Category Archives: Genome

As Silicon Valley is gearing up to fight against the novel coronavirus, NVIDIA is putting its GPU technology to use by enabling researchers and gamers to join the on-going efforts.

Covid-19

GPUs are not only meant to enhance the gaming experience through fast graphics or accelerating the training and inference of machine learning models. They also play a crucial role in assisting the scientific community involved in researching genome analysis and sequencing.

To fight the growing threat of novel coronavirus, NVIDIA is making its platform, Parabricks, free for 90 days to any researcher working on sequencing the novel coronavirus and the genomes of people afflicted with COVID-19.

Genome analysis is a computationally intensive effort that needs a high performance computing environment powered by CPUs and GPUs. Sequencing platforms such as DNBSEQ-T7 from MGI generate as much as 6 TerraBytes of data every day, which is analyzed by scientists performing whole genome sequencing. According to NVIDIA, these systems will generate about 20 ExaBytes of data by 2025 more than Twitter, YouTube and astronomy combined. Interestingly, it would take all the CPUs in every cloud and more than 200 days to run genome analysis.

Parabricks, an Ann Arbor, Michigan-based startup, built a platform based on GPU to speed up the process of analyzing whole genomes all 3 billion base pairs in human chromosomes from days to under an hour.

As platforms like DNBSEQ-T7 generate more data, analysis has becomes a major bottleneck in both time and cost perspectives. Parabricks solution addresses both of these barriers to accelerate the genomic analysis.

Parabricks platform is powered by NVIDIA CUDA-X and benefits from CUDA, cuDNN and TensorRT inference software and runs on NVIDIA entire computing platform from NVIDIA T4 to DGX to cloud GPU instances.

Earlier this year, NVIDIA acquired Parabricks with a goal to release the companion technology that accelerates single-cell and RNA analysis.

The Parabricks acquisition helped NVIDIA to officially offer genome sequencing and analysis on its HPC platform.

By making Parabricks accessible to the research community, NVIDIA aims to dramatically reduce the time for variant calling on a whole human genome from days to less than an hour on a single server.

Since Parabricks is available as a part of NVIDIA GPU Cloud (NGC), it is expected to run on major cloud platforms and NVIDIAs own appliances including DGX-1. Researchers with access to NVIDIA GPUs can fill out a form to request access to Parabricks.

Apart from offering Parabricks free for 90 days, NVIDIA is also encouraging gamers to participate in the Folding@Home project, a distributed computing project for disease research that simulates protein folding, computational drug design and other types of molecular dynamics.

Folding@home is a collaborative project focused on disease research. The problems they deal with rely on many calculations that can be effectively offloaded to idle PCs running in homes and offices for globally distributed processing. The project is managed by Washington University in St. Louis School of Medicine.

NVIDIA is joining Intel and AMD in an effort to utilize unused GPU computing power on PCs and gaming machines to fight against COVID-19.

NVIDIA is putting its best technology to use in fighting COVID-19 through the 90 day free trial of Parabricks and by participating in the Folding@Home project.

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How NVIDIA Is Using Its GPU Technolgy To Fight Against COVID-19 Virus - Forbes

When the new coronavirus (formally known as SARS-CoV-2) was identified in China in January, scientists around the world were ready to respond. The viruss entire genetic makeup, or genome, was published online within days. By comparison, during the SARS coronavirus outbreak in 2003, this took almost three months, after the disease was originally blamed on chlamydia.

Advances in the technology have brought down the cost of gene sequencing significantly and the machines are now small enough to fit in the palm of your hand. This has made it easier for a large number of samples to be sequenced around the world.

You can see from the sequences how the virus spreads, the speed at which it's spreading and estimate the number of people that are infected. As we get more and more sequences, the more and more accurate the numbers are, said Professor Anne-Mieke Vandamme from KU Leuven, Belgium.

Next-generation sequencing, or NGS, can generate enormous amounts of data, and the challenge becomes finding ways to analyse it properly.

In 2015, Prof. Vandamme led a project called VIROGENESISto develop new tools to help analyse and interpret the data that comes from sequencing, particularly for laboratories that were not used to dealing with sophisticated genetic analysis.

When we were doing the project, there were only mainly research labs that had NGS. Now everyone has NGS, she said.

