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Data is central to offering an innovative, personalized approach to healthcare. Personalized medicine, or precision medicine, is a growing field, with the aim to apply scientific processes, technology and evidence to optimize for the prevention, diagnosis, treatment and wider disease management of individual patients.

COVID-19 has demonstrated that access to data literally has life-or-death consequences in healthcare delivery. Data is the lifeblood of healthcare: either you can test, treat and trace the virus, or succumb to the will of an invisible enemy, as coined by David Nott. The hospitals and healthcare systems set up to share data quickly and efficiently have been able to adapt to new, expanding flows of information on the coronavirus, while those ill-equipped to participate in data-sharing efforts have struggled to flatten the curve.

Yet recognizing the value of data collaboration and actually designing, establishing and administering a data consortium segregates the global healthcare ecosystem. Many want to share data to improve clinical outcomes for patients, but far fewer are actively participating in data-sharing initiatives.

Genomic data exemplifies that health data can have value beyond the rationale for its initial collection; genomic data at scale can provide answers to how we prevent, diagnosis, and treat disease. Genomic data in isolation isnt incredibly insightful, but larger datasets linked to de-identified clinical health records and phenotypic data can serve as a treasure trove of information on our most complex and destructive diseases.

As the global health community continues to understand the benefits of data collaboration and the value of participating in a data consortium, how can we advance data interoperability in genomics and other types of sensitive health data and globally deliver a more personalized approach to healthcare?

Genomic data in isolation isnt incredibly insightful, but larger datasets linked to de-identified clinical health records and phenotypic data can serve as a treasure trove of information on our most complex and destructive diseases.

The biggest perceived challenge to creating a data consortium is how to build and use the technology that enables such data sharing and interoperability.

Yet the technology solution is evident amid a range of other proof of concept examples led by the Global Alliance for Genomics and Health and other international collaborations: a federated data system.

In fact, developing and delivering a federated data system and associated management system has been solved before in other applications. The global network of genomic data established and managed by ELIXIR is an example of how aligned organizations with common interests can relatively quickly build a functional federated data system for life sciences data.

Challenges such as managing the security of the query in flight to the data system, and similarly securing the return result, require attention, but can be solved. The scale of genomic data storage presents a formidable challenge, with the annual storage requirements predicted to be 2 40EB (EB = 10^18 b) commonly compared to multiples of the total global astronomy data or the universe of YouTube data. Multiple technologies ranging from novel storage media to compression standards should support this need.

Where the challenge does become more formidable is the real need to link clinical records to genomic data. A genomic variant (a variation in an individuals DNA) coupled with a longitudinal health record is vastly more informative than either piece of data alone. Data ontologies and standards will likely become universal over the coming years, but the vast investment in legacy data systems such as Electronic Health Records (EHRs) will make it very difficult to migrate such pre-existing data to a standardized, machine-readable format. Solving this challenge, however, is possible by aligning the needs of organizations and focusing on a specific use case to start with as a shared dataset.

The application of precision medicine to save and improve lives relies on good-quality, easily-accessible data on everything from our DNA to lifestyle and environmental factors. The opposite to a one-size-fits-all healthcare system, it has vast, untapped potential to transform the treatment and prediction of rare diseasesand disease in general.

But there is no global governance framework for such data and no common data portal. This is a problem that contributes to the premature deaths of hundreds of millions of rare-disease patients worldwide.

The World Economic Forums Breaking Barriers to Health Data Governance initiative is focused on creating, testing and growing a framework to support effective and responsible access across borders to sensitive health data for the treatment and diagnosis of rare diseases.

The data will be shared via a federated data system: a decentralized approach that allows different institutions to access each others data without that data ever leaving the organization it originated from. This is done via an application programming interface and strikes a balance between simply pooling data (posing security concerns) and limiting access completely.

The project is a collaboration between entities in the UK (Genomics England), Australia (Australian Genomics Health Alliance), Canada (Genomics4RD), and the US (Intermountain Healthcare).

The Australian Genomics Health Alliance (Australian Genomics) is an example of a national-scale genomic data consortium that has driven considerable value for partner organizations, collaborators, the health system and individuals and families participating in the research. It operates as a collaborative network of clinicians, researchers and academics dedicated to sharing data to advance scientific knowledge, improve patient outcomes and inform policy.

The clinical, phenotypic and genomic data generated through Australian Genomics research is managed in scalable, standardized systems established to facilitate data sharing. The tools and guidelines implemented by the collaboration are designed to empower Australians to contribute to data sharing, if they choose.

With 25 million people in Australia, international collaboration and data sharing are critical to increase the power and maximize the value of the countrys health and genomic datasets particularly in the context of rare diseases.

The formation of international genomic data consortia is a compelling means to achieve this. With trusted partners, defined governance and agreed standards and approaches, a data consortium delivers the value of data sharing, mitigates security risks and provides the opportunity to learn from other genomic initiatives globally.

The World Economic Forum, Australian Genomics and Genomics4RD in Canada set out to better understand how to provide a clear governance model to drive global innovation via federated data access while still mitigating potential privacy or security risks.

