Thursday, January 20, 2022

Rapid Test Hacking: Swabbing the Throat?

 Recently, there has been a twitter craze associated with using at-home rapid tests in a new way. While the tests are supposed to be used as nasal swabs, some people have become convinced that swabbing the throat is a better and more effective way to see if someone is positive for COVID. 

This article from NPR Goats & Soda ( discusses this phenomenon and whether it has any scientific merit. The authors discuss how in other countries, such as the UK and Canada, rapid tests are designed to swab the throat. Interestingly, this idea of throat swabbing is linked to the omicron variant specifically. 

This is because some researchers believe that unlike previous variants omicron replicates in the throat prior to replicating in the nose. This means, in theory, that someone could swab their nose and test negative but then swab their throat and test positive. This phenomenon appears to be backed by a study conducted in South Africa. For people with any other COVID variant, the throat swabs were only 71% effective at recognizing it while the nasal swabs recognized it every time. However, for the omicron variant, nasal swabs were 86% effective while throat swabs were 100% effective. 

However, there are some holes that I think it’s important to recognize in this research. The sample size of patients in this study was fairly small, with less than 400 people total. Furthermore, the study used PCR tests rather than the rapid antigen tests that people have been using at home in the United States. Finally, the NPR article states that the research has not undergone peer review, so it is difficult to say whether the methods and conclusions are sound. 

However, several individuals in the United States have tried to informally test whether throat swabs are more effective. One advocate for this approach is Micheal Mina, a former epidemiologist and immunologist at Harvard. Other health experts such as infectious diseases expert Jill Weatherhead of Baylor College says that this approach could just be producing a higher rate of false positives rather than a lower rate of false negatives. It is also important to note that the swab sticks are designed for use in the nostrils, so it may be dangerous for people to stick them down their throats (perhaps accidentally injuring their tonsils). As of right now, the FDA has warned against using the testing kits as throat swabs. 

-Sophia (from Week 2)

Monday, January 17, 2022


 One very interesting statistic, that was first noticed in France and surrounding European countries, is that there is a significant increase of flu infections that seems to follow the increase in COVID cases because of the Omicron variant. People are calling this a “Twindemic” because of this similarity between the rise in COVID cases and the rise in flu cases. This year’s version of flu has reached endemic levels in many cities in France and is at a pre-endemic level in many other parts of the country. One thing that the WHO is finding is that flu vaccination coverage for the flu variants this year are not as high as they would have hoped they would be this year, and this is likely the cause of this increase in cases. Furthermore, this strand of flu virus seems to be quite severe, already causing 72 severe cases of the flu with 6 deaths this year in France.

The reason people are concerned about this so called “Twindemic” is because it has been going on for quite a long time and doesn’t seem to be slowing down. Furthermore, it is spreading at a faster rate than was expected of the flu virus this year. The flu virus is very versatile, seeing as it changes and adapts consistently as people become immune to other strands. This makes creating a vaccine for it very difficult, and that is the reason a person has to get a new flu vaccine every single year. So, what I said earlier about how the vaccination coverage is low this year means that the vaccine that is being used, based off a prediction of what the flu virus would be like this year, is not as effective as one would hope. Since December of 2021, this flu strain seems to be very severe and very contagious and rising in cases alongside COVID-19 Omicron cases. Some people are saying this strand of the flu could lead to a very long flu season that leads all the way into the summertime.

-Lauren Burch

Tuesday, January 11, 2022

Study Says Previous Common Cold Coronavirus Infection Could Protect Against COVID-19

According to a study published Monday in Nature Communications, people who build up high levels of immune cells from previous coronaviruses that cause the common cold could have some protection against COVID-19. Human Coronavirus has several different types including common human coronaviruses: 229E (alpha coronavirus), NL63 (alpha coronavirus), OC43 (beta coronavirus) and HKU1 (beta coronavirus). Other types include MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS), SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS), and SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19)according to CDC: 

People around the world commonly get infected with human coronaviruses 229E, NL63, OC43, and HKU1. The researchers were curious about why some people exposed to SARS-CoV-2 don't necessarily get infected, and it turned out that these people have high concentration of T memory cells from previous coronavirus infection. The study found that T cells created from other coronaviruses can recognize SARS-CoV-2 and provide immune protection. This elicits new ways to generate universal vaccines that targets the common proteins shared by the coronaviruses family to protect against future variant infection. 

