Tag Archives: mutation

New COVID variant identified in France — but experts say we shouldn’t fear it

Scientists have identified a previously unknown mutant strain in a fully vaccinated person who tested positive after returning from a short three-day trip to Cameroon.

Academics based at the IHU Mediterranee Infection in Marseille, France, discovered the new variant on December 10. So far, the variant doesn’t appear to be spreading rapidly and the World Health Organization has not yet labeled it a variant of concern. Nevertheless, researchers are still describing and keeping an eye on it.

The discovery of the B.1.640.2 mutation, dubbed IHU, was announced in the preprint server medRxiv, in a paper still awaiting peer review. Results show that IHU’s spike protein, the part of the virus responsible for invading host cells, carries the E484K mutation, which increases vaccine resistance. The genomic sequencing also revealed the N501Y mutation — first seen in the Alpha variant — that experts believe can make COVID-19 more transmissible.  

In the paper, the clinicians highlight that it’s important to keep our guard and expect more surprises from the virus: “These observations show once again the unpredictability of the emergence of new SARS-CoV-2 variants and their introduction from abroad,” they write. For comparison Omicron (B.1.1.529) carries around 50 mutations and appears to be better at infecting people who already have a level of immunity. Thankfully, a growing body of research proves it is also less likely to trigger severe symptoms.

Like many countries in Europe, France is experiencing a surge in the number of cases due to the Omicron variant.

Experts insist that IHU, which predates Omicron but has yet to cause widespread harm, should not cause concern – predicting that it may fade into the background. In an interview with the Daily Mail, Dr. Thomas Peacock, a virologist at Imperial College London, said the mutation had “a decent chance to cause trouble but never really materialized. So it is definitely not one worth worrying about too much at the moment.”

The strain was first uploaded to a variant tracking database on November 4, more than two weeks before Omicron was sequenced. For comparison, French authorities are now reporting over 300,000 new cases a day thought to be mostly Omicron, with data suggesting that the researchers have identified only 12 cases of IHU over the same period. 

On the whole, France has good surveillance for COVID-19 variants, meaning health professionals quickly pinpoint any new mutant strains. In contrast to Britain, which only checks three in ten cases for variants. The paper’s authors state that the emergence of the new variant emphasizes the importance of regular “genomic surveillance” on a countrywide scale.

Pfizer vaccine appears to work against a key variant mutation, study shows

The coronavirus vaccine developed by Pfizer and BioNTech appears to be effective against the mutations that have emerged in South Africa and the UK, according to new laboratory studies. The news has been largely welcomed but it’s not being seen as definitive proof yet about how the vaccine will perform against these mutations.

Image credit: Flickr / Marco Verch

Coronaviruses frequently mutate as they pass from human to human and, for the most part, don’t significantly alter the virus. Still, a handful of mutations appears to allow the virus to spread faster. These changes happen in the virus’s spike proteins, which are crucial because they enable the virus to enter and take over human cells.

Working with researchers from the University of Texas, Pfizer carried out a study on blood taken from 20 patients who had been given the Covid-19 vaccine. They created two forms of the virus, one with and one without the mutation, and bathed those viruses in the blood samples. Results showed the immune system could take out the new mutation.

The research, which hasn’t been peer-reviewed yet, suggested the vaccine worked to neutralize the so-called N501Y mutation, which has been reported in the variants of the virus discovered in the UK and South Africa. These forms of the virus are spreading faster, which raised questions about the level of protection of vaccines.

“These findings are good news for the likely effectiveness of the Pfizer/BioNTech vaccine against these new variants of SARS-CoV-2,” Michael Baker, an epidemiologist at the University of Otago, told CNBC. “In other words, the Pfizer vaccine is likely to induce immunity that covers the two new more infectious variants.”

Nevertheless, the findings are limited, as the study doesn’t look at the full set of mutations found in either of the new rapidly spreading variants. Researchers now hope to have more information in the next few weeks on whether the vaccines work against the other mutations found in the UK and South Africa variants.

“While it’s reassuring that one mutation within these variants is not associated with escape from vaccines, at least in the laboratory, we urgently need data on these mutations, and preferably on the variant virus with a combination of mutations, as these may act differently in combination” Deepti Gurdasani, a clinical epidemiologist at Queen Mary University of London, told CNBC.