The result is an 8-Step Guide to Sharing Sensitive Health Data in a Federated Data Consortium Model. From finding trustworthy partners (Step 1) to determining a common problem where federating data is beneficial (Step 2), to aligning on incentives and capacities (Step 3), to identifying resourcing (Step 4), to designing and deploying a governance model (Steps 5 and 6), to structuring data (Step 7), to deploying the API technology (Step 8), creating a new health data consortium requires a custom process and extensive dialogue to ensure success and long-term viability.

Eight steps to follow to build a federated data consortium

Image: World Economic Forum

Accessing large volumes of pre-collected health data for further analysis beyond a single countrys border will unlock new innovations and discoveries, but also produce new risks to patient privacy and data security. While it is impossible to implement a singular policy safeguarding against all potential hazards of participating in a health data consortium, it is possible to create a consortium governance model by following a calculated development process. Creating a governance model will foster a cohesive, symbiotic relationship between institutions with otherwise differing models of consent, operations, security and technology. It is possible to optimize for the best outcomes policy and implementation.

Beyond technical frameworks, operational, legal and ethical frameworks of genomic data sharing will allow for transformation in healthcare delivery, enriched reference databases representative of all ethnicities, large genomic data resources available for clinical deliberation and scientific discovery, and an informed, empowered patient community.

Originally posted here:
Increasing the value of genomic data with global genomic data consortia - World Economic Forum

BRISBANE, Calif.--(BUSINESS WIRE)--Sangamo Therapeutics, Inc. (Nasdaq: SGMO), a genomic medicine company, today announced that it has executed a global licensing collaboration agreement with Novartis to develop and commercialize gene regulation therapies to address three neurodevelopmental targets, including autism spectrum disorder (ASD) and other neurodevelopmental disorders. The collaboration will leverage Sangamos propriety genome regulation technology, zinc finger protein transcription factors (ZFP-TFs), to aim to upregulate the expression of key genes involved in neurodevelopmental disorders.

At Sangamo, we believe that we can engineer zinc finger proteins to address virtually any genomic target, and we are building a broad pipeline of wholly owned and partnered programs with the goal to bring our genomic medicines to patients. In the case of the central nervous system, there are potentially hundreds of neurological disease gene targets that may be addressable by our zinc finger platform, said Sandy Macrae, CEO of Sangamo. Partnering Sangamos proprietary technology with Novartis deep experience in neuroscience drug development is a powerful combination which expands Sangamos pipeline and allows us to tackle challenging neurodevelopmental conditions. Our goal in this collaboration is to create genomic medicines for patients with neurodevelopmental disorders, such as autism, that can potentially alter the natural history of these complex lifelong disorders.

This collaboration with Sangamo is part of our commitment to pioneering the next generation of neurodevelopmental treatments, said Jay Bradner, President of the Novartis Institutes for BioMedical Research. The goal is to create new gene regulation therapies that act at the genomic level, moving us beyond the symptom focused treatments of today and toward therapies that can address some of the most challenging neurodevelopmental disorders.

Sangamos ZFP-TF genome regulation technology, which is currently delivered with adeno-associated viruses (AAVs), functions at the DNA level to selectively repress or activate the expression of specific genes to achieve a desired therapeutic effect. The collaboration will leverage ZFP-TFs engineered by Sangamo scientists in an effort to upregulate, or activate, the expression of genes that are inadequately expressed in individuals with certain types of neurodevelopmental disorders.

Under the terms of the agreement, over a three-year collaboration period, Novartis has exclusive rights to ZFP-TFs targeted to three undisclosed genes which are associated with neurodevelopmental disorders, including ASD and intellectual disability. Novartis also has the option to license Sangamos proprietary AAVs. Sangamo is responsible for certain research and associated manufacturing activities, all of which will be funded by Novartis, and Novartis assumes responsibility for additional research activities, investigational new drug-enabling studies, clinical development, related regulatory interactions, manufacturing and global commercialization.

Under the collaboration agreement, Novartis will pay Sangamo a $75 million upfront license fee payment within thirty days. In addition, Sangamo is eligible to earn up to $720 million in other development and commercial milestone payments, including up to $420 million in development milestones and up to $300 million in commercial milestones. Sangamo is also eligible to receive from Novartis tiered high single-digit to sub-teen double-digit royalties on potential net commercial sales of products arising from the collaboration.

About Sangamo Therapeutics

Sangamo Therapeutics is committed to translating ground-breaking science into genomic medicines with the potential to transform patients lives using gene therapy, ex vivo gene-edited cell therapy, and in vivo genome editing and gene regulation. For more information about Sangamo, visit http://www.sangamo.com.

