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Drug-resistant SARS-CoV-2 variants found in immunocompromised patients

Individuals with compromised immunity and persistent COVID-19 infections can harbor drug-resistant variants of the SARS-CoV-2 virus, which have the potential to spread to the general population found researchers at Weill Cornell Medicine, the College of Veteri

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Individuals with compromised immunity and persistent COVID-19 infections can harbor drug-resistant variants of the SARS-CoV-2 virus, which have the potential to spread to the general population found researchers at Weill Cornell Medicine, the College of Veterinary Medicine at Cornell University and the National Institutes of Health's (NIH) National Institute of Allergy and Infectious Diseases (NIAID).

In the study, published Sept. 18 in Nature Communications, researchers isolated drug-resistant strains of SARS-CoV-2 from people who had not cleared the virus after two to three months of infection and treatments with antiviral drugs.

One variant showed resistance to antivirals Paxlovid and remdesivir while another strain had mutations associated with a decreased sensitivity to remdesivir and a third antiviral drug, the monoclonal antibody sotrovimab.

The risk in emerging mutations is the possibility of transmitting these new resistant variants to the general population with fewer viable treatment options available. We have to come up with better treatments for immunocompromised patients and consider investigating combinations of therapies." Dr. Mirella Salvatore, study's co-senior author, associate professor of medicine at Weill Cornell Medicine and infectious disease physician at NewYork-Presbyterian/Weill Cornell Medical Center

Dr. Elodie Ghedin, senior investigator and chief of the Systems Genomics Section in NIAID, is co-senior author. Dr. Mohammed Nooruzzaman, research associate in the Diel Lab at the College of Veterinary Medicine at Cornell University, and Katherine Johnson, senior bioanalyst contractor in NIAID, are co-first authors.

Unique challenges in treating persistent COVID infections

While people with working immune systems can typically clear SARS-CoV-2 within days, those who are immunocompromised may continue to harbor and shed the virus for longer, even without symptoms. They also often receive multiple antiviral treatments over time, which may lead to the emergence of drug-resistant variants.

To understand the rise of antiviral drug resistance, the researchers focused on 15 individuals with compromised immune systems who received remdesivir, and in some cases, nirmatrelvir-ritonavir (Paxlovid). They found nine patients had developed virus variants with mutations to the nsp12 protein that is the target of remdesivir and four had viruses with mutations to the nsp5 protein, the target of Paxlovid. These mutations helped the virus persist despite common antiviral treatments.

One person had a virus resistant to both drugs. "For the first time, we isolated virus from a patient's nose 77 days after disease onset that was resistant to Paxlovid and also to remdesivir," Dr. Salvatore said. "It is concerning that some of these patients may have viable virus in their nasal secretions so far into the disease."

Combination therapies may be the answer

The researchers found that when they grew the isolated virus in lab cell cultures, two drugs simultaneously were effective in clearing the drug-resistant strain. "These findings indicate that combination therapy may be a better option to treat COVID-19 in highly vulnerable immunocompromised patients," said co-senior author Dr. Diego Diel, associate professor of population medicine and diagnostic sciences with the College of Veterinary Medicine at Cornell University.

The researchers also found that the resistant strain replicated as well as the original SARS-CoV-2 virus in cell culture. Next, using a preclinical model, they tested whether the virus could spread through contact. They discovered this variant was as transmissible as the wildtype virus without the mutations.

It is generally assumed that when a virus acquires drug-resistance mutations, it loses some of its fitness, meaning it may not replicate or transmit from person to person as well—this study shows that isn't the case. The authors will further investigate how mutations associated with therapeutics impact the virus's ability to thrive and spread.

This research highlights the importance of including cohorts of immunocompromised COVID-19 patients when evaluating the efficacy of antivirals. "When the virus has more time to evolve in a host who does not clear the infection early, therapeutic strategies will need to be reassessed," said the authors.

This work was funded in part by NIAID grant R01AI166791-01, by the Division of Intramural Research of the NIAID/NIH and the National Center for Advancing Translational Science of the NIH grant UL1TR002384.

Nooruzzaman, M., et al. (2024). Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. Nature Communications. doi.org/10.1038/s41467-024-51924-3.

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Related questions

01Please can you give an overview of the current drug discovery paradigm? In what ways do you think it needs to be leaner?