One of the tools developed, called Genome Detective, can take the raw data from the sequencing machine, filter out results from non-viruses, piece together the genome and use that to identify the virus. It does not rely on any prior guesses or hypotheses, so it can even identify viruses that have not been seen before. This was used to confirm the first case of COVID-19 in Belgium, identifying it as a SARS-related coronavirus.

You can see from the sequences how the virus spreads, the speed at which it's spreading and estimate the number of people that are infected.

Professor Anne-Mieke Vandamme, KU Leuven, Belgium

Online sharing

The power of gene sequencing comes from comparing the results across different cases. Prof. Vandamme says that it has been fantastic to see the level of collaboration internationally: There is a lot more online sharing of data and sequences ... compared to the past because we have a lot more online sharing tools available.

One of these tools is NextStrain, an online resource that uses genome data to monitor the evolution of disease-causing organisms such as viruses in real time. It has tracked several outbreaks including Zika, Ebola and Dengue and has even been used to inform World Health Organization policy on seasonal flu.

Research papers typically take months to be published an aeon in the current race to tackle the pandemic. The need to share information quickly has encouraged greater sharing of preprints, drafts of papers that have not yet been through peer review.

The push towards open science, open data and preprinting has really changed the way we experience the scientific discourse in this outbreak compared to previous ones, said Professor Richard Neher, from the University of Basel, Switzerland, who leads the NextStrain project.

NextStrain already has over 700 genomes of the new coronavirus, which it can use to trace the outbreak by detecting new mutations in the virus. The mutations do not necessarily affect how the virus behaves, but they can act as a genetic signature to link cases that are related. Like tracing your ancestry through a DNA test, a virus sequenced in Madrid, for instance, could have mutations that suggest it originated from an outbreak in Italy.

In the current pandemic, it gives us a lower bound on how often the virus has been introduced to a specific location, Prof. Neher said.

NextStrain publishes a weekly situation report that analyses these trends. The team was able to estimate that the outbreak in Iran may have been introduced by a single person, whereas at least four different introductions were responsible for the outbreak in the UK, as of 13 March.

(Sequencing cases) will become even more important because as we start cracking down on (the pandemic), which we hopefully will achieve, it will tell us how many transmission chains are still circulating and whether the virus is being transported from one region to another, said Prof. Neher.

He believes that, as the virus continues to spread, it will accumulate more genetic diversity and it will give us more information on how the virus is being transmitted.

Genetic blueprint

Despite the genetic blueprint of the new coronavirus being readily available, it still does not tell us very much about how it differs from other coronaviruses. Much of what we know has come from seeing how it has spread through the population. It is now clear how different it is to previous coronavirus outbreaks, such as SARS and MERS.

They were certainly much less easy to transmit, and also had a very different presentation in that only a few people were asymptomatic. One of the many challenges that we are facing here is that people that have only very mild symptoms have been substantial in transmitting this virus,' said Prof. Neher.

That is much harder to control because you have to convince somebody who is basically healthy to distance themselves from others.

Yet, it is not clear why that is the case. The traits of the virus, such as its infectiousness and severity, are driven by its proteins that are responsible for invading our cells and replicating the viral genome.

Sequencing a genome these days is pretty fast, but for proteins its different, said Dr Charlotte Uetrecht, from the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Germany. She studies coronavirus proteins through a project calledSPOCkS MS.

My lab is producing the proteins (of the new coronavirus) right now. So we want to see whether they behave the same (as other coronaviruses). We usually need to produce the proteins and purify them to a certain extent so we can look at them. So it's a lot more laborious than sequencing.

Even small changes to the viral proteins can significantly influence how they interact with each other. Dr Uetrecht studies these fleeting associations, which are crucial for the virus to replicate.

We know a bit about how that looks, but we don't really understand which of the proteins need to associate for a new genome to be produced, she said.

Although understanding these processes could provide new targets for antiviral drugs, Dr Uetrecht says that historically there has been little interest in studying coronaviruses as they have had little relative impact until now.

The case numbers were low for SARS and MERS andinterest fell after the outbreaks, she says. 'The common-cold-causing coronaviruses were not (considered) dangerous.'