Forward Looking Statements

This press release contains forward-looking statements regarding Sangamo's current expectations. These forward-looking statements include, without limitation, statements relating to the potential to develop, obtain regulatory approvals for and commercialize safe and effective therapies to treat neurodevelopmental disorders and the timing and availability of such therapies, the potential for Sangamo to receive upfront licensing fees and earn milestone payments and royalties under the Novartis collaboration and the timing of such fees, payments and royalties, the potential to use ZFP-TF technology to upregulate specific genes involved with neurodevelopmental disorders, the therapeutic potential of Sangamos zinc finger platform and other statements that are not historical fact. These statements are not guarantees of future performance and are subject to risks and uncertainties that are difficult to predict. Factors that could cause actual results to differ include, but are not limited to, risks and uncertainties related to: the evolving COVID-19 pandemic and its impact on the global business environment, healthcare systems and the business and operations of Sangamo and Novartis; the research and development process; the unpredictable regulatory approval process for product candidates across multiple regulatory authorities; the manufacturing of products and product candidates; the commercialization of approved products; the potential for technological developments that obviate technologies used by Sangamo and Novartis; the potential for Novartis to breach or terminate the collaboration agreement; and the potential for Sangamo to fail to realize its expected benefits of the Novartis collaboration. There can be no assurance that Sangamo will earn any milestone or royalty payments under the Novartis collaboration or obtain regulatory approvals for product candidates arising from these collaborations. Actual results may differ from those projected in forward-looking statements due to risks and uncertainties that exist in Sangamo's and Novartis operations and business environments. These risks and uncertainties are described more fully in Sangamo's filings with the U.S. Securities and Exchange Commission, including its most recent Quarterly Report on Form 10-Q for the quarter ended March 31, 2020 and Annual Report on Form 10-K for the year ended December 31, 2019. Forward-looking statements contained in this announcement are made as of this date, and Sangamo undertakes no duty to update such information except as required under applicable law.

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Sangamo Announces Global Collaboration With Novartis to Develop Genomic Medicines for Autism and Other Neurodevelopmental Disorders - Business Wire

Dr. Florence Haseltines resume is robust, if not intimidating: She has attended and taught at world-renowned universities, and received awards for championing womens health and advocating for womens rights. Most recently, she transformed the North Texas Genome Center at the University of Texas at Arlington into a COVID-19 testing facility for students.

Haseltine, 77, leveraged her personal connections, built on 27 years of working at the national level, to make sure that the center has the supplies necessary for testing. And that will promote her aspirations for the center: to study why the novel coronavirus appears to affect men more than women.

From a young age, she was determinedly curious about the differences between men and women. I kept asking my father, who was a scientist, why there are two sexes, and he tried hard to explain it, she said. I kept bugging him so much that finally one day he threw up his arms and said, When you grow up, you figure it out.

Haseltines career has centered on this question she asked her dad. After studying at the University of California at Berkeley and MIT, and getting her M.D. from the Albert Einstein College of Medicine, she trained as a reproductive endocrinologist and researched in vitro fertilization at Yale University. Her work helped couples struggling to have children. The Yale Fertility Center was one of the first clinics in the U.S. to offer in vitro fertilization.

In 1985, Haseltine became the Director of the Center for Population Research at the National Institute of Child Health and Human Development at the National Institutes of Health. Working there for nearly three decades, she helped increase federal funding for womens health research.

In 2018, a few years after Haseltines retirement, the president of UTA recruited her as a faculty member. The prospect of studying the human genome, or all of our genetic material, seemed like a perfect reason for her to return to academia.

Her career was influenced by her younger brother, William Haseltine. He developed some of the methodologies and technology used in genomics research as the founder of the biotechnology company Human Genome Sciences. It was clear if I was to make a second jump [in academia], it would be into the genome, she said.

When Haseltine first came to UTA, she planned to study why certain diseases affect men and women differently, and why, in some cases, one sex might suffer from more severe symptoms.

She thought that it might be due to differences between the sexes when it comes to some genetic information that determines our immune response. In particular, she wants to investigate a group of genes called human leukocyte antigens, or HLA.

HLA genes serve as an early warning for the immune system. These genes provide pieces of proteins made by foreign invaders, like a virus, to specialized immune cells that can then fight and eliminate the pathogen.

To proceed with the research, the North Texas Genome Center needed federal certification for processing human samples to diagnose, prevent and treat diseases. Last summer, Haseltine brought Anajane Smith, a researcher who studied HLA genes in Seattle, out of her own retirement to help the center get certified.

Haseltine knew Smith since the age of 6. They parted ways after college when she took a job on the East Coast and Smith took a position on the West Coast. Even after all this time, Smith jumped in to help when Haseltine needed her expertise.

With Smiths guidance, the North Texas Genome Centers officials got their required certification in January. Then the pandemic struck Texas and the university encouraged the centers director, Jon Weidanz, to shift the centers focus to testing for COVID-19.

Through personal relationships, Haseltine got the supplies necessary to test for SARS-CoV-2, the virus that causes COVID-19. She reached out to Dr. Mary Lake Polan, whom she had mentored at Yale University in 1975.

She has the ability to deal with people, so that, as focused as she is, she doesnt put them off, said Polan. They want to help her.

Polan is a board member of Quidel Corp., a company that makes diagnostic health care products. Haseltine was able to get one of the companys SARS-CoV-2 assays or products that analyze COVID-19 tests the day that the assay was approved by the Food and Drug Administration.

Then she needed to make sure that the assays worked with the UTA centers equipment. She needed the genetic material, or the RNA, of SARS-CoV-2 to test the assays.

She contacted Scott Weaver, a colleague from the Global Virus Network, an international coalition of scientists dedicated to managing viral diseases.

Weaver, director of the Institute for Human Infections & Immunity at the University of Texas Medical Branch, gave Haseltine some SARS-CoV-2 RNA from the universitys World Reference Center on Emerging Viruses and Arboviruses.

