BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: #rapidtest

A “CRISPR” Way to Test for Melioidosis

By

On March 23, 2024

In Student Post

Melioidosis is a deadly tropical disease that flies under the radar. Around 150-200 thousand people get it every year, and more than half of people diagnosed die. One of the largest problems of this disease is that it takes several days to diagnose, meaning it takes several days for patients to receive the correct treatments. However, a new test, using CRISPR, could change that.

A new test has been invented that uses CRISPR to detect a genetic target that is specific to Burkholderia pseudomallei, which is the bacteria that causes meliondosis. The new test can detect the gene with almost a 94% sensitivity. It was developed by researchers at the Mahidol-Oxford Tropical Medicine Research Unit, Chiang Mai University, Vidyasirimedhi Institute of Science and Technology in Thailand, and the Wellcome Sanger Institute in the UK. The results of this new CRISPR test mean that thousands of people could be saved annually from meliondosis, with an easy to use rapid test.

The disease is caused by Burkholderia pseudomallei, which is found in water and soil of sub tropical and tropical regions. It enters the body through cuts on the skin, ingestion, or inhalation. One of the reasons it’s difficult to diagnose is that the symptoms range from pneumonia to those of a chronic infection. This, paired with the fact its more common in rural areas, causes this disease to be under reported.

Currently, melioidosis is diagnosed in patients after bacterial samples are cultured, which takes three to four days. But, in Thailand, 40% of patients die after just a couple days while waiting for the tests to come back. Currently, there is no vaccine for this disease, but it can be treated with an antibiotic such as carbapenem. However, due to the range of the symptoms, many other and or wrong antibiotics are prescribed, which wastes time and money.

To develop a new test, researchers identified a genetic target specific to B. pseudomallei by analyzing over 3,000 B. pseudomalleigenomes. Their new test called CRISPR-BP34, ruptures bacterial cells and using a recombinase polymerase amplification reaction to amplify the bacterial target DNA for increased sensitivity. In addition to this, a CRISPR reaction is used to provide specifics. The researchers collected samples from about 100 people with the disease and 200 without, in order to test the legitimacy of the test. The new test got results in just four hours and enhanced the sensitivity from about 66% to almost 94%.

This relates to our study of the immune system in AP Biology. As we’ve learned in Biology, first macrophages and neutrophils are the first responders, and they attempt to engulf and destroy the disease. The helper T-cells try and coordinate the response while killer T-cells are attempting to destroy the disease. And cytokines signal molecules to come help defeat the disease. While these attempts by our body is unsuccessful more often than not, it still displays the immune system response learned in AP Biology.

This new test will help save thousands of lives by making diagnoses faster, which will allow the correct treatment to be given in hours, instead of days. This is truly a groundbreaking invention.

Where else do you think CRISPR can be used?

Had you ever heard of Melioidosis before?

Why do you think there is such a large range of symptoms for Melioidosis?Melioidosis world map distribution

Testing!

By

On January 10, 2021

In Student Post

When you hear the word “COVID -19 testing” what comes to mind? I have this vivid image of a cotton swab being pushed up my nose. But what exactly is testing? Why is it so important? And what are the types of testing available for our use?

We’ve all heard that testing is important but why? To summarize a supplementary article, COVID testing “leads to quick identification of cases, quick treatment for those people and immediate isolation to prevent spread” (Dr. Eduardo Sanchez). When discovered at an early stage, COVID will be less a threat to a person because doctors can plan accordingly while COVID is still less severe. Even when a person discovers they have COVID not as early as hoped, testing helps to identify anyone who came into contact with infected people so they too can be quickly treated. Contact tracing would not be possible without testing because a person would never know if they are spreading the virus. The only way to be better safe than sorry is to get tested. Someone may show symptoms that are COVID-like but there is still a chance that it could be a common cold, or allergies. It is important to confirm COVID suspicion.

Now that we know why testing is important, what kind of testing is out there? What I found in this FDA article is what I like to call a family of tests; there are numerous different tests to take.

