News Article | February 22, 2017
A laboratory in Wuhan is on the cusp of being cleared to work with the world’s most dangerous pathogens. The move is part of a plan to build between five and seven biosafety level-4 (BSL-4) labs across the Chinese mainland by 2025, and has generated much excitement, as well as some concerns. Some scientists outside China worry about pathogens escaping, and the addition of a biological dimension to geopolitical tensions between China and other nations. But Chinese microbiologists are celebrating their entrance to the elite cadre empowered to wrestle with the world’s greatest biological threats. “It will offer more opportunities for Chinese researchers, and our contribution on the BSL‑4-level pathogens will benefit the world,” says George Gao, director of the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology in Beijing. There are already two BSL-4 labs in Taiwan, but the National Bio-safety Laboratory, Wuhan, would be the first on the Chinese mainland. The lab was certified as meeting the standards and criteria of BSL-4 by the China National Accreditation Service for Conformity Assessment (CNAS) in January. The CNAS examined the lab’s infrastructure, equipment and management, says a CNAS representative, paving the way for the Ministry of Health to give its approval. A representative from the ministry says it will move slowly and cautiously; if the assessment goes smoothly, it could approve the laboratory by the end of June. BSL-4 is the highest level of biocontainment: its criteria include filtering air and treating water and waste before they leave the laboratory, and stipulating that researchers change clothes and shower before and after using lab facilities. Such labs are often controversial. The first BSL-4 lab in Japan was built in 1981, but operated with lower-risk pathogens until 2015, when safety concerns were finally overcome. The expansion of BSL-4-lab networks in the United States and Europe over the past 15 years — with more than a dozen now in operation or under construction in each region — also met with resistance, including questions about the need for so many facilities. The Wuhan lab cost 300 million yuan (US$44 million), and to allay safety concerns it was built far above the flood plain and with the capacity to withstand a magnitude-7 earthquake, although the area has no history of strong earthquakes. It will focus on the control of emerging diseases, store purified viruses and act as a World Health Organization ‘reference laboratory’ linked to similar labs around the world. “It will be a key node in the global biosafety-lab network,” says lab director Yuan Zhiming. The Chinese Academy of Sciences approved the construction of a BSL-4 laboratory in 2003, and the epidemic of SARS (severe acute respiratory syndrome) around the same time lent the project momentum. The lab was designed and constructed with French assistance as part of a 2004 cooperative agreement on the prevention and control of emerging infectious diseases. But the complexity of the project, China’s lack of experience, difficulty in maintaining funding and long government approval procedures meant that construction wasn’t finished until the end of 2014. The lab’s first project will be to study the BSL-3 pathogen that causes Crimean–Congo haemorrhagic fever: a deadly tick-borne virus that affects livestock across the world, including in northwest China, and that can jump to people. Future plans include studying the pathogen that causes SARS, which also doesn’t require a BSL-4 lab, before moving on to Ebola and the West African Lassa virus, which do. Some one million Chinese people work in Africa; the country needs to be ready for any eventuality, says Yuan. “Viruses don’t know borders.” Gao travelled to Sierra Leone during the recent Ebola outbreak, allowing his team to report the speed with which the virus mutated into new strains1. The Wuhan lab will give his group a chance to study how such viruses cause disease, and to develop treatments based on antibodies and small molecules, he says. The opportunities for international collaboration, meanwhile, will aid the genetic analysis and epidemiology of emergent diseases. “The world is facing more new emerging viruses, and we need more contribution from China,” says Gao. In particular, the emergence of zoonotic viruses — those that jump to humans from animals, such as SARS or Ebola — is a concern, says Bruno Lina, director of the VirPath virology lab in Lyon, France. Many staff from the Wuhan lab have been training at a BSL-4 lab in Lyon, which some scientists find reassuring. And the facility has already carried out a test-run using a low-risk virus. But worries surround the Chinese lab, too. The SARS virus has escaped from high-level containment facilities in Beijing multiple times, notes Richard Ebright, a molecular biologist at Rutgers University in Piscataway, New Jersey. Tim Trevan, founder of CHROME Biosafety and Biosecurity Consulting in Damascus, Maryland, says that an open culture is important to keeping BSL-4 labs safe, and he questions how easy this will be in China, where society emphasizes hierarchy. “Diversity of viewpoint, flat structures where everyone feels free to speak up and openness of information are important,” he says. Yuan says that he has worked to address this issue with staff. “We tell them the most important thing is that they report what they have or haven’t done,” he says. And the lab’s international collaborations will increase openness. “Transparency is the basis of the lab,” he adds. The plan to expand into a network heightens such concerns. One BSL-4 lab in Harbin is already awaiting accreditation; the next two are expected to be in Beijing and Kunming, the latter focused on using monkey models to study disease. Lina says that China’s size justifies this scale, and that the opportunity to combine BSL-4 research with an abundance of research monkeys — Chinese researchers face less red tape than those in the West when it comes to research on primates — could be powerful. “If you want to test vaccines or antivirals, you need a non-human primate model,” says Lina. But Ebright is not convinced of the need for more than one BSL-4 lab in mainland China. He suspects that the expansion there is a reaction to the networks in the United States and Europe, which he says are also unwarranted. He adds that governments will assume that such excess capacity is for the potential development of bioweapons. “These facilities are inherently dual use,” he says. The prospect of ramping up opportunities to inject monkeys with pathogens also worries, rather than excites, him: “They can run, they can scratch, they can bite.” Trevan says China’s investment in a BSL-4 lab may, above all, be a way to prove to the world that the nation is competitive. “It is a big status symbol in biology,” he says, “whether it’s a need or not.”
