Thursday, June 4, 2020

The Basics Of COVID-19 Testing In The PH

The Basics Of COVID-19 Testing In The PH


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With 244,800 tests conducted to date, the Department of Health (DOH) has discussed in detail the complexities of Covid-19 testing, the wide range of factors affecting its speed and accuracy, as well as the health and safety of the healthcare workers facilitating the testing.

In a May 18 Beat Covid-19 virtual presser, Health Undersecretary, Dr. Maria Rosario Singh-Vergeire was joined by ThinkWell’s senior policy advisor, Dr. Maria Eufemia Yap and the executive director of the University of the Philippines Manila-National Institutes of Health (UP-NIH), Dr. Eva Maria Cutiongco-dela Paz, who detailed the entire testing process — from specimen collection to data validation and analysis.

ThinkWell is an international health systems development organization that has been instrumental in maximizing the country’s testing strategy by ramping up the capacities of current subnational laboratories and encouraging the private sector to set up Covid-19 laboratories and train laboratory personnel.

The UP-NIH is a licensed Covid-19 laboratory and trains laboratory personnel for biosafety and molecular biology.

Testing samples

“Medyo masalimuot ang proseso ng testing para sa Covid-19. Una sa lahat, kailangan [sa] prosesong ito [ang] nirerekomenda ng WHO — ang RT-PCR methodology (Testing for Covid-19 is a complicated process. First, the process has to be recommended by the WHO — the RT-PCR methodology),” said Yap, referring to the use of Reverse Transcription Polymerase Chain Reaction (RT-PCR) test — the gold standard for Covid-19 testing worldwide, which remains unequalled in terms of accuracy.

Yap said Covid-19 testing is a manual process which starts with the arrival of sample specimens in the laboratory.

“Tatlong malalaking bahagi po na ginagawa dito. Ang una, pagdating po ng samples sa laboratoryo…kailangan pong i-record ng mabuti ang datos tungkol sa sample na ito. Dapat siguraduhin [pong tama ang] pag-record at pag-label ng mga samples (There are three major parts done here. First, once the samples arrive at the laboratory, data about the sample should be recorded carefully. The recording and labeling of samples should be correct),” she said.

The samples containing live viruses are unpacked inside a biosafety cabinet which should also be contained and situated inside a biosafety laboratory.

“Ang unang [step sa actual testing] ay ang pag-extract ng RNA. Ito po ay ginagawa ng isang medical technologist sa loob po ng apat na oras para [makuha nya] ang [komponent] ng virus na siya namang ilalagay sa tinatawag nilang PCR machine (The first step in actual testing is the extraction of the RNA. This is done by medical technologists for about four hours to get the component of the virus which would then be put onto the so-called PCR machine),” said Yap, referring to the ribonucleic acid or RNA extraction process where the presence of the virus is then checked using the PCR machine for two hours.

Yap estimated that it takes eight hours to process a single Covid-19 sample.

“Siyempre umiiksi ito kapag medyo sanay na ‘yung ating mga [medical technologists]. Pero hindi po talaga mapapabilis ito sa kadahilanan na dapat may karampatang ingat talaga na kailangan gawin (The process shortens when the medical technologists get the hang of it. But this cannot be expedited for the reason that there should be caution in doing so),” she said.

“Hindi po ito katulad ng nagpapa-test tayo ng sa diabetes o kaya sa cholesterol na pag kinuhanan tayo ng dugo, matapos ilagay sa makina, [at] makalipas ang ilang oras, nariyan na agad ang resulta (This is not the same as when we get tested for diabetes or cholesterol that when blood is extracted and placed on a machine, after a few hours, the results are out),” Yap said.

Biosafety in licensing a testing laboratory

Before a Covid-19 testing laboratory is licensed by the DOH, it undergoes a five-stage licensing process designed to ensure that the facility and its personnel are capable of handling the specimens without the risk of contamination and further spread of infection.

In going through this process, dela Paz highlighted that it is not easy for a molecular laboratory to get licensed.

She said the laboratory must have a safe facility, trained personnel, appropriate equipment, and adequate supply to be licensed.

