Category Archives: Genome

An epidemiologist answers the biggest questions she's getting about coronavirus. Wochit

SAN FRANCISCO At least eight strains of the coronavirus are making their way around the globe, creating a trail of death and disease that scientistsare tracking by their genetic footprints.

While much is unknown, hidden in the virus's unique microscopic fragments are clues to the origins of its original strain, how it behaves as it mutates and which strains are turning into conflagrations while others are dying out thanksto quarantine measures.

Huddled in once bustling and now almost empty labs, researchers who oversaw dozens of projects are instead focused on one goal:tracking the currentstrains of the SARS-CoV-2 virus that cause the illness COVID-19.

Labs around the world are turning their sequencing machines, most about the size of a desktop printer, to the task ofrapidly sequencing the genomes of virus samples taken frompeople sick with COVID-19.The information is uploaded to a website called NextStrain.org that shows how the virus is migrating and splitting into similarbut new subtypes.

Investigation:How federal health officials mislead states and derailed the best chance at containment.

While researcherscaution they'reonly seeing the tip of the iceberg, the tiny differences between the virus strains suggest shelter-in-place orders are working in some areas and thatno one strain of the virus ismore deadly than another. They also say it does not appear the strains will grow more lethal as theyevolve.

The virus mutates so slowly that the virus strains are fundamentally very similar to each other, said Charles Chiu, a professor of medicine and infectious disease at the University of California, San Francisco School of Medicine.

A map of the main known genetic variants of the SARS-CoV-2 virus that causes COVID-19 disease. The map is being kept on the nextstrain.org website, which tracks pathogen evolution.(Photo: nextstrain.org)

The SARS-CoV-2 virusfirst began causing illness in China sometimebetween mid-November and mid-December. Its genome is made up of about 30,000 base pairs. Humans, by comparison, have more than 3 billion. So fareven in the virus's most divergent strainsscientists have found only 11 base pair changes.

That makes iteasy to spot new lineages as they evolve, said Chiu.

The outbreaks are trackable. We have the ability to do genomic sequencing almost in real-time to see what strains or lineages are circulating, he said.

So far, mostcases on the U.S. West Coast are linked to a strainfirst identified in Washington state. It may have come from a man who had been in Wuhan, China, the virus epicenter, and returned home on Jan. 15. It is only three mutations away from the original Wuhan strain, according to work done early in the outbreakby Trevor Bedford, a computational biologist at Fred Hutch, a medical research center in Seattle.

On the East Coast there are several strains, including the one from Washington and others that appear to have made their way from China to Europe and then to New York and beyond, Chiu said.

Death rate soars in New Orleans coronavirus 'disaster' that could define city for generations

Charles Chiu, MD, PhD, director of the UCSF-Abbott Viral Diagnostics and Discovery Center, inserts a tray of Universal Transport Medium (UTM) or vials for the collection, transport, maintenance and long term freeze storage of viruses into a Biomatrix sorter that the Chiu Lab will be using, starting Monday to study the genes of the Coronavirus.(Photo: Susan Merrell/UCSF)

This isnt the first time scientists have scrambled to do genetic analysis of a virus in the midst of an epidemic. They did it with Ebola, Zika and West Nile, but nobodyoutside the scientific community paid much attention.

This is the first time phylogenetic trees have been all over Twitter, said Kristian Andersen, a professor at Scripps Research, a nonprofit biomedical science research facility in La Jolla, California, speaking of the diagrams that show the evolutionary relationships between different strains of an organism.

The maps are available on NextStrain, an online resource for scientists that uses data from academic, independent and government laboratories all over the world to visually track the genomics of the SARS-CoV-2 virus. It currently represents genetic sequences of strains from 36 countries on six continents.

While the maps are fun, they can also be little dangerous said Andersen. The trees showing the evolution of the virus are complex and its difficult even for experts to draw conclusions from them.

Remember, were seeing a very small glimpse into the much larger pandemic. We have half a million described cases right now but maybe 1,000 genomes sequenced. So there are a lot of lineages were missing, hesaid.

The basics on the coronavirus: What you need to know as the US becomes the new epicenter of COVID-19

COVID-19 hitspeople differently, with some feeling only slightly under the weather for a day, others flat on their backs sick for two weeks and about 15% hospitalized. Currently, an estimated1% of those infected die. The rate varies greatly by country and experts say it is likely tied to testing rates rather than actual mortality.

Chiu says it appears unlikely the differences are related to people being infected withdifferent strains of the virus.

The current virus strains are still fundamentally very similar to each other, he said.

The COVID-19 virus does not mutate very fast. It does so eightto 10 times more slowly than the influenza virus, said Anderson, making its evolution rate similar to other coronaviruses such as Ebola, Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).

Its also not expected tospontaneously evolve into a form more deadly than it already is to humans. The SARS-CoV-2 is so good at transmitting itself between human hosts,said Andersen,it is under no evolutionary pressure to evolve.

Chius analysis shows Californias strict shelter in place efforts appear to beworking.

Over half of the 50 SARS-CoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state. Another 30% are associated with health care workers and families of people who have the virus.

Only 20% are coming from within the community. Its not circulating widely, he said.

Thats fantastic news, he said, indicating the virus has not been able to gain aserious foothold because of social distancing.