News Article | January 6, 2016
A Swiss company is set to become the first firm to capture carbon dioxide from the air and sell it on a commercial scale, a stepping stone to larger facilities that could one day help to combat global warming. Around July, Climeworks will start capturing some 75 tonnes of CO per month at its plant near Zurich, then selling the gas to nearby greenhouses to boost crop growth. Another company — Carbon Engineering in Calgary, Canada, which has been capturing CO since October but is yet to bring it to market — hopes to show that it can convert the gas into liquid fuel. Facilities worldwide already capture the gas from power-plant exhausts, but until 2015 only small demonstration projects sucked it up from air. Human trials will get under way for treatments that use DNA-editing technologies. Sangamo Biosciences in Richmond, California, will test the use of enzymes called zinc-finger nucleases to correct a gene defect that causes haemophilia. Working with Biogen of Cambridge, Massachusetts, it will also start a trial to look at whether the technique can boost a functional form of haemo-globin in people with the blood disorder β-thalassaemia. Scientists and ethicists hope to agree on broad safety and ethical guidelines for gene editing in humans in late 2016. And this year could see the birth of the first gene-edited monkeys that show symptoms of the human disorders they are designed to model. Physicists think there is a good chance that they will see the first evidence of gravitational waves — ripples in space-time caused by dense, moving objects such as spiralling neutron stars — thanks to the Advanced Laser Interferometer Gravitational-Wave Observatory (Advanced LIGO). And Japan will launch Astro-H, a next-generation X-ray satellite observatory that, among other things, could confirm or refute the claim that heavy neutrinos give off dark-matter signals known as bulbulons. Hints of a potential new particle from the supercharged Large Hadron Collider (LHC), which has been running at record energies since last June, could become clearer as the machine rapidly accumulates data. Even if the particle is not confirmed, the LHC could still unearth other exotic phenomena, such as glueballs: particles made entirely of the carriers of the strong nuclear force. Scientists will soon hear whether funding for research that makes viruses more dangerous can resume. In October 2014, the US government abruptly suspended financial support for ‘gain-of-function’ studies. These experiments could increase understanding of how certain pathogens evolve and how they can be destroyed, but critics say that the work also boosts the risk of, for example, accidental release of deadly viruses. A risk–benefit analysis was completed in December 2015, and the US National Science Advisory Board for Biosecurity will issue recommendations in the next few months on whether to resume funding — potentially with tightened restrictions on the research. One lucky research group will win a $50-million grant for heart-disease research from Internet giant Google and the American Heart Association. Google’s disease-research portfolio is growing, and neuroscientists are eager to see what Thomas Insel, former director of the US National Institute of Mental Health, will do at the firm, where he has been leading a mental-health effort since November. Private funding could also make its mark in space: the non-profit Planetary Society in Pasadena, California, plans to launch a US$4.5-million mission in April to test its light-driven spacecraft, LightSail. The orbits of Earth and Mars will bring the planets close to each other this year, creating the perfect opportunity for a trip to the red planet. A joint mission between the European Space Agency (ESA) and Roscosmos will capitalize on that chance. Launching in March, ExoMars 2016 will analyse gases in Mars’s atmosphere and test landing technology. Farther afield, NASA’s Juno mission will arrive at Jupiter in July. In September, ESA’s craft Rosetta will make a death dive into the comet it orbits; mourners can console themselves with the launch of NASA’s OSIRIS-REx, a mission to bring back samples from the asteroid Bennu. Hot on the heels of the launch of the US$100-million Dark Matter Particle Explorer (DAMPE) last December, China’s National Space Science Center will launch the second and third space-science probes in its planned series of five. The world’s first quantum communications test satellite will blast off in June, and the Hard X-ray Modulation Telescope — which will scour the sky for energetic sources of radiation, such as black holes and neutron stars — will fly by the end of the year. September will see China complete construction of the 500-meter Aperture Spherical Radio Telescope (FAST), which will supersede Puerto Rico’s Arecibo Observatory as the world’s largest radio telescope. In Hawaii, the team behind the controversial Thirty Meter Telescope, which had its construction permit revoked in December, will try to work out whether and how it can move the project forward. The first results from an ambitious project to analyse the world’s microbial communities are expected this year. The Earth Microbiome Project, which launched in 2010, aims to sequence and characterize at least 200,000 samples of microbial DNA taken from everything from Komodo dragon tongues to soil in the Siberian tundra. The project promises to uncover unprecedented levels of biological diversity. In November, the United States will elect a new president. If a Republican takes the White House, long-debated plans to bury nuclear waste at Yucca Mountain in Nevada may well resurface, and federal funding for climate and social science could face the chop. And if Canada’s Liberal government lives up to its pre-election promises, the country will get a chief science officer, who researchers trust will arrive with a drive to rebuild the depleted ranks of government scientists. Neuroscientists hope to finally identify genes that are crucial to regulating the timing and duration of sleep but have been difficult to tease out, possibly because they also have other functions in the brain. Pinpointing these genes could shed light on sleep disorders and some psychiatric illnesses, which scientists now realize are linked to highly disrupted sleep patterns. The SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) facility will switch on in Jordan towards the end of 2016. The ring-shaped particle accelerator will generate intense light to probe materials and biological structures down to the atomic level. It is the region’s first major international research facility, and a rare collaboration between governments including Iran, Israel and the Palestinian Authority. Support to build a similar facility in Africa is likely to gather pace. And in June, scientists will get to use bright X-ray beams at the world’s first fourth-generation synchrotron, MAX IV in Lund, Sweden.
