Largest discovery of new virus species sheds light on the hidden virosphere.
Artificial intelligence (AI) has been used to reveal details of a diverse and fundamental branch of life living right under our feet and in every corner of the globe. These viruses not only play significant roles in human health but are also prevalent in extreme environments, highlighting their crucial roles in ecosystems and offering insights into viral evolution and diversity.
Using a machine learning tool, researchers have discovered 161,979 new species of RNA virus, a breakthrough that could dramatically enhance our understanding of Earth’s biodiversity and assist in identifying millions more viruses yet to be characterized.
Published on October 9 in the journal Cell and conducted by an international team of researchers, the study is the largest virus species discovery paper ever published.
Unprecedented Viral Diversity Unveiled
“We have been offered a window into an otherwise hidden part of life on earth, revealing remarkable biodiversity,” said senior author Professor Edwards Holmes from the School of Medical Sciences in the Faculty of Medicine and Health at the University of Sydney.
“This is the largest number of new virus species discovered in a single study, massively expanding our knowledge of the viruses that live among us,” Professor Holmes said. “To find this many new viruses in one fell swoop is mind-blowing, and it just scratches the surface, opening up a world of discovery. There are millions more to be discovered, and we can apply this same approach to identifying bacteria and parasites.”
The Role of RNA Viruses in Extreme Environments
Although RNA viruses are commonly associated with human disease, they are also found in extreme environments around the world and may even play key roles in global ecosystems. In this study they were found living in the atmosphere, hot springs, and hydrothermal vents.
“That extreme environments carry so many types of viruses is just another example of their phenomenal diversity and tenacity to live in the harshest settings, potentially giving us clues on how viruses and other elemental life-forms came to be,” Professor Holmes said.
Advancements in Viral Identification via AI
The researchers built a deep learning algorithm, LucaProt, to compute vast troves of genetic sequence data, including lengthy virus genomes of up to 47,250 nucleotides and genomically complex information to discover more than 160,000 viruses.
“The vast majority of these viruses had been sequenced already and were on public databases, but they were so divergent that no one knew what they were,” Professor Holmes said. “They comprised what is often referred to as sequence ‘dark matter’. Our AI method was able to organize and categorize all this disparate information, shedding light on the meaning of this dark matter for the first time.
The AI tool was trained to compute the dark matter and identify viruses based on sequences and the secondary structures of the protein that all RNA viruses use for replication.
Future Directions and Applications of AI in Virology
It was able to significantly fast-track virus discovery, which, if using traditional methods, would be time intensive.
Co-author from Sun Yat-sen University, the study’s institutional lead, Professor Mang Shi said: “We used to rely on tedious bioinformatics pipelines for virus discovery, which limited the diversity we could explore. Now, we have a much more effective AI-based model that offers exceptional sensitivity and specificity, and at the same time allows us to delve much deeper into viral diversity. We plan to apply this model across various applications.”
Co-author Dr Zhao-Rong Li, who researches in the Apsara Lab of Alibaba Cloud Intelligence, said: “LucaProt represents a significant integration of cutting-edge AI technology and virology, demonstrating that AI can effectively accomplish tasks in biological exploration. This integration provides valuable insights and encouragement for further decoding of biological sequences and the deconstruction of biological systems from a new perspective. We will also continue our research in the field of AI for virology.”
Professor Holmes said: “The obvious next step is to train our method to find even more of this amazing diversity, and who knows what extra surprises are in store.”
Reference: “Using artificial intelligence to document the hidden RNA virosphere” by Xin Hou, Yong He, Pan Fang, Shi-Qiang Mei, Zan Xu, Wei-Chen Wu, Jun-Hua Tian, Shun Zhang, Zhen-Yu Zeng, Qin-Yu Gou, Gen-Yang Xin, Shi-Jia Le, Yin-Yue Xia, Yu-Lan Zhou, Feng-Ming Hui, Yuan-Fei Pan, John-Sebastian Eden, Zhao-Hui Yang, Chong Han, Yue-Long Shu, Deyin Guo, Jun Li, Edward C. Holmes, Zhao-Rong Li and Mang Shi, 9 October 2024, Cell.
