Tag Archives: omicron

Rapid COVID test would be the key to end the pandemic?

The COVID pandemic might enter the late stage due to the low toxicity of new COVID variants, such as the Omicron variant. However, the omicron variant has high transmissibility than other variants. How could we stop the transmission and end the pandemic? Maybe a rapid COVID test could be the solution. Let’s understand why a quick COVID test would be essential.

There are two types of tests, diagnostic tests and antibody tests. Diagnostic tests are usually used to determine if we have an active COVID-19 infection. If tested for positive COVID, we need to take steps, potential treatment, and quarantine to isolate ourselves from others to prevent transmission. On the other hand, an antibody test is measured to determine the antibodies produced from the immune system in response to the COVID virus. It means that we could not use an antibody test to identify active COVID-19 infection. When should we get a COVID test? There are several conditions, you should do a COVID test, either molecular or antigen tests. 1. If you have any COVID symptoms, including fever or chills, cough, shortness of breath (difficulty breathing), fatigue, muscle or body aches, headache, loss of taste or smell, sore throat, congestion, or runny nose, nausea, or vomiting, diarrhea. Even you are fully vaccinated, you should have a COVID test. 2. If you have had close contact with someone who tested positive for COVID-19. The definition of close contact is to stay with a COVID-positive person within 6 feet for more than 15 minutes. 3. If you had any activities that might put you at high risk for COVID-19, such as traveling, attending a significant social event, crowded indoor gathering. Last, sometimes the workplace or school might establish a screening program to maintain a COVID-free environment. Depending on the program regulation, you might need to do the COVID test weekly.

Figure1, the real-time viral RNA replicates through reverse transcription-polymerase chain reaction (RT-PCR), and the cycle threshold (Ct) value is measured. When the Ct value is smaller, the higher the viral RNA is measured.

The diagnostic tests consist of molecular tests and antigen tests. The primary method is nucleic acid amplification tests (NAATs) in the molecular test. Its amplifying methods are divided into two groups, reverse transcription-polymerase chain reaction (RT-PCR), isothermal amplification including nicking endonuclease amplification reaction (NEAR), transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), clustered regularly interspaced short palindromic repeats (CRISPR), strand displacement amplification (SDA). Both amplifying methods measure the amount of viral RNA in the body, but the isothermal amplification method might shorten the time to get the Ct (cycle threshold) value. What is Ct value? In the RT-PCR, we used the fluorescent probe to measure the total amount of RNA in each cycle, and the number of cycles reaching the threshold is called the Ct value. In other words, when the Ct value is lower, there are more viral RNA to be detected. In current regulations, there is no standard for Ct value in NAATs. In general, the test result would be positive in COVID-19 viral RNA detection when the Ct value is between 35-40. This is why some people might receive a negative COVID test before the international flight but for a test positive after entering the U.S. On the other hands, the antigen test measures the protein from the virus to identify the infection. Usually, the antigen test is less sensitive to the COVID virus detection but has a shorter time to receive the result than NAATs. Here is the summary table to compare the NAATs and antigen tests:

Table1. Comparison between NAATs and antigen tests

The antigen test could provide a quick and cheap result to screen people who have a potential infection in a community, but it might need to repeat the test to confirm the result by NAAT. For example, in a community screening, we should use an antigen test as a rapid COVID test to quickly screen the people who might have contact with the COVID-19 virus. If a person does not have any symptoms of COVID-19, and the result of the antigen test shows positive, then this person needs to do additional NAAT to determine whether this person has COVID-19 or not. If a person has COVID symptoms, and the antigen test result shows negative, this person still needs a NAAT to confirm the infection. If the final result is positive in COVID-19, then quarantine would be required to stop the virus transmission. Also, if there is an outbreak in the community, serial testing should be done every 3-7 days until there are no new COVID-19 cases for 14 days.

Figure 2, the COVID-19 viral RNA accumulates in the infected body while the viral antigen also increases in the body for antigen test. The sensitivity of viral detection is higher by NAATs than antigen tests.

In sum, the COVID-19 pandemic might enter the late stage because the new variant shows a high transmission rate but less toxicity to humans, and what we need to do to prevent any recent outbreak from breaking down the medical system is frequent rapid COVID test to maintain a COVID-free environment. Then we could get back to our normal life soon.


