Laboratory support for COVID-19
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COVID-19
By now, you have heard of the global pandemic of COVID-19 that has taken more than 100,000 lives in the United States as of today June 10, 2020, with 7.3M confirmed cases globally. You have also been affected by the continuing lockdown and restriction of things that you will normally be doing in your daily lives. You now have a "new normal" that you have to deal with. You have been asked to "stay home" and do not go out if you are not an essential worker or if you are not going for groceries. So, for this reason, you have heard of and you are affected by COVID-19. You may not have been exposed or even infected with the disease, but events around you have gotten you to ask questions on "what is COVID-19?" How is it transmitted? How is it diagnosed? What is the treatment? and when is the vaccine coming out? And, when are all these restrictions ending? My write up today is not to focus on COVID-19 information as an official source of authentic information. That is the work of global public health institutions including the World Health Organization, the Center for Disease Control and Prevention (CDC), or the federal government website. Please consult these websites for official information.
Laboratory Diagnostics of COVID-19.
To understand what it takes to diagnose COVID-19 is to understand what we are looking for in persons under investigation (PUI), who is exposed to the disease. COVID-19 is a viral disease caused by severe acute respiratory syndrome-corona virus-2, also called the SARS-CoV-2 virus, which is a novel or new mutations of previously known coronaviruses such as Ebola or Middle East Respiratory Syndrome (MERS). This belongs to a group of coronaviruses that attacks the respiratory tract causing severe and acute respiratory disorders in PUIs. For this reason, diagnosis is to confirm the presence or absence of the SARS-CoV-2 virus in the respiratory tracks of infected individuals. Because coronaviruses have sharp end-pointed follicles that look like "crowns or corona" they turn to attach themselves to surfaces of the host until they are transferred to areas close to the lungs where they "bound" to the cells to replicate or mutate.
Standard Laboratory Technique
To confirm the presence or absence of the virus, the method must be specific to identify ONLY the SARS-CoV-2 and not other viruses (also called sensitivity, true positive). At the same time, the method shows the absence of the virus; otherwise, MUST identify those without the virus (specificity, true negative). We shall get back on this terms later, but for now, the most accurate laboratory test of coronaviruses is the polymerase chain reaction, or PCR, which determine the deoxyribonucleic acid (DNA) fingerprint of the virus. Advances in this technology has led to the development of high sensitivity and specific testing methods of this platform. This type of test is base on the molecular structure of the virus using the nucleic acid test (NAT), which helps to detect the "fingerprint" of the virus; extraction, amplification, and detection in the visible region of the light spectrum. The specific DNA region of the virus that is detected conforms to the specific visible region of the light spectrum that can be seen or visualized through light scattering devices.
COVID-19 Testing
With the explanation of the general principles of molecular diagnostics (NAT or PCR), let's specifically discuss the identification of the SARS-CoV-2 virus that is responsible for COVID-19. The one characteristic of this virus is that its structure is of ribonucleic acid (RNA) instead of DNA, the main difference between the two is the type of nucleic acid - sugar ribose and a nucleobase. Discussion on the differences between the two is outside the scope of this write-up. However, RNA could be converted into a detectable DNA by reverse transcription or reverse transcriptase (RT) which allows the visibility of the nucleic acid structure of coronavirus by PCR. Hence the standard method for the detection and diagnosis of the COVID-19 virus is the reverse transcription-polymerase chain reaction (RT-PCR) method. This method has been validated and found to be 99.9% specific and sensitivity to coronavirus and specifically on the SARS-CoV-2 virus.
