Scientists found compounds in a Brazilian tree that hit SARS-CoV-2 on multiple fronts, revealing a promising new lead in the search for COVID-19 treatments. Researchers have found that galloylquinic acids extracted from the leaves of Copaifera lucens Dwyer, a tree native to Brazil and found mainly in the Atlantic Forest, can act against SARS-CoV-2 in [...]

Sheeppox is a highly contagious, often fatal viral disease that was largely eradicated from much of European livestock in the 20th century. But there is still the occasional regional outbreak, such as the one that afflicted many flocks of sheep in Greece last year. In order to reconstruct how the virus has evolved over the last 3,500 years, scientists extracted and sequenced sheeppox DNA preserved in the animal skins used for the parchment of numerous medieval manuscripts. They reported their findings in a new paper published in the journal Science Advances.

“The recording of ancient DNA of pathogens has completely changed our understanding of infectious disease in the past, and here we show that parchment can also preserve animal pathogen DNA. It is possible that archives and libraries around the world also contain the genetic traces of disease outbreaks in animals in the past,” said co-author Louis L’Hôte, a graduate student at University College Dublin. “These genomes help us understand how these pathogens evolved and how they impacted past societies—such as sheeppox virus, which we show has been affecting Eurasian sheep herds for at least three and a half millennia.”

Per the authors, the earliest known written evidence of sheeppox infection dates to the first century CE, when Roman accounts described outbreaks of skin lesions ("pustules") in the animals. There are more frequent mentions of deadly outbreaks of "pockes" or "variola" in sheep by the Middle Ages, recorded in various agricultural texts and accounting documents in France, Spain, and England. There seemed to be a decline in outbreaks in 17th-century France, although frequent outbreaks re-emerged in the 18th and 19th centuries, often with high mortality rates in the flocks. Great Britain did not experience a sheeppox resurgence until 1847.

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Scientists who were instrumental in shutting down the Covid lab-leak theory admitted in private "we can’t rule it out" months after publishing a paper closing down the possibility, newly released messages show.

The post The Messages That Show Covid Scientists Secretly Suspected a Lab Leak appeared first on The Daily Sceptic.

BU virologist Nancy Sullivan says the Bundibugyo outbreak in the Democratic Republic of the Congo underscores the need for broader outbreak preparedness. The death of a nurse marked the moment health officials recognized that something dangerous was spreading. The illness was Bundibugyo virus, a rare but potentially deadly infection now driving a growing outbreak in [...]

Nitrogen is an essential building block of proteins, amino acids, and DNA. Without nitrogen, cells can’t function or reproduce. Nitrogen is abundant in the atmosphere as dinitrogen gas, but plants and animals can’t access atmospheric nitrogen. Instead, we rely on biologically available forms like ammonia and nitrate. 

Specialized microbes can transform atmospheric nitrogen into ammonia via a process called biological nitrogen fixation. Nitrogen-fixing soil bacteria have a unique protein complex, the nitrogenase complex, that facilitates this nitrogen transformation. The nitrogenase complex is activated by a group of genes known as nif genes. 

Legume plants like peanuts, peas, and beans have nitrogen-fixing bacteria in the soil zone around their roots, called the rhizosphere. The symbiotic relationship between nitrogen-fixing soil bacteria and legume plants supplies most of the biologically available nitrogen to life on Earth.

However, one piece of the puzzle remains unexplored: the role of soil viruses in these nitrogen transformations, referred to as the nitrogen cycle. Viruses are microscopic particles made up of genetic material and proteins, but they can’t reproduce without a host cell. Scientists consider viruses to be biological entities that are halfway between living and non-living.

To reproduce, viruses contact a host cell and inject their genetic material into it. The virus’s genetic material takes over the host cell’s genome and forces the cell to produce proteins that assemble into new viruses. As new viruses are created, they can incorporate genes from the host cell into their own genetic material. Genes that are transferred from a host cell to a virus are known as auxiliary metabolic genes (AMGs). Viruses can carry AMGs and pass them to other hosts or use them to increase their own ecological fitness. 

