is a contentious issue.Nakita nila na very clear na naka-splice siya... There are some reports this might be due to a lab error, kaya they are making sure na tunay po talaga ito."

(Again this is a contentious issue. They saw clearly that it was spliced... There are some reports this might be due to a lab error, that's why they are making sure it's real.)

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