News Article | March 8, 2016
An American company that bills itself as a pioneer in tracking emerging epidemics made a series of costly mistakes during the 2014 Ebola outbreak that swept across West Africa - with employees feuding with fellow responders, contributing to misdiagnosed Ebola cases and repeatedly misreading the trajectory of the virus, an Associated Press investigation has found. San Francisco-based Metabiota Inc. was tapped by the Sierra Leonean government and the World Health Organization to help monitor the spread of the virus and support the response after Ebola was discovered circulating in neighboring Guinea in March 2014. But emails obtained by AP and interviews with aid workers on the ground show that some of the company's actions made an already chaotic situation worse. WHO outbreak expert Dr. Eric Bertherat wrote to colleagues in a July 17, 2014, email about misdiagnoses and "total confusion" at the Sierra Leone government lab Metabiota shared with Tulane University in the city of Kenema. He said there was "no tracking of the samples" and "absolutely no control on what is being done." "This is a situation that WHO can no longer endorse," he wrote. Metabiota chief executive officer and founder Nathan Wolfe said there was no evidence his company was responsible for the lab blunders, that the reported squabbles were overblown and that any predictions made by his employees didn't reflect the company's position. He said Metabiota doesn't specialize in outbreak response and that his employees stepped in to help and performed admirably amid the carnage of the world's biggest-ever Ebola outbreak. "Metabiota's team worked tirelessly, skillfully and at substantial potential danger to themselves to assist when most of the world was still ignoring the problem," he said in an email. "We are proud of our team efforts which went above and beyond the call of duty." Wolfe said some of the problems flagged were misunderstandings - and that others were planted by commercial rivals. The complaints about Metabiota mirror the wider mismanagement that hamstrung the world's response to Ebola, a disease that has killed upward of 11,000 people. Previous AP reporting has shown that WHO resisted sounding the alarm over Ebola for two months on political, religious and economic grounds and failed to put together a decisive response even after the alert was issued. The turmoil that followed left health workers in Kenema bereft of protective equipment or even body bags and using expired chlorine, a crucial disinfectant. WHO said Metabiota was well-placed to help when Ebola broke out in West Africa because of its expertise with Lassa, a related disease. The agency declined to give any detail about how it dealt with the complaints from senior staff about the firm or the status of their current relationship. In Sierra Leone, Sylvia Blyden, who served as special executive assistant to the country's president in the early days of the outbreak, said Metabiota's response was a disaster. "They messed up the entire region," she said. She called Metabiota's attempt to claim credit for its Ebola work "an insult for the memories of thousands of Africans who have died." Wolfe, a swashbuckling scientist sometimes described as the Indiana Jones of virology, has focused his company's work on disease hotspots like West Africa in a bid to sniff out the next big threat. In his book, "The Viral Storm," Wolfe writes that his work is aimed at hunting down "the first moments at the birth of a new pandemic" to prevent its global spread. With a doctorate in immunology and infectious diseases from Harvard, Wolfe, 45, has found some serious backers. Metabiota and its nonprofit sister company Global Viral have received millions in funding from USAID, Google and the Skoll Foundation, among others. The Department of Defense alone has granted more than $18 million worth of contracts to the firm, federal records show. In the early months of the outbreak, with WHO and the Centers for Disease Control and Prevention thin on the ground, Metabiota said it stepped in to help at the request of the Sierra Leonean government. An account posted to its website says Metabiota provided "critical support" in the earliest days of the outbreak, organizing training, jointly running Sierra Leone's Ebola laboratory, assisting with outbreak logistics and producing daily reports for the government. Messages saved to ProMed, a mailing list for outbreak watchers, are upbeat, describing Metabiota's tests and how it was teaching Sierra Leoneans how to set up Ebola isolation wards. On May 12, senior Metabiota scientist Dr. Jean-Paul Gonzalez said preparedness work had "ultimately protected, or at least uniquely prepared, Sierra Leone." But there were already reports of suspected infections in the country and, within weeks, the virus tore through Sierra Leone, overwhelming the hospital in Kenema where Metabiota shared the 700-square-foot (65-square-meter) lab with Tulane. To some at Tulane, which had a long-established research project at the lab, Metabiota's missteps were predictable. The two groups worked side-by-side in an uneasy relationship that observers said sometimes tipped into open conflict. Tulane microbiology professor Bob Garry questioned whether Gonzalez was the right person to teach Sierra Leoneans how to protect themselves from Ebola. In 1994, the French researcher was at the center of a safety scare at Yale University after he accidentally infected himself with the rare Sabia virus and didn't notify officials there for more than a week. The university put more than 100 people under surveillance and ordered Gonzalez to take a remedial safety course. Garry said that should have raised a red flag. "Do you really want the person who infected himself with hemorrhagic fever going around explaining to people how to be safe?" he asked. Gonzalez referred questions to a Metabiota press representative, who said in an email that the incident happened more than 20 years ago and that Gonzalez has extensive lab safety experience. But Garry also faced questions; the WHO emails obtained by AP complaining about the Kenema lab are as critical of Tulane as they are of Metabiota. Garry acknowledged mistakes but said they were understandable given the chaotic circumstances. "We didn't have the personnel and the infrastructure that was needed to handle the onslaught of cases that were coming," he said. "We were doing the best we had with what we had there." "THEY WERE AT WAR" As the death toll mounted in July, scientists from WHO, the United States and Canada were voicing concerns about what Metabiota and its Tulane colleagues were doing at the Kenema lab, according to the emails obtained by AP and interviews with those on the ground at the time. When Gary Kobinger, head of special pathogens at the Public Health Agency of Canada, double-checked some of the facility's work in mid-July, he found worrying discrepancies in four of eight tests and identified up to five people wrongly diagnosed with Ebola, among them a worker with the medical charity Doctors Without Borders. Kobinger told AP in a telephone interview that the misdiagnoses he caught suggested many more had gone unnoticed. "If you detect two, three, four, five, how many are out there?" he said. The mistakes were doubly dangerous in a country where many mistrusted international workers, who were suspected of spreading Ebola deliberately, said Bertherat, the WHO outbreak expert. Attempts to reassure a jittery public could be "totally ruined if the population does not trust anymore in the diagnostic of the medical teams," he wrote in an email. Bertherat proposed two fixes for the problematic lab: WHO could either train Metabiota and Tulane staffers, or close down the facility and transfer all testing to another lab. He told his boss on July 18, 2014, that shutting down the shared lab was the "more prudent" option. Five days later, Geneva-based WHO staffer Pat Drury emailed the agency's chief, Dr. Margaret Chan, with criticism