Tag Archives: vaccine

How do we make 2 successful COVID mRNA vaccines?


According to COVID data from World Health Organization (2022/02/28), total COVID cases have reached 400 million, and the COVID-induced death is close to 6 million people. On the bright sight, the COVID vaccines have been administered over 10 billion doses, and around 4 billion people are fully vaccinated now. Among the FDA-approved COVID vaccine, the primary modality is mRNA-based vaccines from Moderna or Pfizer/BNT. In February 2022, Moderna announced establishing subsidiaries in four Asian countries, including Taiwan, and planning to manufacture COVID vaccine and other mRNA-based drugs in Taiwan. What is the procedure to make an mRNA vaccine and mRNA-based drugs? Here I will explain how the lipid nanoparticles with mRNA are manufactured.

Figure 1, the mechanism of gene therpay: DNA transcripts into RNA which could translate into proteins in cells.

Mechanism of gene therapy

First, we need to know what mRNA is. In our cells, chromosomes composed of DNA and proteins in the nucleus control the gene expression by different DNA fragments. Additionally, the mechanism is that first, the DNA in the nucleus transcripts into messenger RNA (mRNA), and the mRNA would translate into protein to be expressed in the cells (Figure 1 ). Also, that’s why mRNA plays an essential role in molecular biology. To produce the mRNA, we would need a lot of DNA templates for in vitro transcription (IVT), and the easier way to collect a large number of DNA templates is to clone the desired DNA template into a plasmid and transforms it into E. coli, to use E. coli to grow and produce a lot of plasmids for IVT. After collecting the plasmids from E. coli, we would use enzymes to isolate the DNA template to make the RNA through IVT reactions. (Figure 2) The mRNA structure comprises the RNA coding region, untranslated region, capping, and poly-A tail. (Figure 3) Therefore, we need to add 5′ capping and 3′ poly-A tail to the IVT RNA before purification. The mRNA production is a simple reaction, but several essential elements affect the mRNA efficacy.

Key elements in IVT reaction

First, we need to add a T7 promoter in the DNA template because T7 RNA polymerase is required in the IVT. Second, the RNA coding region should be designed by codon-optimization to prevent the single-strand RNA from forming secondary structure to decrease the efficacy. Third, there is an untranslated region (UTR) on each side of the coding region. Although the UTR would not be translated into protein, these regions could affect the efficacy of mRNA in the cells. Additionally, a good UTR sequence could improve protein production in vitro and in vivo and alleviate the immune response triggered by the mRNA. In the biotech company, the UTR sequences are confidential because they could highly affect mRNA therapeutics’ efficacy. Last, the 5′ cap is also a crucial element in mRNA synthesis. In the COVID vaccine from Pfizer and Moderna, the capping system, CleanCapⓇ is from another mRNA biotech company, Trilink, to minimize the immune response in the body and increase the vaccine efficacy. Therefore, the whole production of mRNA is pretty complicated. I will prepare another blog to introduce the IVT reaction and the following procedure to produce mRNA.

Figure 2, scalable production of DNA template for in-vitro transcription (IVT) reactions.
Figure 3, The mRNA structure comprises the RNA coding region, untranslated region, capping, and poly-A tail.

Lipid nanoparticles production

Next, after purification of capped mRNA with polyA tail, we could mix the mRNA and lipid-like materials to manufacture the lipid nanoparticles (LNP). In the previous blog (introduction to gene therapy), I have introduced how cationic lipid-like materials form LNP under acidic conditions by electrostatic interaction. The critical factor in LNP production is mixing because well-mixing could allow the cationic materials and anionic nucleic acids to form a more compact structure and smaller nanoparticles. To make those mRNA-based LNP with less than 100 nanometers in diameter, we used a microfluidic device with a micromixer to better mix the organic phase (lipid-like materials) and aqueous phase (nucleic acids) by chaotic advection (Figure 4). The smaller size of LNP could prevent liver filtration after administration. Furthermore, another essential step is how we purify the LNP and remove the residuals during the process to minimize the side effects of the mRNA-based vaccine.

Figure 4, microfluidic device with micromixer is used to produce lipid nanoparticles with mRNA.


Although the whole process looks pretty simple, every step in manufacturing is critical to maintaining a safe and efficient vaccine. There is still a lot of work we could do in research to improve the mRNA therapeutics: How we design the coding sequences UTR sequences. How we develop a new capping system and nucleotides to alleviate immune response. Also, currently, all the FDA-approved mRNA-based vaccines are used non-degradable materials to deliver mRNA. Most scientists and biotech companies are working on new degradable materials in RNA therapeutics. Therefore, if you are interested in gene therapy, maybe you could consider contributing to the field of mRNA therapeutics.