  1. the U.S. Centers for Disease Control and Prevenetion, www.cdc.gov
  2. Paul Drain, Rapid Diagnostic Testing for SARS-CoV-2. N Engl J Med 2022; 386:264-272 DOI: 10.1056/NEJMcp2117115

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Omicron, BA.2 subvariant, is it the last variant in the pandemic?

Up to date, the COVID pandemic has not been ended due to the high contagious variant, omicron. The omicron variant has been found in four subvariants, BA.1, BA.1.1.529, BA.2, and BA.3 by World Health Organization (WHO). BA.1 is known as the original omicron variant, which was detected in most countries worldwide in early 2022; however, BA.1 is overtaken by BA.2 in Denmark, Nepal, Philippines, United Kingdom…etc. With the emergence of BA.2, BA.3 and Delta variants gradually disappear in most cases. Since researchers predicted that BA.2 will eventually become the dominant variant globally due to its higher transmission, what do we need to know about this subvariant?

Researchers have claimed that subvariant BA.2 is a stealth variant because, in BA.1 subvariant, it loses one of the three target genes we used in a standard PCR, but BA.2 does not. In other words, with a standard PCR test, if the expected result shows the absence of the particular gene, we could conclude that it is omicron, BA.1. But we could not find the same pattern in BA.2 and easily missed spotting this variant. That is why we call it a stealth variant. However, in my opinion, it is not invisible to us, and the only reason we cannot detect it is due to the wrong technique. Also, according to the evolution tree, BA.2 subvariant has been found on a different track than the original omicron subvariant, BA.1. Therefore, scientists have argued whether we need to set Omicron BA.2 as a new COVID variant.

On the other hand, in a report from Denmark, Omicron BA.2 has been found to have a higher transmission rate than BA.1 subvariant because of these different mutations. Additionally, BA.2 subvariant has been the dominant subvariant of COVID-19 in Denmark since January 2022. In the study, scientists collected the data to follow the spreading of Omicron variants within Danish households from December 2021 to January 2022. The result shows that the secondary transfection rates from infected people are 29% and 39% with Omicron BA.1 and BA.2, respectively. This means that BA.2 subvariant could be spread out more quickly than BA.1 subvariant and other COVID variants. In the study, BA.2 subvariant would have a higher possibility for breakthrough infection in fully vaccinated individuals and those with booster vaccination. Also, scientists found that the transmissibility of BA.2 from unvaccinated primary cases is increased when compared to BA.1. Fortunately, researchers did not observe the same pattern in vaccinated individuals. That is, although the BA.2 subvariant could infect fully vaccinated people with and without booster shots, these vaccinated people are less likely to spread the new COVID Omicron BA.2 subvariant. It seems that COVID vaccine could potentially stop the spread of Omicron BA.2 subvariant.

The cumulative COIVD-19 cases by date. The figure was adapted from Johns Hopkins University on 2/9/2022

In the original Omicron variant, BA.1, animal studies and clinical data have shown that BA.1 subvariant is less toxic to humans because it mainly accumulates in the upper respiratory tract and less in the lower respiratory and lung. It means more minor damage to the lung and a lower severity/death rate. And now we are curious that what about subvariant BA.2? Although we do not know the toxicity of BA.2 yet, in the current data, which claimed that Omicron subvariant BA.2 is likely to have the same severity rate as subvariant BA.1. Moreover, at the end of January 2022, Denmark decided to lift all the domestic COVID-19 related restrictions, including wearing masks, despite the increase in COIVD cases. This might indicate that although the omicron variant is more contagious, this virus no longer qualifies as a critical threat to the country with a high vaccination rate. More than 80% of the population has been fully vaccinated in Denmark, and over 60% have received the booster shot. This is excellent news to us to know that the end of the pandemic might be close. However, even though the Omicron variant has a lower severity rate, its high transmissibility might cause the crush of the medical system. For example, the new COVID cases by omicron variant since December 2021 has reached ~20% of the cumulative cases in the United States. This is an alarming number to me. Within 2 months, more than 20 million cases were reported in the United States, and these cases might break down the medical system. In sum, to end the pandemic, please wear a surgical mask (N95 or KN95 are even better.) and get COVID vaccine. With these, I believe that we could have our regular lives soon.