of both Tulane and Metabiota, referring to their shared facility as two labs. "Both labs do not meet international standards for Biosecurity," he said, adding that "several patients have been wrongly tested positive." Metabiota founder Wolfe said "we did wonderful lab work as far as I'm concerned." Errors in the shared facility stopped once "other groups" were pulled from the testing and, in any case, he noted that Metabiota tested over 1,800 samples. Even if any mistakes were made, he said the error rates were well within ranges seen elsewhere. Wolfe did not name the "other groups," but documents and interviews show Metabiota and Tulane blamed each other. "On the surface, they were collaborating," Kobinger said. But in reality, "they were at war." U.S. health official Austin Demby, who was sent to evaluate the lab's work at the request of the CDC and Sierra Leone, said initial diagnostic tests carried out by Metabiota and Tulane clashed as often as 30 percent of the time. Errors raised the risk that the virus could be spread further by sending infected patients home or confining otherwise healthy people to infectious Ebola wards. In a July 21 email to CDC and State Department officials, Demby put the blame at Tulane's door, saying Metabiota's tests were always closer to the mark and that Tulane's "add no real value to the diagnosis." But Tulane's Garry said Metabiota's staff stirred confusion by not following protocol. Wolfe said that was "simply false." The lab's set-up also was worrisome. Used needles littered the place, according to a worker who spoke on condition of anonymity because the worker was not authorized to speak to the media. Demby said in his email that the lab lacked an ultraviolet light for decontamination and didn't have enough space to process blood samples safely. "The cross contamination potential is huge and quite frankly unacceptable," he wrote. Tulane pulled the plug on its tests soon thereafter and the lab's results improved. Kobinger credited Metabiota researcher Nadia Wauquier - "the hero of that whole gang" - with tightening procedures, but eventually the company was relieved of its testing duties and the CDC took over. Both Tulane and Metabiota say they stepped aside voluntarily. Outside the lab, the training touted by Metabiota unnerved some fellow responders. Anja Wolz, an emergency coordinator with Doctors Without Borders, told AP in an interview that she saw Metabiota workers enter the homes of suspected Ebola patients without protective gear and without decontaminating themselves before leaving high-risk areas. "They didn't even have chlorine with them to wash their hands," she said, adding that Metabiota project coordinator James Bangura told her they didn't need the critical disinfectant. "I didn't go inside the Metabiota lab," she said. "I refused to go because I had already seen enough." Aid workers also complained that Metabiota employees including Bangura and a Ugandan consultant hijacked the outbreak response in Kenema, which was supposed to be directed by WHO. Metabiota staffers "are systematically obstructing any attempt to improve the existing surveillance system and there are a lot of improvement(s) needed," WHO Ebola coordinator Philippe Barboza said in an August 8, 2014, email. The next day, he argued that WHO should pull its outbreak staff from Kenema so they wouldn't be tarred with Metabiota's failures, writing he was "very concerned of the potential reputational risk for WHO." British disease expert Chris Lane echoed Barboza's concerns. In a message to Barboza, he lamented that "much good work was achieved prior to the arrival of the Metabiota field staff." Barboza and Lane declined comment on the arguments. Metabiota officials acknowledged the dispute but downplayed it. "It is inaccurate to suggest a major conflict between WHO and Metabiota," Wolfe said, noting that Bangura was awarded a Sierra Leonean presidential silver medal for his Ebola efforts. Nevertheless, the disagreement was serious enough that Metabiota said it fired the consultant and pulled Bangura from Kenema. The consequences went beyond office politics. In one email, Barboza said 1 million euros in funding proposed by the International Rescue Committee was being held up because the donors wanted "a clear WHO leadership." Some responders said one of the most disturbing mistakes Metabiota employees made was misreading the epidemic. Wolz, of Doctors Without Borders, said she recalled a meeting in the early summer as cases began multiplying "when I said that the outbreak was completely out of control." She said Metabiota responded, 'No, we know where we are, everything is OK.'" Kobinger, the Canadian scientist, said Bangura would interpret temporary dips in the number of cases to mean that the outbreak was dissipating. He said he couldn't fathom that reasoning given the number of Ebola-positive samples pouring into his own lab in nearby Kailahun. Though Bangura said he did not personally make any estimates, Kobinger said Bangura told him in July that the outbreak would be over in "two or three weeks." Any suggestion Metabiota wrongly forecast the Ebola epidemic is rejected by Wolfe, who once wrote that his career is focused on creating systems "that can accurately detect pandemics early, determine their likely importance, and, with any luck, crush those that have the potential to devastate us." Wolfe told AP that his company couldn't be held responsible for the predictions of employees seconded to Sierra Leone's Health Ministry. "We didn't make forecasts. We loaned individuals to the ministry," Wolfe said. "So the notion that somehow it's a Metabiota forecast is simply completely inaccurate." Fellow responders may not have grasped the distinction. On Aug. 11 - just three days after WHO had declared the crisis a global emergency - Metabiota employees presented a slideshow to an Ebola task force. Next to a bar chart showing a slowdown in cases were the words: "The outbreak is stabilizing." "This is the kind of report we get from Metabiota epidemiologists," she emailed colleagues from the presentation. "They are sending wrong messages. The outbreak is clearly not stabilizing." It was only in the second half of August that Kenema numbers began falling and, even then, the virus was merely moving to more populated areas. Nearly two years after the virus was first discovered circulating near its border, Sierra Leone still is not officially Ebola-free. "THEY MESSED UP ON EBOLA" Despite doubts about Metabiota's performance, Wolfe's firm has largely been congratulated on its work in West Africa. In December 2014, it won a European Union grant to help validate new tests and treatments for the disease, something a company official said was in recognition of "the critical contributions our team has made in supporting the current outbreak." In 2015, the company raised some $30 million in investment from four U.S. investment firms intended to "support Metabiota's efforts to further develop and deliver epidemic risk management worldwide," according to a press release. Even WHO has publicly credited Metabiota for its work during the outbreak. Months after Senga, one of its employees, complained privately about Metabiota's optimistic predictions in Kenema, she wrote a sunnier account on WHO's website. "The fact that they were already there helped a lot," she wrote in a post called "Ebola Diaries." Tulane and Metabiota employees already being established in Kenema "made our case investigations and contact tracing work a lot easier," she wrote. Guillaume Lachenal, a medical historian at Paris Diderot University who has followed Metabiota's work in Africa, said it was indecent of the company to claim Ebola as a success story. "They messed up on Ebola. That can happen," he said. "To make a success story out of their Ebola response, that's quite something." Satter and Cheng also reported from London. Krista Larson contributed to this report from Kenema, Sierra Leone. Lisa Leff contributed from San Francisco.