There was not much research into coronaviruses at all, until SARS. I know a few people who have been working on coronaviruses since the '90s, and they were not very well regarded they had a hard time getting funding. It was considered a boring, irrelevant virus.

Now, it is very interesting again.

The research in this articleis supportedby the EU. If you liked this article, please consider sharing it on social media.

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Covid-19: How unprecedented data sharing has led to faster-than-ever outbreak research - Horizon magazine

Newswise Inside the molecular diagnostics laboratory at Johns Hopkins Hospital in Baltimore, while health care workers and hospital staff work tirelessly to process patient tests to detect the virus causing the COVID-19 pandemic, two biologists from the Johns Hopkins Applied Physics Laboratory (APL) are working alongside them.

Peter Thielen and Tom Mehoke, members of APLs Research and Exploratory Development Department, are waiting for the positive tests. Certainly, positive tests are no cause for celebration; but for Thielen and Mehoke, they are an invaluable sample and a key to learning more about the rapidly spreading virus.

With software and molecular biology approaches developed in part at APL in Laurel, Maryland, Thielen and Mehoke are using hand-held DNA sequencers to conduct immediate on-site sequencing of the SARS-CoV-2 genome the virus that causes COVID-19.

This information allows us to track the evolution of the virus, Thielen said. It gives us a sense of where the new cases coming into Baltimore couldve originated, and insight into how long transmission may have occurred undetected. There are a lot of things we can glean from that.

Topping that list is the ability to see how quickly the virus mutates integral information for mapping its spread, as well as developing an effective vaccine. Influenza, for example, mutates constantly. Thats why its necessary to vaccinate against different strains of the flu each year.

The virus causing COVID-19, Thielen said, does not appear to be mutating as fast.

When this virus was first sequenced in China, that information was helpful in starting the process to develop a vaccine, Thielen explained. What were doing informs whether or not the virus is mutating away from that original sequence, and how quickly. Based on the mutation rate, early data indicates that this would likely be a singlevaccine rather than one that needs to be updated each year, like the flu shot.

In the near-term, the mutations inform how the virus is spreading.

With the United States continuing to ramp up testing and mitigation capabilities, the ability to understand how outbreaks are linked gives public health departments another tool for evaluation. Mutations can explain how long the virus may have gone undetected and the supposition that there are likely far more cases than diagnosed, and can advise on what measures to put in place (such as the social-distancing efforts and closings that are ongoing nationwide).

Sequencing of the virus genome is being performed by scientists all over the globe as they work to trace the source of regional outbreaks. In northern California, for example, news reports suggest that genome sequencing has linked the Bay Area outbreak to the Grand Princess cruise ship, which linked back to the virus found in Washington State, which likely came from China.

Thats the type of insight a DNA fingerprint, if you will that Thielen and Mehoke will gain as more virus genomes are sequenced from the Baltimore and Washington, D.C., regions.

As part of the Johns Hopkins Center of Excellence for Influenza Research and Surveillance, Thielen and Mehoke have sequenced the genome of influenza for years in their work at APL, and are currently transitioning similar capabilities directly to the diagnostic laboratory at Johns Hopkins Hospital.

Theyve completed analysis of the first four COVID-19 samples, with upward of 100 in the queue from the Baltimore/Washington, D.C. area, and expect many more in the coming weeks.

Operating remotely using just hand-held sequencers and laptop computers, and at the mercy of how long the tests take to return results before they can be transferred to them, Thielen and Mehokes initial method was multiday. But, at the end of last week they validated a new process that enables same-day sequencing one that can be done by the hospital staff members already administering the diagnostic tests.

Ultimately, its what theyve been preparing for.

In the last nine months, Thielen and Mehoke held two workshops with the National Institutes of Health Fogarty International Center to help train scientists from low- and middle-income countries on how to use the hand-held sequencers to do this work.

We were doing that to prepare as many researchers as we can, in the event that there would be a future pandemic, Thielen said. Its here.

The latest workshop was held last week, where they trained stateside researchers to do the same type of on-site sequencing in their own laboratories. Participants included researchers at the Walter Reed Army Institute of Research, the U.S. Naval Research Laboratory, the University of Maryland, Johns Hopkins Hospital, Johns Hopkins Bloomberg School of Public Health, Auburn University, the University of California, Berkeley, and Kansas State University. Due to recent national travel restrictions, it was held virtually.