With Haseltines help, staff at the North Texas Genome Center recently ran their first successful assays. Staff started processing tests from student athletes this month, and will continue to do so every four weeks thereafter. Other students can be tested after they return to campus if they show symptoms. And students will have no out-of-pocket costs for testing, according to a UTA spokesperson.

Haseltine now has the opportunity to join other members of the scientific community in studying why SARS-CoV-2 seems to affect men more than women. Haseltine and Weidanz have a hunch that certain forms of some HLA genes could offer a protective role against COVID-19 in women.

Science can be an incredibly competitive field. So the amount of cooperation by scientists to work together and fight COVID-19 stunned many, including Haseltine. Ive had a lot of people help me in my life, but Ive never seen this level of cooperation, she said. Everybody wants to do whatever they can.

Gina Mantica reports on science for The Dallas Morning News as part of a fellowship with the American Association for the Advancement of Science.

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How a renowned scientist used her personal network to transform UTA's North Texas Genome Center into a COVID-19 testing facility - The Dallas Morning...

Novartis has agreed to license Sangamo Therapeutics zinc finger protein transcription factors (ZFP-TFs) to develop gene regulation therapies for neurodevelopmental disorders that include autism spectrum disorder and intellectual disability, the companies said, through a collaboration that could generate more than $795 million for Sangamo.

Through Sangamos ZFP-TFs, the companies plan over three years to develop treatments addressing three target genes associated with neurodevelopmental disorders, by upregulating the expression of key genes that are inadequately expressed in individuals with certain neurodevelopmental disorders.

The goal is to create new gene regulation therapies that act at the genomic level, moving us beyond the symptom focused treatments of today and toward therapies that can address some of the most challenging neurodevelopmental disorders, Jay Bradner, president of the Novartis Institutes for BioMedical Research, said in a statement. This collaboration with Sangamo is part of our commitment to pioneering the next generation of neurodevelopmental treatments.

Sangamos ZFP-TF genome regulation technology, now delivered via adeno-associated viruses (AAVs), is designed to selectively repress or activate the expression of specific genes to achieve a desired therapeutic effect, at the DNA level.

While AAVs have many advantages that make them well-suited for gene therapy, Novartis says, they also have one disadvantage: They cant carry large genes. The collaboration is designed to enable the companies to target diseases caused by mutations in one copy of a large gene.

The gene for a ZFP-TF is small enough to fit inside an AAV, Ricardo Dolmetsch, head of neuroscience at the Novartis Institutes for BioMedical Research, explained in a post on the companys blog. We can use it to increase the production of a large gene in someone who still has one intact copy of the gene. This dramatically expands the range of diseases that we can potentially target with gene therapy because many diseases are caused by the loss of a single copy of a gene.

Each of Sangamos ZFP-TFs is engineered to bind to a target region of genomic DNA in a highly specific and selective manner. They can be designed to precisely modulate the expression of targeted genes to varying extents. After identifying its target, the ZFP-TF recruits other proteins that help switch genes on or off.

The zinc finger nuclease technology is remarkable, Macrae told GEN in January. Its one of the commonest transcripts in the body. Its natural and human, and its very, very adaptable. The individual units are modular, so one is always able to come up with a solution for any part of the genome.

For its part, Sangamo reasons that it can engineer zinc finger proteins to address virtually any genomic target.

We are building a broad pipeline of wholly owned and partnered programs with the goal to bring our genomic medicines to patients, stated Sangamo CEO Sandy Macrae. In the case of the central nervous system, there are potentially hundreds of neurological disease gene targets that may be addressable by our zinc finger platform.

For Sangamo, the collaboration with Novartis is the second signed this year that focuses on applying ZFP-TFs toward treating neurological disorders. In February, Sangamo launched a potentially more than $2.7 billion partnership to develop and commercialize Sangamo gene regulation therapies. The collaboration included ST-501 for tauopathies including Alzheimers disease, ST-502 for synucleinopathies including Parkinsons disease, a third treatment targeting an undisclosed neuromuscular disease target, and additional treatments for up to nine additional undisclosed neurological disease targets over five years.

In its latest partnership with Novartis, the Swiss pharma giant will have exclusive rights to ZFP-TFs targeting the genes, which are undisclosed, during the three-year collaboration period.

Novartis also has the option to license Sangamos AAVs. Sangamo has agreed to oversee specified research and associated manufacturing activities, all of which will be funded by Novartiswhile Novartis agreed to oversee additional research activities, investigational new drug-enabling studies, clinical development, related regulatory interactions, manufacturing, and global commercialization.

Novartis agreed to pay Sangamo a $75 million upfront license fee within 30 days, plus up to $720 million tied to achieving development and commercial milestonesconsisting of up to $420 million in development milestones and up to $300 million in commercial milestones.

Sangamo is also eligible to receive from Novartis tiered high single-digit to sub-teen double-digit royalties on potential net commercial sales of products arising from the collaboration.

Partnering Sangamos proprietary technology with Novartis deep experience in neuroscience drug development is a powerful combination which expands Sangamos pipeline and allows us to tackle challenging neurodevelopmental conditions, Macrae added.