News Article | November 23, 2016
A groundbreaking study of the virosphere of the most populous animals - those without backbones such as insects, spiders and worms and that live around our houses - has uncovered 1445 viruses, revealing people have only scratched the surface of the world of viruses - but it is likely that only a few cause disease. The meta-genomics research, a collaboration between the University of Sydney and the Chinese Centre for Disease Control and Prevention in Beijing, was made possible by new technology that also provides a powerful new way to determine what pathogens cause human diseases. Professor Edward Holmes, from the Marie Bashir Institute for Infectious Diseases & Biosecurity and the School of Life and Environmental Sciences, who led the Sydney component of the project said although the research revealed humans are surrounded by viruses in our daily lives, these did not transfer easily to humans. "This groundbreaking study re-writes the virology text book by showing that invertebrates carry an extraordinary number of viruses - far more than we ever thought," Professor Holmes said. "We have discovered that most groups of viruses that infect vertebrates - including humans, such as those that cause well-known diseases like influenza - are in fact derived from those present in invertebrates," said Professor Holmes, who is also based at the University's multidisciplinary Charles Perkins Centre. The study suggests these viruses have been associated with invertebrates for potentially billions of years, rather than millions of years as had been believed - and that invertebrates are the true hosts for many types of virus. The paper, "Redefining the invertebrate RNA virosphere," is published tonight in Nature. "Viruses are the most common source of DNA and RNA on earth. It is all literally right under our feet," Professor Holmes said. The findings suggest viruses from ribonucleic acid, known as RNA - whose principal role is generally to carry instructions from DNA - are likely to exist in every species of cellular life. "It's remarkable that invertebrates like insects carry so very many viruses - no one had thought to look before because most of them had not been associated with human-borne illnesses." Although insects such mosquitoes are well-known for their potential to transmit viruses like zika and dengue, Professor Holmes stressed that insects should not generally be feared because most viruses were not transferable to humans and invertebrates played an important role in the ecosystem. Importantly, the same techniques used to discover these invertebrate viruses could also be used to determine the cause of novel human diseases, such as the controversial 'Lyme-like disease' that is claimed to occur following tick bites. "Our study utilised new techniques in meta-genomics, which we are also using to provide insights into the causes of human-borne diseases," said Professor Holmes, who is also a National Health and Medical Research Council Australia Fellow. "The new, expensive technologies available to researchers which have allowed us to do this landmark project, provide the ultimate diagnostic tool." Professor Holmes and his collaborators are conducting human studies using these new techniques to analyse Lyme-like disease and other clinical syndromes. This paper describes a landmark 'meta-transcriptomics' analysis of ~220 species of invertebrates from nine diverse animal phyla that have not previously been studied with respect to viral diversity and evolution. What we discovered is a picture of phylogenetic and genomic diversity that fundamentally changes our understanding of RNA virus evolution and re-writes the virology text book. The meta-sequencing study profiled more than 220 invertebrate species across nine animal phyla and discovered more viruses than have been documented in any one study. The research fills major gaps in the understanding of RNA and reveals viruses evolve in a far more complex way than was previously thought. For example, the study has found that viruses can capture genes (including from the animals they infect), lose genes and transfer genes among themselves. Together, the data from this new research present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution. It enables us to re-examine and re-define the invertebrate virosphere, providing a new perspective on the fundamental patterns and processes of viral evolution.
News Article | December 28, 2016
A Queensland man who is allegedly keeping a cluster of illegal rabbits at his Brisbane home faces up to $60,000 in fines under the state’s tough anti-rabbit laws. Brisbane City Council received 11 complaints of rabbit sightings in the inner-city suburb of Red Hill in 2016 and a spokesman said they are believed to belong to the same person. Rabbits are a restricted animal in Queensland and it is illegal to keep them as pets, under strict biosecurity laws. But, according to local media reports, a number of domestic rabbits have been spotted on footpaths and in suburban backyards in Red Hill and some had even been hit by cars. In a statement, a council spokesman said the rabbits had been traced back to one property. “Council understands the source of the rabbits is a local resident, who is keeping the animals on his property,” they said. “Council is working with the resident to have the rabbits removed.” Council was not able to say how many rabbits were at the house, how they had escaped, or whether the man had been charged. Rabbits are classed as “restricted matter” under the Biosecurity Act 2014. Anyone found to have sold, traded or given a rabbit in any way, or to have kept one as a pet, or to have transported it, or to have fed one for any purpose other than baiting it, faces a fine of up to $60,950. The penalties have recently increased. The Queensland government has faced continuing pressure to change the law by pet owners who say they should be able to keep rabbits as pets provided they are microchipped and desexed. Alyson Shepherd, who runs the Facebook page Legalise Pet Rabbits in Queensland, said cases like this, when rabbits have reportedly roamed uncontrolled, damaged their campaign. “It’s something we are completely against in our fight to legalise rabbits,” she told Guardian Australia. “We are completely angry about this because it’s now going to be a burden in our fight.” Shepherd brought her pet rabbit with her when she moved to Queensland from Melbourne, driving it across the border at Tweed Heads past the signs warning of what was then a $44,000 fine for rabbit ownership. She says pet rabbits are common in Queensland, despite the law, and a number of veterinary clinics are prepared to treat them so long as they are desexed. “There are people here in Queensland and there are vets who look after them,” she said. “We call them long-eared guinea pigs.” It may work as a code name in veterinary clinics but a rabbit owner who tried the same argument on police in March had to surrender the bunny to a rabbit sanctuary in Grafton, back across the border in rabbit-friendly New South Wales. Shepherd said the law was “ridiculous”, particularly because Queensland had not outlawed the keeping of domestic mice, rats, or cats, all of which are significant feral pests. According to Queensland’s Department of Agriculture and Fisheries, domestic rabbits are banned because they can easily interbreed with wild populations if they escape or are released, boosting wild numbers. Queensland’s rabbit-proof fence makes it the only state to have a significant area that is largely free of rabbits, and pet rabbits threaten that status, the department said. The department does issue permits for the use of rabbits for “certain forms of public entertainment… e.g. magic shows and circuses” and for scientific research but not to be kept as pets. Rabbits were released in Victoria as hunting fodder in 1859 and quickly multiplied. The wild rabbit population in Australia is currently estimated at 400m.