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Johns Hopkins APL Biologists Sequencing Genome of the Virus Causing COVID-19 - Newswise

Scientists should start sequencing the genomes of coronavirus patients. We should look for DNA differences between patients who are severely affected and those with mild symptoms. This could allow us to predict who else would be vulnerable and advise them to take precautions. We may be able to use this knowledge against the coronavirus epidemic before a vaccine is widely available.

In particular, it would be valuable to know if key DNA variations are shared by those rare people who are young and appeared to be healthy but developed severe symptoms from the coronavirus. We might then be able to predict which doctors and nurses are most at risk and remove them from the front line.

Of course, we dont yet know if accurate predictions will be possible. We dont even know if someones chances of severe symptoms from the coronavirus are affected by their genes. We could, however, answer these questions relatively cheaply and rapidly by using commonplace DNA sequencing technology.

Read more: Will warmer weather stop the spread of coronavirus?

We would need to sequence the whole genomes of coronavirus victims who need intensive care and compare them with the genomes of people who have only mild symptoms. With only a few thousand genomes from each category, we could quickly find out if there is mileage in this approach.

It may be that just one or two genes are involved. Perhaps broken genes involved in the immune system or lung cell surfaces. If so, we could quickly discover them using a method called genome-wide association study. If just a couple of broken genes make all the difference, a genetic test for coronavirus susceptibility could be simple to make, cheap and accurate.

It may be that there are thousands of genes involved. Perhaps a complex mix of genes involved in lung physiology, upper respiratory tract shape, and many other things we have never even thought of. If this is the case, working out exactly what is going on could take decades. But we need answers within weeks or months.

Here we can draw on an unexpected source of inspiration: we can use a method called genomic prediction, which has been used successfully for decades by plant and animal breeders, but is seldom used in medicine. It enables the prediction of complex traits from whole-genome sequences, even when we do not understand what any of the genes are doing.

With this approach, we do not need to spend several years working out what exactly is going on. We can construct a score from a persons whole-genome sequence that predicts their susceptibility. These scores could be obtained at the cost of (we estimate) only a few hundred pounds per person.

We took a genomic prediction approach last year for ash trees, which are dying from a fungal epidemic. By comparing the genomes of healthy versus dying trees, we discovered over 3,000 points in their genomes that contribute to susceptibility. Some of these were in genes that had known functions in host defences, but for many others, we had no idea what they did. Yet we did not need that knowledge to predict the susceptibility of other ash trees with a useful level of accuracy.

Read more: Ash dieback: one of the worst tree disease epidemics could kill 95% of UKs ash trees

We should do similar studies on humans and coronavirus. Of course, there would be more complex issues of privacy and consent than we had to deal with for ash trees. But tens of thousands of human genomes have already been sequenced around the world, so the issues around consent have been well explored. For some coronavirus patients, their genome will already be in a database.

Should we find that we can make accurate predictions, the moral and psychological challenges would be severe. Where should tests be deployed? Will people respond appropriately if they are predicted to be at risk (or not)? How would it affect health insurance? But difficult challenges are faced in every decision that we have to make in our battle against the virus.

Read more: Homemade hand sanitiser recipes that could help protect against coronavirus

Research on the genetic basis of susceptibility to the coronavirus could be done quickly and without diverting resources from research on treatments and vaccines. It might show that predictions are impossible. It might show that accurate predictions can be made. We dont know. But we need to find out. If it worked, it might protect thousands of lives before a vaccine is widely available.

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Coronavirus: sequencing the DNA of patients screened for coronavirus might save lives - The Conversation Africa

Nvidia is making its Parabricks tool available for free for 90 days (with the possibility of extension, depending on needs) to any researcher currently working on any effort to combat the ongoing novel coronavirus pandemic and spread of COVID-19. The tool is a GPU-accelerated genome analysis toolkit, which leveraged graphics processing power to take a process that previously took days, but that through its use can be accomplished in just a matter of hours.

Researchers will still need access to Nvidia GPUs for running the Parabricks genetic sequencing suite, but they won't have to pay anything for the privilege of running the software. This is a big advantage for anyone studying the new coronavirus or the patients who have contracted the illness. The GPU-maker is also providing links to different cloud-based GPU service providers to lower that barrier to entry, as well.