It's like a wildfire, Chiu said. A few sparks might fly off the fire and land in the grass and start new fires. But if the main fire is doused and itsembers stomped out, you can kill offan entire strain.In California, Chiu sees a lot of sparks hitting the ground, most coming from Washington,but they're quickly being put out.

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An example wasa small cluster of cases in Solano County, northeast of San Francisco. Chius team did a genetic analysis of the virus that infected patients there and found it was most closely related to a strain from China.

At the same time, his lab was sequencing a small cluster of cases in the city of Santa Clara in Silicon Valley. They discovered the patients there had the same strain as those in Solano County. Chiu believes someone in that cluster had contact with a traveler who recently returned from Asia.

This is probably an example of a spark that began in Santa Clara, may have gone to Solano County but then was halted, he said.

The virus, he said, can be stopped.

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China is an unknown

So far researchers dont have a lot of information about the genomics of the virus inside China beyond the fact that it first appeared in the city of Wuhan sometime between mid-November and mid-December.

The viruss initial sequence was published on Jan. 10 by professor Yong-Zhen Zhang at the Shanghai Public Health Clinical Center. But Chiu says scientists dont know if there was justone strain circulating in China or more.

It may be that they havent sequenced many cases or it may be for political reasons they havent been made available, said Chiu. Its difficult to interpret the data because were missing all these early strains.

Researchers in the United Kingdom who sequenced the genomes of viruses found in travelers from Guangdong in south China found those patients strains spanned the gamut of strains circulating worldwide.

That could mean several of the strains were seeing outside of China first evolved there from the original strain, or that there are multiple lines of infection. Its very hard to know, said Chiu.

There's a new symptom of coronavirus, docs say: Sudden loss of smell or taste

While there remain many questions about the trajectory of the COVID-19 disease outbreak, one thing is broadly accepted in the scientific community: Thevirus was not created in a lab but naturally evolved in an animal host.

SARS-CoV-2s genomic molecular structure thinkthe backbone of the virus is closest to a coronavirus found in bats. Parts of its structure also resemble a virus found in scaly anteaters, according to a paper published earlier this month in the journal Nature Medicine.

Someone manufacturing a virus targetingpeople would have started with one that attacked humans, wrote National Institutes of Health Director Francis Collinsin an editorial that accompanied the paper.

Andersen was lead author on the paper. He said it could have been a one-time occurrence.

Its possible it was a single event, from a single animal to a single human, and spread from there.

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8 strains of the coronavirus are circling the globe. Here's what clues they're giving scientists. - USA TODAY

Credit: B.C. Centre for Disease Control

B.C. researchers with ready-to-launch projects applicable to combatting the COVID-19 pandemic are being urged to tap into a new funding avenue that could deliver as much as $250,000.

Genome BC, a non-profit known for facilitating genomics research across the province, launched a rapid-response funding program Thursday (March 26) that could get funds approved for projects within days.

Researchers, scientists and innovators based on the West Coast will be prioritized for funding, but Genome BC is not closing the door on any out-of-province projects that are endorsed by another regional genome centre.

The initiative is optimized for speed while maintaining high review standards and balanced decision-making, Pascal Spothelfer, president and CEO of Genome BC, said in a statement.

By investing in ideas to deliver short-term impacts, we increase our chances to overcome challenges of this pandemic more quickly.

Genome BC has been funding COVID-19 research since at least February, supporting thelaunch of a $150,000, six-month pilot studywith the B.C. Centre for Disease Control.

That project integrates genomic analysis into the BCCDCs own coronavirus tracking methods.

The goal is to turn around genome sequences from patients within 24-48 hours, which would allow B.C. experts to quickly determine if the strain has a close relative thats already appeared in the province or if its a new introduction already documented in another country or province.

So it really helps us understand transmission and that can be really important information when investigating a cluster of cases or trying to understand how an organism is spreading throughout the community, Natalie Prystajecky, a BCCDC microbiologist overseeing COVID-19 test development, toldBusiness in Vancouverlast month.

torton@biv.com

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Ready-to-launch COVID-19 projects can tap $250k from Genome BC - Business in Vancouver

The cerebral cortex is the relatively thin, folded, outer gray matter layer of the brain crucial for thinking, information processing, memory, and attention. Not much has been revealed about the genetic underpinnings that influence the size of the cortexs surface area and its thickness, both of which have previously been linked to various psychiatric traits, including schizophrenia, bipolar disorder, depression, attention deficit hyperactivity disorder (ADHD), and autism.Now, for the first time, more 360 scientists from 184 different institutions including UNC-Chapel Hill have contributed to a global effort to find more than 200 regions of the genome and more than 300 specific genetic variations that affect the structure of the cerebral cortex and likely play important roles in psychiatric and neurological conditions.

The study was led by co-senior authors Jason Stein, PhD, assistant professor in the Department of Genetics at the UNC School of Medicine; Sarah Medland, PhD, senior research fellow at the QIMR Berghofer Medical Research Institute in Australia; and Paul Thompson, PhD, associate director of the Mark and Mary Stevens Neuroimaging and Informatics Institute at the University of Southern California. Ten years ago, these scientists cofounded the ENIGMA Consortium, an international research network that has brought together hundreds of imaging genomics researchers to understand brain structure, function, and disease based on brain imaging and genetic data.

