Polymerase Chain Reaction (PCR) is a method of producing millions or billions of specific DNA. This allows for the detection of the genetic materials (RNA or DNA) of a specific virus present in the given sample. For the measurement of the PCR, the real-time RT-PCR machine is mostly used nowadays. Here, we will be discussing the process of PCR tests and the list of health sectors present within Nepal that are doing the PCR tests. We will also be talking about the differences between the PCR test in comparison to that of the rapid antigen test.
How does the covid PCR test work?
There are three main steps involved in the process of PCR test for the diagnosis of the coronavirus. They are as follows.
1. Sample Collection
In this step, the sample is collected from the nasopharynx or oropharynx or the saliva of the person with the help of a swab. The sample is enclosed within a closed tube. Then it is sent to the laboratory for further analysis.
The sample can consist of a number of RNA, DNA, etc. So we need to extract the required component from all the available components.
In the case of SARS-CoV-2 coronavirus, RNA is the genetic material. So, RNA is extracted from the available sample.
3. PCR Machine
After the required material has been extracted from the sample, it is now time for carrying out the PCR test with the help of PCR machine.
We have already stated that with the help of PCR, the available DNA molecule becomes amplified. Thus it becomes easier to detect the virus in the sample. But, in the case of coronavirus, the genetic material is RNA. Hence it needs to be converted into the DNA sequence before carrying out the test. So for this reason, an RT-PCR machine is used.
RT-PCR is a type of PCR in which an RNA template generates complementary DNA (cDNA), with the help of a reverse transcriptase enzyme.
The RT- PCR machine will carry out the following steps for the analysis of the virus.
Denaturation is the process of the breakdown of the proteins or nucleic acids (such as DNA) by applying an external force, heat, pressure, or changing the pH value. Denaturation causes the breakdown of the structure of the protein or the nucleic acids.
In the case of the DNA, denaturation causes the breakdown of the double-stranded DNA into two separate strands. For this purpose, the nucleic acid is heated to 92 – 94°C for a short period of time. This causes the breakdown of the hydrogen bond present between the two strands. This method of the breakdown of double-stranded DNA into a single strand by heating is known as denaturation (melting) of the DNA molecule.
(Note:- Remember that the temperature of the DNA solution should not exceed 94°C. Temperature above this can also cause the breakdown of the phosphodiester bond. Thus the nucleotide sequences will get damaged. )
The other name of annealing is hybridization. In this process, the temperature of the sample solution is reduced from 94°C to 50 – 70 °C. In this process, the RNA primers bind to the two separate strands. The nucleotide present in the RNA primers should be complementary to the mother strand DNA. Also, the specific primer only binds to a certain viral cDNA and not with other cDNAs.
A temperature of about 72°C is applied to the DNA solution for about 30 seconds to 3 minutes. During this time, Taq polymerase is attached at the end of the RNA primer. This allows attaching the nucleotides, at the end of the primer causing its extension.
Thus at the end of the single-chain reaction, a single DNA multiplies to two DNAs.
The PCR undergoes a number of chain reactions, causing the doubling of the DNA strands in each cycle. Hence, within 37 cycles, single specific DNA gives out millions or billions of DNAs. This huge number of DNA in a sample becomes useful for the analysis of disease-causing organisms.
What is real-time RT – PCR?
The conventional method of the RT-PCR only gives the result at the end of the test. So, to overcome this defect a new method has been developed. It is known as real-time RT-PCR. As the name suggests, real-time RT-PCR gives the result when the test is being carried on.
Just like the Ebola virus, this technology is also used for the detection of the coronavirus. Nowadays, a Taqprobe consisting of the fluorophore is covalently attached to the oligonucleotide probe. This fluorophore emits out fluorescence light whenever a new DNA molecule is formed.
In the case of SARS-CoV-2 coronavirus, for every specific cDNA molecule formation, fluorescence light will be emitted.
PCR Test Result
PCR test is determined on the basis of the Ct-value (cycle threshold value). Ct-value refers to the number of cycles required to amplify the cDNA before it becomes detectable to the PCR machine. Inside the real-time RT-PCR machine, it is possible with the help of the emission of fluorescence light.
When the intensity of the fluorescence light crosses the set threshold value, the cycle threshold value is obtained. Thus the test becomes relevant. A low ct-value indicates that the signal quickly reaches or crosses the threshold value. This implies that there is a higher load of the virus in the given test sample.
The ct-value can differ from one virus to another. For SARS-CoV-2 coronavirus, the benchmark of the cycle threshold value can range from around 24 – 35. This value can differ from one laboratory to another. If the ct-value is equal to or less than the set value, then the test is considered positive.
PCR Test Result Accuracy
The result of the PCR test is highly accurate and reliable. There are two types of results that we can get from the PCR test. They are as follows.
If the result of the PCR test is positive, then the person is likely to be a covid patient. In such a case you need to take care of yourself. You need to follow the guidelines of the doctors.
If the result of the PCR test is negative, then there can be three possible conclusions. The first conclusion is that the person is not infected with the coronavirus. The other conclusion is that the person has recently been infected by the virus. Thus, there is not sufficient virus in the body due to which, it is not detected in the sample. The other reason can be that the sample had not been collected or tested properly.
Even if the result is negative, you should not forget that there is always a chance of infection in the future. Hence, you should always be careful.
PCR Test Price
Nepal Government has set the price for the PCR test in governmental hospitals and laboratories at RS 1000/ PCR. Similarly, for the private sectors, the price has been set to Rs 2000/PCR. So, the health sector can charge less than the set price. But, if the organization is charging you more than the price set by the government, you should complain about it to the governmental body.
