What exactly is a nucleic acid test? Can you detect when the virus mutates?

With the OUTBREAK of COVID-19, “nucleic acid testing” is coming into view.
How does this work?
Why is there a certain probability of error?
Is there a better way to detect a mutating virus?

Recently, Yin Ye, CEO of BGI, said, “In the future, infection detection technology will focus on more accurate, faster, cheaper and more convenient development.”

Bvu staff analyzes virus samples

Fluorescent labeling makes viruses’ visible ‘

Nucleic acid tests look for traces of the virus that leave behind when it is in the body to tell if there is an infection.

Nucleic acids, of which deoxyribonucleic acid (DNA) is the genetic material of almost all living things, and ribonucleic acid (RNA) is the genetic material of many coronaviruses, are a necessary component of known life on Earth.
A viral nucleic acid test looks for viral RNA in a sample.

Its outer layer is the envelope and protein, and inside is its genetic material, RNA (image from the Web)

“The kit developed by BVU this time is a fluorescent RT-PCR nucleic acid detection method.”
Yin ye said.

The specific process is that the samples collected from the respiratory tract are strictly sealed and sent to the laboratory, where the nucleic acid extraction reagent is added by professionals and equipment to release the RNA of the virus.

The second step is to use a substance called “reverse transcriptase” in the kit to “reverse” the virus RNA into a specific DNA, and with the help of some special substances in the kit, this specific DNA amplification (PCR).
At the same time of amplification, the fluorescent probe in the kit is “activated” to release the fluorescent signal.
Each time the specific DNA is amplified, the fluorescence signal increases a little.
A PCR detector records the process.

Under normal circumstances, if there is a novel Coronavirus in the sample, the value recorded by the detector will show an gradually increasing S-shaped curve, i.e. the test result is positive.

Virus detection in the past life

Thousands of years of research have been carried out to find the hidden virus in the body, and nucleic acid tests for the virus now go deep into the molecular level.
This novel Coronavirus detection is also the first large-scale use of molecular biology technology to combat newly discovered pathogens in human history.

The human eye can only see objects larger than 0.1 mm in diameter, while most viral microbes are at most one-fiftieth of that size, so ancient doctors could only diagnose by “looking, listening, asking and cutting”.

In 1670, The Dutch scientist Leeuwenhoek improved the microscope, tiny organisms into people’s field of vision, the detection of pathogens also developed.
In the 19th century, The German bacteriologist Charles Koch suggested that if the same microorganisms could be found in the bodies of patients with the same infectious diseases, they could be extracted and cultured to help determine the pathogen of such diseases.
Since then, methods such as smear staining of pathogen samples have appeared successively.

With the deepening of the research on immune mechanism, a variety of immune detection techniques have been developed in accordance with the principles of anti-epidemic and specific combination of antigen in immunology.
The fluorescent probe is one of them.

“We have developed a novel coronavirus specific probe so that if the probe can be matched with the nucleic acid of the sample to be tested, the signal of the marker can be observed, thus proving the existence of a novel Coronavirus.”
Yin ye said.

However, sometimes it is difficult to detect the virus because the nucleic acid level in the patient’s body is too low.
“So ‘amplification’ becomes a key step in detection.
If the viral nucleic acid degrades from sampling to testing, or if too much RNA is lost, ‘false-negative’ results are also likely.”
Yin ye said.

What if the virus keeps mutating

One of the reasons infectious diseases are so dangerous is that viruses constantly mutate and form new diseases.
Covid-19, for example, is poorly understood, so there is a lack of sophisticated prevention and treatment in the early stages of infection, and it is difficult even to diagnose its pathogen.

“At this point, mNGS technology can be used to help quickly diagnose and define the pathogen of infection, and timely carry out accurate treatment for patients.”
Yin ye said.

MNGS, also known as pathogen metagenomic sequencing, is another detection technology for viral RNA in addition to real-time fluorescent RT-PCR.
When used for novel Coronavirus detection, PCR results are faster, while mNGS takes 24-72 hours, so it is less used.

When using mNGS detection, it is necessary to grasp the gene sequence of the virus and then analyze it through sequencing instruments.
Infection can be confirmed when the virus gene sequence detected in the sample is highly homologous with the novel Coronavirus sequence.
It is worth mentioning that, unlike the FLUORESCENT probe used for PCR, mNGS detection can detect multiple viruses simultaneously.

This method can be used in the diagnosis of emerging diseases.
“In 2017, a Filipino sailor suffered from consciousness disorder and other symptoms in tangshan port. The hospital and BGI used mNGS technology and detected mycobacterium tuberculosis in the cerebrospinal fluid sample of the patient within 30 hours, proving that the patient was infected with tuberculous meningitis.”
Yin ye Shared.

“Molecular diagnostic techniques such as mNGS, particularly the cost of sequencing technology to further reduce and further improve the detection speed and performance, and complex pathogen diagnosis will also no longer difficult, human perception of microbes will be more comprehensive, more clear,” Yin Ye said that “age of infection, infection disease of precision medical comprehensive coming.”

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