The World Health Organization (WHO) said in December that health authorities were “urgently investigating” whether the N501Y mutation may have any impact on vaccine performance. The variant that emerged in South Africa is of particular concern, as it carries two other mutations in the spike protein that aren’t present in the UK strain.

Still, if the variants eventually mutate in a way that diminishes the efficacy of the vaccines, we aren’t back at square one. The Pfizer and Moderna’s vaccines use mRNA and can potentially be recoded within a few months to combat new variants. However, while the technology allows for it, this has never been tested before.

More than 88.1 million people have so far tested positive for coronavirus worldwide, with 1.9 million deaths, according to data compiled by Johns Hopkins University. Meanwhile, the vaccine campaign is moving along around the world, with more than 17.5 million shots already given in 38 countries, data by Bloomberg showed.

The paper with the results of the study can be accessed here.

Gene mutation doesn’t make women diagnosed with breast cancer more likely to die

Angelina Jolie made headlines when she underwent preventative surgery after learning she had an up to 87% chance of developing breast cancer. Doctors had found that the star had mutations in BRCA genes which increase a woman’s risk of breast cancer by four-to-eightfold. Now, new findings suggest that Jolie may have been too rushed.

Credit: Wikimedia Commons.

Credit: Wikimedia Commons.

Scientists at the University of Southampton, UK, recently reported that women who carry a mutation in the BRCA1 or BRCA2 genes are not more likely to die after a breast cancer diagnosis than non-carriers. What’s more, carrying these mutations might, in fact, boost the odds of beating cancer if the diagnosis is triple-negative breast cancer.

BRCA mutations can cause cancer because the DNA self-repair mechanisms can malfunction. Besides breast cancer, these mutations have been linked to an increased risk of ovarian and prostate cancers.

“Women diagnosed with early breast cancer who carry a BRCA mutation are often offered double mastectomies soon after their diagnosis or chemotherapy treatment” compared to non-mutation carriers, study co-author Diana Eccles of the University of Southampton said in a statement.

“Our findings suggest that this surgery does not have to be immediately undertaken along with the other treatment.”

The study involved 2,733 British women aged 18-40 who had been diagnosed with breast cancer between 2000 and 2008. About 12 percent of the patients had a BRCA mutation, yet again confirming the association between this ‘faulty gene’ and breast cancer. Roughly 30 to 60 percent of BRCA1 or BRCA2 carriers will develop breast cancer in their lifetime, compared to an estimated 12 percent of women in the general population.

After the women’s medical records were tracked for up to ten years, researchers found that 651 of 678 total deaths were due to breast cancer. Most importantly, they uncovered that there was no difference in overall survival two, five, or ten years after diagnosis for women with and without a BRCA mutation. Actually, those with a BRCA mutation had slightly higher survival rates for the first two years after diagnosis, in the case of patients with triple-negative breast cancer.

About a third of those with the BRCA mutation had a double mastectomy to remove both breasts after being diagnosed with cancer, the same surgery Jolie went through. This surgery did not appear to improve their chances of survival at the 10-year mark, according to the findings published in The Lancet Oncology.

The findings might come as a welcomed breath of fresh air for many young women newly diagnosed with breast cancer, particularly those who are BRCA carriers. It means that they can take time to discuss whether radical breast surgery is the right choice for them as part of a longer-term risk-reducing strategy.

“So long as women are treated appropriately and are safe there is no crashing hurry … they need to be given the space to get as much information as they can and not feel like they need to do it all at once,” Fran Boyle, Professor of Medical Oncology at the University of Sydney told the SMH. 

“This important topic needs more prospective research as preventive surgical measures might have an effect on what might be a very long life after a diagnosis of breast cancer at a young age,” wrote Peter Fasching from the Friedrich-Alexander University Erlangen-Nuremberg, Germany.

Alcohol byproduct causes DNA mutations that might lead to cancer

A new study published in Nature brings sorrow to all alcohol consumers, be they light or heavy users. An older study showed a significant link between cancer and light drinking, but researchers haven’t quite established a causation between the two. Now, Ketan J. Patel, a Cambridge geneticist, and his team discovered that an alcohol metabolite — acetaldehyde — causes significant DNA  damage in the blood stem cells of mice.

After drinking alcohol, the body converts it into smaller parts, one of them being acetaldehyde, a toxic compound. When the body is over-flushed with acetaldehyde, the molecule accumulates within the cells and starts to cause DNA and chromosomal damage.