PCR Test in Kathmandu
PCR test is available in various hospitals (government/private), clinics, and diagnostic centers in Kathmandu. Among all of them, here we will be listing some of the major centers for carrying out the PCR test in Kathmandu.
|Health Centers||Government/ Private||Address||Contact|
|Bir Hospital||Government||Kanti Path, Kathmandu||01-4221988|
|Tribhuvan University and Teaching Hospital (TUTH)||Government||Maharajgunj, Kathmandu||01-4412303|
|National Public Health Laboratory (NPHL)||Government||Teku, Kathmandu||01-5352421|
|Sukra Raj Tropical and Infectious Disease Hospital||Government||Teku, Kathmandu||01-4253396|
|Patan Academy of Health Sciences (PAHS)||Government||Lagankhel, Lalitpur||01-5545112|
|Nepal Armed Police Force (APF) Hospital||Government||Balambu, Kathmandu||01-4315224|
|Prasuti Griha||Government||Thapathali, Kathmandu||01-4260405|
|Nepal Korea Friendship Hospital||Government||Madhyapur Thimi, Bhaktapur||01- 6633442|
|Birendra Army Hospital||Government||Chhauni, Kathmandu||01-4274019|
|B & B Hospital||Private||Gwarko, Lalitpur||01-55531930|
|HAMS Hospital||Private||Dhumbarahi, Kathmandu||01-4377404|
|Grande International Hospital||Private||Dhapasi, Kathmandu||01-5159266|
|Norvic International Hospital||Private||Thapathali, Kathmandu||O1-5970032|
PCR Test in Nepal
In the above paragraph, we had made a list of health sectors present within Kathmandu valley. Now we will be making a list of other health sectors present which provides PCR test in Nepal.
|BP Koirala Institute of Health Sciences||Government||Buddha Road, Dharan||025-525555|
|Koshi Hospital||Government||Rangeli Road, Biratnagar||021-570103|
|Mechi Hospital||Government||Bhadrapur, Mechi||023-520172|
|Birat Medical College and Teaching Hospital||Private||Koshi Rajmarga, Biratnagar||021-421063|
|Provincial Public Health Laboratory 2||Government||Dhanusa||041-590267|
|Gajendra Narayan Singh Hospital||Government||Rajbiraj Road 3, Saptari||031-520155|
|Gaur Hospital||Government||Gaur, Rautahat||55-520091|
|Provincial Public Health Laboratory 5||Government||Bhairahawa||071-543978|
|Nepalgunj Medical College||Private||Kohalpur||081-540401|
|Gulmi COVID-19 Lab||Government||Gulmi|
|Rapti Academy of Health Sciences||Government||Ghorahi, Dang||082-5544253|
|Karnali Academy of Health Sciences||Government||Military Road, Karnali||087-520115|
|COVID-19 Testing Laboratory||Government||Dailekh|
|Seti Provincial Hospital||Government||Dhangadhi||091-525911|
|Dadeldhura Hospital Laboratory||Government||Dadeldhura||096-410372|
|Baitadi Hospital Laboratory||Government||Baitadi|
|Bajhang Hospital Laboratory||Government||Bajhang|
|Trishuli Hospital||Government||Trishuli, Nuwakot||010-560231|
PCR Test Home Service
Due to the lockdown in several parts of Nepal, people are forced to stay inside their houses. So, different organizations have come forward to provide home-based health services. Below is a list of health sectors that collects swab sample from the house and the insolation centers. They do tests and then give the report to the people. Besides these, few of them even provide online counseling to patients infected with the coronavirus and other health-related issures.
|Nirog Medical Care at Home||Sallaghari, Bhaktapur||9851071337,
|Srideep Diagnostic & Medical Center Pvt. Ltd||Balaju (near Bysdhara), Kathmandu||01-4357706
|MedEx Nursing||Thapathali, Kathmandu||9801865201
|People Home Care||Khumaltar, Lalitpur||9841452600
|Doc At Home||Anamnagar, Kathmandu||9813228343
|Himalayan Home Care & Nursing Agency||Chabahil, Kathmandu||9808126895
|Universal Health Services Nepal||Kathmandu Valley, Narayanghat||9801191917
|Salina Home Care & Research Center||Kathmandu Valley||9803989521
|Florence International Home Care||Putalisadak, Kathmandu||01-5902133
|Crystal Diagnostic Pvt. Ltd||Sinamangal, Kathmandu||01-4561021
PCR Vs Antigen Test
When it comes to the testing of the coronavirus, there are two main methods. Besides the PCR test, the other type is the antigen test. The antigen test is also known as the rapid test or the rapid antigen test.
Both of them are swab tests. However, there are few differences between these two tests. Some of them are stated below.
|Antigen Test (Rapid Test)||RT-PCR Test|
|Rapid Test is based on the analysis of the protein of the coronavirus.||RT-PCR Test is based on the analysis of the RNA (genetic material) of the coronavirus.|
|The test report will take not more than 30 mins.||The test report can take about 1 – 2 days.|
|It provides lower accuracy in comparison to that of the RT-PCR test.||It is considered a gold standard for measurement as it provides higher accuracy.|
|If the result of the test is negative but the person is symptomatic, then the person needs to do the RT-PCR test. If the result of the RT-PCR test is positive, then the person is considered to be a covid patient.||If the result of the test is positive, then the person is considered to be a covid patient.|
|It can be conducted easily at any place. For example, in vehicles, roads, etc.||You need to have sophisticated labs to carry out the test.|
|It is quite cheap||It is quite expensive|