The advantage of RT-PCR molecular diagnosis is its universality for viral identification, outside the coronavirus and hence with the outbreak of the pandemic, the method can be repurposed easily to detect emerging viral diseases. This was the situation when the first SARS-CoV-2 viral structure or fingerprint was isolated and shared by China to the scientific community in the early days of the outbreak. As soon as the viral DNA was isolated and confirmed, the existing technology was repurposed to provide specific and sensitive detection range in the visible light spectrum. To re-purpose the existing instruments to detect COIVD-19, the major PRC technology manufacturers such as Roche, Abbott, and Cepheid quickly developed "tool kits" that allow for the capture, extraction, amplification and identification of SARS-CoV-2 virus on their existing technological platforms of RT-PCR. This strategy has helped the world in general, and developing countries in particular, to respond to the diagnosis of COVID-19 during the pandemic.
The major disadvantage of RT-PCR technology is dependent on highly skilled laboratory personnel as well as the high cost of this technology. The instruments are high throughput with the ability to conduct almost 1000 tests per day on one instrument when adequately managed or utilized. However, sample preparation and extraction is an extremely labor-intensive process and has to be done manually, which sometimes hinders the number of "runs" that can be done in a day. But, with the inclusion of Cepheid GeneXpert Cartridge, which is a single-use tool kit, that incorporates automatic amplification, makes that instrument a game-changer in the molecular diagnosis of COVID-19 in developing countries.
Serology - Antigen and Antibody Techniques
Over and above the standard laboratory method, there is growing research in developing simple rapid diagnostics tests (RDTs) that can easily be used at patients or near patients level, thereby eliminating or minimizing the need for laboratory-based testing techniques. In this research, the use of invitro-diagnostics devices (IVD) that employs immunoglobin (IgM or IgG; antigen or antibody) from the blood samples of recovered patients for serological testing. As of writing this piece, there are more than 1000 different types and designs of serological testing devices that are outside the scope of my current blog. However, suffice to say that WHO has not recommended any of these testings for the diagnosis of COVID-19. This area of research continues to evolve and data for specificity and sensitivity of these devices for COVID-19 is still scanty and being developed. We will return to this topic in the future and how developing reliably validated RDTs will be a game-changer in diagnostics access to COVID-19 detection and management. For additional guidance and information on how these tests could be introduced in the national tiered network of developing countries, see my recent publication on this subject: https://ajlmonline.org/index.php/ajlm/article/view/1244/1493
Reference:
1. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
2. https://www.cdc.gov/coronavirus/2019-ncov/index.html
3. https://www.coronavirus.gov/
4. https://ajlmonline.org/index.php/ajlm/article/view/1244/1493
Quality Matters Blog
COVID-19
By now, you have heard of the global pandemic of COVID-19 that has taken more than 100,000 lives in the United States as of today June 10, 2020, with 7.3M confirmed cases globally. You have also been affected by the continuing lockdown and restriction of things that you will normally be doing in your daily lives. You now have a "new normal" that you have to deal with. You have been asked to "stay home" and do not go out if you are not an essential worker or if you are not going for groceries. So, for this reason, you have heard of and you are affected by COVID-19. You may not have been exposed or even infected with the disease, but events around you have gotten you to ask questions on "what is COVID-19?" How is it transmitted? How is it diagnosed? What is the treatment? and when is the vaccine coming out? And, when are all these restrictions ending? My write up today is not to focus on COVID-19 information as an official source of authentic information. That is the work of global public health institutions including the World Health Organization, the Center for Disease Control and Prevention (CDC), or the federal government website. Please consult these websites for official information.
Laboratory Diagnostics of COVID-19.
To understand what it takes to diagnose COVID-19 is to understand what we are looking for in persons under investigation (PUI), who is exposed to the disease. COVID-19 is a viral disease caused by severe acute respiratory syndrome-corona virus-2, also called the SARS-CoV-2 virus, which is a novel or new mutations of previously known coronaviruses such as Ebola or Middle East Respiratory Syndrome (MERS). This belongs to a group of coronaviruses that attacks the respiratory tract causing severe and acute respiratory disorders in PUIs. For this reason, diagnosis is to confirm the presence or absence of the SARS-CoV-2 virus in the respiratory tracks of infected individuals. Because coronaviruses have sharp end-pointed follicles that look like "crowns or corona" they turn to attach themselves to surfaces of the host until they are transferred to areas close to the lungs where they "bound" to the cells to replicate or mutate.
