the westminster news
Published by the students of Westminster School
By Kimi Weng ‘24
SARS-CoV-2, also known as COVID-19, is a virus that has been going around the world for almost three years following its first appearance in Wuhan China in 2019. This virus has troubled people’s lives, including the Martlets': at the beginning of last year, all students at Westminster had to obtain a negative PCR test result to be on campus. However, have you ever wondered what a COVID PCR is?
PCR stands for Polymerase Chain Reaction, a method that is widely used in Molecular Biology for amplifying a target sequence of DNA, and it is often used in areas like forensics and medical science. The process of PCR is like doing a “Ctrl + F” to look for a sentence in an enormous document, then “Ctrl + C” and “Ctrl + V” to produce millions of copies of that same sentence.
There are two types of PCRs: PCR and qPCR. PCR is an endpoint qualitative reaction that is analyzed using gel electrophoresis to separate fragments based on their size and charge. However, the type of PCR that is most frequently used to test for COVID is called qPCR, which stands for quantitative PCR. qPCR is more efficient than PCR because it does not require gel electrophoresis. It uses mainly two fluorescents, SYBR Green or Taqman probe, to show results instead. Higher fluorescence indicates higher copies of target sequences.
COVID-19 is a non-living virus that infects humans by binding and entering cells. It sends its viral genetic information in the form of RNA and instructs the cells to produce more viruses. According to the Centers for Disease Control and Prevention (CDC), “symptoms may appear 2-14 days after exposure to the virus”. PCR helps identify infections after exposure and before the symptoms by amplifying the virus. Since the genetic material of the COVID virus is in the form of RNA and PCR only targets DNA, we use reverse transcription first to change RNA to DNA. Therefore, the PCR conducted for COVID is called RT-qPCR, Reverse-transcription quantitative PCR. Every time you do a COVID PCR, a nasal swab is required to collect your genetic material to run the RT-qPCR in a laboratory.
But how do you know if you are positive or negative? The qPCR machines in the laboratory will monitor the intensity of fluorescence in the PCR tubes and produce graphs as below. The presence of fluorescence indicates that there is a presence of COVID. The “Ct” in the graph stands for cycle threshold, which indicates the first time fluorescence is observed. The lower the Ct means more target copies are present, which means that the patient is more heavily infected with COVID, thus a positive result is concluded.
COVID PCR only targets and amplifies around 20 base pairs (letters of A, T, C, and G in DNA) among 3,300,000,000 base pairs in a single human genome. For example, one of the sequences that the World Health Organization published for COVID PCR is 17 base pairs long: ATGAGCTTAGTCCTGTTG. But the actual process of amplifying the target sequence of DNA is more complicated than just finding those base pairs. PCR contains three steps:
To more readily detect the target sequences, the denaturation-annealing-extension cycle would usually be repeated 35 to 40 times. This entire process would take about an hour, resulting in millions of copies of the target DNA sequences.
In China, There are small stations on the streets and in neighborhoods to perform PCR tests. They put 10 swabs in the same PCR tube to maximize efficiency while maintaining the accuracy of the test. All citizens have to have negative COVID PCR test results within 72 hours, and sometimes 48 hours, to enter public areas like restaurants and stores. They would receive a “green QR code” on their phone about 5 hours after the swab, the code indicating their negative PCR result. If the PCR result comes out positive, they will test the 10 people, whose samples were in the tube, one-by-one to find the infected person. With more than 1.4 billion people in China and with such efficiency, there are more than one million COVID PCRs conducted every hour.
According to the World Health Organization Director-General Tedros Adhanom Ghebreyesus, “We are much closer to being able to say that the emergency phase of the pandemic is over — but we're not there yet.” We should not disregard the existence of the virus, and have it catch us off guard, but we should also not stress too much over its existence, and let it impede us from living our meaningful lives.
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Protocol: Real-time RT-PCR assays for the detection of SARS-COV-2 ... (n.d.). Retrieved December 4, 2022, from https://www.who.int/docs/default-source/coronaviruse/real-time-rt-pcr-assays-for-the-detection-of-sars-cov-2-institut-pasteur-paris.pdf?sfvrsn=3662fcb6_2
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Stewart, D. (2021). Pcr illustration of amplification curves. What is qPCR? photograph, Lexa Gene. Retrieved December 4, 2022, from https://lexagene.com/product-info/what-is-qpcr/
 qPCR is also called RT (Real-time) PCR, so RT-qPCR is also called RT (Reverse-transcription) RT (Real-time) PCR