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Novartis Taps Sangamo Zinc Finger Tech for Gene Regulation Therapies - Genetic Engineering & Biotechnology News

For A-J Media

For the first time, the raw genetic material that codes for bats unique adaptations and superpowers such as the ability to fly, use sound to move effortlessly in complete darkness, survive and tolerate deadly diseases and resist aging and cancer has been fully revealed and published in Nature.

Bat1K, a global consortium of scientists dedicated to sequencing the genomes of every one of the 1,421 living bat species, has generated and analyzed six highly accurate bat genomes that are 10 times more complete than any bat genome published to date, in order to begin to uncover bats unique traits.

"Given these exquisite bat genomes, we can now better understand how bats tolerate viruses, slow down aging and have evolved flight and echolocation," said Emma Teeling of University College Dublin, co-founding director of Bat1K and senior author on the paper. "These genomes are the tools needed to identify the genetic solutions evolved in bats that ultimately could be harnessed to alleviate human aging and disease."

As part of the consortium, two researchers in Texas Tech Universitys Department of Biological Sciences, associate professor David A. Ray and doctoral candidate Kevin Sullivan, played a pivotal role in the genome analysis.

"Our lab was tasked with analyzing the portions of each genome that are made up of transposable elements, parts of the genome that can move around and potentially disrupt or alter function," Ray said. "We found that, unlike most other groups of mammals, bats have an exceptionally diverse transposable element repertoire. This suggests their genomes may have the ability to change and adapt to novel environments above and beyond what a typical mammal can do. This may explain what appears to be their increased ability to tolerate viruses and live longer, healthier lives than would be expected given their size."

Ray explained that a perfectly assembled genome would have the same number of pieces as there are chromosomes for that species. For example, humans have 23 pairs of chromosomes so a very good assembly would consist of 23 pieces of assembled DNA. In contrast, bad genome assemblies have thousands of pieces, meaning the assembly is very fragmented. Because these bat genomes have very few pieces, the researchers refer to them as "exquisite" genomes.

To generate these exquisite bat genomes, the Bat1K team used the newest technologies of the DRESDEN-concept Genome Center, a shared technology resource in Dresden, Germany, to sequence the bats DNA, and generated new methods to assemble these pieces into the correct order and to identify the genes present.

"Using the latest DNA sequencing technologies and new computing methods for such data, we have 96-99% of each bat genome in chromosome-level reconstructions an unprecedented quality akin to, for example, the current human genome reference, which is the result of over a decade of intensive finishing efforts," said senior author Eugene Myers, director of Max Planck Institute of Molecular Cell Biology and Genetics, and the Center for Systems Biology in Dresden. "As such, these bat genomes provide a superb foundation for experimentation and evolutionary studies of bats fascinating abilities and physiological properties."

The team compared these bat genomes against 42 other mammals to address the unresolved question of where bats are located within the mammalian tree of life. Using novel phylogenetic methods and comprehensive molecular data sets, the team found the strongest support for bats being most closely related to a group called Ferreungulata that consists of carnivores (which includes dogs, cats and seals, among other species), pangolins, whales and ungulates (hooved mammals).

To uncover genomic changes that contribute to the unique adaptations found in bats, the team systematically searched for gene differences between bats and other mammals, identifying regions of the genome that have evolved differently in bats and the loss and gain of genes that may drive bats unique traits.

"Our genome scans revealed changes in hearing genes that may contribute to echolocation, which bats use to hunt and navigate in complete darkness," said senior author Michael Hiller, research group leader in the Max Planck Institute of Molecular Cell Biology and Genetics, the Max Planck Institute for the Physics of Complex Systems and the Center for Systems Biology. "Furthermore, we found expansions of anti-viral genes, unique selection on immune genes, and loss of genes involved in inflammation in bats. These changes may contribute to bats exceptional immunity and points to their tolerance of coronaviruses."

The team also found evidence that bats ability to tolerate viruses is reflected in their genomes. The exquisite genomes revealed "fossilized viruses," evidence of surviving past viral infections, and showed that bat genomes contained a higher diversity than other species providing a genomic record of historical tolerance to viral infection.

Given the quality of the bat genomes, the team uniquely identified and experimentally validated several non-coding regulatory regions that may govern bats key evolutionary innovations.

"Having such complete genomes allowed us to identify regulatory regions that control gene expression that are unique to bats," said senior author Sonja Vernes of the Max Planck Institute for Psycholinguistics and co-founding director of Bat 1K. "Importantly, we were able to validate unique bat microRNAs in the lab to show their consequences for gene regulation. In the future we can use these genomes to understand how regulatory regions and epigenomics contributed to the extraordinary adaptations we see in bats."

This is just a beginning. The remaining approximately 1,400 living bat species exhibit an incredible diversity in ecology, longevity, sensory perception and immunology, and numerous questions remain regarding the genomic basis of these spectacular features. Bat1K will answer these questions as more and more exquisite bat genomes are sequenced, further uncovering the genetic basis of bats rare and wonderful superpowers.

This study was funded in part by the Max Planck Society, the European Research Council, the Irish Research Council and the Human Frontier Science Program.