Researchers from the Medical Research Council’s lab of molecular biology at Cambridge University genetically engineered mice by deleting the genes that controlled the formation of acetaldehyde dehydrogenase 2 (ADLH2). Acetaldehyde dehydrogenases are a group of enzymes that are one of the natural mechanisms of alcohol degradation. Their purpose is to convert acetaldehyde into acetic acid. Basically, they rendered the mice unable to produce ADLH2.

Via Pixabay/lisichik

Next, they gave the mice diluted ethanol and then analyzed their genome to see what had happened. They discovered that acetaldehyde had altered their DNA by causing double-stranded breaks, which can lead to cancer.

Scientists were amazed when they saw that mice lacking the ALDH2 enzyme had four times the DNA damage in their blood stem cells when compared with mice that possessed the enzyme.

“We saw huge amounts of DNA damage in these cells. Bits of DNA were deleted, bits were broken and we even saw parts of chromosomes being moved about and rearranged,” Patel, the lead author said.

Via Pixabay/Goyaines

Another part of the experiment was to establish the methods through which the body repairs the damage done by acetaldehyde. Patel’s team learned that cells have a coordinated way of dealing with acetaldehyde poisoning.

“There are lots of ways cells can fix DNA damage,” says Patel in a press release. “What we’ve shown is that when damage happens as a result of breaking down alcohol, there’s a hierarchy when selecting the best way to carry out repairs.”

The most frequently chosen way was the Fanconi anemia repair pathway — a rare genetic disease resulting in impaired response to DNA damage. Other methods used were the non-homologous end-joining repair pathway and the homologous recombination pathway.

Either way, the news is not that great for drinkers. Of course, it would be best if all mankind could renounce drinking alcohol once and for all, but let’s face it: that’s not happening any time soon.

psychosis madness

Icelandic family of ten psychotic members helps identify new psychosis-related mutation

psychosis madness

Credit: Pixabay.

Studies on twins and families have time and time again found the risk of developing psychotic disorders is higher if siblings previously developed such a condition. This tells us that there’s an interplay of genetic factors that puts people at risk of developing mental illnesses. Identifying which genes or set of genes are responsible could help countless people but much like the unfortunate minds of the patients, such information is often hidden under a tangled mess of code. Yet in what can be considered a breakthrough, scientists have managed to find a new gene linked to psychosis.

A rare mutation

Large-scale genome-wide association studies have previously identified genetic variants that can be linked to psychosis among the general population. Such studies are useful but they often turn up with potentially ‘risky’ genes that have a small effect. Studies that attempt to uncover rare genetic variants that are rarely seen in the general population are much harder to come by. These are desirable and valuable because such genes must greatly raise the risk of psychosis within some families and are also associated with more severe forms of psychosis like schizophrenia.

One peculiar family from Iceland, however, seems to singlehandedly offer more insight into psychosis than dozens of studies before them. Here’s how.

The family in question has 10 members suffering from psychosis. Six are diagnosed with schizophrenia, two schizoaffective disorder while the last two have psychotic bipolar disorder. Without exception, each of them has hallmarks of psychotic symptoms like delusions and hallucinations.

After the genomes of each member was sequenced and thoroughly analyzed, the international team of researchers from  Iceland, Finland, and Germany found a common denominator — all ten members carry a disrupting mutation in the RBM12 gene. Later, they found a family with a similar history mental illness from Finland where the psychotic members also carried this same mutation.

“In addition to identifying RBM12 … the work reported here provides a template for future familial studies of psychosis, suggesting that the mutations involved are likely to be recent, may be incompletely penetrant for psychosis, but lead to related phenotypes in carriers unaffected by psychosis, and are likely to act in concert with other sequence variants,” corresponding author Kari Stefansson, with Decode/Amgen and the University of Iceland, said in a statement.

That being said, of course, you can have psychosis without an RBM12 mutation. Just the same, you can carry the mutation and not be psychotic. Case in point, a dozen other Icelanders, all descended from the family in question, had the same RBM12 mutation but didn’t express psychosis symptoms. It’s a predisposition. The new findings, however, offer hope for the development of new drugs that can ease psychotic symptoms, especially those very severe forms of delusion and hallucination, by pinpointing potential biological pathways to target. As we find more psychosis-associated mutations such as RBM12, doctors can get a better grasp of the neurobiological mechanisms at work behind psychosis.