We've cut down drastically on genomic sequencing times in the past few years, but they still require a massive amount of computing hardware, and Parabricks, which was acquired by Nvidia late last year, has developed technology that makes it possible to sequence an entire human genome in less than an hour -- and that's using a single server, not an entire server farm.

Speed is of the essence when it comes to every aspect of the continued effort to fight the spread of the virus, and the severe respiratory illness that it can cause. One of the biggest challenges that scientists and researchers working on building potential drug therapies and vaccines for the novel coronavirus face is lack of solid, reliable information. The more sequencing that can be done to understand, identify and verify characteristics of the genetic makeup of both the virus itself and patients who contract it (both during and post-infection), the quicker everyone will be able to move on to potential treatments and immunotherapies.

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Nvidia makes its GPU-powered genome sequencing tool available free to those studying COVID-19 - Yahoo Tech

A doctor in Germany prepares a swab to test for coronavirus infection.

By Robert F. ServiceMar. 22, 2020 , 12:15 PM

As the United States races to ramp up testing for the pandemic coronavirus using technology based on the tried-and-true polymerase chain reaction (PCR), alternative approaches are beginning to roll out that could make it easier and quicker for people to learn whether they have been infected. Some methods modify the standard PCR test, which amplifies tiny bits of genetic material to enable detection, whereasothers sequence the virus directly or use the genome editor CRISPR.

Faster and cheaper tests are coming, says Evan Jones, CEO of OpGen, a rapid diagnostics company. However, he adds, developing new kinds of tests is going to take time. Some of the new tests are coming online now, but others will likely take months to validate and ready for widespread distribution.

Testing, testing, testing has been the mantra repeated again and again by World Health OrganizationDirector-General Tedros Adhanom Ghebreyesus. Diagnostic assays that identify active infections in people are vitally important for public health efforts, not just for individuals health concerns. Widespread diagnostic testing, along with isolation of the infected, contact tracing, and quarantining of those contacts, seems to have been key in South Koreas work to suppress virus spread.

In the United States, the slow rollout of coronavirus PCR tests has been widely attributed to a combination of stringent rules aimed at ensuring their reliability and a complex web of companies and health care systems responsible for developing, carrying out, and paying for tests. The Trump administration says testing is accelerating. On 16 March, at a White House press conference, U.S. Health and Human Services Assistant Secretary for Health Brett Giroir saidthe country would be able to process 1 million tests by the end of the week, and 2 million the following week. But the actual numbers arent close to that yet. According to data compiled by the COVID Tracking Project, a nonprofit collaboration of public health officials and journalists counting tests given in the United States, 191,541 PCR diagnostics have been performed as of 22 March, with 24,345 of them positive for the virus.

On 29 February, the U.S. Food and Drug Administration (FDA) posted new rules to allow for emergency use authorizations of coronavirus tests beyond the ones being made and distributed by the U.S.Centers for Disease Control and Prevention. Academic virology labs, public health departments, and companies sprang to work creating their own PCR tests. Today, some four dozen organizations have received FDA approval for their tests. Among the largest are diagnostic companies, such as Roche Molecular Systems, which received FDAs green light for its test this week. It will initially supply some 400,000 tests per week in the United States and 3 million globally, according to Alexandra Valsamakis, the companys chief medical officer. Other large companies have recently gained approval for their tests as well, including Thermo Fisher Scientific and Abbott Laboratories.

University virology labs have also leaped into the breach to help diagnose cases in their vicinity. This past week, for example, doctors at the University of Pittsburgh Medical Center (UPMC) began to use a homemade PCR test to check for infection in Allegheny county. For now, its number of tests remains small, about 100 per week. We definitely wished we had started it sooner, says Alan Wells, who heads UPMCs clinical laboratories.

PCR is the most commonly used test for diagnosing coronavirus because its highly accurate. (SeeHow does the most common coronavirus test work?) But other problems limit it. Its not getting the turnaround we need, says Steven Wolinsky, an infectious diseases physician at Northwestern University. Each test takes about 4 hours once a sample reaches a centralized testing lab, with the time split between sample preparation and the actual PCR test. With transport and queues, getting a result can take 2 to 4 days. In that time, infected people may spread the virus to many others.

