Oct 2, 2020

Palawan’s COVID-19 testing laboratory, an exclusive close look

Dr. Frederick Dalingding is the pathologist and head of the rapid polymerase chain reaction (PCR) for COVID-19 laboratory in ONP.

Pathologist Dr. Frederick Dalingding stands in front of the TB Culture Laboratory that was turned into a COVID-19 testing laboratory at the Ospital ng Palawan (ONP).

The Ospital Ng Palawan (ONP) on May 15 acquired its temporary license to operate as a coronavirus disease (COVID-19) laboratory, marking a landmark step towards effective infectious disease monitoring in the province.

Dr. Frederick Dalingding is the pathologist and head of the rapid polymerase chain reaction (PCR) for COVID-19 laboratory in ONP.

Granting Palawan News an exclusive walkthrough of the facility, he explained how the ONP’s existing tuberculosis (TB) culture laboratory was reconfigured for coronavirus testing.

The centerpiece of the ONP’s COVID-19 laboratory is a GeneXpert machine, typically used for TB and human immunodeficiency virus (HIV) viral load testing. Health officials say the machine is at par with the real-time PCR (RT-PCR) machine dubbed as the “gold standard” in COVID-19 confirmatory test.

 

 

Dubbed as “the next best thing”, GeneXpert analyzes the actual molecular structure of the virus. Specifically, it detects two viral components, namely N2-gene and E-gene.

Compared to the “conventional” RT-PCR test that utilizes three rooms, GeneXpert is a “closed-system” laboratory that serves as its “advantage” as it squeezed the processing into just one cartridge.

“Ang advantage nito is sa closed-system laboratory, nami-minimize ‘yong cross-contamination dahil lahat ng processing sa isang cartridge na lang,” Dalingding said.

The Process

Dalingding explained that the entire testing process will have three phases: pre-analytic, analytic, and post-analytic. The analytic phase, where the conclusive result may be read, can be generated within two hours.

However, Dalingding said the whole process would entail about three days, which is still faster compared to when samples were being sent to Manila that yield results within ten days at most.

“From pre- to post-analysis, three days. Pero ‘yong actual reading, or analytic phase, two hours lang ‘yon,” Dalingding said.

The pre-analytic phase involves clerical work and extraction of samples from the patient. This is a critical stage in testing, especially that the samples would need to be as “acceptable” as possible to the GeneXpert machine. Otherwise, it will yield a “presumptive” result which would start the whole testing cycle again.

“Hindi puwedeng madugo ‘yong sample. ‘Yong swab, na ilalagay sa tube, would also need a fluid viral transport medium. Kapag madugo or iba yong viral transport, hindi puwedeng i-run sa machine or magkakaroon ng false result,” Dalingding said.

The analytic phase would entail the actual run of samples into the GeneXpert machine. ONP’s COVID-19 laboratory will only be scheduled as it would also hold its regular testing for equally important monitoring of TB and HIV.

 

Dr. Frederick Dalingding, who will head the COVID-19 Testing Laboratory shows Palawan News the storage area where collected specimen will be placed before it is tested in the lab.

“Selected day lang dahil ang TB at HIV testing hindi naman puwedeng i-stop,” Dalingding said.

He explained that the laboratory would undergo rigorous daily decontamination. The staff, composed of three medical technologists and Dalingding himself as the pathologist, will follow a strict daily safety checklist prior to the start of their testing operations. Donning on proper personal protective equipment (PPE) alone would take 30 minutes to an hour.

“There is no emergency in a pandemic. We have to make sure safety is always prioritized because it is highly infectious. Every day, may checklist ang staff,” Dalingding said.

Upon entering the facility, he said airflow will have to be checked using a smoke test. This is to ensure that the air flows in one direction towards the virus filters or cabinets, to avoid contamination or outbreak within the testing center.

“We are a biosafety level two, kaya usually preparation pa lang three hours, during the shift na 8 a.m. to 5 p.m., nauubos for preparation,” Dalingding said.

During the analytic phase, the swab sample would be inserted into the cartridge. The machine can hold four cartridges and generate results in two hours. In an eight-hour shift, the team can only do four cycles. This limits the testing into 16 per day.

“Isa pa lang ‘yong machine natin. Hopefully, dumating na ‘yong sinabi nilang two additional,” Dalingding said.

The results may yield to: positive, negative, presumptive, invalid, or error; depending on the quality of samples.

“Kapag na-detect ‘yong N2 gene and E gene, that automatically means positive. If it only detects E gene, it is only presumptive or re-test dapat,” Dalingding said.

ONP was only given “more than 100” cartridges out of the 3,000 that were purchased from the United States (US).

“Limited sa ngayon ang cartridges, especially one cartridge is to one test, kaya we will strictly follow the guidelines,” Dalingding said.

 

Dr. Frederick Dalingding while being interviewed by Palawan News.

Under the Department of Health (DOH) Memorandum No. 2020-0180 issued on April 16, persons were classified under four categories including A) those who have moderate to severe symptoms and with exposure to a COVID-19 positive patient; B) are the patients showing mild symptoms and with travel history or a direct exposure with a confirmed case, or the “vulnerable” group such pregnant women and the elderlies; C) those under mild cases; and D) the returning “local stranded individuals”, or those who have a travel history from a place with known local transmission of the deadly infection.

“Priority natin ‘yong intubated patients or serious or severe condition,” Dalingding said.

The post-analytic phase involves reading and analysis of the result by the pathologist. Presumptive or invalid results were carefully reviewed and would generally determine a re-test for the patient.

“For error or presumptive result, may series of cycle, usually uulit from the start. Kaya for one patient, sinasabing may nagagamit na dalawa o tatlong cartridges to have a conclusive result,” Dalingding said.

In an earlier report, Dr. Dean Palanca, incident commander from the City Health Office (CHO), reiterated that the DOH algorithm would determine if an individual would be subject to the COVID-19 testing.

Palanca said that they were anticipating “at least 100” cartridges from the DOH, and pointed out that the local government was looking for other suppliers.

“May budget para bumili, at tina-try pa din namin kung makakakuha tayo somewhere else para may buffer tayo at hindi umasa sa DOH cartridges,” Palanca added.

With limited testing capability due to the number of personnel and resources, Dalingding is still grateful for the first step taken as the city and the province leaps for expanded COVID-19 testing.

“Hindi naman ito paran fastfood drive-through. This is still better compared to samples being sent to Manila,” Dalingding added.

(With reports from Celeste Anna Formoso and Ruth Rodriguez)

 

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