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By Tristan Mañalac
VERA FILES
A couple of weeks ago, two months ago, even when SARS-CoV-2 spread worldwide, everything seemed fine in the Philippines. Today, easily more than 5,000 people have tested positive for the virus across the country and at least 300 have lost their lives. Counts are expected to worsen in the coming weeks.
As anxiety and frustration mount, widespread testing of COVID-19 has become, almost overnight, the common call of political comment online, an indication of how (or not) a government is dealing with the crisis.
After all, as Dr. Tedros Adhanom Ghebreysus, Director-General of the World Health Organization put it, “You can’t fight a fire blindfolded.”
On March 22, people turned to the Internet to echo this sentiment. Under the motto #MassTestingNowPH, the online rally called on the government to greatly expand its testing capabilities and make the kits free. The mainstream media is also inundated with almost daily accounting of these kits: how many come in and where, which is cheaper than that, and we’ve been tricked into accepting poor donations.
But the tests for COVID-19 will need much more than the kits. The whole process involves so many other elements (reagents, machines, infrastructure, human resources) without which the test kits will be useless.
The clock begins to mark the time the swabs are collected. Viruses can only survive for so long in the open air before their genetic material begins to break down. At refrigerator temperatures, shelf life can extend to approximately one week. Beyond that, however, samples should be stored in sub-zero conditions, at least –70orC, to be precise.
And so, in a race against time, a technician collects the samples, one from the throat and the other from the bottom of the nose, on the furthest back wall, and immerses them in sterile tubes of a liquid called viral transport medium. Inside a cooler filled with ice and under layers of packaging, the virus remains for the rest of the trip.
Back in the lab, before any further action is taken on the samples, the viruses must be deactivated to keep technicians safe. Heat is one way to accomplish this, according to Dr. Neil Andrew Bascos, PhD, Assistant Professor at the Diliman National Institute of Molecular Biology and Biotechnology at the University of the Philippines. Some chemicals, particularly those involved in the next step, also work.
Viruses keep their genetic material (ribonucleic acid, in this case, instead of the typical deoxyribonucleic acid in humans and animals) sealed within their fat and protein layers. They must be opened before the SARS-CoV-2 test kits can hope to detect anything.
The process of isolating RNA from samples is facilitated by dedicated kits. The specifics vary from kit to kit, but overall, the goal is to open up the cells and the viral particles they contain, shut down the molecules that can destroy genetic material and hijack RNA, away from the rest of the intracellular dirt.
(The kits belong to sets of reagents that have been calibrated to work analytically well with each other. They also include inserts with instructions for use. Some RNA extraction kits, for example, will have five tubes of reagents. This is also the case with the Homegrown SARS-CoV-2 test kits containing three tubes).
Unfortunately, reaching this viral stem load is arguably the most difficult step in the entire test flow diagram, and it’s a major bottleneck in the process, says Dr. Bascos. Each batch of RNA extraction samples, about 20 tubes, can take hours of work and a bag full of supplies. Even before the actual testing of SARS-CoV-2 begins, the lab will have already gone deep into its inventories.
Up to this point, the test facility has just prepared the samples for actual virus detection. What results is a solution that, in a word, is messy. It will contain RNA from the virus, if present, but also from cells, bacteria, and anything else in the subjects’ throats when swabs were collected. This is where the SARS-CoV-2 test kits come in.
These kits are based on a leading technique in molecular biology called a polymerase chain reaction (PCR), which targets a specific stretch of DNA and subjects it to 30 cycles of DNA replication, copying it one and again. If present in the sample, the PCR will have amplified the target sequence, allowing easy detection.
But not just any PCR machine will work. The genetic material for SARS-CoV-2 is RNA, not the typical DNA typically handled by normal PCR machines. Testing centers need to use kits and machines that first reverse transcribe the virus RNA into DNA and then measure the number of copies produced in real time, after each PCR cycle.
This process is called quantitative reverse transcription PCR, and although basic PCR machines are a dime in laboratories across the country, machines that can perform this more advanced technique are rare.
I should go without saying that, every step of the way, handlers and technicians must be very careful and more liberal with the use of disinfectants. These are highly infectious viruses, after all, and the threat of contamination will always be present.
Improper handling and opening of sample tubes after heat inactivation can lead to the formation of aerosols, risking infection by laboratory technicians, says Dr. Bascos. The risks persist throughout the process, which is why the tests are carried out in laboratories that have a biosafety level of 2+.
These facilities are built with the special purpose of containing threats inside. Airflow in laboratories, for example, must be inward to prevent aerosols and droplets from seeping into adjacent hallways and non-laboratory rooms. Laboratories must also come equipped with sterilization equipment and biosafety cabinets, which allow technicians to safely handle potentially infectious samples.
To date, the Health Department has authorized 16 laboratories as test facilities. These labs have shown that they can reliably detect SARS-CoV-2 in patient samples without putting their own people at risk.
Currently, while the scope of Evidence remains limited, the threat of a broken pipeline remains far away. Labs still have their RNA extraction kits before the health crisis, and supply stocks (plates, pipet tips, all different types of tubes, among others) should still be fine.
But because demand is skyrocketing around the world, it can be increasingly difficult for the country to maintain a secure supply chain for these essential, but often invisible, parts of the testing process. Continuing without thought can stifle efforts to contain the outbreak.
Dr. Bascos knows that. And so do many other experts and authorities who understand COVID-19 testing comprehensively. By themselves and in silent collaborations, these people are trying to prepare what they can, helping the country contain a problem before it explodes in a disaster.
VERA Files is published by veteran journalists who analyze current problems in depth. Vera is Latin for “true”).
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