Another new dimension is now being added to the coronavirus diagnostic landscape: home tests, which involve mailing a sample taken at home to a lab. Tomorrow, for example, Everlywell expects to begin toshipkits to homes and retail pharmacies. These tests will start with screening questions, either online or at a retailer, to determine whether a person is likely to have been exposed to the virus. If they are, they can receive a nasopharyngeal sampling kit by mail or can buy one from a local retailer. A person will be given detailed instructions to administer their own swab, insert it into a protective vial, and overnight mail it to one of dozens of diagnostic labs (which partnered with Everlywell and already have FDA approval) for PCR analysis.

Frank Ong, Everlywells chief medical and scientific officer, says the company expects to quickly ramp up from offering thousands of such tests per day to tens of thousands. Although each test will still likely require a 4-day wait for results, Ong says, this home sampling strategy carries major benefits: It will protect health care workers from exposure to potential infection and free up their time. We need to make sure we give them the bandwidth to take care of patients, Ong says. Other companies, including Nurx and Carbon Health, say theyre now shipping limited supplies of their own home sampling kits.

Most PCR tests for the new virus are being done with big, expensive automated machines that do many tests at once. Major hospitals or diagnostic facilities have them, but another option beginning to roll out now is smaller, less expensive devices that also do nucleic acid amplification. These could be used by smaller hospitals and even individual doctors offices.

On Friday, for example, Cepheid, which sells small PCR systems for rapidly detecting influenza viruses, tuberculosis bacteria, and other microbes, received FDA emergency use approval for a severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) test cartridge that slots into the companys GenXpert system, a device the size of espresso machine that can produce a diagnostic result in as little as 45 minutes. Cepheid officials say that 23,000 such systems are in place worldwide, with 5000 in the United States. On 19 March, GenMark received FDA emergency use approval for its own coronavirus tests, which run on similar-sizemachines that use a proprietary electrochemical approach to detect target genetic material in less than 2 hours. Other companies rushing to deliver point-of-care diagnostic machines include Mesa Biotech, HiberGene, Mobidiag, and QuantuMDx.

So, too, are companies such as Oxford Nanopore and Fulgent Genetics, which instead of using PCR directly sequence any genetic material in a sample and then look for matches to, say, the new coronavirus. This high-speed gene sequencing approach could help characterize the coronavirusgenome to better understand how the virus is evolving, but it could alsobe a diagnostic in certain situations, such as remote sites without access to PCR. Oxford Nanopores handheld devices have been used in Ebola outbreaks, and the company sent many to China early in the pandemic.

The fastest way to test for the coronavirus may ultimately be offered by companies using the CRISPR genome editor, better known for adding or deleting DNA in cells. Two U.S. companies, Mammoth Biosciences and Sherlock Biosciences, say they have created CRISPR-based tests and are in the process of validating them with patient samples before seeking emergency use approval by FDA. The technique starts with a patient sample, extracts viral RNA, and uses a fast nucleic acid amplification test called loop-mediated amplification to make just enough RNA for the test to detect. Researchers then add two components of a CRISPR genome editor, a protein called CAS12 that cuts DNA or RNA and a guide RNA that slots into CAS12 and helps it search out a sequence corresponding to a piece of the coronavirus genome. If CAS12 and its guide find a match in the RNA, CAS12 binds to that matched RNA, which activates CAS12 to cut it and go on to cut any other short RNA or DNA strands in the vicinity, including copies of a strand designed to liberate color-changing molecules when CAS12 cuts them free. The upshot can be a simple color change on a test strip.

The technique excels at hunting for small snippets of genetic material, says Jennifer Doudna, a biochemist at the University of California (UC), Berkeley, a CRISPR pioneer, who is chair of Mammoth Biosciencess science advisory board.

In a preprint posted 10 March on medRxiv, researchers at Mammoth Biosciences and UCSan Franciscoreport that tests on clinical samples produced results with accuracy rates comparable to PCR in just 30 minutes. It uses a simple paperlike strip with a colored line that appears with a positive result. The company is discussing with partners manufacturing test kits that would allow rapid and cheap diagnosis of SARS-CoV-2 infection at home without requiring medical know-how, says Trevor Martin, Mammoths CEO.

