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genomes

Scientists Create First Viruses Designed By AI, What Does This Mean For The Future Of Medicine?

Scientists have created the first viruses that were designed using artificial intelligence. This feat is being highly debated within the scientific community as both a major milestone advancement for medicine, and a potential threat if this technology isn’t protected. 

Dr. Brian Hie is a chemical engineer at Stanford University in California, who utilized genome language models to design functioning genomes for bacteriophages. The models are the genetic equivalent to the language models used for AI chatbots, and bacteriophages are the specific viruses that only infect bacteria, so they’re used to treat patients with persistent infections. 

The viruses were then made in the laboratory and specifically put against E. coli in a dish, according to the research recently published in the journal Science. “The ability to rapidly design genomes and tune them for specific bugs while overcoming resistance could transform phage therapy and expand biotechnological toolkits,” the researchers wrote. 

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On the other hand, the scientists have also stated that the new work raised “important biosafety, biocontainment, and biosecurity consideration,” telling other people who are designing whole genomes to “consult both safety and security professionals throughout the project.”

Professor Tom Inglesby and Dr. Mori Hanke at the Center for Health Security at Johns Hopkins University wrote an accompanying article in which they emphasized the researchers safety warnings: 

“Although this is promising for life sciences applications, it also raises urgent biosafety and biosecurity questions. The ability to compose viral genomes using generative AI now exists; the governance to safely steer it does not.”

Dr. Hie and his colleagues mapped out in their article how they used AI models named Evo1 and Evo2 to design the new viral genomes. The models were specifically trained with genetic data from 2 million bacteriophages.

To keep the focus on the bacteriophages that can be utilized in medicine, the scientists made sure to carefully exclude any genetic codes for viruses that can infect living beings so the AI training doesn’t design any dangerous viruses. 

The AI worked to generate thousands of potential genomes, and the researchers chose about 300 to then make in a lab. Those genomes were then dropped into bacteria which read the genetic code and created the new bacteriophages. 

Only 16 bacteriophages were viable, however, the makeup of them were able to overcome resistance in two different strains of E. coli

Professor Inglesby and Dr. Hanke said that although only 16 out of the 300 were viable, the work proves that generative AI can create viral genomes, and there should be safeguards put into place to ensure that the technology can never be used to create pathogens that can infect plants, animals, and especially humans. 

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“Such genomes might encode new pathogens that … cannot be contained by existing countermeasures,” they wrote

Tom Ellis, a professor of synthetic genome engineering at Imperial College London, stated that this work was very impressive, but when it comes to creating more complex genomes, there’s a lot more work to actually be done. 

“This is literally the smallest and easiest genome to make,” he said. 

“An AI trained on the genetic code of dangerous bugs could be used to design more harmful viruses,” the Guardian reported that Ellis said. 

“But controlling access to genetic data and having restrictions on making genomes that look dangerous would help. Governments are working hard to do this already,” he added.

“But honestly, the threat from full AI design and writing of a genome of a virus or bacteria is very overblown when we consider that just taking existing pathogens and making gain-of-function changes to their genomes is so much easier and much more likely to be a real pathogenic threat.”

Dr. Filippa Lentzos, a reader in science and international security at King’s College London, stated that one of the biggest things to now look out for with this type of work is making sure no scientific groups try to manufacture anything involving DNA. 

“It’s important to see the bigger governance picture and not focus regulation solely on the AI model,” she said

“A layered approach makes more sense: safeguards around model development and access, responsible research review, synthesis screening, and established laboratory biosafety and biosecurity.”

vaccine

China Deploys Drones and Mosquito-Eating Fish to Combat Chikungunya Outbreak

Southern China is grappling with a major outbreak of chikungunya, a mosquito-borne viral illness that has rapidly infected thousands in recent weeks—marking one of the country’s largest recorded surges since the disease was first detected there nearly 20 years ago.

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Arizona Resident Dies from Rare Case of Pneumonic Plague

A resident of Coconino County, Arizona, has died from pneumonic plague, the first fatal case reported in the area since 2007. While local officials are stressing that the death appears unrelated to a recent and mysterious die-off of prairie dogs near Flagstaff, both incidents are drawing renewed attention to a disease more often associated with medieval history than modern life.

The individual, whose identity and demographic details have not been disclosed, reportedly arrived at Flagstaff Medical Center’s emergency department and died that same day, according to local health officials.

A spokesperson for Northern Arizona Healthcare (NAH) confirmed that the individual died from a “severe lung infection caused by the Yersinia pestis bacterium” and that “despite appropriate initial management and attempts to provide life-saving resuscitation, the patient did not recover.”

“NAH would like to remind anyone who suspects they are ill with a contagious disease to contact their health care provider. If their illness is severe, they should go to the emergency Department and immediately ask for a mask to help prevent the spread of disease while they access timely and important care.”