This study was only possible due to a huge scientific collaboration of more than 60 sites involved in MRI scanning and genotyping participants, Stein said. This study is the crown jewel of the ENIGMA Consortium, so far.

The researchers studied MRI scans and DNA from more than 50,000 people to identify 306 genetic variants that influence brain structure in order to shed light on how genetics contribute to differences in the cerebral cortex of individuals. Genetic variants or variations are simply the slight genetic differences that make us unique. Generally speaking, some variants contribute to differences such as hair color or blood type. Some are involved in diseases. Most of the millions of genetic variants, though, have no known significance. This is why pinpointing genetic variants associated with cortex size and structure is a big deal. Stein and colleagues consider their new genetic roadmap of the brain a sort of Rosetta stone that will help translate how some genes impact physical brain structure and neurological consequences for individuals.

Among the findings of the research:

Most of our previous understanding of genes affecting the brain are from model systems, like mice, Stein said. With mice, we can find genes, knock out genes, or over express genes to see how they influence the structure or function of the brain. But there are a couple of problems with this.One problem is, quite simply, a mouse is not a human. There are many human-specific features that scientists can only study in the human brain.

The genetic basis for a mouse is very different than the genetic basis for humans, Stein said, especially in in the noncoding regions of the genome.

Genes contain DNA, the basic human code that, when translated into action, creates proteins that do things, such as help your finger muscles type or your heart beat or your liver process toxins. But only about 3 percent of the human genome codes for proteins. The vast majority of the human genome is called the noncoding genome. Much of this region is not shared between mice and humans. This noncoding genome consists of tiny molecular switches that can modulate the expression of other genes. These switches dont directly alter the function of a protein, but they can affect the amounts of a protein that is expressed. Turns out, most genetic variants associated with psychiatric disorders are found in the noncoding region of the genome.

These findings can now be a resource for scientists to help answer important questions about the genetic influences on the brain and how they relate to numerous conditions.ReferenceGrasby et al. (2020) The genetic architecture of the human cerebral cortex. Science. DOI: https://doi.org/10.1126/science.aay6690

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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The First Genetic Map of the Cerebral Cortex - Technology Networks

There are endless viruses in our midst, made either of RNA or DNA. DNA viruses, which exist in much greater abundance around the planet, are capable of causing systemic diseases that are endemic, latent, and persistentlike the herpes viruses (which includes chicken pox), hepatitis B, and the papilloma viruses that cause cancer. DNA viruses are the ones that live with us and stay with us, Denison said. Theyre lifelong. Retroviruses, like H.I.V., have RNA in their genomes but behave like DNA viruses in the host. RNA viruses, on the other hand, have simpler structures and mutate rapidly. Viruses mutate quickly, and they can retain advantageous traits, Epstein told me. A virus thats more promiscuous, more generalist, that can inhabit and propagate in lots of other hosts ultimately has a better chance of surviving. They also tend to cause epidemicssuch as measles, Ebola, Zika, and a raft of respiratory infections, including influenza and coronaviruses. Paul Turner, a Rachel Carson professor of ecology and evolutionary biology at Yale University, told me, Theyre the ones that surprise us the most and do the most damage.

Scientists discovered the coronavirus family in the nineteen-fifties, while peering through early electron microscopes at samples taken from chickens suffering from infectious bronchitis. The coronaviruss RNA, its genetic code, is swathed in three different kinds of proteins, one of which decorates the viruss surface with mushroom-like spikes, giving the virus the eponymous appearance of a crown. Scientists found other coronaviruses that caused disease in pigs and cows, and then, in the mid-nineteen-sixties, two more that caused a common cold in people. (Later, widespread screening identified two more human coronaviruses, responsible for colds.) These four common-cold viruses might have come, long ago, from animals, but they are now entirely human viruses, responsible for fifteen to thirty per cent of the seasonal colds in a given year. We are their natural reservoir, just as bats are the natural reservoir for hundreds of other coronaviruses. But, since they did not seem to cause severe disease, they were mostly ignored. In 2003, a conference for nidovirales (the taxonomic order under which coronaviruses fall) was nearly cancelled, due to lack of interest. Then SARS emerged, leaping from bats to civets to people.The conference sold out.

SARS is closely related to the new virus we currently face. Whereas common-cold coronaviruses tend to infect only the upper respiratory tract (mainly the nose and throat), making them highly contagious, SARS primarily infects the lower respiratory system (the lungs), and therefore causes a much more lethal disease, with a fatality rate of approximately ten per cent. (MERS, which emerged in Saudi Arabia, in 2012, and was transmitted from bats to camels to people, also caused severe disease in the lower respiratory system, with a thirty-seven per cent fatality rate.) SARS-CoV-2 behaves like a monstrous mutant hybrid of all the human coronaviruses that came before it. It can infect and replicate throughout our airways. Thats why it is so bad, Stanley Perlman, a professor of microbiology and immunology who has been studying coronaviruses for more than three decades, told me. It has the lower-respiratory severity of SARS and MERS coronaviruses, and the transmissibility of cold coronaviruses.

