Belagavi is at the number 3 position in the state for the number of COVID-19 positive patients in Karnataka with only Bengaluru and Mysuru above it.
As on date as many as results of 243 samples are awaited. That is a huge number and even after such a hike in the number of cases Belagavi does not have a COVID lab.
Now it has come to light that the Indian council of medical research has approved the use of the virology laboratory in the ICMR National Institute of Traditional medicine (NITM) in Nehru Nagar Belagavi as a COVID 19 testing laboratory and the officers in charge say testing of throat swab samples could begin in 2-3 days.
By Sunday the swab samples from Belagavi could be tested in Belagavi itself making it easy to get the results early. The list of Belagavi for the lab was visible on the ICMR website.
The new laboratory at the NITM will have a fully equipped laboratory to conduct the Reverse transcription-polymerase chain reaction (RT-PCR) tests to determine the presence of SARS- COV 2 virus that causes COVID 19.
A test for COVID19 uses a ‘reverse transcription-polymerase chain reaction’ (RT-PCR). The RNA in the sample is extracted and converted to DNA, which is then amplified using “primers”–short synthesized fragments of nucleic acid. A fluorescent dye (called a “probe”) is introduced, and the sample illuminates only in the presence of DNA.
Here’s how a COVID-19 test is conducted.
Step 1: Sample Collection
The specimen is collected through throat and nasal swabs, and inserted into a virus-transposing medium and sent to the lab.
Step 2: Extracting RNA
The genetic material in the coronavirus, which originates in animals, is an RNA–ribonucleic acid–and not DNA (deoxyribonucleic acid) like in humans. The next step is to separate the RNA from everything else in the sample–human cells, proteins, enzymes–that would chew up that viral genetic code. This is done using a centrifugal process by adding chemicals, where the RNA collects at the bottom of the sample. This process is also automated when large samples are to be tested.
Step 3: Conversion to DNA
The RT enzyme is used to convert the RNA into DNA–going from one strand to two. In order to set up this reaction, you need a “master mix”, which usually contains nucleotides (to make new DNA), taq DNA polymerase (an enzyme to amplify the DNA), PCR buffers (to create optimal conditions for taq DNA polymerase) and magnesium salts.
Step 4: Amplifying the DNA
Primers–short synthesised fragments of nucleic acid–are added to help define the area to be amplified. This mixture is then added to the PCR machine, which raises and decreases the temperature alternately for 15-20 seconds. In one cycle, temperature is raised to separate the DNA strand and cool it down. “Usually, [the temperature is raised to] between 55 and 60 deg C, and at this time, the primers will bind,” Ravi said. “The next step is to raise the temperature to 72 deg C at which the new strand will be synthesised. This whole thing is called one cycle. For RT-PCR, one has to do 40 such cycles and this approximately takes an hour, and each cycle is about one one-and-a-half minutes.”
Step 5: Results
Once enough DNA is produced in the PCR machine, it is ready to be detected. A fluorescent dye or ‘probe’ is added to the test-tube. If there is DNA present, it starts to glow. “As the number of copies of DNA increases, so does the amount of light emitted, Ravi said. “A special light-measuring instrument in the PCR machine reads these fluorescence patterns to determine which samples have the virus in them and which don’t.”
Step 6: Ensuring accuracy
Controls are introduced to ensure that the test is accurate. There is a positive control (a known COVID positive sample), a negative control (a known negative sample) and an internal control, which is usually a “housekeeping gene”–genes required for the maintenance of basic cellular function.
“Internal controls ensure whether the sample collection was done correctly,” Ravi said. “If the swab has not touched the throat properly, then you will not have human self-image. If this housekeeping gene does not come positive in the PCR, the test is not valid.”
“In one hour, PCR will be over and then the machine will figure out whether the required DNA has been amplified or not,” Ravi added. “Whenever you run a test, you need to know that it was working properly. You will have to have several controls. The purpose of control is to know that every process in the test is working.”