DOI: 10.1016/j.cell.2024.09.027
The researchers declare no competing interests. The research was supported by the National Natural Science Foundation of China, the Shenzhen Science and Technology Program, the Natural Science Foundation of Guangdong Province, the Guangdong Province “Pearl River Talent Plan” Innovation and Entrepreneurship Team Project, the Hong Kong Innovation and Technology Fund (ITF) and the Health and Medical Research Fund. Professor Holmes is funded by a National Health and Medical Research Council of Australia Investigator grant and by AIR@InnoHK administered by the Innovation and Technology Commission, Hong Kong Special Administrative Region, China.

News
Small antibodies provide broad protection against SARS coronaviruses
Scientists have discovered a unique class of small antibodies that are strongly protective against a wide range of SARS coronaviruses, including SARS-CoV-1 and numerous early and recent SARS-CoV-2 variants. The unique antibodies target an [...]
Controlling This One Molecule Could Halt Alzheimer’s in Its Tracks
New research identifies the immune molecule STING as a driver of brain damage in Alzheimer’s. A new approach to Alzheimer’s disease has led to an exciting discovery that could help stop the devastating cognitive decline [...]
Cyborg tadpoles are helping us learn how brain development starts
How does our brain, which is capable of generating complex thoughts, actions and even self-reflection, grow out of essentially nothing? An experiment in tadpoles, in which an electronic implant was incorporated into a precursor [...]
Prime Editing: The Next Frontier in Genetic Medicine
By Dr. Chinta SidharthanReviewed by Benedette Cuffari, M.Sc. Discover how prime editing is redefining the future of medicine by offering highly precise, safe, and versatile DNA corrections, bringing hope for more effective treatments for genetic diseases [...]
Can scientists predict life longevity from a drop of blood?
Discover how a new epigenetic clock measures how fast you are really aging from just a drop of blood or saliva. A recent study published in the journal Nature Aging constructed an intrinsic capacity (IC) clock [...]
What is different about the NB.1.8.1 Covid variant?
For many of us, Covid-19 feels like a chapter we’ve closed – along with the days of PCR tests, mask mandates and daily case updates. But while life may feel back to normal, the [...]
Scientists discover single cell creatures can learn new behaviours
It was previously thought that learning behaviours only applied to animals with complex brain and nervous systems, but a new study has proven that this may also occur in individual cells. As a result, this new evidence may change how [...]
Virus which ’causes multiple organ failure’ found at popular Spanish holiday destination
British tourists planning trips to Spain have been warned after a deadly virus that can cause multiple organ failure has been detected in the country. The Foreign Office issued the alert on its dedicated website Travel [...]
Urgent health warning as dangerous new Covid virus from China triggers US outbreak
A dangerous new Covid variant from China is surging in California, health officials warn. The California Department of Public Health warned this week the highly contagious NB.1.8.1 strain has been detected in the state, making it the [...]
How the evolution of a single gene allowed the plague to adapt, prolonging the pandemics
Scientists have documented the way a single gene in the bacterium that causes bubonic plague, Yersinia pestis, allowed it to survive hundreds of years by adjusting its virulence and the length of time it [...]
Inhalable Nanovaccines: The Future of Needle-Free Immunization
The COVID-19 pandemic highlighted the need for adaptable and scalable vaccine technologies. While mRNA vaccines have improved disease prevention, most are delivered by intramuscular injection, which may not effectively prevent infections that begin at [...]
‘Stealthy’ lipid nanoparticles give mRNA vaccines a makeover
A new material developed at Cornell University could significantly improve the delivery and effectiveness of mRNA vaccines by replacing a commonly used ingredient that may trigger unwanted immune responses in some people. Thanks to [...]
You could be inhaling nearly 70,000 plastic particles annually, what it means for your health
Invisible plastics in the air are infiltrating our bodies and cities. Scientists reveal the urgent health dangers and outline bold solutions for a cleaner, safer future. In a recent review article published in the [...]
Experts explain how H5 avian influenza adapts to infect more animals
A new global review reveals how rapidly evolving H5 bird flu viruses are reaching new species, including dairy cattle, and stresses the urgent need for coordinated action to prevent the next pandemic. Since its [...]
3D-printed device enables precise modeling of complex human tissues in the lab
A new, easily adopted, 3D-printed device will enable scientists to create models of human tissue with even greater control and complexity. An interdisciplinary group of researchers at the University of Washington and UW Medicine [...]
Ancient DNA sheds light on evolution of relapsing fever bacteria
Researchers at the Francis Crick Institute and UCL have analyzed ancient DNA from Borrelia recurrentis, a type of bacteria that causes relapsing fever, pinpointing when it evolved to spread through lice rather than ticks, and [...]