It may take months to finalize the test and get regulatory approval for it, so it likely wont be ready in the crucial weeks ahead. But it could be ready if the spread of the coronavirus continues. Some predict the virus will also recede but then have a resurgence of infections in the fall. Getting results wouldnt require PCR machines operated by trained technicians, Martin says. It would be a game changer for our response to emerging diseases, Martin says.

Even as companies and academic labs are scaling up their PCR-based diagnostic efforts, hospitals and testing sites around the country report that they are facing a more immediate crunch: Many are running out of chemicals and other materials that enable the tests, such as the swabs to collect samples from patients and the reagents needed by PCR. Benjamin Pinsky, a Stanford University pathologist who developed a PCR-based diagnostic test in use in Northern California, says his lab is facing rolling shortages of different supplies, most notably the kits used to extract RNA from viral samples, before it can be loaded into PCR machines.

This has been a big challenge, Pinsky says. Weve had to be very nimble in dealing with this, constantly switching suppliers or even chemical procedures, which must be validated before they can be used on patient samples. His team has even sent pleas over Twitter to the Stanford community and regional biotech companies calling for donations of reagent assemblies, such as kits from Zymo and Qiagen. And even though donations have been pouring in, supplies are still running short, Pinsky says.

Reagent companies are trying to respond. For example, Qiagen, a major supplier of RNA extraction kits, announced Tuesday that its employees are working around the clock to increase production from 1.5 million kits per month to 6.5 million per month by the end of April and further increases later.

Pinsky, for one, says hes ready for companies to take over coronavirus testing entirely from academics such as himself. Im hopeful these companies will be able to provide the testing they have promised, Pinsky says. That remains to be seen.

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The standard coronavirus test, if available, works wellbut can new diagnostics help in this pandemic? - Science Magazine

Ever since the Human Genome Project began in the late 1980s, genetics and DNA have become topics of mass interest. The book Genome: The Autobiography of a Species in 23 chapters states that the genome is a book that wrote itself, continually adding, deleting, and amending for over four billion years.

For Dr Surendra Chikara, who has been working in the field for close to 20 years now, the idea of founding Bione, a healthcare startup, was a no-brainer.

Monitoring the present coronavirus outbreak scenario in the country, we have included new parameters to our Longevity Plus kit. The new updated kit provides information about the susceptibility of a person to viruses like coronavirus, SARS-like viruses, HIV, Hepatitis C virus, etc. This could be based on an individuals genetic makeup or the patterns of living, Surendra says.

Dr Surendra, Founder of Bione

Surendra says a recent addition to the Bione Genetic test can check an individuals susceptibility to coronavirus. He adds that the platforms microbiome test, combined with its predictive analytics tools and artificial intelligence, can provide tailored recommendations to individuals to strengthen their microbiome and improve their immunity.

A research paper titled 'Evidence of gastrointestinal infection of SARS-CoV-2 revealed that 23.29 percent patients infected with SARS CoV-2 showed positive results in stool after showing negative in respiratory samples. Hence, the gut microbiome test is the only way to know when a virus is no longer in your system, Surendra says.

Surendra started his career with recombinant DNA technology and worked with Dr Gita Sharma, who had created the first r-DNA vaccine for Hepatitis-B in India.

My journey in genomics started under her support and guidance. It was the time when human genome sequencing and next-generation sequencing were starting to gain importance. We were in discussions to bring D2C technology to India, but the Indian healthcare market was not ready for direct-to-consumer genetic testing," Surendra says.

This is a huge problem that all my networks were aware of. We all know that the future of the global pharmaceutical industry lies in developing precision medicines tailored for individuals based on their genes, and clinical risk for developing a disease. Indian genetic data is highly diverse and a number of breakthroughs can happen. At Bione, we are doing our part to be part of this bigger picture of making India disease-free, Surendra says.

The different types of kits depend on the number of tests covered, and include Longevity kit, Longevity Plus Kit, and MyMicrobiome kit. The Longevity Plus kit covers over 415 parameters, including health, personalised medicine, fitness, and wellness.

The team claims that it also covers a parameter that determines specific gene variants that may contribute to enhance resistance to viruses like coronavirus, HIV, Hepatitis C, and many others.

