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PCR Test- Price, Procedure, Result and Analysis for Covid

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.

2. Extraction

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.

PCR Steps

The RT- PCR machine will carry out the following steps for the analysis of the virus.

1. Denaturation

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. )

2. Annealing

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.

3. Extension

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.

Positive

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.

Negative

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.

Health Sectors Government/Private Address Contact
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
Narayani Hospital Government Birgunj 051-521993
Gajendra Narayan Singh Hospital Government Rajbiraj Road 3, Saptari 031-520155
Bardibas Hospital Government Bardibas 044-550597
Gaur Hospital Government Gaur, Rautahat 55-520091
Provincial Public Health Laboratory 5 Government Bhairahawa 071-543978
Bheri Hospital Government Nepalgunj 081-520120
Nepalgunj Medical College Private Kohalpur 081-540401
Gulmi COVID-19 Lab Government Gulmi
Rapti Academy of Health Sciences Government Ghorahi, Dang  082-5544253
Province Hospital Government Surkhet 083-520200
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
 Doti Hospital Government Doti
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.

Health Centers Address Contact
Nirog Medical Care at Home Sallaghari, Bhaktapur 9851071337,

9851143704

Srideep Diagnostic & Medical Center Pvt. Ltd Balaju (near Bysdhara), Kathmandu 01-4357706

9849913719

Luniva Care Kathmandu 9841307041

9847694499

MedEx Nursing Thapathali, Kathmandu 9801865201

01-4101765

People Home Care Khumaltar, Lalitpur 9841452600

9818731766

Doc At Home Anamnagar, Kathmandu 9813228343

9801846558

Himalayan Home Care & Nursing Agency Chabahil, Kathmandu 9808126895

9801048950

01-4493206

 

Universal Health Services Nepal Kathmandu Valley, Narayanghat 9801191917

9801191915

Salina Home Care & Research Center Kathmandu Valley 9803989521

9860497366

9823010006

Florence International Home Care Putalisadak, Kathmandu 01-5902133

9822975307

Crystal Diagnostic Pvt. Ltd Sinamangal, Kathmandu 01-4561021

01-4561020

01-4561030

9802301020

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

 

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