HOW DOES CORONAVIRUS TESTING WORK AND WHY DO WE HAVE FEW LABS CONDUCTING COVID-19 TESTS IN NIGERIA?
Coronaviruses are viruses in the subfamily Orthocoronavirinae, in the family Coronaviridae, order Nidovirales, and realm Riboviria. The main symptoms of COVID-19, the disease caused by the coronavirus SARS-CoV-2, are fever, dry cough and shortness of breath.
According to the
, diagnostic testing for COVID-19 is critical to tracking the virus and suppressing its transmission.
At a Covid-19 media briefing on Monday, the director-general of the
Tedros Adhanom Ghebreyesus said, 'We have a simple message for all countries: test, test, test,” The question is; why is the most populous black nation on earth lagging behind on the simple aspect of testing, testing, and testing? To answer, we need to understand how CODID-19 is tested and confirmed. As a holder of a diploma in Laboratory science, and a plant breeder with a background on molecular breeding, I reckon I can delve into this topic with the hope that experts that come across this piece might correct me where I falter.
Coronavirus mainly affects the upper respiratory tract and causes pneumonia which is the prime symptom in COVID-19 infection. It enters the lungs through Angiotensin-converting enzyme 2 (ACE2) receptors via endocytotic pathways. Once it's in, it affects the body. Now that it is inside the body, the goal is how to detect it and be sure its coronavirus, not common cold or flu. The coronavirus is a plus (+) strand RNA virus with proteins such as S protein, M protein, N protein, and E protein which are necessary for the survival of the virus. The viral genome encodes for all these proteins (S, M, N, and E). since the genome encodes for these proteins, it means once you are infected the detection of RNA corresponding to these proteins becomes easier. Regions for encoding the enzymes (proteins) include the orf1a and orf1b which encodes for the replicate. This process is important for viral DNA replication. If any of this fragment or a combination of the fragments is detected in a patient's sample then he/she is said to be possibly infected by the virus. Otherwise, these fragments can never be detected in an uninfected person.
The detection of the coronavirus can be achieved using real-time quantitative PCR analysis called reverse-transcription polymerase chain reaction. Real-time PCR analysis is a technique used to understand the presence or absence of certain RNA or transcripts in a sample. It can also tell how much it is present in a sample. Depending on the protocol/guideline you are using (shown in picture), the PCR uses primers to detect a portion of the viral genome as present or absent in the sample. Whatever PCR strategy a lab or country uses, its certain to detect the presence or absence of the viral genome. In order to detect the virus, the lab scientists or any health care official takes a sample which is either blood or the sputum. RNA is extracted from that and the total RNA is converted to cDNA. If the sample has a viral RNA, the viral RNA will also be converted to cDNA. Afterward, specific primers and a dye are introduced to amplify the portion of this cDNA. Now, if the cDNA is not present, the amplification will not take place and that can be absolutely and quantitatively detected by real-time PCR. The dye helps immensely in this process because when it binds to our DNA of interest, it creates a fluorescence which is apparent. As the PCR cycles move on, more SYBR Green molecules bind to the amplified DNA and the signal amplifies over time. You can detect a fold change from a control sample versus a patient sample. The E protein transcript level will be several folds higher than a control sample that is not infected. This is a confirmatory test for coronavirus infection. This technique is very accurate.
In order to finish one round of test, it should take 24 - 72 hours (from sample collection to final report) or conservatively, let's say one week!! Why then does it take 'forever' for the
to test and confirm cases? and why can't we use University labs with PCR machines to help in this National emergency?
The test for the coronavirus requires a kit, specialized equipment, and specially trained personnel. The requirement for all tests to be conducted at the NCDC labs can be shelved to make it easier for commercial and academic laboratories other certified labs that already have the necessary equipment and trained personnel to test patient samples. Since all the labs including the NCDC labs do not and cannot develop their test kits, we are all left with the option of importing. NCDC can be at the forefront of procuring the kits and distributing it to all partners and also ensure they are used judiciously. The results from the various labs can be routinely picked at random for quality control by the NCDC.
But let's discuss the economics of testing for COVID-19!! How much does it really cost a lab to do a PCR test? That’s hard to calculate. To do a PCR test one needs a bunch of chemical reagents. For many infections, such as HIV, there are manufacturers around the world supplying kits with all the reagents the laboratory needs. But SARS-CoV-2 was only discovered a couple of months ago and no such pre-packaged commercial kit yet exists for it. So until such kits are available — which should be soon — laboratories have to source the various chemicals, using a protocol developed by the World Health Organisation. However, one estimate here in South Africa puts the cost of testing at a range of ZAR400 to ZAR1200 which in today's exchange is between Naira 8180.51 to Naira 24541.54. I will be glad if the
can confirm the information that it costs around N10,000.00 to test one sample which is freely done by the FGN!!! Let us assume it will cost NCDC N10000 - N50000 to test each sample, that will amount to 100 - 250 million Naira to test 5000 samples. That is if we also assume just 5000 cases are serious and also fulfill all criteria to be tested. That's a lot of money, huh? NO. For the government and donors, who recently came together and raised loads of monies, that is a chicken change as compared to what was raised. A billion Naira from
to test 40,000 - 200,000 suspected cases in Nigeria. Don't worry, more money will remain that will go into equipping our isolation spots and buying respirators and ventilators and all the gears necessary to equip our health personnel in this war. Currently, our hospitals are lacking in ventilators (some reports say we have about 400 ventilators) and other basic gears necessary to save not only patients' lives but the lives of our health workers as well.
Putting into account the national emergency we are facing, I am sure the import fees for supplying these valuable kits can be waived by the federal government. Why then aren't we supplying, distributing and testing as we should be doing according to recommendations from the
? We also need to consider the fact that with the massive increase in tests, the process (2 weeks to obtain the result of the test) will probably start taking longer as a backlog builds. Can we afford that? I know some might be worried about the security protocols surrounding such sensitive tests. This is a totally valid worry but when we consider the NCDC is working to set up more Labs across the nation which will take time to come into operation. It, therefore, becomes a wise move to upgrade the security clearances of some of the existing Labs in the Universities to handle such tests as a matter of expediency. Nigeria, please let's get it right this time!!! God bless the Federal Republic of Nigeria.
Muhammad Ahmad Yahaya
Lecturer, Sorghum/Sunflower Breeder
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