With the current drug discovery paradigm, it takes up to 15 years to translate an idea, such as hypothesizing a certain protein is important in a disease and testing this with targeting the protein with a drug, all the way through to proof of concept. The drug has to be filed with the regulatory authorities, having done all the safety and efficacy testing. It's a long process and it's also very costly. Estimates vary, but it's currently reckoned to cost over 1 billion dollars per drug. That’s partly because you have to pay for all the drugs that didn't make it. By the time you've taken a protein target and you've made a whole load of molecules that affect that target in the way you want them to, you've probably already spent a couple of years on it and then you have to take the best molecule through the appropriate safety testing in animals before proceeding to phase 1 testing in people. Even if you get to phase 1 testing, where you are just giving it to human volunteers for the first time, not even patients, about 95% of the compounds at the stage then fail to make it all the way through to the market. So, you’ve only got a 5% success rate. The odds are not good and, essentially, it is why so many companies have had to merge because, over time, this is becoming less and less sustainable as a business model.

Source: www.news-medical.net ↗
02There is considerable excitement around AI in drug development. Where do you see the largest gap between hype and reality, and where is AI perhaps underappreciated?

AI is moving so quickly that in the gap between answering this and publication, I could be proved wrong! With that caveat, there is a lot of hype around AI drug discovery campaigns. AI is certainly a substantial part of many discovery programs today and has been applied in drug discovery for many years. However, we need to be realistic about what AI is doing, where humans remain central, and how that balance may vary. AI agents are an area that has emerged relatively recently and continues to evolve quickly. They can complete tasks for example data extraction and reporting with guidance from experts, helping to generate larger, more standardized datasets over time. They can also help build closed-loop systems that connect computation and experiment directly, with strategic direction still coming from expert scientists. However, care and oversight is needed with these systems to validate their actions. I also think people often equate AI with generative AI, but there are many other AI systems which are underappreciated. For example, the GNN property prediction models and task-specific predictive tools we discussed earlier can be extremely valuable. Some of these methods receive less attention simply because they have already become familiar in drug discovery.

Source: www.news-medical.net ↗
03What comes next?

We are now testing the drug in patients with earlier-stage pancreatic cancer, prescribing it while their tumors are still operable and before their cancer spreads.

Source: www.news-medical.net ↗
04How does vitamin D strengthen the immune system?

More specifically, the study showed that the female patient produced very few cathelicidins, which is a natural toxin found in the immune cells of the lungs needed to fight tuberculosis. In most people infected by tuberculosis, tuberculosis bacteria attack the immune cells of the lungs. The immune cells fight the bacteria by eating them. But the tuberculosis bacterium has developed various evasive mechanisms that reduce the immune cells’ ability to digest and thus to kill the Mtb. “You could say that the tuberculosis bacterium has developed a way to lull the immune cells to sleep. This enables the disease the hide inside the immune cells, making it invisible to other parts of the immune system,” Martin Kongsbak-Wismann explains. This is where vitamin D enters the picture. Because vitamin D is able to counteract the soporific effect of the tuberculosis bacteria by making the immune cells produce more of the cathelicidin toxin. “Cathelicidin is like a microscopic needle that is able to pierce the tuberculosis bacteria. And when it does, it weakens the bacteria’s soporific effect on the immune cells. This restores the immune cells’ ability to kill tuberculosis bacteria,” says Martin Kongsbak-Wismann and adds: “We were amazed by the effect of vitamin D. In immune cells from healthy control subjects, vitamin D improved the cells’ ability to fight Mtb, whereas in the female patient’s immune cells we saw no response to vitamin D. This shows that vitamin D is key to the immune system’s ability to fight Mtb and prevent tuberculosis.” Al-Jaberi, F.A.H., et al. (2022) Reduced vitamin D-induced cathelicidin production and killing of Mycobacterium tuberculosis in macrophages from a patient with a non-functional vitamin D receptor: A case report. Frontiers in Immunology. doi.org/10.3389/fimmu.2022.1038960.

Source: www.news-medical.net ↗
05What supplements really work?

The bulk of vitamins and supplements containing fish oil, biotin, and vitamins A, C, and E can potentially promote nail and hair growth. You can find dietary supplements with higher concentrations of vitamins and minerals that aid skin, hair, and nail health. Fish oil supplements make nails and hair shiny. Fish oil also serves as an agent that can decrease signs of aging. If sun exposure damages the skin, the omega-3 fatty acids in fish oil can help. Biotin, also known as B7, increases hair density and strengthens it. It is found naturally in bananas, eggs, and milk. Vitamins are vital for skin health as well. Vitamin A reduces acne flairs and helps with changes due to aging like wrinkling. A vitamin A deficiency may increase the risk of acne because it becomes difficult for dead skin to slough off hair follicles, blocking pores. Vitamin B lowers the risk of precancerous growths and nonmelanoma skin cancer. Vitamin C is an antioxidant. It leads the fight against free radicals to help stimulate collagen and brighten skin. It also helps to prevent the formation of unneeded melanin that causes uneven skin pigmentation.

Source: www.medicinenet.com ↗
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Peptide Therapy Guide Editorial Team

Editorial team for Peptide Therapy Guide.

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