This also posts other questions: why do some of the coronaviruses non-pathogenic or only generate mild symptoms like a cold while others lead to severe respiratory disease? What are the differences between the different strains? Understanding the key determinant of the pathogenic coronavirus strains can also help with universal vaccine production. 

-- Wenqi Song 


Saturday, January 8, 2022

Are At-home Testing Kits Actually Reliable?

Coming back from winter break, everyone was required to immediately do an at-home antigen testing kit. It took 15 minutes and as soon as everyone got a negative result, we socialized mask-less like everything was normal. And this was great and all, but it got me wondering. How reliable are these at-home testing kits? Should we all be more cautious rather than immediately trust that everyone did the test correctly? Do we even know that this test can detect the new Omicron virus?

I recently found a post about this, on the Washington Post, saying at-home testing kits are very useful, however results are not always as accurate as you think. The kits are very useful in detecting a protein in the virus that causes COVID. Furthermore, it can detect the Omicron virus as well as other versions of COVID. However, because Omicron is a virus that primarily affects the upper respiratory tract, it would be more useful to use saliva to detect the virus rather than the typical nasal swab. Even with this, the FDA still recommend following the nasal swab instructions to have the most accuracy with the at-home testing. A PCR test using saliva, however, would still be the most accurate form of testing.

While at-home testing does have its perks, it also has its flaws. The at-home testing kit does not detect if you are still contagious on the last few days of infection. It also does not detect Omicron on the first few days of infection. So, while someone may get a negative test, they should treat it with caution if they have symptoms or came into contact with someone who tested positive. This means that the blind trust that my friends and I had with our at-home testing kits may have been a bit too fast to trust them, but we are all still negative, so perhaps there is some truth to them after all.

-Lauren Burch

Board, Editorial. “Opinion | Those Rapid at-Home Virus Tests Are Useful. but Look at Results with Caution.” The Washington Post, WP Company, 8 Jan. 2022,

Friday, January 7, 2022

CORBEVAX Subunit Vaccine Pioneered for COVID-19 in Low Income Countries

     This article in NPR Goats & Soda ( a new COVID-19 vaccine called CORBEVAX that is currently being manufactured for distribution in low and middle income countries such as India. CORBEVAX is not an mRNA vaccine, which makes it different from the Pfizer and Moderna COVID-19 vaccines that are very common in the United States.

    CORBEVAX is a subunit vaccine, which means that it uses proteins from the SARS-CoV-2 virus in order to mount an immune response. Other highly successful vaccines that make use of this technology are the Hepatitis B vaccine and the Human Papillomavirus (HPV) vaccine. 

    Interestingly, researchers Peter Hotez and Maria Elena Bottazzi from the Baylor College of Medicine began developing this vaccine during the first pandemic of SARS in the early 2000s. As we discussed in class, the global response to SARS was mounted very effectively, causing the outbreak to decline quickly. As a result, their vaccine was never tested. I thought this was really interesting, and I wonder how common it is that vaccines are created and then never tested/used because the spread of the virus decreases to such a large extent within the population. For instance, were U.S. scientists developing vaccines for the recent outbreaks of Zika/Ebola in case they ever spread rapidly through our country? Or do we tend to be more reactive than proactive, waiting to make vaccines until it’s almost too late?

    When the COVID-19 pandemic began, the scientists decided to see if they could use the same technology for SARS-CoV-2. Interestingly, though, the scientists said that no one wanted to fund or support their work because subunit vaccines were not as “innovative” as the mRNA vaccines that companies like Pfizer and Moderna were making. This statement confused me because I don’t understand why a vaccine technology would need to be “innovative” in order for people to want to support it. I would think that people would be more wary of novel vaccine technologies. As we learned in class, subunit vaccines for HPV and Hepatitis B are highly effective in preventing disease, so why would funders hesitate to support a technology that they know has worked well in the past? 