One reason that SARS-CoV-2 may be so versatile, and therefore so successful, has to do with its particular talent for binding and fusing with lung cells. All coronaviruses use their spike proteins to gain entry to human cells, through a complex, multistep process. First, if one imagines the spikes mushroom shape, the cap acts like a molecular key, fitting into our cells locks. Scientists call these locks receptors. In SARS-CoV-2, the cap binds perfectly to a receptor called the ACE-2, which can be found in various parts of the human body, including the lungs and kidney cells. Coronaviruses attack the respiratory system because their ACE-2 receptors are so accessible to the outside world. The virus just hops in, Perlman told me, whereas its not easy to get to the kidney.

While the first SARS virus attached to the ACE-2 receptor, as well, SARS-CoV-2 binds to it ten times more efficiently, Kizzmekia Corbett, the scientific lead of the coronavirus program at the National Institutes of Health Vaccine Research Center, told me. The binding is tighter, which could potentially mean that the beginning of the infection process is just more efficient. SARS-CoV-2 also seems to have a unique ability, which SARS and MERS did not have, to use enzymes from our human tissueincluding one, widely available in our bodies, named furinto sever the spike proteins cap from its stem. Only then can the stem fuse the virus membrane and the human-cell membrane together, allowing the virus to spit its RNA into the cell. According to Lisa Gralinski, an assistant professor in the Department of Epidemiology at the University of North Carolina at Chapel Hill, this supercharged ability to bind to the ACE-2 receptor, and to use human enzymes to activate fusion, could aid a lot in the transmissibility of this new virus and in seeding infections at a higher level.

Once a coronavirus enters a personlodging itself in the upper respiratory system and hijacking the cells hardwareit rapidly replicates. When most RNA viruses replicate themselves in a host, the process is quick and dirty, as they have no proofreading mechanism. This can lead to frequent and random mutations. But the vast majority of those mutations just kill the virus immediately, Andersen told me. Unlike other RNA viruses, however, coronaviruses do have some capacity to check for errors when they replicate. They have an enzyme that actually corrects mistakes, Denison told me.

It was Denisons lab at Vanderbilt that first confirmed, in experiments on live viruses, the existence of this enzyme, which makes coronaviruses, in a sense, cunning mutators. The viruses can remain stable in a host when there is no selective pressure to change, but rapidly evolve when necessary. Each time they leap into a new species, for example, they are able to hastily transform in order to survive in the new environment, with its new physiology and a new immune system to battle. Once the virus is spreading easily within a species, though, its attitude is, Im happy, Im good, no need to change, Denison said. That seems to be playing out now in humans; as SARS-CoV-2 circles the globe, there are slight variations among its strains, but none of them seem to affect the viruss behavior. This is not a virus that is rapidly adapting. Its like the best car in the Indy 500. Its out in front and there is no obstacle in its path. So there is no benefit to changing that car.

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From Bats to Human Lungs, the Evolution of a Coronavirus - The New Yorker

EVRY, France--(BUSINESS WIRE)--Regulatory News:

IntegraGen (Paris:ALINT), a company specializing in the transformation of data from biological samples into genomic information and diagnostic tools for oncology, today announced Dana-Farber Cancer Institute will utilize the companys MERCURY cloud-based software as part of their analysis and reporting process for sequencing data obtained from tumors of cancer patients. Dana-Farber plans to utilize MERCURY to assist in the analysis of sequencing data obtained from small and large targeted gene sequencing panels as well as data derived from whole exome and genome sequencing.

Genomic profiling of tumors can assist in the identification of pathogenic molecular alterations which drive a patients cancer and enable the implementation of precision medicine-based approaches to treatment, stated Annette S. Kim M.D., Ph.D., Co-Director of the Dana-Farber Cancer Institutes new Interpretive Genomics Program within the Department of Oncologic Pathology. The program is Co-Directed by Keith L. Ligon, MD PhD, Director of the Dana-Farber Center for Patient Derived Models. MERCURY provides us with a tool to rapidly interpret large scale and complex genomic sequencing data with the added ability of customization to meet our specific analysis and reporting needs to support clinical research and clinical trials.

IntegraGen is excited about Dana-Fabers decision to utilize MERCURY and look forward to interacting with another world leader in cancer care related to the utilization of our cloud-based bioinformatic tools, said Larry Yost, General Manager of IntegraGen, Inc. We are convinced that the use of MERCURY will aid in the better understanding of the etiology of a patients cancer and assist with the realization of the benefits of precision medicine by transforming large-scale sequencing data into actionable results. We are also looking forward to continuing the development and expansion of our genomic interpretation software tools in North America.

MERCURY is a user-friendly genomic interpretation tool for oncology designed to assist pathologists and oncologists to rapidly transform raw data obtained via high-throughput sequencing into a clinical molecular report for clinical and research use. The cloud-based tool minimizes the complexity, time and cost associated with the clinical interpretation and identification of variants that may be of interest in the therapeutic management of patients. MERCURY utilizes the Google Cloud technology to ensure a secure environment for data analysis and storage which is compliant with the latest information security requirements.

About IntegraGen

IntegraGen is a company specializing in the analysis of the human genome and performs adaptive and quickly interpretable analyses for academic and private laboratories. For the management of cancers, which are characterized by a genetic disruption of cells, IntegraGen provides researchers and doctors with universal and individualized therapeutic guidance tools allowing them to adapt the treatment to the patient's genetic profile.

