October 2020
GENEWS
FEATURE
23
lab, meaning that the laboratory can only perform diagnosing and testing of swab samples. Since the start of operations, the lab has received thousands of samples from Los Baños, and around Laguna- all directed to their facility for testing and diagnosis. Thus, it was important that the protocols and procedures of the UPLB-CMDL were up to guidelines and were strictly followed to ensure that all the samples undergo proper testing. Showcasing some of UPLB-CMDL’s biosafety and security features As we see in television news, the norm for healthcare workers in hospitals and laboratories includes wearing full protective equipment: isolation suits, gloves, face shields, respirators or masks, and other equipment strictly fitted to them. Aside from protective equipment, UPLB-CMDL has eleven (11) out of thirteen (13) negative pressure rooms to further ensure safety of the staff and the lab’s surroundings. The rooms possibly have contaminated air, so the negative pressure prevents the air from reaching other areas. Double high-efficiency particulate air (HEPA) filters enable the filtration of the air from the contaminated areas before flowing out of the laboratory. Each room also has CCTVs with access in the administration room. If these protective gears and systems weren’t present, what would happen? Think of the game Among Us, but COVID-19 is the impostor, and is always ready to attack. “How does UPLB-CMDL deal with the swab samples they receive?“ Dr. Diaz stated that their workflow system resembled a factory assembly line, since different personnel carry out the tasks. However, the difference is that different rooms of isolation shelters every personnel. The workflow starts with the samples being collected from partner institutions.
Then, RNA extraction using spin columnbased kits occurs. The kits isolate and aid in purifying the RNA, so that no contaminants are present. Next, they prepare the PCR mix in the reagent room. They combine the PCR mix and extracted RNA in the template room. Then, real time RT-PCR amplification allows the generation of samples, showing fluorescence, which is the basis of the test result. We might think, is the sample from swabbing enough to give us results? The answer is no, but that’s where RT-PCR comes in. Reverse Transcription Polymerase Chain Reaction (RT-PCR) amplification works by transcribing the starting material (RNA) to DNA, and then copying and multiplying it to detectable amounts and then analyzed. “How do they diagnose which samples are positive and which samples are negative?” Three controls accompany the PCR amplification: positive control, internal control, and no template control. According to Dr. Diaz, these function in verifying the purity of the RNA, or if the gene for the SARSCoV-2 is present (positive control), verifying the purity of the RNA and the correctness of RNA extraction, which is the internal control, and verifying the purity of the PCR mix and the correctness of the whole workflow process, that is, the absence of template control. They repeat the PCR process when the controls are faulty. How they identify which ones are positive and negative all boils down to the cycle threshold (also called cq or ct). Dr. Diaz defined the cycle threshold as the number of cycles wherein the fluorescence curve surpasses the given threshold. Different diagnostic kits have varied ct indicated on the kits. For example,
when the indicated ct of the internal control is 27, the fluorescence and ct value seen in negative samples are beyond this threshold, but only to an extent. Negative samples show no amplification curve, only following the curve of the internal control. On the other hand, the fluorescence seen in positive samples are amplified within the ct of 27, say, the ct value of the positive samples is 25. Therefore, we see that the lower the ct value of the amplified sample, the more the sample contains the specific SARS-CoV-2 gene. The fluorescence seen increases as the amplified gene for SARS-CoV-2 increases, and we say the sample is positive when the fluorescence amplification is lower than the expected cycle threshold. Late sample amplifications are one of the challenges that Dr. Diaz and her team encounter during this process. Late amplifications are those that are not within the threshold considered positive, but still showed amplification too far into the threshold considered negative. She explained that they deal with this by repeating the run of the samples. After the second PCR run, and late amplification still ensued, they recommend re-swabbing of the individual. Laboratories, like the UPLB-CMDL, healthcare professionals, and government aid, are critical to us during these trying times. The journey of the UPLB-CMDL was a maze of obstacles and tests; still, they continue to face these challenges head on. The UPLB-CMDL, headed by Dr. Diaz, is always ready to fight with the country in this battle against COVID-19. Suits on, ready, fight!
Genes Towards Justice: Outstanding Paper Progresses Filipino Forensics by DANIEL VARIAS (Isochore)
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xploring genetic diversity in Filipinos has value not only in reconstructing how human pre-history unfolded in this region of the world but also in its social impact in improving forensic DNA practice in the country.
During its 42nd Annual Scientific Meeting held on July 8-10, 2020, the National Academy of Science and Technology (NAST) awarded one of this year’s Outstanding Scientific Paper Award to the work entitled “Filipino DNA variation at 36 Y-chromosomal short tandem
repeat (STR) marker units.”. The Special Genomics Issue of the Philippine Journal of Science published the paper in 2019. Researchers from the DNA Analysis Laboratory, Natural Sciences Research
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