“Today’s capacity for whole-exome and whole-genome sequencing makes it likely that additional high-penetrance, familial mutations will be discovered,” Stefansson and co-authors wrote in their paper published in Nature Genetics.

 

Mutation in daisies near Fukushima might not be caused by radiation

via Twitter user

Image via Twitter User San Kaido

After a twitter user and photographer from a city 110 km from Fukushima posted photos of mutated flowers, people started to freak out all over the internet that these plants suffered mutations due to the devastating nuclear incident from 2011 in Fukushima, Japan. According to the photographer @san_kaido, the radiation level near the daisies was measured at 0.5 μSv/h at 1m above the ground, which in fact is not much higher than the normal values.

In other words, no reason to freak out.

via

Fasciated strawberries via reddit

The mutation of plants, daisies in our case, is not really that uncommon in nature as you might expect. The process that causes these deformations is called fasciation and it can be caused by the hormonal imbalances, infections, genetics and even environment which also includes bacterial and viral infections, some types of fungi, insect attack and also the exposure to chemicals (mostly in agriculture). Yep, lots of things can cause it.

It surprisingly common in strawberries and even tomatoes. They may look odd, but consuming these fruits and vegetables that went through fasciation is harmless to the human body. Also the good part is that fasciation isn’t contagious so you can have a plant with mutations near other normal plants and they won’t be affected in any way.
According to Scott Morris on Garden Toolbox:

“It should be noted that just because a plant has fasciation, it doesn’t mean it will still be affected when it dies and comes back the next year – there’s no guarantee. In many cases it has been reported that plants are 100 percent fine the following year and show no sign of being fasciated, especially in perennial plants. Do bear in mind, that if the cause is genetic, there is a strong chance of reoccurrence and you may very well have to dispose of the plant completely.”

via reddit

Fasciated daisy in natural environment via reddit

At the same time it is important not to forget that it is a possibility that the plants were actually affected by radiation, according to a study from 2009 by the researchers at Japan’s National Institute of Agrobiological Sciences, it seems that the fasciation can be induced by gamma-irradiation:

The proportion of plants showing stem fasciation increased with gamma-irradiation … Each single mutant also showed stem fasciation at a low frequency without gamma-irradiation, while gamma-irradiation induced stem fasciation. Importantly, in wild-type plants, the frequency of stem fasciation was very low (<0.1 percent) [but] were induced by gamma-irradiation.

Whether or not these daisies suffered the mutation due to radiation or not it is important to keep in mind that nature is strange, and sometimes, strange things happening are completely natura. Until further research and experiments it is better that we think about all the possibilities and question everything.

Ashlyn Blocker, the teenager that can't feel pain. (c) Justin Heckert

How a girl that doesn’t feel pain at all might help create the painkillers of tomorrow

Some people are born with the innate ability, or better said disability, of not feeling pain – whatsoever. It’s not that they can’t feel anything, quite on the contrary – they still have a sense of texture, they feel pressure, they can feel a hug or handshake just like anyone, they experience warmth or coldness and so on – it’s just that any sensation that passes a certain threshold, effectively becoming pain, isn’t registered with these people.

That’s really weird, right? For a bit of insight into what’s it like living without physical pain, I’d recommend you read this NY Times piece on Ashlyn Blocker, a normal looking teenager from a small town called Patterson, GA  who at first glace isn’t significantly different from any other kid her age. In the article, however, you’ll find out how she never cried as a baby, how she first burned her hand when she was only two years old or how later on in her teens she constantly bruised herself and had broken bones.

“The girl who feels no pain was in the kitchen, stirring ramen noodles, when the spoon slipped from her hand and dropped into the pot of boiling water. It was a school night; the TV was on in the living room, and her mother was folding clothes on the couch. Without thinking, Ashlyn Blocker reached her right hand in to retrieve the spoon, then took her hand out of the water and stood looking at it under the oven light. She walked a few steps to the sink and ran cold water over all her faded white scars, then called to her mother, “I just put my fingers in!” Her mother, Tara Blocker, dropped the clothes and rushed to her daughter’s side. “Oh, my lord!” she said — after 13 years, that same old fear — and then she got some ice and gently pressed it against her daughter’s hand, relieved that the burn wasn’t worse.” excerpt from the NY Times article.