IntegraGen has forty-six employees and generated revenue of 8.3 million in 2019. Based in the Gnopole d'Evry, IntegraGen is also located in the United States in Cambridge, MA. IntegraGen is listed on Euronext Growth in Paris (ISIN: FR0010908723 - Mnemo: ALINT - Eligible PEA-PME).

For more information, visit http://www.integragen.com

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IntegraGen Announces Leading U.S. Cancer Center to Use MERCURY Cloud-based Tool for Oncology Sequencing Data Interpretation and Reporting - Business...

To battle the COVID-19, the population is majorly relying on the health care workers. Consequently, interacting with patients suffering from a contagious virus, leaves them as the most vulnerable. 20% of the globally infected cases (1,701) during the SARS coronavirus epidemic in 2003, were health care workers.

While age is a focal risk factor for the COVID-19, health workers of any age are extremely vulnerable. Hazardous consequences of the virus do not limit itself to the individuals infected. The capacity of the health care system is incredibly affected after every case of COVID-19 in a healthcare worker.

Health workers consequently risk exposure to viral particles more than the general public, and can possibly result in worse cases. For this reason, a large number of younger Chinese doctors have died.

Moreover, with the number of patients increasing, protective equipments are facing shortage. Meanwhile, less developed parts of the worlds, have fewer and/or inadequate health care facilities, along with overburdened staff that result in exceptionally high risks. The added stress and long duty hours only increases the vulnerability of the immune systems of health workers. Eventually, hospitals turn into a hub for the transmission of COVID-19.

Numerous doctors in Wuhan died due to the COVID-19, but were the first to raise the alarm, despite being silenced by Chinese authorities.

However, many institutions can fail in providing protection to their health care workers. Two nurses IN Dallas, were infected with Ebola in 2014, and while CDC had claimed it to be a result of breach in protocol, the nurses explained how there were no established protocols in the first place. The CDC repeated this with a Californian nurse who requested a test after developing symptoms of COVID-19 after dealing with an infected patient.

China had insisted that 13 was the number of infected doctors, causing everyone to think that the spread within hospitals could be prevented by the standard protocol and was not a concern for six weeks.

However, on the day of February 14th, the number had jumped to 1,716 and by February 20th, the World Health Organization had reported 2,055 lab-confirmed COVID-19 cases among health workers only. The estimated number had come up to 3,200 by March 3rd.

On the contrary, Italy had been reporting high rates of infected health care workers. They reported about 8.5 percent of their total infected cases, to be health workers, which would be 20 percent of their health care workforce. Meanwhile in Spain, over 4,000 infected cases had been found in the health care workforce.

Unfortunately, no matter what circumstances, the risk factor, less or more, will always exist for health care workers due to the nature of their job and workplace environment. Performing certain tasks like CPR, intubation, ventilation, and resuscitation, require the worker to maintain less than a safe distance between them and the patient. Hence, the best of circumstances do not exist.

Even today, there is a shortage of N95 masks, gowns, suits, and goggles, causing an increase in risks and uncertainty for the health care workers.

A shortage of staff (either the infected victims or the ones unwilling to take substantial risks) could cause redundancy of perfect supply chains, with more beds, more hospitals etc. Even If health workers were the only one to receive vaccines, it would still lessen the risk of the collapse of the health systems. However, CEO of a vaccine company has told the financiers that a potential vaccine for the COVID-19 is expected to be available to some health workers.

When there will be no doctors to treat, and no nurses to care, the death rates will increase exponentially from COVID-19 along with the other usual killers.

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Experts Say Mapping of Cannabis Genome Could Potentially Improve Crops And Health - Cannabis Health Insider

By Robert Langreth

In a few short weeks, Seattle-based biologist Trevor Bedford, 38, has emerged as one of the most famous epidemiologists in the world. His frequent tweets are seized upon by many of the globes top scientists and health policy makers. So far he has more than 170,000 Twitter followers, with thousands more joining every day.

But, unlike traditional epidemiologists, this disease detective working from his lab at the Fred Hutchinson Cancer Research Center, doesn't do field work to track down Covid-19 patients contacts. Instead, Bedford and a handful of colleagues spanning the globe from Seattle to Basel, Switzerland, and Wanaka, New Zealand analyse hundreds of virus genomes from patient samples to trace where outbreaks came from, how they spread from one corner of the Earth to the next and, most important, detecting early signs of infection clusters.

The teams analytic approach relies on tracking how viruses mutate over time as they spread from person to person. In the case of the coronavirus, whose RNA consists of about 30,000 genetic bases or letters, it mutates about twice a month. These minor mutations tend not to change the potency of the virus. But they provide clues for genetic detectives to chart how they shift subtly over time, allowing them to create sprawling family trees, or phylogenies, that show how the coronavirus has spread from one part of the world or country to the next.

So far Bedfords findings, which he summarizes promptly on Twitter, have been eerily on the mark, fueling his sudden celebrity status among fellow scientists and public health experts.

Trevor Bedford offered some of the most careful analysis of this pandemic from the very beginning, former Food and Drug Administration Commissioner Scott Gottlieb wrote in a March 14 tweet. His estimates on the emerging epidemic in U.S. should be taken very seriously.