Coconino County encompasses a swath of northern Arizona, including part of Grand Canyon National Park. While human cases of plague are extremely rare in the U.S., the bacterium Yersinia pestis, the culprit behind the Black Death outbreak in the 1340s, still lingers in parts of the American Southwest.

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The Centers for Disease Control and Prevention (CDC) reports roughly seven human plague cases annually across the country, with the vast majority occurring in rural areas of western states. Since 2000, only 15 plague-related deaths have been recorded nationwide.

This latest case involves pneumonic plague, the rarest and most virulent form of the disease, which attacks the lungs and can spread through respiratory droplets. In contrast, the more common bubonic plague is typically transmitted via flea bites and affects the lymphatic system.

Bubonic plague may still lead to painful, swollen lymph nodes known as buboes, but it can be easily cured if treated with antibiotics early. Pneumonic plague can trigger symptoms such as fever, fatigue, chills, and severe pneumonia within a week of exposure.

Although the patient’s case is believed to be isolated, county officials have launched an investigation into a concurrent spike in prairie dog deaths northeast of Flagstaff. Trish Lees, a communications manager for Coconino County, told the Arizona Republic that the total number of deceased prairie dogs is still being assessed.

Despite the timing, health authorities have stated that as of right now, there is no evidence linking the recent death to the prairie dog die-off. However, the county has issued precautionary guidelines for residents and visitors to reduce potential exposure to Yersinia pestis.

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These include avoiding sick or dead animals, steering clear of rodent burrows when camping, refraining from sleeping directly on the ground, and using insect repellents. Tucking pants into socks is also recommended for extra protection against fleas.

“Report prairie dog die-offs. Prairie dogs are highly susceptible to plague but are not considered a long-term reservoir of the disease. They typically die off quickly after infection, making them an indicator species for plague presence. Active prairie dog colonies are not harmful, but a sudden reduction/die-off in prairie dog colonies may indicate the presence of disease.”

While Yersinia pestis is known to persist in rodent populations, particularly in the Southwest, human infections remain exceedingly rare and person-to-person transmission of pneumonic plague is even rarer. In fact, the last confirmed case of such transmission in the U.S. occurred in Los Angeles more than a century ago, in 1924.

Arizona itself has reported only seven plague cases since 2006. Yet the region is no stranger to other zoonotic diseases, including hantavirus, rabies, and West Nile virus, which are considered endemic to the area.

“Our hearts go out to the family and friends of the deceased,” said Coconino County Board of Supervisors Chair Patrice Horstman. “We are keeping them in our thoughts during this difficult time. Out of respect for the family, no additional information about the death will be released.”

Showerheads And Toothbrush Heads Are A Breeding Ground For Viruses, But They’re Actually Beneficial To Our Health 

The warm and damp environments that exist in our bathrooms create an ideal breeding ground for microbes, specifically around our showerheads and toothbrushes. However, these specific microbes and viruses aren’t necessarily a bad thing, as they have evolved to hunt, attack, and absorb specific bacterial species that may be bad for us.

covid

New Covid Variants Account For 50% Of Current US Cases, According To CDC

Covid-19 cases in the US have been on the rise this summer. The KP.3 Covid-19 variant is the current strain that is dominating the cases, according to the US Centers for Disease Control and Prevention (CDC). Their data also showed that another variant, known as KP.3.1.1, is also one of the most dominant strains currently. 

The CDC’s Nowcast data tracker showed the projections of the COVID-19 variants for a two-week period starting on July 7 and ending on July 20. The KP.3 variant accounted for 32.9% of positive infections, followed by KP.3.1.1, at 17.7%. Combined, the two variants make up 50.6% of cases,” according to Ahjané Forbes for USA Today

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From June 23rd to July 6th, CDC data showed that the KP.3 strain accounted for 33.7% of cases, however, the strain decreased in presence by .8% while KP.3.1.1 increased by 10.9% from 6.8% between July 6th and July 20th. 

CDC Spokesperson Rosa Norman told USA Today that “the symptoms associated with KP.3 are similar to those from JN.1. These symptoms can appear between two and 14 days after exposure to the virus and can range from mild to severe.

The CDC said “you should seek medical attention if you have the following symptoms: trouble breathing, persistent pain or pressure in the chest, new confusion, inability to wake or stay awake, or are experiencing pale, gray, or blue-colored skin, lips, or nail beds.”

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The CDC data stated that “COVID-19 test positivity has risen 12.6% within the past week.”

On July 16, the CDC said that “COVID-19 infections are growing in 42 states, stable or uncertain in 6 states, and declining to zero.”

Data shows that “four states had the biggest increase of 5.6% in positive COVID-19 cases from July 6 to July 13, 2024.”