News Article | February 15, 2017
Invasive species, from feral pigs to Japanese knotweed, can devastate ecosystems. They damage crops, clog rivers, and cost farmers and homeowners billions of dollars to control each year. People aren’t the only ones suffering: The invaders have been linked to the decline of some four in every 10 endangered or threatened species in the United States. Now, the first-ever look at just how quickly these species have spread reveals more bad news: Since 1800, the rate at which alien species have been reported around the world has skyrocketed, with almost 40% of them discovered since 1970. “There are no signs of a slowdown [except for mammals and fish], and we have to expect more new invasions in the near future,” says study leader Hanno Seebens, an ecologist at the Senckenberg Biodiversity and Climate Research Centre in Frankfurt, Germany. He cautions that not all nonnative or “alien” species are a problem—only those that adversely affect the environment, which are known as “invasive.” To figure out how to help scientists deal with the problem, Seebens first had to find out how big it was. To do so, he and a team of researchers from across Europe, Asia, and the United States combed through more than 500 years of records from scientific publications, books, and unpublished works taken from more than 280 countries and islands. The documents revealed the very first sightings of alien species in each region, from squirrels to mosquitoes. Altogether, the scientists found 16,926 records of alien species of plant, mammal, insect, bird, and fish, they report today in Then, the team analyzed the speed at which new incursions were taking place, broken down by major taxonomic groups. Since 1800, that speed has increased for all groups, with the absolute number of new species reaching 1.5 sightings per day in 1996. Part of this is inevitably because of better recordkeeping over time, says Mark Hoddle, an entomologist at the University of California (UC), Riverside, who was not involved in the work. But Hoddle, who directs the Center for Invasive Species Research at UC Riverside, adds that the key trends are not surprising. The introduction of nonnative plants exploded in the 1800s thanks to the growth of globalized trade, and it has remained high ever since. Mammals and fish peaked around 1950. But other groups, including algae, mollusks, and insects rose steeply after 1950, thanks to climate change and the post–World War II wave of global trade. For those plants and animals that can easily stow away in the ballast of ships, there is a strong correlation between the spread of nonnative species and the market value of goods imported into each region. One glimmer of hope is that biosecurity measures that limit the movement of species and pathogens between countries—which have been growing in use since the early 20th century—seem to be having an effect. Since the early 1950s, for example, the speed of fish and mammals spreading beyond their native habitats has decreased, going from more than 150 sightings per year to just 24 from 1996 to 2000. In New Zealand, the study found a significant decline in the number of new alien plants since the 1990s, which coincides with the country’s 1993 Biosecurity Act and the Hazardous Substances and New Organisms Act 1996. These acts regulate imports using a white list of permitted species, and they require a risk assessment for all new species entering the country. As an island, says Hoddle, New Zealand has a distinct advantage. For countries without such geographically distinct borders, preventing the introduction of nonnative species is much harder. He says success requires science-based policy that accommodates increasing tourism and trade. “The good news is that biosecurity and quarantine measures [have worked] for some more obvious taxa, so we know we can take actions that have positive outcomes,” says Margaret Stanley, an ecologist at the University of Auckland in New Zealand, who was not involved in the new analysis. The challenge now, she adds, is to set policies that prevent more inconspicuous nonnative species from becoming established. Conservationists hope that better awareness of the threats of species, coupled with improved global biosecurity, will continue to slow the spread of nonnative species. Some researchers predict the rate of spread will reach a saturation point before tailing off. Unfortunately, Seebens’s data suggest that may be a long way off.
News Article | February 15, 2017
For the German translation, please visit here. On Friday February 3rd, 2017, Make Magazine (Germany) published "Biohacking: Federal Office warns against Do-It-Yourself kits", pointing to the German federal government's declaration on GM projects. This declaration, published by the German government on January 25th, 2017, as “"Genetic engineering with biology kits: simple, but potentially criminal", outlines the current legislation for the handling of “DIY genetic engineering kits” bought from abroad (North America). Who can do genetic engineering experiments, and where can they do them? These are the types of questions that very frequently arise in European countries as the accessible science movement gains momentum worldwide. Unfortunately, each European country has slightly different rules, making it difficult to get a straight answer. Since the DIYbio and Maker movements are growing rapidly around the world and Making with Biology outside of universities and corporations is now an exciting and feasible exercise no longer relegated to the realm of science fiction, it is important for governments to clearly delineate the current laws and regulations. In fact, looking at the German DIYbio Google Group, the legal uncertainties surrounding DIYbio in the home are brought evident. The German government along with Make: have done Europe a service in clarifying the rules in Germany. Initially when reading the Make: article using Google Translate (as many native English speakers would do), it comes across as polarizing, and even suggests that the products are potentially “criminal kits.” After a careful read, one would realize that the intention is not to crackdown on biohacking or limiting access to hands-on biology education but that it is rather a timely reminder of the containment level and environment required in Germany to complete genetic engineering tasks. For this, we see the German government's move to clarify the current rules as a positive undertaking. Furthermore, the Make: article closes on a constructive note with a link to information about how non-scientists in Germany can learn about biotechnology and genetic engineering. The “Accessible Bio” companies recommend that all European countries follow Germany’s lead and clearly and concisely communicate GM regulations to DIYbio and makers in their countries, as