Three weeks ago, when U.S. authorities still thought they might have the coronavirus somewhat under control, Bedford was among the first to argue that it had already been circulating undetected in the Seattle area for weeks. Virus-genome analyses suggested to Bedford that the very first patient in Washington in January, a 35-year-old man who had recently visited Wuhan, China, somehow infected someone else, allowing the disease to spread undetected for all that time around the Seattle area.

There are some enormous implications here, Bedford said in a nine-part Twitter thread on February 29 that has since been retweeted thousands of times. I believe we're facing an already substantial outbreak in Washington State that was not detected until now due to narrow case definition requiring direct travel to China.

This genome work differs markedly from traditional epidemiology that focuses heavily on identifying infected patients and tracking all their contacts. Instead of talking to people about who they have been in contact with and shoe-leather epidemiology, we use the genetics of pathogens to see how they are spreading and how they are transmitting around the world, says Emma Hodcroft, a molecular epidemiologist at the University of Basel who works closely with Bedford.

Genome sequencing has gradually become a more and more powerful tool over for tracking diseases. In the 2014 Ebola outbreak in West Africa, genome analyses helped trace the origin to a transmission strain that had been missed, allowing the disease to spread quietly for months in Sierra Leone. But that work took months to perform. Recently, genome sequencing has become a standard tool for tracing the source of bacteria-tainted produce.

Twitter has also become a crucial tool. Bedford says he has long written Twitter threads to accompany his scientific papers. But the coronavirus has moved so swiftly he hasn't had time for scientific papers lately. Once the first genome came out in January, I basically started doing science over Twitter, he says.

Along with the science sometimes comes an inspirational call to arms. We can bring this epidemic under control, he wrote in a thread that was retweeted 5,000 times. This is the Apollo program of our times. Let's get to it.

In his 19-part March 18 Twitter thread, Bedford offers way to do just that. One path out of the crisis, he says, could be via a massive effort to roll out in-home testing kits and drive-through sites to spot cases early on and then combine those with cellphone location data to trace all the previous movements of those who test positive.

He says he finds his newfound Twitter fame a bit bewildering. This has been very, very surreal, says Bedford, who's been working 16-hour days since the outbreak started. I am getting all this attention for doing this, and meanwhile everyone else's lives are being upended in terrible ways.

One of his key collaborators, Richard Neher, is a computational biologist at the University of Basel. Neher says the two scientists hit upon the idea of tracking virus evolution in real time using an interactive website after meeting at a conference at the University of California Santa Barbara in 2014. Their original idea was focused on influenza evolution, with the goal of helping vaccine makers predict which strains are likely to spread around the world in the next flu season. But over time their website, Nextstrain.org, evolved to include data from multiple outbreaks including Zika, Enterovirus D68 and Ebola.

When the coronavirus hit, Bedford and Neher had customized software ready to roll for rapidly analyzing hundreds of virus genomes. We hit the ground running here because all of this basic infrastructure was in place, Neher says.

Since then, Nextstrain has become a 24/7 operation, staffed with researchers at Bedfords and Nehers labs in Seattle and Basel, along with another scientist in New Zealand. With global coverage, someone is always on call to start analyzing data as soon as a new viral genome is released to gisaid.org, a website where scientists are posting the information. It takes about 20 to 30 minutes to analyze a new viral genome, allowing the website to be updated frequently.

Bedford sees his work as expanding, not replacing, the utility of existing virus-tracing methods, providing new data streams to complement traditional epidemiology. And while the evidence he gathers stops short of proving a chain of transmission, my suspicion is almost everything we have seen in the Seattle area is part of the same transmission chain, he says.

He started analyzing coronavirus genomes from China as soon as they began to flow into public databases on January 10th. At the time, health authorities were claiming that the virus had limited ability to spread between people. But Bedford found something alarming: The viral genomes were too similar to derive from viruses from different animals infecting people on multiple occasions. Instead, the genome data suggested that someone had acquired it from a single infected animal around early December and it had been spreading from person to person ever since.

This genomic data represented one of the first and strongest indications of sustained epidemic spread, Bedford said in a Jan. 31 blog post. I spent the week of Jan 20 alerting every public health official I know.

Bedford and Neher are limited by the amount of genome data that is available. So far almost 1,000 patients have had their viral genomes analyzed, out of more than 350,000 people who have been infected. There are few virus genome sequences from New York, which has surpassed Washington as the hardest-hit state in the country. Overwhelmed testing centers often don't have manpower to spare to do genome analysis when so many people are having trouble getting test results.

Even so, a basic picture is emerging: Most of the coronavirus clusters now spiraling out of control in Europe and the United States likely date back to community spread that had been quietly percolating for many weeks.

We were thinking , Neher says, it was all in China and China's problem, but that was not true."

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Eerily on the mark, a gene detective's coronavirus findings raise hope and fear in equal measure - Economic Times

A colorized image of cells from a patient infected with the coronavirus SARS-CoV-2. The virus particles are colored pink. The image was captured from a scanning electron micrograph. NIAID/Flickr hide caption

A colorized image of cells from a patient infected with the coronavirus SARS-CoV-2. The virus particles are colored pink. The image was captured from a scanning electron micrograph.

As the new coronavirus continues to spread around the globe, researchers say the virus is changing its genetic makeup slightly. But does that mean it is becoming more dangerous to humans? And what would the impact be on any future vaccines?