Standard Laboratory Technique
 |
| A picture of coronavirus structure showing "crowns" |
COVID-19 Testing
With the explanation of the general principles of molecular diagnostics (NAT or PCR), let's specifically discuss the identification of the SARS-CoV-2 virus that is responsible for COVID-19. The one characteristic of this virus is that its structure is of ribonucleic acid (RNA) instead of DNA, the main difference between the two is the type of nucleic acid - sugar ribose and a nucleobase. Discussion on the differences between the two is outside the scope of this write-up. However, RNA could be converted into a detectable DNA by reverse transcription or reverse transcriptase (RT) which allows the visibility of the nucleic acid structure of coronavirus by PCR. Hence the standard method for the detection and diagnosis of the COVID-19 virus is the reverse transcription-polymerase chain reaction (RT-PCR) method. This method has been validated and found to be 99.9% specific and sensitivity to coronavirus and specifically on the SARS-CoV-2 virus.
 |
| Examples of DNA and RNA nucleic acid structure |
The major disadvantage of RT-PCR technology is dependent on highly skilled laboratory personnel as well as the high cost of this technology. The instruments are high throughput with the ability to conduct almost 1000 tests per day on one instrument when adequately managed or utilized. However, sample preparation and extraction is an extremely labor-intensive process and has to be done manually, which sometimes hinders the number of "runs" that can be done in a day. But, with the inclusion of Cepheid GeneXpert Cartridge, which is a single-use tool kit, that incorporates automatic amplification, makes that instrument a game-changer in the molecular diagnosis of COVID-19 in developing countries.
Serology - Antigen and Antibody Techniques
Over and above the standard laboratory method, there is growing research in developing simple rapid diagnostics tests (RDTs) that can easily be used at patients or near patients level, thereby eliminating or minimizing the need for laboratory-based testing techniques. In this research, the use of invitro-diagnostics devices (IVD) that employs immunoglobin (IgM or IgG; antigen or antibody) from the blood samples of recovered patients for serological testing. As of writing this piece, there are more than 1000 different types and designs of serological testing devices that are outside the scope of my current blog. However, suffice to say that WHO has not recommended any of these testings for the diagnosis of COVID-19. This area of research continues to evolve and data for specificity and sensitivity of these devices for COVID-19 is still scanty and being developed. We will return to this topic in the future and how developing reliably validated RDTs will be a game-changer in diagnostics access to COVID-19 detection and management. For additional guidance and information on how these tests could be introduced in the national tiered network of developing countries, see my recent publication on this subject: https://ajlmonline.org/index.php/ajlm/article/view/1244/1493
Reference:
1. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
2. https://www.cdc.gov/coronavirus/2019-ncov/index.html
3. https://www.coronavirus.gov/
4. https://ajlmonline.org/index.php/ajlm/article/view/1244/1493
Quality Matters Blog
You brought back my Biology 101 lectures Dr. Farouk! Thanks for the good overview on how the SARS-CoV-2 virus is detected in the laboratory. For the IVDs that have been developed and continue to be developed, how widely are they being used globally? Though the WHO has not recommend them, the USFDA did grant emergency use authorization for a particular type I think. Why has the WHO not recommended at least this one?
ReplyDeleteGreat questions and thanks for visiting and reading my post. Yes, WHO's mandate is to recommend guidance and give direction on what is to be done. It is also the mandate of the regulatory agency to issue emergency authorization. Now, for US FDA to issue authorization they consider existing data on quality and safety of the products. But because of emergency situation as a result of the pandemic, there is limited data to assure the quality and safety of products. With the IVD under development now, FDA is still monitoring post authorization data to makes sure that the products are continuously working as authorization. An example is the authorization of hydroxy-chloroquine by US FDA based on the data and now that authorization was revoked with the availability of new evidence.
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