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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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Antiviral pills for COVID-19

Up to date, there are two oral antiviral pills with FDA emergency use authorization, Paxlovid from Pfizer, Molnupiravir from Merck. With these drugs, I believe that the COVID pandemic could end soon. What are those drugs? How does it work to treat COVID?

On December 22nd, 2021, the U.S. FDA issued an emergency use authorization (EUA) for Pfizer antiviral pills. Paxlovid could treat mild to moderate COVID-19 in adults and pediatric patients who are older than 12 years old and more than 40 kg. Additionally, Paxlovid could be prescribed and taken within 5 days of symptom onset. However, Paxlovid could not be utilized for the pre-exposure or post-exposure prevention of COVID-19 or any treatment for severe COVID-19. In the clinical trial, the result shows that Paxlovid could significantly reduce the proportion of people with COVID-19 induced hospitalized or died by 88%. Since we have known that Paxlovid could effectively treat COVID-19 within 5 days of symptom starting, we are interested in how Paxlovid works to treat COVID. One Paxlovid consists of 2 tablets of nirmatrelvir and 1 tablet of ritonavir and the patient should take these twice a day for 5 days. (30 tablets in total for one treatment). Nirmatrelvir in Paxlovid could inhibit a COVID protein to stop the virus from replicating, and ritonavir could enhance the stability of nirmatrelvir and help it to maintain at a high concentration in the body. Its potential side effects are impaired sense of taste, diarrhea, high blood pressure, and muscle aches. Furthermore, Paxlovid might have a significant drug interaction with certain drugs, and it would lead to HIV-1 drug resistance for those people who have uncontrolled or undiagnosed HIV-1 infection. Last, due to the potential damage in the liver and kidney, Paxlovid is not recommended for patients with severe kidney or severe liver impairment.

One day later(12/23/2021), the U.S. FDA issued a EUA for Merck’s Molnupiravir to treat mild to moderate COVID-19 in adults. Additionally, similar to Paxlovid, Molnupiravir should be prescribed and taken within 5 days of symptom onset. One important thing for Molnupiravir is that it can not be taken for patients who are younger than 18 years old because Molnupiravir might affect bone and cartilage growth. The mechanism to treat COVID-19 is that Molmupiravir could introduce errors into the COVID virus’ genetic code to prevent the virus from replicating. In the clinical trial, the result indicates that with Molnupiravir only 6.8% of patients were hospitalized or died compared to 9.7% of patients who received placebo. The treatment of Molnupiravir is to orally take 4 capsules (200 milligrams) twice a day for 5 days. (40 capsules in total) Its potential side effects are diarrhea, nausea, and dizziness. Moreover, from animal studies, Molnupiravir has been found to potentially cause fetal harm in pregnant women. Therefore, this drug is not recommended for use during pregnancy.

In conclusion, both Paxlovid and Molnupiravir could effectively prevent hospitalization or death, but these antiviral drugs could not be a substitute for vaccination or a booster shot. Please receive an FDA-approved COVID-19 vaccine and booster shot to maintain enough immune protection from COVID-19 including the omicron variant.


  1. the U.S. Food and Drug Administration

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

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.

What engineers can do in biomedical field?

An engineer is trained to solve problems through science and math. We can see engineers everywhere in our lives, such as civil engineers, chemical engineers, electrical engineers, and software engineers, to improve our daily lives. What can engineers do in the biomedical field? A pioneer, professor Robert Langer, an internationally well-known biomedical engineer and inventor, is a perfect example illustrating how engineers can contribute to biomedical science. Dr. Langer holds the title of David H. Koch Institute Professor at the Massachusetts Institute of Technology (MIT) as well as that of Senior Lecturer on Surgery at Harvard University’s Medical School. It is worth to mention that being an Institute Professor at MIT is the highest honor that can be awarded to a faculty member. Besides, Dr. Langer has more than 1,500 published papers and over 1,400 issued patents and pending patents worldwide. In his research, he focuses on solving biomedical problems from an engineering aspect, such as developing materials for drug delivery, cell engineering, and tissue engineering. Here we have some examples to demonstrate how engineers contribute to the field.