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Texas Tech researchers involved in analyzing first reference-quality bat genomes - LubbockOnline.com

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New research reveals the genetic material that codes for bat adaptations and superpowers.

Those bat powers include the ability to fly, to use sound to move effortlessly in complete darkness, to tolerate and survive potentially deadly viruses, and to resist aging and cancer.

The project, called Bat1K, sequenced the genome of six widely divergent living bat species.

Although other bat genomes have been published before, the Bat1K genomes are 10 times more complete than any bat genome published to date.

One aspect of the paper findings shows evolution through gene expansion and loss in a family of genes, APOBEC3, which is known to play an important role in immunity to viruses in other mammals. The details in the paper that explain this evolution set the groundwork for investigating how these genetic changes, found in bats but not in other mammals, could help prevent the worst outcomes of viral diseases in other mammals, including humans.

More and more, we find gene duplications and losses as important processes in the evolution of new features and functions across the Tree of Life, says Liliana M. Dvalos, an evolutionary biologist and professor in the department of ecology and evolution at Stony Brook University and coauthor of the paper in Nature.

But, determining when genes have duplicated is difficult if the genome is incomplete, and it is even harder to figure out if genes have been lost. At extremely high quality, the new bat genomes leave no doubts about changes in important gene families that could not be discovered otherwise with lower-quality genomes.

To generate the bat genomes, the team used the newest technologies of the DRESDEN-concept Genome Center, a shared technology resource in Dresden, Germany to sequence the bats DNA, and generated new methods to assemble these pieces into the correct order and to identify the genes present. While previous efforts had identified genes with the potential to influence the unique biology of bats, uncovering how gene duplications contributed to this unique biology was complicated by incomplete genomes.

The team compared these bat genomes against 42 other mammals to address the unresolved question of where bats are located within the mammalian tree of life. Using novel phylogenetic methods and comprehensive molecular data sets, the team found the strongest support for bats being most closely related to a group called Fereuungulata that consists of carnivorans (which includes dogs, cats, and seals, among other species), pangolins, whales, and ungulates (hooved mammals).

To uncover genomic changes that contribute to the unique adaptations found in bats, the team systematically searched for gene differences between bats and other mammals, identifying regions of the genome that have evolved differently in bats and the loss and gain of genes that may drive bats unique traits.

It is thanks to a series of sophisticated statistical analyses that we have started to uncover the genetics behind bats superpowers, including their strong apparent abilities to tolerate and overcome RNA viruses, says Dvalos.

The researchers found evidence the exquisite genomes revealed fossilized viruses, evidence of surviving past viral infections, and showed that bat genomes contained a higher diversity of these viral remnants than other species providing a genomic record of ancient historical interaction with viral infections. The genomes also revealed the signatures of many other genetic elements besides ancient viral insertions, including jumping genes or transposable elements.

Funding for the study came in part from the Max Planck Society, the European Research Council, the Irish Research Council, the Human Frontiers of Science Program, and the National Science Foundation.

Source: Stony Brook University

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Genomes reveal the source of bat 'superpowers' - Futurity: Research News

(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.)

William Petri, University of Virginia

(THE CONVERSATION) As millions of people are recovering from COVID-19, an unanswered question is the extent to which the virus can hide out in seemingly recovered individuals. If it does, could this explain some of the lingering symptoms of COVID-19 or pose a risk for transmission of infection to others even after recovery?

I am a physician-scientist of infectious diseases at the University of Virginia, where I care for patients with infections and conduct research on COVID-19. Here I will briefly review what is known today about chronic or persistent COVID-19.

What is a chronic or persistent viral infection?

A chronic or persistent infection continues for months or even years, during which time virus is being continually produced, albeit in many cases at low levels. Frequently these infections occur in a so-called immune privileged site.

What is an immune privileged site?

There are a few places in the body that are less accessible to the immune system and where it is difficult to eradicate all viral infections. These include the central nervous system, the testes and the eye. It is thought that the evolutionary advantage to having an immune privileged region is that it protects a site like the brain, for example, from being damaged by the inflammation that results when the immune system battles an infection.

An immune privileged site not only is difficult for the immune system to enter, it also limits proteins that increase inflammation. The reason is that while inflammation helps kill a pathogen, it can also damage an organ such as the eye, brain or testes. The result is an uneasy truce where inflammation is limited but infection continues to fester.

A latent infection versus a persistent viral infection

But there is another way that a virus can hide in the body and reemerge later.

A latent viral infection occurs when the virus is present within an infected cell but dormant and not multiplying. In a latent virus, the entire viral genome is present, and infectious virus can be produced if latency ends and the infections becomes active. The latent virus may integrate into the human genome as does HIV, for example or exist in the nucleus as a self-replicating piece of DNA called an episome.

A latent virus can reactivate and produce infectious viruses, and this can occur months to decades after the initial infection. Perhaps the best example of this is chickenpox, which although seemingly eradicated by the immune system can reactivate and cause herpes zoster decades later. Fortunately, chickenpox and zoster are now prevented by vaccination. To be infected with a virus capable of producing a latent infection is to be infected for the rest of your life.

How does a virus become a latent infection?

Herpes viruses are by far the most common viral infections that establish latency.