well as recommend appropriate locations where this type of exploration can be done if they are unable to complete the Risk Group 1 experiments at home. For example, in the United Kingdom you can find accredited DIYbio labs such as MadLab and London Biohackspace. In the Netherlands, the Waag Society, La Paillasse in France, and the OpenBiolab in Austria. Efforts are also being made by EKoli, a European “Maker” initiative that aims to standardize and make learning and hands-on genetic engineering possible for Belgium schools. “We’re pursuing and working with government to establish a scalable model for setting up appropriate containment levels in an ad hoc basis in schools, so that this important [genetic engineering] content can be effectively taught.”, says co-founder Deepak Mehta. “We are North American companies building products for North American customers, under the North American regulatory framework. At the moment, it is more complicated for those in European countries who wish to learn about genetic engineering hands-on as the rules are unclear”, says Justin Pahara, Fellow of the Johns’ Hopkins Emerging Leaders in Biosecurity Initiative (ELBI) and former Biosafety Committee member of the Department of Chemical Engineering and Biotechnology at the University of Cambridge. “Safety is one of our greatest considerations, and we encourage everyone who purchases our product(s) to comply with their local containment laws and follow the safety and disposal instructions.” In North America, these DIY, Education, and Design kits do not require regulated containment as they are considered non-harmful to humans or the environment. The regulations for containment in North America begin with potentially hazardous agents and pathogens. “We design our kits and technologies in response to information inequality” says Orkan Telhan, co-founder of Biorealize and faculty of Emerging Design Practices at University of Pennsylvania. "Not everyone has access to the same resources and infrastructure to start learning biology. And anyone who is interested in exploring the world of the living should be able to pursue it, whether it is through DIY Biology, Biohacking, or PhDs in Life Sciences. This diversity is necessary. These educational kits are stepping stones that will turn young curious minds into a growing community of professionals who can design the next generation applications of biology.” “Through our research, we found that once a person reaches the age of 16, they’ve often already decided on a career path based on the opportunities they have had access to”, says Julie Legault, CEO of Amino Labs. “The world needs innovation that leads to more abundant and cheaper medicine - more nutritious and non-animal-based sustainable food options - more eco-friendly and sustainable manufacturing methods — all of which will lead to economic growth. Genetic engineering is a key tool for achieving these goals, and, as a complex topic, is best explored hands-on. Everyone should have the opportunity to unearth their passion for solving humanity’s grand challenges through biology, regardless of their access to university labs.” We see this response as an opportunity to jointly express our commitment to make biology accessible to anyone who would be willing to use it responsibly. We invite the all policy-makers and enforcers of GM laws to consider the following: The mission of “Accessible Bio” companies is mainly to address information inequality. We intend to support biotech education to make it more accessible to those who do not have the resources. We invite all stakeholders to be in dialogue with each other to address the regulatory concerns together. There is no need to contemplate, pass and/or enforce regulation due to fear and unverified opinions. We are always ready to hear new perspectives from everyone who would like to learn genetic engineering with our kits and technologies. We are ready to improve our products to support your interests.
News Article | December 2, 2016
DARPA scientists think they can use insects to deliver genetic changes to crops. Scientists might soon be able to transform wilting, diseased crops into healthy ones by releasing colonies of benign insects onto a field. Current selective breeding techniques can produce plant seeds that are often better at resisting devastating diseases, but this process takes many years. Once a new disease threat hits a mature crop population, there’s no quick antidote available that farmers and scientists can rapidly deploy to protect these plants except for expensive and often toxic pesticides. To address this problem, scientists at the Defense Advanced Research Projects Agency (DARPA) want to capitalize on insects’ natural relationships with plants. They believe the insects can transmit viruses carrying beneficial genetic traits to the plants they feed on. “What we want to do is try to generate tools that will allow us to stabilize the food supply both domestically and internationally,” says Blake Bextine, the DARPA scientist overseeing the program. The agency wants to use an approach called gene therapy to protect and rejuvenate crops from diseases—both naturally occurring ones and biothreats. Gene therapy uses harmless viruses as a vehicle to carry new genetic material to cells in an attempt to correct or reverse disease symptoms. Scientists think insects, which are the natural carriers of most plant viruses, could shuttle defensive genes to crops. Insects can be quickly bred and released within the same growing season. DARPA is soliciting proposals from academic and industry scientists to develop a plant virus capable of carrying and delivering genetic material to a mature plant. Investigators will then have to figure out which insect species would deliver the viruses. Researchers have been working on such a therapy for a bacterial disease called greening, which is transmitted by insects and has decimated Florida’s citrus crop for the past decade. Jacqueline Fletcher, the founder and former director of the National Institute for Microbial Forensics & Food and Agricultural Biosecurity at Oklahoma State University, says the DARPA project could help spur that therapy’s development. Ideally, the technology could be used for important agricultural commodities, such as corn, wheat, and soybeans in the U.S., and cassava, a staple crop in many developing countries, especially in sub-Saharan Africa. Bextine says this approach is preferable to insecticide spray, which can be expensive and inefficient, since substantial amounts of these products never reach their intended target. Spray technology is also much less common in developing countries. For now, the gene therapy experiments will be conducted in laboratories or other contained spaces. DARPA hopes the technology will be ready to be released in the field in four years.