First, Dr. Langer and his colleagues with Bill & Melinda Gates Foundation created pulsatile-release PLGA microspheres for single-injection vaccination1 for developing world. Poly (lactic-co-glycolic acid) (PLGA) is an FDA-approved degradable material for clinical application, and core-shell decoupled microspheres are fabricated by a new microfabrication method (StampEd Assembly of polymer Layers (SEAL))2. Despite the immense increase in vaccine coverage worldwide over decades, vaccine-preventable infectious diseases still claim the lives of approximately 1.5 million children every year because of inadequate distribution and administration of vaccines in the developing countries. Currently, around 19.4 million infants do not receive fully immunized against diphtheria, tetanus, and pertussis. Moreover, 6.6 million of them with one dose of the vaccine remain at risk for these diseases due to lack of full series of doses. With the pulsatile-release PLGA microspheres and SEAL technology, the problem of inadequate distribution and administration of vaccine could be solved, and millions of people in the developing world would benefit.

What engineers can do in biomedical field? 1

Fig. 1, Using different molecular weight of PLGA to control degradation time to release the therapeutics to evoke immune response. (modified from McHugh, K. J. et al. Science, 2017).

Second, Dr. Langer and his colleagues discovered three chemical materials which can suppress foreign body response to minimize fibrosis in rodents and at least 6 months in non-human primates3. These materials were conjugated to alginate hydrogel, and these hydrogel microspheres were transplanted in mice and monkeys. In addition, these anti-fibrotic materials could be applied in cell therapy, such as beta cell replacement treatment for type I diabetes. In type I diabetes, patients’ pancreatic islet cells are destroyed by their own immune system. To date, the most common treatment is a daily insulin injection to control blood glucose. However, insulin injection cannot cure type I diabetes or prevent the many devastating diseases associated with diabetes, such as blindness, hypertension, and kidney disease. Islet cell transplantation could provide an alternative treatment for type I diabetes to avoid daily injection and restore normoglycemia. However, foreign body response is a major challenge for cell therapy. The cellular and collagenous deposition would isolate the transplanted device from the host, which could induce tissue distortion, cut off the nourishment of encapsulated cells, and finally lead to device failure. With these new anti-fibrotic materials, the transplanted device with insulin-producing beta cells could maintain its function in the long term to cure type I diabetes.

What engineers can do in biomedical field? 2

Fig. 2, Three chemical materials can suppress foreign body response to minimize fibrosis in rodents and non-human primates. Encapsulated by these materials, the therapeutic cells can be protected from host immune system and also suppress its immune system to reduce foreign body response.

Third, Dr. Langer’s group developed a combinatorial library of ionizable lipid-like materials to identify mRNA delivery vehicles that facilitate mRNA delivery in vivo and provide potent and specific immune activation4. The cationic lipid-like materials could encapsulate therapeutic mRNA in lipid nanoparticles by electrostatic interaction. To date, mRNA therapeutics is a promising strategy for disease treatment and vaccination. In contrast to DNA therapeutics, mRNA delivery results in transient expression of encoded proteins, and so avoids complications associated with insertional mutagenesis. Currently, mRNA therapeutics, including disease treatment and vaccination, are in the process of clinical trials. For instance, TranslateBio has conducted phase ½ clinical trials in delivering mRNA encoding fully functional cystic fibrosis transmembrane conductance regulator (CFTR) protein to treat cystic fibrosis by nebulization. For COVID-19, Moderna (co-founded by Dr. Langer) and Pfizer all utilize lipid nanoparticles to deliver mRNA encoding for a prefusion stabilized form of spike protein. Moderna also has two mRNA cancer vaccines in phase 1 and phase 2 to target solid tumors and melanoma. These clinical trials with mRNA delivery are incorporated to cationic lipid-like materials to enhance mRNA stability and lead to an increase in intracellular protein expression.

What engineers can do in biomedical field? 3

Fig. 3, Illustration for the formulation of lipid nanoparticles in mRNA delivery

In sum, biomedical engineering is a combination of multiple disciplines, such as engineering, biology, medical science, and chemistry. To date, biomedical engineers have contributed to the biomedical field in different aspects, such as new materials, fabrication methods, and medical devices to improve current medical treatments and solve emerged medical problems, for instance, COVID-19.


1.        Guarecuco, R. et al. Immunogenicity of pulsatile-release PLGA microspheres for single-injection vaccination. Vaccine 36, 3161–3168 (2018).

2.        McHugh, K. J. et al. Fabrication of fillable microparticles and other complex 3D microstructures. Science (80-. ). 357, 1138 LP – 1142 (2017).

3.        Vegas, A. J. et al. Combinatorial hydrogel library enables identification of materials that mitigate the foreign body response in primates. Nat. Biotechnol. 34, 345 (2016).

4.        Miao, L. et al. Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation. Nat. Biotechnol. 37, 1174–1185 (2019).

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