This is a large family of viruses whose genetic material, or genome, is encoded by DNA (and not RNA such as the new coronavirus). Herpes viruses include not only herpes simplex viruses 1 and 2 which cause oral and genital herpes but also chickenpox. Other herpes viruses, such as Epstein Barr virus, the cause of mononucleosis, and cytomegalovirus, which is a particular problem in immunodeficient individuals, can also emerge after latency.

Retroviruses are another common family of viruses that establish latency but by a different mechanism than the herpes viruses. Retroviruses such as HIV, which causes AIDS, can insert a copy of their genome into the human DNA that is part of the human genome. There the virus can exist in a latent state indefinitely in the infected human since the virus genome is copied every time DNA is replicated and a cell divides.

Viruses that establish latency in humans are difficult or impossible for the immune system to eradicate. That is because during latency there can be little or no viral protein production in the infected cell, making the infection invisible to the immune system. Fortunately coronaviruses do not establish a latent infection.

Could you catch SARS-CoV-2 from a male sexual partner who has recovered from COVID-19?

In one small study, the new coronavirus has been detected in semen in a quarter of patients during active infection and in a bit less than 10% of patients who apparently recovered. In this study, viral RNA was what was detected, and it is not yet known if this RNA was from still infectious or dead virus in the semen; and if alive whether the virus can be sexually transmitted. So many important questions remain unanswered.

Ebola is a very different virus from SARS-C0V-2 yet serves as an example of viral persistence in immune privileged sites. In some individuals, Ebola virus survives in immune privileged sites for months after resolution of the acute illness. Survivors of Ebola have been documented with persistent infections in the testes, eyes, placenta and central nervous system.

The WHO recommends for male Ebola survivors that semen be tested for virus every three months. They also suggest that couples abstain from sex for 12 months after recovery or until their semen tests negative for Ebola twice. As noted above, we need to learn more about persistent new coronavirus infections before similar recommendations can be considered.

Could persistent symptoms after COVID-19 be due to viral persistence?

Recovery from COVID-19 is delayed or incomplete in many individuals, with symptoms including cough, shortness of breath and fatigue. It seems unlikely that these constitutional symptoms are due to viral persistence as the symptoms are not coming from immune privileged sites.

Where else could the new coronavirus persist after recovery from COVID-19?

Other sites where coronavirus has been detected include the placenta, intestines, blood and of course the respiratory tract. In women who catch COVID-19 while pregnant, the placenta develops defects in the mothers blood vessels supplying the placenta. However, the significance of this on fetal health is yet to be determined.

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The new coronavirus can also infect the fetus via the placenta. Finally, the new coronavirus is also present in the blood and the nasal cavity and palate for up to a month or more after infection.

The mounting evidence suggests that SARS-CoV-2 can infect immune privileged sites and, from there, result in chronic persistent but not latent infections. It is too early to know the extent to which these persistent infections affect the health of an individual like the pregnant mother, for example, nor the extent to which they contribute to the spread of COVID-19.

Like many things in the pandemic, what is unknown today is known tomorrow, so stay tuned and be cautious so as not to catch the infection or, worse yet, spread it to someone else.

This article is republished from The Conversation under a Creative Commons license. Read the original article here: https://theconversation.com/does-coronavirus-linger-in-the-body-what-we-know-about-how-viruses-in-general-hang-on-in-the-brain-and-testicles-142878.

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Does coronavirus linger in the body? What we know about how viruses in general hang on in the brain and testicles - Huron Daily Tribune

BETHESDA, Md., July 30, 2020 /PRNewswire/ --The ACMG Foundation for Genetic and Genomic Medicine announced today that Nasha Fitter has been elected to its board of directors. The ACMG Foundation is a national nonprofit foundation dedicated to facilitating the integration of genetics and genomics into medical practice. The board members are active participants, serving as advocates for the ACMG Foundation and for advancing its policies and programs. Ms. Fitter was elected to a two-year term starting immediately.

ACMG Foundation President Bruce R. Korf, MD, PhD, FACMG said, "I am delighted to welcome Nasha Fitter to the ACMG Foundation board as a public member.Nasha has a passion for improving the lives of individuals who are affected with genetic conditions, and also has extraordinary skills in business, education and technology.She is superbly qualified to represent the interests of the public on the ACMG Foundation board."

Ms. Fitter has a background in healthcare and education. She currently serves as director of Rare and Neurological Diseases at Ciitizen, where she and her team generate regulatory-grade longitudinal data for natural history studies, synthetic control arm and post-approval studies for rare and neurological diseases. She is also co-founder, CEO, and head of research at FOXG1 Research Foundation, an organization she launched after her daughter was diagnosed with FOXG1 syndrome. The foundation is focused on finding a cure for this severe disease and is working to build global expertise on FOXG1 neurobiology and a repository of patient clinical outcomes. Previously, Ms. Fitter founded and served as CEO of Schoolie, a technology company that collected data on school performance across the US and shared actionable analysis with parents and policymakers. She also worked as director of the Global Schools Program at Microsoft Education, Microsoft's premier global program for K12 schools. Ms. Fitter earned a Bachelor of Science from the University of Southern California and an MBA from Harvard Business School.