News Article | November 23, 2016
The meta-genomics research, a collaboration between the University of Sydney and the Chinese Centre for Disease Control and Prevention in Beijing, was made possible by new technology that also provides a powerful new way to determine what pathogens cause human diseases. Professor Edward Holmes, from the Marie Bashir Institute for Infectious Diseases & Biosecurity and the School of Life and Environmental Sciences, who led the Sydney component of the project said although the research revealed humans are surrounded by viruses in our daily lives, these did not transfer easily to humans. "This groundbreaking study re-writes the virology text book by showing that invertebrates carry an extraordinary number of viruses - far more than we ever thought," Professor Holmes said. "We have discovered that most groups of viruses that infect vertebrates - including humans, such as those that cause well-known diseases like influenza - are in fact derived from those present in invertebrates," said Professor Holmes, who is also based at the University's multidisciplinary Charles Perkins Centre. The study suggests these viruses have been associated with invertebrates for potentially billions of years, rather than millions of years as had been believed - and that invertebrates are the true hosts for many types of virus. The paper, "Redefining the invertebrate RNA virosphere," is published tonight in Nature. "Viruses are the most common source of DNA and RNA on earth. It is all literally right under our feet," Professor Holmes said. The findings suggest viruses from ribonucleic acid, known as RNA - whose principal role is generally to carry instructions from DNA - are likely to exist in every species of cellular life. "It's remarkable that invertebrates like insects carry so very many viruses - no one had thought to look before because most of them had not been associated with human-borne illnesses." Although insects such mosquitoes are well-known for their potential to transmit viruses like zika and dengue, Professor Holmes stressed that insects should not generally be feared because most viruses were not transferable to humans and invertebrates played an important role in the ecosystem. Importantly, the same techniques used to discover these invertebrate viruses could also be used to determine the cause of novel human diseases, such as the controversial 'Lyme-like disease' that is claimed to occur following tick bites. "Our study utilised new techniques in meta-genomics, which we are also using to provide insights into the causes of human-borne diseases," said Professor Holmes, who is also a National Health and Medical Research Council Australia Fellow. "The new, expensive technologies available to researchers which have allowed us to do this landmark project, provide the ultimate diagnostic tool." Professor Holmes and his collaborators are conducting human studies using these new techniques to analyse Lyme-like disease and other clinical syndromes. Explore further: Biological factors predict which viruses will cause human epidemics More information: Mang Shi et al, Redefining the invertebrate RNA virosphere, Nature (2016). DOI: 10.1038/nature20167
News Article | November 28, 2016
Every year, thousands of budding biologists compete in the International Genetically Engineered Machine (iGEM) Competition. Their goal is to employ synthetic biology to address pressing global issues. The list of sponsors is pretty much what you would expect for such an event—software companies, scientific journals, organizations focused on clean energy and agriculture. But there's one name on the list that's fairly arresting: the Federal Bureau of Investigation. Why would the FBI care about the projects of high school and college biology students? iGEM is just one of the ways that the FBI is collaborating with the biotech community, says Megan Palmer, a senior research scholar at the Center for International Security and Cooperation at Stanford University. In order to be prepared to respond to an emerging biological threat, no matter if it's an accidental outbreak or a biological attack, the FBI is working to create a culture of trust and transparency with the biotech community. Palmer discussed this topic last week at the Biofabricate conference for synthetic biology and design in New York City. Biological attacks have happened in the past—in 1984, cult members poisoned patrons of 10 salad bars in Oregon with salmonella, sickening more than 750 people; in 2001, anthrax spores mailed to newsrooms and government offices killed five people. Other incidents have sometimes failed because the would-be attackers made some scientific errors, rendering their weapons ineffective, Palmer says. But bioterror incidents are extremely difficult to predict. In the past governments have built the deadliest biological weapons programs, but one worry is that now small groups may also be able to do serious damage, Palmer says. Is the spread of an unlikely or new disease an accident, or could it be intentional? And if it was intentional, it would take a while for law enforcement to figure out who launched it and from where. It makes sense that government agencies like the FBI would want to prevent these sort of attacks before they happen. But there are other challenges there. As technology rapidly becomes more sophisticated, it's not always easy for law enforcement to understand how it works or to ask the right questions to understand threats. In some cases, it's not clear what kind of information authorities would need to estimate risk, or it would be dangerous or unethical to conduct the kinds of experiments they would need to answer those questions. That's why the FBI, along with other government agencies like the Departments of Defense and State, have looked for more opportunities to create trust and transparency with the biohacker community. Spearheaded by Edward You, a supervisory special agent in the FBI's Weapons of Mass Destruction Directorate who is a molecular biologist by training, the relationship between the two is getting cozier. In addition to informing students about the history and risks of a bioterror attack, the FBI launched the International Biosecurity and Prevention Forum designed to get experts to discuss how to prevent biosecurity risks; the agency has also helped support fellowships in responsible biotechnology leadership, including at the Synthetic Biology Leadership Excellence Accelerator Program, which Palmer directs. To the FBI, these efforts aren't just important to stave off a bioterror attack—they also protect the biotech community from harmful actors, as well as the parts of the economy based on that technology, Palmer notes. Individuals and companies in the private sector are stepping up to the responsibility. There are examples of iGEM students acting as white hat biohackers to help biotech companies detect weaknesses in their systems that might enable bioterrorists to get the materials to launch an attack—all in collaboration with the FBI, Palmer says. "There's the overall sense that the government has acknowledged that it is not necessarily the center of influence in technological development," Palmer says. "We're going to start seeing many more examples of partnerships between the government and the private sector where you wouldn't have necessarily expected them before. People should be willing to give them a chance." "There's the overall sense that the government has acknowledged that it is not necessarily the center of influence in technological development." But there's a natural tension between biohackers embedded in fringe communities and government agencies that are traditionally secretive. To Palmer, the key to the collaboration is open communication. So far, it's going well—Palmer says she has been asking the FBI questions about its involvement, what it sees in the field, and why the agency is spending so much time and effort to be involved, and so far she says they have "been willing to have more of those conversations." Still, the relationship has not yet been tested by what Palmer calls a "triggering event," a situation in which people start getting sick and biologists are suspected to be behind it, or one in which the biologists find that the FBI has been monitoring them just a little too closely. If the relationship doesn't withstand a test like that, the trust between the agency and the community would erode. Communication would break down. If biologists and federal agents continue to frame biosecurity as a mutual responsibility, that day will never come. "The efforts of individuals within larger organizations can make all the difference in the framing," Palmer says. So the FBI starts that foundation early. At the iGEM meeting in October, Palmer says, the agency addressed students about the history of bioterror and told them to be aware of suspicious activity. Some kids weren't just inspired to participate, Palmer says—they wanted to be running the conversation. "Lots of these kids may think, 'Well maybe I can be in the FBI, maybe I can be a science advisor to the Department of State,'" Palmer says. "These are people that are trying to cultivate a healthy overall ecosystem of institutions that are working in this space. It's not just 'Us against Them.'" Get six of our favorite Motherboard stories every day by signing up for our newsletter.