To start things off, let’s talk about Diagnostic testing. Diagnostic testing shows if you have an active coronavirus infection. As of right now, there are two types of diagnostic tests: molecular and antigen tests. Molecular tests detect the virus’ genetic material in a sample from the patient’s nose or throat. This is where test results will take longer because they are sent to labs. From there, the lab essentially converts the virus’s RNA into DNA, and then make millions of copies of the DNA to be processed in a machine. The test is “positive” for infection with SARS-CoV-2, the virus that causes COVID-19. Examples of molecular diagnostic tests include nucleic acid amplification test (NAAT), RT-PCR test, and the LAMP test. Next, there is Antigen diagnostic testing. Antigen tests provide results from an active coronavirus infection faster than molecular tests. The downside to these tests are that they have a higher chance of missing an active infection. Sometimes an antigen test may come back negative, but a doctor might still order a molecular test to confirm.

Different from Diagnostic Tests, there are Antibody (different from Antigen) tests. These tests looks for antibodies that are made by your immune system in response to a threat, such as a specific virus. As we learned in biology class, antibodies can help fight infections. These tests are taken by finger stick or blood draw, and the results are quick. The antibody test only shows if you’ve been infected by coronavirus in the past. But do antibodies help diagnose COVID-19? As we learned in class about the Immune System, our body can fight pathogens, bacteria, and viruses that we have been previously exposed to. While this was a popular belief earlier on in the year, sadly, researchers do not know if the presence of antibodies means that you are immune to COVID-19 in the future. It is possible to contract COVID-19 for a second time, therefore adaptive immunity does not apply.

The most common testing that I knew of before researching was rapid testing. Rapid testing can be both a molecular or antigen diagnostic; a doctor uses a mucus sample from the nose or throat. The test can also be taken at home only by prescription of a doctor. The results are available in minutes. There is also saliva testing where a person can spit into a tube; this also keeps the doctor or worker safer from the potentially infected person.

Testing is the best way to keep yourself and those around you safe. While testing is still not 100% accurate, there is currently no better way to confirm if someone has COVID-19 unless he/she get tested. With this pandemic, we can never be too safe!

 

 

 

 

 

Could Rapid Testing Be the Key to Beating COVID-19?

By

On January 2, 2021

In Student Post

A study published by University of Colorado Boulder and Harvard University researchers, states that rapid tests could help the world come close to eliminating COVID-19. The study focused on whether sensitivity of the tests, or turnaround times of getting the results is more important. By using mathematical formulas, different scenarios and three locations (a 10,000 person population, a university setting and in a large city) they came to conclude that when trying to slow the spread, frequency of testing and turnaround time is more important than the sensitivity of the test.

It is important to note the difference between the PCR test and the rapid antigen test. A PCR test, which uses polymerase chain reaction technology (hence the name) to detect traces of the virus’ genetic material. A rapid antigen test does not trace the genetic material but instead looks for specific proteins on the surface of the virus, known as antigens. A PCR test can detect one SARS-CoV-2 RNA molecule for a positive test result, the rapid antigen test needs thousands of virus particles for a positive test result. An antigen is present on the outside of a pathogen. In adaptive response to pathogens, dendritic cells place these antigens on display. The antigens are what allows the T-helper cells to recognize the antigen and trigger the cell mediated and humoral response. Therefore, if your body is fighting against COVID-19, the antigens would be displayed on cells and the rapid test may recognize them.

In one of the scenarios a large city had widespread rapid testing two times a week and they reduced the infections by 80% compared to widespread PCR testing done two times a week that only reduced infection by 58%. This scenario shows that because two thirds of infected people do not show symptoms as they wait for their results they are not quarantining. If people receive the positive tests results sooner, they can self-isolate sooner.

People have felt hesitant about rapid testing since it is less accurate than PCR testing and may miss cases where levels of infected particles are too low. However, it has been shown that there is a short time period where PCR testing will show a positive, and rapid tests won’t. This is because infected particles can go from 5,000 to 1 million in less than 24 hours. During this short window of time it is also likely that the patient is not contagious yet. 

Personally, I think that having more accessible rapid tests will be a huge help to curbing the virus. Even with less sensitivity, if a person tests positive then they self-isolate up to up to 48 hours quicker, if tests results take longer, then even more. This means that less people will get infected. I know that when family members have gotten tested, especially in the beginning of the pandemic, tests took 5 days when the labs were backed up. If they had not been properly quarantined during the 5 days, this could pose a danger to others. Therefore, I think that the accuracy can be put aside for the speed of the test results.

So, what do you think? Is rapid testing the inexpensive, fast, key piece to curbing the infection rate, or is the accuracy of tests more important?

Archives

Powered by WordPress & Theme by Anders Norén

Skip to toolbar