    Eventually, the researchers were able to test the vaccine. The vaccine has high efficacy (90%) against the original strain and almost as high efficacy for the delta variant (80%). Trials are currently underway to see whether it maintains this efficacy against omicron. One thing I learned from this article was that subunit vaccines are harder to modify than mRNA vaccines, which means that it is more difficult to adapt the vaccine technology when new strains of the virus become more common in the population. I think this lack of adaptability may pose a problem for combatting SARS-CoV-2, especially given how quickly new variants seem to be arriving. 

    One of the most important benefits of this vaccine, in my opinion, is its low cost. Each dose costs only about $1.50, which is much more accessible than the $15-20 per dose that the United States is currently paying for the Pfizer/Moderna vaccines. Furthermore, Hotez and Bottazzi have decided to allow any manufacturer to view the “recipe” for the vaccine, meaning that it can easily be manufactured worldwide. According to the NPR article, Pfizer and Moderna have not been transparent in this regard. I think the concept of intellectual property and patents when it comes to vaccines is really interesting, especially when thinking about who stands to benefit from the production and gatekeeping of these vaccines.

-Sophia Nesamoney

Codon Deoptimization As a Novel Way to Develop Live-attenuated Vaccines

I was listening to the podcast This Week in Virology and a very interesting episode caught my interest. The episode talks about a paper published by Dr. LuisMartínez-Sobrido's lab recently that focuses on developing a live-attenuated arenavirus vaccines using codon deoptimization method. Codon deoptimization is something that I've never heard of before but is really effective and meaningful in the field of vaccine development. Their work focuses on one of the arenaviruses - Lassa virus, the cause of Lassa fever, which currently doesn't have FDA approved vaccines. As we all know, many amino acids are coded by more than one codons. However, these codons don't have the same frequencies of being translated because all animals have a codon usage bias. Codon deoptimization is when all the preferred codons are replaced by non preferred codons, thus dramatically reducing the amount of proteins being made. By using codon deoptimization method, they made mutations in one of the nucleoproteins that plays an important part of virus life cycle and largely decreased the viral nucleoprotein translation, ultimately resulting in virus attenuation. 

I found this method really impressive and I think it is a promising way to generate more live-attenuated vaccines for other viruses. One concern mentioned by the paper is that codon deoptimization requires computer algorithms to design viral genomes with proper less preferred codons and the use of these new codons might result in different degrees of attenuation. Further improvement can be done in terms of generating consistent degrees of attenuation. 

Wenqi Song

Thursday, May 6, 2021

Waiving Vaccine Patents Way Too Late

    The Biden administration has surprisingly stated that they will advocate for a COVID-19 vaccine patent waiver. Given the “extraordinary circumstances of the COVID-19 pandemic” the administration plans to advocate for waiving vaccine patent protections. This comes at a time when case numbers are falling in the US but rapidly increasing in other countries like India. The proposal to waive patent protections was drafted by India and South Africa and was backed by many congressional Democrats. According to the US trade representative Katherine Tai, “This is a global health crisis, and the extraordinary circumstances of the Covid-19 pandemic call for extraordinary measures. The administration believes strongly in intellectual property protections, but in service of ending this pandemic, supports the waiver of those protections for Covid-19 vaccines.” Apparently, this news meant that shares for Pfizer and Moderna are plummeting in an all too predictable fashion. 

This news is both surprising and unsurprising to me. Surprising because I wouldn’t expect the US, a country run on a fundamentally capitalist system, to ever support something like this. This country was built upon privatization and profit-driven systems, often without care or concern for the ethics of money making. Vaccine distribution thus far has just been another example of this- even though the vaccines have been developed at a speed unknown to mankind and the power of science could not be more evident at a time when humanity needs it most, the distribution of the vaccine has been so limited because of the inefficiency and cruelty that a capitalist system brings. I’m unsurprised, however, because this backing of the waiving of vaccine patents should have been done long ago. This action to waive intellectual property rights could greatly bolster production and distribution of vaccines, especially to areas where vaccination rates are really low like countries that are poor and under-resourced. If this had been done before vaccines had even come out, perhaps the US could have been vaccinated much faster, and perhaps other countries around the world would have experienced a much more equitable distribution of vaccine supplies. 

-Komal Kumar, 5/03/21