"In the literal sense of 'is it changing genetically,' the answer is absolutely yes," says Marc Lipsitch, an infectious disease epidemiologist at Harvard University. "What is in question is whether there's been any change that's important to the course of disease or the transmissibility or other things that we as humans care about."

So far, "there is no credible evidence of a change in the biology of the virus either for better or for worse," says Lipsitch.

Coronaviruses like all viruses change small parts of their genetic code all the time.

"Viruses mutate naturally as part of their life cycle," says Ewan Harrison, scientific project manager for the COVID-19 Genomics UK Consortium, a new project that tracks the virus in the United Kingdom.

Like flu and measles, the coronavirus is an RNA virus. It's a microscopic package of genetic instructions bundled in a protein shell. When a virus infects a person, the string of genetic instructions enables the virus to spread by telling it how to replicate once it enters a cell. The virus makes copies of itself and pushes them out to other cells in the body. Infectious doses of the virus can be coughed out in droplets and inhaled by others.

Inevitably, viruses "make mistakes in their genomes" as they copy themselves, says Harrison. Those changes can accumulate and carry over to future copies of the virus. Researchers are using these small, cumulative changes to trace the pathway of the virus through groups of people.

So far, researchers who are tracking the genetic changes in SARS-CoV-2 the official name for the coronavirus say it seems relatively stable. It acquires about two mutations a month during this process of spread, Harrison says about one-third to one-half the rate of the flu.

Coronaviruses differ from flu viruses in another key way that reduces the number of mutations. They proofread their own genomes when they copy themselves, cutting out things that don't seem right. "They maintain this ability to keep their genome pretty much intact," says Vineet Menachery, a virologist at the University of Texas Medical Branch. "The mutations that they incorporate are relatively rare."

This added proofreading function means that coronaviruses are also one of the largest RNA viruses. They're about 30,000 nucleotides long double the size of flu viruses. But at 125 nanometers wide, they're still microscopic; 800 of them could fit in the width of a human hair.

Nonetheless, their relatively larger size means "they have a lot more tools in their tool belt" compared with other RNA viruses, says Menachery in other words, more capability of fighting off a host's immune system and making copies of themselves.

Researchers are on alert for changes that might affect how the coronavirus behaves in humans. For instance, if the coronavirus developed ways to block parts of our immune system, it could hide out in our bodies and establish itself better. If it evolved to bind more strongly to human cells, it could enter them more efficiently and replicate more quickly.

But it's not as if the coronavirus needs to become more potent to survive and thrive. It's already replicating itself around the world very successfully, says Justin Bahl, an evolutionary biologist at the University of Georgia. "The viruses themselves are not actually under much pressure to change."

Selective pressures could come from introducing treatments and vaccines that are effective against a narrow group of coronavirus strains. If that happens, strains that aren't targeted by these measures would likely proliferate.

The small genetic changes that researchers have observed so far don't appear to be changing the function of the virus. "I don't think we're going to see major new traits, but I do think that we're going to see different variants emerge in the population," says Bahl.

And that slower rate of change is potentially good news for treatments and vaccines. Researchers think that once a person gains immunity against SARS-CoV-2, either by recovering from an infection or by getting a future vaccine, they will likely be protected against the strains in circulation for "years rather than months," predicts Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center, in an assessment shared on Twitter.

Projects such as the COVID-19 Genomics UK Consortium will use these genetic drifts to track the path of the virus and figure out if there are hospitals or community hubs that are hot spots for contagion, according to Harrison. This will give public health officials a sense of where and how the virus is being transmitted now.

Will the coronavirus surge when schools reopen? Will new strains emerge that develop resistance to drugs or vaccines that are introduced? To answer such questions, Harrison says, the long-term plan is to track the virus in real time and see how it changes as it spreads.

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Researchers Look At How The Coronavirus Is Mutating And Possible Consequences : Goats and Soda - NPR

Regulatory News:

IntegraGen (Paris:ALINT), a company specializing in the transformation of data from biological samples into genomic information and diagnostic tools for oncology, today announced Dana-Farber Cancer Institute will utilize the companys MERCURY cloud-based software as part of their analysis and reporting process for sequencing data obtained from tumors of cancer patients. Dana-Farber plans to utilize MERCURY to assist in the analysis of sequencing data obtained from small and large targeted gene sequencing panels as well as data derived from whole exome and genome sequencing.

"Genomic profiling of tumors can assist in the identification of pathogenic molecular alterations which drive a patients cancer and enable the implementation of precision medicine-based approaches to treatment," stated Annette S. Kim M.D., Ph.D., Co-Director of the Dana-Farber Cancer Institutes new Interpretive Genomics Program within the Department of Oncologic Pathology. The program is Co-Directed by Keith L. Ligon, MD PhD, Director of the Dana-Farber Center for Patient Derived Models. "MERCURY provides us with a tool to rapidly interpret large scale and complex genomic sequencing data with the added ability of customization to meet our specific analysis and reporting needs to support clinical research and clinical trials."

"IntegraGen is excited about Dana-Fabers decision to utilize MERCURY and look forward to interacting with another world leader in cancer care related to the utilization of our cloud-based bioinformatic tools," said Larry Yost, General Manager of IntegraGen, Inc. "We are convinced that the use of MERCURY will aid in the better understanding of the etiology of a patients cancer and assist with the realization of the benefits of precision medicine by transforming large-scale sequencing data into actionable results. We are also looking forward to continuing the development and expansion of our genomic interpretation software tools in North America."