Scientists from China, Spain, and the Czech Republic set out to investigate whether viruses from legume roots could increase local soil nitrogen fixation by expressing nif AMGs or by transferring nif genes to other bacteria. First, they determined the global distribution of viral nitrogen-fixing genes by analyzing about 8.6 million viral genomes from the Integrated Microbial Genomes/Virus database. They looked for the DNA sequences of known nitrogen-fixing genes and the locations where the viruses were sampled. They found that only 0.003% of the viruses in the database had at least 1 nitrogen-fixing gene, but they clustered in the same locations as nitrogen-fixing bacteria. 

The team also found 3 types of viruses that most commonly carried nitrogen-fixing genes: Kyanoviridae, Nudiviridae, and Bronfenbrennervirinae. Kyanoviridae viruses carried a nif gene called nifU. The researchers used a computer program called DRAM-v to confirm that nifU was a fully functional gene and a real tool that viruses could use. 

Next, the team collected soil samples from a cowpea field in Nanjing, China, to test whether the cowpea roots influenced the abundance of viruses using nitrogen-fixing genes. They collected soil from the cowpea rhizospheres and soil away from the plants. They analyzed both viral and bacterial RNA in the soil samples to identify active genes, using a sequencing process called metatranscriptomics. They found that the viral nifU gene was actively expressed in the cowpea rhizosphere samples more than in the non-crop soil. Although about 96% of nifU genes were being expressed by bacteria, viruses contributed about 4%. 

The researchers then assessed whether rhizospheric viruses changed the amount of nitrogen being fixed in these soils. They set up small, enclosed containers of sterile soil and added either bacteria or a mixture of bacteria and viruses extracted from the cowpea rhizospheres. They found that soil with viruses had higher total nitrogen (36 milligrams per kilogram, or mg/kg) than soil without viruses (17 mg/kg). 

Finally, they adjusted the air in each container to have a different form of dinitrogen gas. Atoms of the same element that have different atomic masses are known as isotopes. Nitrogen has 2 stable isotopes: lighter nitrogen-14 and heavier nitrogen-15. Bacteria or viruses that fix nitrogen at natural isotope abundances will take up nitrogen-14. But scientists can track who in the population fixes nitrogen by adding nitrogen-15 to the air, a process called nitrogen-15 stable isotope probing. Nitrogen-fixers will incorporate the heavy nitrogen-15 into their biomass over time and increase their weight, allowing researchers to separate and identify them.

The team grew the bacteria and viruses with nitrogen-15 for 35 days, then used stable isotope probing to separate the nitrogen fixers. They detected viral nifU AMGs among the heavier biomass, confirming that rhizospheric viruses were fixing nitrogen. 

The team concluded that rhizospheric viruses and the viral nifU AMG can increase nitrogen fixation in cowpea soils. The team suggested that although viruses with nitrogen-fixing genes are rare, they can influence the soil nitrogen cycle. They recommended that future researchers further test the contribution of viral nifU genes to plant nitrogen fixation with controlled infection experiments.

The post Viruses help plants obtain nitrogen appeared first on Sciworthy.

A new nanodisc breakthrough lets scientists see viruses more realistically, revealing hidden clues that could lead to better vaccines. Viruses are highly effective at infecting human cells, largely because of specialized proteins that cover their outer surfaces. These proteins are also a key focus for vaccine design. To study them, scientists often create lab-made versions [...]

A groundbreaking AI-designed vaccine aims to protect against not only today’s coronaviruses, but tomorrow’s as well. A new type of universal coronavirus vaccine has passed its first test in humans, marking an important step toward broader protection against future viral threats. Researchers from the University of Cambridge and biotechnology company DIOSynVax (DVX) Ltd reported that [...]