PH Genome Center seeks more personnel amid COVID-19 Delta variant threat

Katrina Domingo, ABS-CBN News

Posted at Jul 27 2021 06:20 PM

MANILA - The Philippine Genome Center chief on Tuesday said the facility is planning to raise the number of its personnel by double to increase the country's sequencing capabilities as the threat of another spike in COVID-19 cases due to the Delta variant looms over the country.

The center currently has 40 molecular biologists, chemists, computer scientists and physicists who extract, prepare, sequence, and analyze some 750 samples every week, said Dr. Cynthia Saloma, executive director of the Philippine Genome Center.

"We're hiring more people. We're doubling our team particularly in the extraction and sequencing side," she said in an online press conference.

"Marami naman tayong (We have a lot of) molecular biology graduates so I don't think it will be a problem," she said.

Between January and July 2021, the Philippines has sequenced 9,351 samples or 0.86 percent of the 1 million COVID-19 cases in the country, Saloma said.

While the World Health Organization's ideal sequence rate should be 5 percent of a country's COVID-19 cases, nearly all countries in the world only do purposive sampling, she said.

"With the exception of Denmark and the United Kingdom... In many countries around the world, it is really purposive sampling. They only sequence in areas of interest," she said.

"Singapore has sequencing capacity but they don't sequence everything," she said.

SEQUENCING NOT A DIAGNOSTIC TOOL

The whole genome sequencing is only meant to "provide us with more information," said Dr. Alethea Deguzman, director of the DOH's Epidemiology Bureau.

"Whole genome sequencing is not a diagnostic tool. When you find out you have a variant of concern, pareho pa din ang ginagawa natin sa kanila [as with other COVID-19 patients]," she said.

"Yung mga core - prevent, detect, isolate, treat, reintegrate - it is still the same response whether we have a variant of concern or not," she said. 

As of July 25, the Philippines has confirmed 1,773 Alpha variant carriers, 2,019 Beta variant carriers, 119 Delta variant carriers, and 2 Gamma variant carriers in the country.

WHY SEQUENCING TAKES A WHILE

The DOH earlier said sequencing a batch of samples from COVID-19 patients may take between 5 and 7 days.

"The whole process of genome sequencing takes time," Saloma said.

The process involves 4 steps: RNA (ribonucleic acid) Extraction, Library Preparation, Sequencing and Data Analysis, she said.

The extraction of RNA from samples would take about 1 and half to 3 hours, while library preparation - which would adhere to the sequencing flowcell and allows the sample to be identified - may last up to 7 hours, she said.

Samples would then be sequenced with the length of the process depending on what type of machine was used.

The Genome Center's smallest sequencing machine can run up to 48 samples at a time and needs 18 hours for the process to be completed, while its largest apparatus can accommodate up to 750 samples with a 25-hour run time.

The final step is analyzing the data to identify which COVID-19 mutation or variant is present in the sample. It may take up to 2 days to fully analyze a sequenced sample.

"There is a lot of thinking process and vetting that happens," said Dr. Eva Marie Dela Paz, executive director of the National Institute of Health.

"There is a proportionality. The less number of RT-PCR positive [cases] they have, they will be able to sequence more," she said.

The Philippines is planning to open sequencing laboratories in the Visayas and Mindanao to further boost the country's capacity, but Saloma said that more funding is required.

The national government earlier allocated P362 million for COVID-19 genome sequencing, but the fund would only cover supply of reagents or chemicals used in tests, testing kits and other logistical requirements until the end of the year, the DOH earlier said.

"Kung may mag-donate lang sana, maka-start sila right away," the Genome Center chief said, referring to the proposed laboratories in Visayas and in Mindanao. 

"Kung magbigay lang ng pondo agad, we can help them."

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