  1. Johns Hopkins University, Coronavirus resource center
  2. Meredith Wadman, Scienceinsider 2022 doi: 10.1126/science.ada0810
  3. UK Health Security Agency
  4. Frederik L. et al, “Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households”, medRxiv, doi: https://doi.org/10.1101/2022.01.28.22270044 

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COVID-19 and the variants

In December 31st 2019, first case of coronavirus disease 2019 (COVID-19) was reported to World Health Organization (WHO). On March 11th 2020, WHO declared COVID-19 a pandemic and US government declared COVID-19 a national emergency after 2 days. On December 31st, 2019, the first coronavirus disease 2019 (COVID-19) case was reported to the World Health Organization (WHO). On March 11th, 2020, WHO declared COVID-19 a pandemic, and the U.S. government declared COVID-19 a national emergency after 2 days. The COVID-19 is caused by a novel coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which emerged in December 2019 from Wuhan, China. COVID-19 might cause respiratory symptoms, such as fever, cough, shortness of breath, fatigue, body aches, and headaches. Some people might lose their taste or smell. Additionally, it might induce more severe diseases like SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome). Its transmission could be spread in three ways: First, an infected person could exhale tiny droplets and particles containing the virus. If another person is nearby within 6 feet, this healthy person might get the virus from these particles. Second, these small droplets and particles with the virus might land on the eyes, nose, or mouth through an infected person’s coughs or sneezes. Third, if your hand has a virus on it, and you use it to touch eyes, nose, or mouth, then you might get an infection. To protect ourselves and our family, wearing a medical-grade mask is an important step because the surgical mask constitutes an electrospinning fibers layer with static electricity to capture the virus. Moreover, keeping 6 feet distance from others might also lower the risk of getting an infection. The last way to protect ourselves from COVID-19 is vaccine administration. Up to date, there are three FDA-approved vaccines in the U.S., Moderna mRNA-based vaccine, Pfizer mRNA-based vaccine, and Johnson & Johnson adenovirus-based vaccine. These vaccines could effectively stimulate the immune response to allow our bodies to produce antibodies to fight coronavirus.

Interestingly, the name coronavirus is not named from Corona beers. It actually means crown structure because coronavirus has spike proteins on its capsid, and it looks like a crown. These spike proteins play an essential role not only in virus transmission but also in vaccine development. In the transmission process, the spike protein would bind to a typical protein receptor on the cell surface of human throat and lung cells, called ACE2 receptor (Figure 1), and fuse with human cells to transfect it. On the other hand, scientists have developed a COVID vaccine to produce antibodies to target the spike proteins. While the COVID virus has been widely spread, more and more variants appear with mutations in spike protein. For example, the Alpha variant of COVID-19 has ten mutations in the sequence of spike protein which could help the virus to bind to the human cell easier. Up to date, there are five significant variants that exit after pandemic: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). The Alpha variant was first found in the United Kingdom in September 2020. The Beta variant was discovered in South Africa in May 2020. The Gamma variant was documented in Brazil in November 2020. In 2021, Delta, the primary variant, was identified in India in October 2020. In 2022, the Delta variant was replaced by a higher infectious version, the Omicron variant, which occurred in multiple countries from November in 2021. At least 36 mutations were found in the omicron variant in the spike protein. These mutations might be the reason that omicron has become the most contagious variant in the world. Although the transmission rate of the omicron variant is higher than other variants, the toxicity/ damage to the lung is lower. In recent animal studies, scientists have discovered that the infection sites of the omicron variant would result mainly in the upper respiratory tract but less in lower respiratory and lung damages. This might imply that the pandemic would end soon because the trend of viral mutation would be a higher transmission rate but lower toxicity to humans.

Figure 1, The structure of coronavirus is constituted of single strand of RNA and envelop with spike protein which could bind to ACE2 receptor on human cells. Adapted from an image by Davian Ho for the Innovative Genomics Institute.

In sum, although the omicron variant might affect our daily lives, we could protect ourselves and our family by three methods described above, mask, 6 feet distance, and vaccine. If you have not received the COVID vaccine, please remember to get it, including a booster shot, to get full protection. With the oral pill from Pfizer (PAXLOVID) and Merck (molnupiravir), I believe the pandemic would end soon, and everyone could have a normal life again.


  1. U.S. Centers for Disease Control and Prevention https://www.cdc.gov
  2. Megan Scudellari, Nature 595, 640-644 (2021)
  3. Leung, N.H.L. Transmissibility and transmission of respiratory viruses. Nat Rev Microbiol19, 528–545 (2021). https://doi.org/10.1038/s41579-021-00535-6

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Jason(Yen-Chun) Lu, All right reserved.