The CDC recommends that every US resident who’s 6 months old and older should be diligent and receive their updated 2024-2025 Covid-19 vaccination.

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Former CDC Director Believes Next Pandemic Will Be Caused By The Bird Flu

Robert Redfield, former director of the US Centers for Disease Control and Prevention (CDC), recently stated that the next pandemic could be caused by the bird flu. 

Additionally, the World Health Organization recently announced the first human death from bird flu in Mexico, and the virus itself has been found in cattle across dairy farms in the US, according to reports

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“I really do think it’s very likely that we will, at some time, it’s not a question of if, it’s more of a question of when we will have a bird flu pandemic,” Redfield said to NewsNation last week. 

He also discussed that the mortality rate will likely be much higher in a bird flu pandemic versus what the world experienced during the Covid-19 pandemic. The Covid-19 pandemic had a mortality rate that was 0.6%, and Redfield predicts the mortality “for the bird flu would probably be somewhere between 25 and 50%.”

The Hill reported that by late May, the CDC had found the third case of an individual diagnosed with bird flu within three months. Each case was found in a farmworker, but were unrelated to each other. The main symptoms included a cough and pink eye. 

As of right now, there is no direct evidence that suggests the virus is spreading amongst humans right now. 

Health experts and researchers found that in order for the bird flu to be able to connect to a human receptor, five amino acids have to change their key receptors. If that does occur, the virus would spread like Covid-19 did. 

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“Once the virus gains the ability to attach to the human receptor and then go human to human, that’s when you’re going to have the pandemic,” Redfield said

“I think it’s just a matter of time.”

While Redfield stated that it’s hard to predict how long it would take for the amino acids to change, but the fact that it’s been detected in cattle across the US is concerning. 

The CDC reported that more than 40 herds of cattle have been infected with the virus. They’ve been following wastewater treatment sites to track where the virus is originating from, and said that there’s low risk of the virus spreading throughout the public. 

The cattle infected live in the vicinity of pigs, which could allow the virus to evolve from pigs to humans, however, Redfield stated there’s more of a severe risk that the virus will be grown in a lab and spread that way. 

“I know exactly what amino acids I have to change because in 2012, against my recommendation, the scientists that did these experiments actually published them. So, the recipe for how to make bird flu highly infectious for humans is already out there,” he said.

dog

Mysterious Dog Respiratory Illness: What We Know And How To Protect Your Canine Companions

Dog owners throughout the US are worried about their furry friend’s health after a new mysterious respiratory illness has begun making dogs sick. Here’s what we know about this new bacterial infection.

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Study Finds Regular Physical Activity Could Reduce Covid-19 Risk 

According to a data analysis published in the British Journal of Sports Medicine, regular exercise can lower the risk of developing Covid-19 or getting seriously ill when one contracts the virus. The data suggests that about 20 minutes of exercise a day yielded the greatest results. 

The study stated that a weekly total of 150 minutes of moderately intense exercise or 75 minutes of vigorous physical activity would give the greatest results. 

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“Regular physical activity seems to be related to a lower likelihood of adverse Covid-19 outcomes,” the team of researchers wrote. 

“Our analysis reveals that individuals who engage in regular physical activity have a lower likelihood of Sars-CoV-2 infection, Covid-19 hospitalization, severe Covid-19 illness and Covid-19-related death than physically inactive individuals, independent of design and instrument used.”

In general, exercise has a protective effect when it comes to respiratory infections. Regular physical activity reduces one’s chances of obesity, type 2 diabetes, and a multitude of other illnesses, most recently Covid-19. 

The researchers emphasized that the analysis was relatively limited, so the results shouldn’t be taken at face value. The team attempted to quantify the specific threshold of physical activity needed to make an actual difference in lessening the risk of contracting Covid-19, or lessening the severity should one become infected. 

The study observed data from 1.8 million adults, 54% of which were women, and the median age of each individual was 53. 

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The data analysis showed that, overall, “those who included regular physical activity in their weekly routine had an 11% lower risk of infection with Sars-CoV-2, the virus that causes Covid.”

Those individuals also had a 36% lower risk of hospitalization, a 44% lower risk of severe Covid-19, and a 43% lower risk of death from Covid-19. 

The research team also warned that the data was a result of “observational studies, differing study designs, subjective assessments of physical activity levels, and concerned only the Beta and Delta variants of Sars-CoV-2 rather than Omicron, all of which could weaken the findings.”

“There are plausible biological explanations for what we found. Regular moderate-intensity exercise may help to boost the body’s anti-inflammatory responses, as well as cardiorespiratory and muscular fitness, all of which may explain its beneficial effects on Covid-19 severity,” the researchers said. 

“Our findings highlight the protective effects of engaging in sufficient physical activity as a public health strategy, with potential benefits to reduce the risk of severe Covid-19.”

