Why So many backlogged in Covid-19 test?
1. Because there are too many samples to be processed in a day. Not only the new case sample, but the lab also received repeat samples from inpatient and previous negative patients. If there are 1000 negative samples within 2 previous weeks, then there will be 1000 samples already booked to be processed this week. Unless decided that the person does not require repeated samples (asymptomatic, low-risk patients).
2. WHO recommends using 2 gene detection for Covid-19. If other labs use different gene then it will be much difficult. As far as I know, most labs in Malaysia use the same genes / similar genes detection. So this would make things much easier. Back to the 2 genes detection part, if one gene is detected and the other not detected, then how to interpret it? It will require repeat testing in such situation. As COVID-19 is a very new virus, and we understand only that much, it is better to repeat the test rather than make assumptions.
Our lab, for example, use E gene detection and Rdrp (RNA dependant RNA polymerase) gene detection. The E genes is a 'universal' genes which can be detected in many strain of bat coronavirus SARS virus/ SARS related virus. Rdrp gene is the specific genes for COVID-19 developed based on the sequencing result done from Wuhan strain.
If E gene is detected and Rdrp not detected (E+/Rdrp -), it would be easy to say that COVID-19 negative..... but hold on... This will become more complicated. As for our experience, Rdrp can be detected late in the cycle of PCR. Maybe after 40th cycles. (You have to understand cycle threshold to follow this). So, what if the E genes detected at 38th cycles, and Rdrp detected at 44th cycles? = E + /Rdrp -).
To make it more complicated, E genes are specific for SARS and SARS related viruses. So, if in the above situation, can we say the patient had SARS? No, because SARS was eliminated since 2004. We don't want to trigger more panic. Certain parties recommended that all E positive classified as COVID-19 nevertheless. How to be sure?
Repeat the test. Refer for sequencing et cetera et cetera.
This equals time. TAT will increase.
3. Control issues. For every PCR test, control is a must. Control is the baseline to make sure our positive is real positive and negative is real negative. Some assays also require internal control instead of only positive and negative control. Control, no matter how high quality the assay is, how good our technician, will have a problem once in a while. "Control not in" or "control got problem" is a nightmare. Control needs to be run with every batch of PCR test. If one control has issued ( example control positive turn out to be negative or vice versa), the whole batch needs to be repeated. Wasting half day. If for other well-established assays, such a problem will prompt the lab to reject the assay and find other companies or different assay to be used. But in this pandemic, all assays are for emergency use only. This translated into - no one knows definitely how the primer and probe would react since we are doing everything in emergency protocol now. Only enough evaluations have been done before the assays expedite approval by WHO and FDA. We have to rely on whatever we have for now.
4. The most advance PCR would take only 1-2 hours for extraction and the amplification process. The so so PCR especially the one that needs to be done manually will take a few hours for extraction and a few hours for the amplification and detection. Usually, it will take a half-day to get the results.
5. Backlogged will be there unless we add more PCR devices, more lab involved and more staff involved. And to make sure the reagent always sufficient.
6. To those hidden front-liner working in the lab, even if you are not published glamorously in media, you are all amazing. You all deserves much respects. You all are nagged every day to produce the results and yet you all never complain on how hard your life is in this pandemic.
Disclaimer: Different lab will have their own assays and ways to validate the results. Some lab only use 1 gene detection to expedite the results. However, rest assure, all labs are following strict quality control to make sure our result reliable for the epidemiological and clinical use.
2. WHO recommends using 2 gene detection for Covid-19. If other labs use different gene then it will be much difficult. As far as I know, most labs in Malaysia use the same genes / similar genes detection. So this would make things much easier. Back to the 2 genes detection part, if one gene is detected and the other not detected, then how to interpret it? It will require repeat testing in such situation. As COVID-19 is a very new virus, and we understand only that much, it is better to repeat the test rather than make assumptions.
Our lab, for example, use E gene detection and Rdrp (RNA dependant RNA polymerase) gene detection. The E genes is a 'universal' genes which can be detected in many strain of bat coronavirus SARS virus/ SARS related virus. Rdrp gene is the specific genes for COVID-19 developed based on the sequencing result done from Wuhan strain.
If E gene is detected and Rdrp not detected (E+/Rdrp -), it would be easy to say that COVID-19 negative..... but hold on... This will become more complicated. As for our experience, Rdrp can be detected late in the cycle of PCR. Maybe after 40th cycles. (You have to understand cycle threshold to follow this). So, what if the E genes detected at 38th cycles, and Rdrp detected at 44th cycles? = E + /Rdrp -).
To make it more complicated, E genes are specific for SARS and SARS related viruses. So, if in the above situation, can we say the patient had SARS? No, because SARS was eliminated since 2004. We don't want to trigger more panic. Certain parties recommended that all E positive classified as COVID-19 nevertheless. How to be sure?
Repeat the test. Refer for sequencing et cetera et cetera.
This equals time. TAT will increase.
3. Control issues. For every PCR test, control is a must. Control is the baseline to make sure our positive is real positive and negative is real negative. Some assays also require internal control instead of only positive and negative control. Control, no matter how high quality the assay is, how good our technician, will have a problem once in a while. "Control not in" or "control got problem" is a nightmare. Control needs to be run with every batch of PCR test. If one control has issued ( example control positive turn out to be negative or vice versa), the whole batch needs to be repeated. Wasting half day. If for other well-established assays, such a problem will prompt the lab to reject the assay and find other companies or different assay to be used. But in this pandemic, all assays are for emergency use only. This translated into - no one knows definitely how the primer and probe would react since we are doing everything in emergency protocol now. Only enough evaluations have been done before the assays expedite approval by WHO and FDA. We have to rely on whatever we have for now.
4. The most advance PCR would take only 1-2 hours for extraction and the amplification process. The so so PCR especially the one that needs to be done manually will take a few hours for extraction and a few hours for the amplification and detection. Usually, it will take a half-day to get the results.
5. Backlogged will be there unless we add more PCR devices, more lab involved and more staff involved. And to make sure the reagent always sufficient.
6. To those hidden front-liner working in the lab, even if you are not published glamorously in media, you are all amazing. You all deserves much respects. You all are nagged every day to produce the results and yet you all never complain on how hard your life is in this pandemic.
Disclaimer: Different lab will have their own assays and ways to validate the results. Some lab only use 1 gene detection to expedite the results. However, rest assure, all labs are following strict quality control to make sure our result reliable for the epidemiological and clinical use.
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