Pain, like all sensations we experience, is there for a purpose. It’s there to  protect us, to warn us if we’ve strayed too far, it lets us know that we’re in danger and we need help, and best of all it tells us that we need to stop whatever it is we’re doing that causes the pain. Some people, however, are on the other side of fence. There are millions of people in the world suffering from diseases that induce chronic, unbearable pain. Some of these people need to live with an acute sensation of pain for the rest of their lives, and most of the time painkillers don’t cut it or induce side effects that turns the patient into an emotional train wreck (see painkiller epidemic in America).

X-men – Subject 1 – mutation: “can feel no pain”

A team of European researchers recently analyzed the genome of an anonymous girl or woman from Germany, dubbed “Index Subject 1”, that in most respect is just like Ashlyn – she can’t feel any pain. Photos published in a paper about her show severe injuries to her head, face and knee, the latter of which she has fractured multiple times. After comparing her genome with several human genome databases, such as “1,000 Genomes,” which includes all the genes of 1,092 people from 14 populations, the researchers identified a specific gene mutation in Index Subject 1 that couldn’t be found in  in any of the human genome databases they scoured.

This almost unique mutation (the researchers have since found a male also carrying it Index Subject 2 – to no surprise, the man can’t also feel pain)  affected a gene called SCN11A  that  makes a protein that controls how much sodium goes in and out of cells in the human body. Sodium channels are indispensable for relaying information back and forth nerve endings in the body, and apparently the  particular type of sodium channel that was mutated in Index Subject 1 is abundant in nociceptors, the types of nerves that sense pain. The pieces of puzzles seem to fit nicely, however intuitive how this may all seem, the scientists still had to test this assumption.

They introduced the mutated gene into 101 lab mice. Of these, 11  gave themselves self-inflicting wounds suggesting that they couldn’t feel the pain. Also, to be sure, the researchers injected the mice with a chemical that caused their paws to swell up. The mice which underwent the successful mutation didn’t try to protect the swollen paw like the other, normal mice did. When subjected to high temperature, the mutated mice showed no sign of discomfort, again compared to normal mice. Also, as another important indicator, mutated mice bowels didn’t move as well as normal mice – digestive issues, sometimes severe, are common among people who can’t experience pain.

The findings published in Nature are nothing short of remarkable, hinting that indeed this single gene mutation is what causes some people, like Ashlyn, to live in world without physical pain. By better understanding the sodium channel mechanics, it’s foreseeable that one day researchers might be able to craft painkillers that exploit the symptoms of Index Subject 1, but with temporary effects. Remember, pain is good.

Researchers observe antibodies evolve against HIV

For the first time, scientists have observed in a patient the evolution of an immune molecule that recognizes different HIV types and adapt accordingly.

hivA neutralizing antibody, or NAb is an antibody which defends a cell from an antigen or infectious body by inhibiting or neutralizing any effect it has biologically. They’re your body’s elite force, who get sent in whenever something bad happens. By revealing how these molecules develop when adapting to different HIV strains, researchers can make vaccines that elicit similar antibodies that can protect people from becoming infected with HIV.

Barton Haynes of Duke University School of Medicine in Durham, North Carolina and his team found that neutralizing antibodies developed only after the population of viruses in the patient had diversified – something which has been suspected for quite a while, but not observed.

“This is a really beautiful demonstration,” says William Schief, a protein engineer specializing in vaccine design at the Scripps Research Institute in La Jolla, California. “It poses the question for the vaccine-design field of how much of that viral diversity we need to incorporate into our vaccine regimens to try to elicit broadly neutralizing antibodies.”

A big problem in dealing with HIV is that different strains adapt and change so often that it’s very hard for researchers to keep up with them, so they often focus on broadly effective vaccines, which aren’t quite as effective in some cases.

But getting human cells to make broadly neutralizing antibodies – that’s a much better approach, and one which is much more difficult, as scientists observed. The antibody that Haynes and his colleagues describe today, dubbed CH103, recognizes fewer HIV viruses than some other broadly neutralizing antibodies, but it is also much less complicated than the vaccines, which makes it much more possible to recreate.

“A message of our paper is that broad neutralizing antibodies don’t have to be as complicated as we thought, and therefore may be more easily induced,” says Haynes.

The team will now focus on mutating the antibody in order to strengthen its effects.

“The big question now is, once one has activated that germline B cell, how does one get that B cell to undergo maturation to produce a broadly neutralizing antibody?” Schief says.

Via Nature