About her election to the ACMG Foundation Board of Directors, Ms. Fitter said, "In the next few years we will see the immense power of genetic medicine in saving and transforming people's lives. I am thrilled to be joining an organization at the forefront of this incredible science and look forward to working with such a diverse and experienced board."

A complete roster of the ACMG Foundation board can be found at http://www.acmgfoundation.org.

About the ACMG Foundation for Genetic and Genomic Medicine

The ACMG Foundation for Genetic and Genomic Medicine, a 501(c)(3) nonprofit organization, is a community of supporters and contributors who understand the importance of medical genetics and genomics in healthcare. Established in 1992, the ACMG Foundation supports the American College of Medical Genetics and Genomics (ACMG) mission to "translate genes into health." Through its work, the ACMG Foundation fosters charitable giving, promotes training opportunities to attract future medical geneticists and genetic counselors to the field, shares information about medical genetics and genomics, and sponsors important research. To learn more and support the ACMG Foundation mission to create "Better Health through Genetics" visit acmgfoundation.org.

Kathy Moran, MBA [emailprotected]

SOURCE American College of Medical Genetics and Genomics

http://www.acmgfoundation.org

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Nasha Fitter Elected to Board of Directors of the ACMG Foundation for Genetic and Genomic Medicine - PRNewswire

The European Sustainable Agriculture through Genome Editing (EU-SAGE) network and its members from 132 European research institutes and associations urge the European Council, European Parliament, and the European Commission to reconsider their stance ongenome editing, which is one of the tools needed to achieve the Sustainable Development Goals. In an open statement, the EU-SAGE network said that developing new crop varieties need tools that are safe, easy, and fast, and the latest addition to these tools is precision breeding or genome editing.

The use of precision breeding techniques, however, has been halted in Europe on July 25, 2018, due to the ruling of the European Court of Justice which placed all crops developed through this technique under prohibitively strict GMO regulations, even if no foreign DNA was introduced in the crops.

The open statement strongly recommends the following to the European Council, the European Parliament, and the European Commission:

For more details, read thenews release from VIB. Read theopen statement here.

Source: ISAAA

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132 Research Institutes and Associations Urge the EU to Reconsider Stance on Genome Editing - Seed World

Our collective pandemic experience has made us keenly aware that bats have an uncanny ability to carry around deadly viruses, but somehow still survive.

There is a lot we don't yet know about this enviable virus resistance - along with other bat abilities, such as extreme longevity - but new highly-detailed genome sequences may provide some clues.

"Thanks to a series of sophisticated statistical analyses we have started to uncover the genetics behind bats' 'superpowers,' including their strong apparent abilities to tolerate and overcome RNA viruses," said Stony Brook University evolutionary and conservation biologist Liliana Dvalos.

By comparing the genomes of six bat species with other mammal genomes, the researchers have found evidence that the immune systems of bats functions in a unique way to other mammals. And better understanding exactly how they fight off viruses could help us do the same.

These virus resisting superpowers have allowed bats to thrive in many environments around the world. They now make up 20 percent of all living mammal species, with over 1,400 identified bat species.

And despite their ability to carry germs, they play vital roles in our ecosystems.At least 500 plant species depend on bat pollination (like bananas, mangos, and agave), other plants depend on their poop, and some species keep insects in check (including pesky mosquitoes) by devouring them.

Understanding their resistance and its unfortunate virus-incubating side effect, could help us co-exist more safely.

Dvalos and colleagues sequenced and compared the genomes of six very different bat species: insectivorousRhinolophus ferrumequinum,Molossus molossus,Pipistrellus kuhliiandMyotis myotis, frugivorousRousettus aegyptiacusand omnivorousPhyllostomus discolor.

They then compared these with 42 other mammal genomes, allowing them to find the parts that differ in bats, and therefore identify the genetic instructions that code for unique bat traits.

As well as a strong evolution on hearing-related genes - likely connected to their incredible echolocation abilities - the team found bats have lost a family of mammalian genes involved in our immune system. These include some immune-stimulating inflammation genes associated with autoimmune diseases in humans.

Changes in another group of immunity genes called APOBEC were also seen. These genes have been lost, expanded or duplicated across different bat species. They create enzymes involved in blocking a virus's ability to insert its genes into their host genome - a critical part of the virus's ability to replicate.

"More and more, we find gene duplications and losses as important processes in the evolution of new features and functions across the Tree of Life," explained Dvalos.

Within the bat genome the team also found what we might think of as fossilsed viruses - old bits of virus genes that were inserted into the bat genome and then passed on through generations.

Humans have these fossil viruses too and they provide a record of viral infections through our evolutionary history, like a genetic memory.

The bat genome had a higher diversity of these virus fossils, and they revealed bats have survived viruses that were previously thought to only infect birds.

Taken together, these findings support growing evidence that bats can tolerate and survive viral infections better than most mammals, because their immune system works differently.

"Our reference-quality bat genomes provide the resources required to uncover andvalidate the genomic basis of adaptations of bats, and stimulate new avenues ofresearch that are directly relevant to human health and disease," the researchers wrote in their paper.

Maybe bats can one day share their antivirus superpowers with us as well as their germs.

This research was published in Nature.

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Bats Can Survive Carrying Deadly Viruses, And We're Starting to Figure Out How - ScienceAlert