“Sobrang importante po [nang] prosesong ito because we have to make sure na ligtas ang mga taong gagawa ng test sa loob ng laboratoryo (This is a very important process because we have to make sure that the personnel who would be doing this inside the laboratory are safe),” she said, adding that the accreditation is not really the end of the story.

“May kasama pa pong proficiency testing na binibigyan po ang mga [laboratories] ng unknown samples ng RITM [na] tama po dapat ang mailabas nilang resulta ng ating mga pasyente na nag-undergo ng RT-PCR testing (Proficiency testing is included, wherein laboratories are given unknown samples by RITM, and that the results of patients who undergo RT-PCR testing should be correct),” she said.

Dela Paz stressed the importance of biosafety training in assessing, mitigating, and protecting the laboratory personnel, which does not only pertain to the medical technologists processing the tests but also to the laboratory aides who transport the sample from the hospital to the laboratory.

“Kasama po sa mga biosafety training ang disinfection, sterilization, decontamination of materials before they are discarded. Lahat po ito ay tinutuunan ng mabuting pansin, tine-train po properly ang personnel ng sa gayon tayo po ay nasa isang safe environment (Biosafety training includes disinfection, sterilization, decontamination of materials before they are discarded. All this are given attention and personnel are trained properly on this to ensure a safe environment),” she said.

Concerns in ramping up PH’s testing capacity

One of the challenges in ramping up the country’s testing capacity is ensuring a stable supply of RNA extraction kits considering its shortage due to increased global demand.

While some laboratories have the needed machines which could have increased our testing capacity, the specific extraction kit requirement of these machines remains also a challenge.

“Hindi po lahat ng available sa merkado ay pwedeng gamitin ng ilan sa mga laboratoryo natin. Maliban po dun, medyo hirap po tayong kumuha dahil ang karamihan po nito ay inaangkat mula sa ibang bansa. Kung kaya’t nakiki-kompetensya tayo sa mga ibang bansa na pare-parehong nangangailangan ng kits na ito (Not all that are available in the market can be used in our laboratories. Aside from that, it is a bit hard to get them because most are imported from other countries. We are competing with other countries that also need them),” Yap said.

The current supply is also depleting faster as we establish more swabbing centers and orders to replenish them usually take two weeks to arrive.

“Kung mayroon mang kulang ngayon, hindi po pwede pumunta lamang sa tindahan at um-order at mag-deliver agad (In case we lack them, placing orders and having them delivered aren’t easy),” she added.

When asked on how the government could possibly resolve these challenges, Yap highlighted the distribution efforts of the entire public sector and the generosity of several private partners who made available their extraction kits especially to provincial laboratories.

Causes of backlog

Yap said the backlog in reporting is a result of multiple factors. One of which is the reporting schedule or the cut-off time.

She shared that test results are normally transmitted at the time the machine has not yet finished processing all samples.

“’Yung makina po [ng] PCR, meron lang ho ‘yan na 96 na butas pero 44 lang po ang pwedeng gamitin dun sa kadahilanan na meron pa pong kailangan na ilagay na ibang mga sample na pang-verify doon sa mga tine-test (The PCR machine has 96 holes but only 44 can be used because there are other samples to be placed that would verify those being tested),” she said.

The second factor is the human element. In the absence of an automatic extractor, Yap shared that extraction is done by the laboratory personnel. This, according to her, requires a certain degree of familiarity without which the process might take time to finish.

“Ikatlong factor ho nito, marami sa LGU [ang] nagsipag-swab na po. Ang dami ng sample so ‘yung ating mga [laboratories] medyo nao-overwhelm din sila sa dami… kaya ‘di rin sila nakakatapos (Third factor, a lot of LGUs now are doing swab testing. The samples are piling up and so the laboratories get a little overwhelmed with the number… that’s why it’s taking time),” she said.

When asked for insights on how to possibly resolve these challenges, Yap said “nakikita ko po na sa [pagtutulungan] po ng mga laboratoryo, tapos nandyan po ang DOH…at ang private sector na willing naman pong tumulong sa amin, tingin ko po ay mararating din po at matatapos din po ‘yang backlog natin (with the cooperation of laboratories, the DOH, and the private sector willing to help us, I think we can do this and finish the backlog).”

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