MERCURY is a user-friendly genomic interpretation tool for oncology designed to assist pathologists and oncologists to rapidly transform raw data obtained via high-throughput sequencing into a clinical molecular report for clinical and research use. The cloud-based tool minimizes the complexity, time and cost associated with the clinical interpretation and identification of variants that may be of interest in the therapeutic management of patients. MERCURY utilizes the Google Cloud technology to ensure a secure environment for data analysis and storage which is compliant with the latest information security requirements.

About IntegraGen

IntegraGen is a company specializing in the analysis of the human genome and performs adaptive and quickly interpretable analyses for academic and private laboratories. For the management of cancers, which are characterized by a genetic disruption of cells, IntegraGen provides researchers and doctors with universal and individualized therapeutic guidance tools allowing them to adapt the treatment to the patient's genetic profile.

IntegraGen has forty-six employees and generated revenue of 8.3 million in 2019. Based in the Gnopole d'Evry, IntegraGen is also located in the United States in Cambridge, MA. IntegraGen is listed on Euronext Growth in Paris (ISIN: FR0010908723 - Mnemo: ALINT - Eligible PEA-PME).

For more information, visit http://www.integragen.com

View source version on businesswire.com: https://www.businesswire.com/news/home/20200326005546/en/

Contacts

Contacts IntegraGen Bernard COURTIEUPresident and CEO

Laurence RIOT LAMOTTEChief Financial Officercontact@integragen.com Tel: +33 (0)1 60 91 09 00

NewCap Investor and Media RelationsLouis-Victor DELOUVRIERintegragen@newcap.eu Tel: +33 (0)1 44 71 98 53

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IntegraGen Announces Leading U.S. Cancer Center to Use MERCURY Cloud-based Tool for Oncology Sequencing Data Interpretation and Reporting - Yahoo...

The UK government has backed their leading clinicians and scientists this week with new resources to map how COVID-19 spreads and evolves using whole-genome sequencing. Through a 20 million investment, the consortium will look for breakthroughs that help the UK respond to this and future pandemics, and save lives.

The COVID-19 Genomics UK Consortium COG-UK comprised of the NHS, Public Health Agencies and academic institutions including the University of Birmingham will deliver large scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the Government.

Samples from patients with confirmed cases of COVID-19 will be sent to a network of sequencing centres which currently includes Birmingham, Belfast, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield.The Wellcome Trust Sanger Institutewill provide large-scale sequencing capacity and additional support.

The University of Birmingham, led byNick Loman, Professor of Microbial Genomics and Bioinformatics in theInstitute of Microbiology and Infection, have deployed a real-time genome sequencing facility established at the University capable of sequencing genomes of the virus causing COVID-19 from patients in the West Midlands in less than 24 hours.

Professor Loman says: This is a remarkable collaboration which brings together Birmingham and the UKs incredible depth of expertise and knowledge in viral sequencing and genomics. An open and distributed model of sequencing involving both academia, the NHS and our public health bodies is the right way to ensure results are delivered quickly to decision-makers. We are now well positioned to return deep insights into understanding the rapidly-accelerating pandemic of COVID-19, easily the most pressing infectious disease emergency we have faced in two generations in the UK.

The governments investment is well-timed to accelerate the pace of viral genome sequence production and ensure this information is openly available to epidemiologists and virologists worldwide. This will provide an unprecedented real-time view of COVID-19 virus evolution.

Understanding viral evolution is important for understanding how the virus is spreading in local, national and international settings. It provides valuable epidemiological information revealing the chains of transmission that must be stopped in order to stop this outbreak.

We also stand to observe how the virus adapts to a human host over time, and how human interventions including drug treatments and eventually vaccines, exert pressure on the virus.

The consortium benefits from two major initiatives in which the University of Birmingham has played a pivotal role: ARTIC and CLIMB.The CLIMB project,which recently secured funding for a further five years with the CLIMB-BIG-DATA project, will provide the data analysis pipelines, computing and storage capacity required to analyse the large genome datasets produced by the consortium, as well as facilitating national and international research capabilities.

The ARTIC project,funded by a Wellcome Trust Collaborative Award, is a collaborative project to put genomics at the heart of outbreak response. Dr Josh Quick, a UKRI Future Leaders Fellow in the Institute of Microbiology and Infection rapidly developed a method for sequencing coronavirus, released to researchers back in January, and which has already been widely adopted across the world. This method builds on work previously successfully used to trace epidemics of Ebola virus and Zika virus.

Dr Quick says: Based on previous experiences with Ebola and Zika virus we were able to rapidly develop an approach to sequencing the COVID-19 virus rapidly using a targeted method. The importance of this method is that it works well even when only miniscule amounts of virus are present in the sample, something we commonly see. It has been used to generate the first genomes from countries including Brazil, Scotland, Wales and Northern Ireland with nanopore sequencing and we have helped over 50 groups in over 20 countries establish genome sequencing capabilities in their own labs.

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University of Birmingham joins COVID-19 Genomics UK Consortium - insideHPC