“Given the heterogeneity and risk of publication bias, further studies with standardized methodology and outcome reporting are now needed,” they wrote. 

Thousands Of New Viruses Discovered In The Ocean, According To New Study

More than 5,000 new virus species have been discovered throughout our world’s oceans according to a new study. Researchers at The Ohio State University analyzed tens of thousands of water samples from around the world looking for new RNA viruses, or viruses that use RNA for genetic material. 

These types of viruses are typically understudied when compared to DNA viruses, however, Covid-19 is a type of RNA virus, so scientists and researchers all around the globe have been trying to gain a greater understanding of them. 

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The diversity of the newfound viruses was so great that the researchers have “proposed doubling the number of taxonomic groups needed to classify RNA viruses, from the existing five phyla to 10 phyla. Phylum is a broad classification in biology just below kingdom,” study lead author Matthew Sullivan, a professor of microbiology at The Ohio State University, said in a statement

“There’s so much new diversity here – and an entire new phylum, the Taraviricota, were found all over the oceans, which suggests they’re ecologically important,” he explained. 

“Studies of RNA viruses have usually focused on those that cause diseases. Some well-known RNA viruses include influenza, Ebola and the coronavirus that causes COVID-19. But these are just a tiny slice of RNA viruses on Earth.”

“We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply,” Sullivan said in the statement.

For the study, published in the journal Science, the researchers “analyzed 35,000 water samples taken from 121 locations in all five of the world’s oceans.”

The researchers team are all members of the Tara Oceans Consortium, a worldwide project created to study the impact of climate change specifically on the ocean. 

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The researchers examined genetic sequences that were extracted from plankton; small aquatic organisms. Plankton is known to be a common host for RNA viruses. By focusing on sequences that belonged to RNA viruses, they were able to find the ancient gene known as RdRp, which is found in all RNA viruses, but absent from other types of viruses. 

The researchers were able to identify over 44,000 sequences with the ancient gene. Since the RdRp gene is billions of years old, it has been able to evolve, which makes it harder for the scientists to determine the actual evolutionary relationship between the sequences and how they changed. 

“Overall, we identified about 5,500 new RNA virus species that fell into the five existing phyla, as well as the five newly proposed phyla, which are named Taraviricota, Pomiviricota, Paraxenoviricota, Wamoviricota and Arctiviricota.”

“Virus species in the Taraviricota phylum were particularly abundant in temperate and tropical waters, while viruses in the Arctiviricota phylum are abundant in the Arctic Ocean,” the researchers wrote.

“Understanding how the RdRp gene diverged over time could lead to a better understanding of how early life evolved on Earth,” the authors said.

“RdRp is supposed to be one of the most ancient genes — it existed before there was a need for DNA. So we’re not just tracing the origins of viruses, but also tracing the origins of life,”study co-first author Ahmed Zayed, a research scientist in microbiology at Ohio State, said in the statement. 

Ancient 15,000-Year-Old Viruses Appear In Melting Glacier Ice

Century-old moss that has been frozen away in the depths of a Tibetan Glacier has melted to reveal ancient viruses, giving scientists a real glimpse into the organisms that lived tens of thousands of years ago on Earth, as well as the history of their ecosystems.

“The melting has also created some concerns about ancient viruses coming back to haunt us. Melting will not only lead to the loss of those ancient, archived microbes and viruses, but also release them to the environment in the future,” microbiologist Zhi-Ping Zhong wrote in a new study.

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Scientists luckily have access to technology that can keep the ice samples completely sterilized, which makes it easier to work with when it comes to analyzing what exactly is in the ice. Recently, scientists identified dozens of 15,000-year-old viruses from the Guliya ice cap of the Tibetan Plateau.

“These glaciers were formed gradually, and along with dust and gases, many, many viruses were also deposited in that ice. These microbes potentially represent those in the atmosphere at the time of their deposit.”

“These are viruses that would have thrived in extreme environments, with signatures of genes that help them infect cells in cold environments – just surreal genetic signatures for how a virus is able to survive in extreme conditions,” said microbiologist Matthew Sullivan, who also worked on the study.

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When the scientists compared the genetic sequence of the recent discovery they found that a majority of the viruses present in the ice core samples were bacteria that infect Methylobacterium; this classifies the group of bacteria responsible for the methane cycle of ice in a glacier.

These types of bacteria are typically found in plant or soil habitats, which indicates to the researchers that the viruses likely were deposited in the ice through dust particles that lifted from soil tens of thousands of years ago.

“These frozen viruses likely originate from soil or plants and facilitate nutrient acquisition for their hosts.”

“We know very little about viruses and microbes in these extreme environments, and what is actually there,” says Earth scientist Lonnie Thompson.

“How do bacteria and viruses respond to climate change? What happens when we go from an ice age to a warm period like we’re in now?”