The MyMicrobiome kit identifies and quantifies the microbiome in the gut, based on which a personalised diet is recommended.

Surendra says scientific research has shown that the gut microbiome plays an important role in the function and maintenance of our immune system. In ideal conditions, this microbiome-immune system alliance allows the initiation of protective responses against germs.

The platform also offers sample collection, with samples collected from an individuals homes. A pick-up is arranged as per your convenience by Bione. The DNA sequencing is done in a well-equipped lab by expert scientists, after which a detailed report is prepared.

Bione gXplore is a user-friendly, informative, and interactive app-based platform. On it, you can go through your report and easily understand the results of DNA analysis.

Slots with genetic or food and nutrition counsellors are provided as a free-of-cost service. The expert team of counsellors guides you to proactively plan your and your familys health and lifestyle choices.

The Bione team consists of experts from global institutions and domains of genomics, genetics, bio-IT, genome informatics, quality assurance, sales, marketing, genetic/nutrition/fitness counselling, and fundraising leads. The startup has a total team size of 39 people.

The startup also runs a lab with scientists, bioinformaticians, and genetic counsellors. The team is applying for ISO 9001:2015, followed by CAP and CLIA accreditation to follow global standards.

Bione is projecting to test 20,000 to 30,000 samples in the first year of operations. Tests are priced between Rs 15,000 to Rs 65,000, with the option of paying in EMIs. Customers can choose the package based on their needs.

The startup has raised angel funding from a clutch of undisclosed investors.

Currently, startups like The Gene Box and Hyderabad-based MapMyGenome work on providing preventive solutions based on an individuals genetic makeup.

He says the startup's high tech lab is using advanced technologies, including whole genome sequencing, while the competition is still working with array technology with limited markers.

(Edited by Kanishk Singh)

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How healthtech startup Bione aims to use genetic testing in the fight against coronavirus - YourStory

This will help to develop a vaccine and understand the evolution of the virus.

Russian scientists have managed to sequence the first complete genome of the coronavirus, the Russian Health Ministry confirmed on March 19.

"This coronavirus is new to us, so it is essential to have an opportunity to identify the path of its spread and entry into the territory of our country, and its mutations. This information will help develop vaccines and antiviral drugs to treat the coronavirus, said Dmitry Lioznov, acting head of the Smorodintsev Research Institute of Influenza, whose specialists decoded the genome.

Soon, this data will be sent to the World Health Organization database so that scientists from other countries can have access to it.

In the meantime, scientists from the VECTOR State Research Center of Virology and Biotechnology in Novosibirsk have managed to take pictures of COVID-19 under a microscope. This is what the virus that has affected thousands of people on the planet looks like:

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Russian scientists take the first photo of a novel coronavirus and fully decode its genome (PHOTOS) - Russia Beyond

The new NextSeq 550 sequencing machine at UCSFs clinical lab on Berry Street looks like a microwave with a computer keyboard, but to microbiologist Charles Chiu, it is the key to Californias fight against the deadliest, most invasive virus to strike humanity in decades.

The professor of medicine at UCSF will be using the black contraption, installed Friday, to sequence the genomes of the viruses infecting hundreds of COVID-19 patients in the Bay Area during the next few weeks.

We will be running this 24 hours a day, said Chiu, wearing a white lab coat and purple rubber gloves as he fiddled with the keyboard and opened the door to a compartment where slides holding genetic material are scanned. I see no reason why we cant sequence the genomes of every case.

Chiu, 48, of San Francisco is one of the top infectious disease specialists in the world. He has assembled an expert team of scientists who have also used his research lab on 16th Street to find critical clues about where the viral outbreaks in the Bay Area came from and how quickly the disease is spreading.

His work, which includes tracking mutations and the spread of infection, is a crucial cog in our understanding of what makes this unique coronavirus tick and, eventually, how we might control or eradicate it and similar viruses.

A married father of 13- and 11-year-old boys, Chiu was born in Missouri to immigrants from Taiwan. He is director of the UCSF-Abbott Viral Diagnostics and Discovery Center. It was one of the first labs to sequence strains of the H1N1 influenza virus, which was associated with the 1918 Spanish flu pandemic. Chiu has sequenced 2,000 unusual strains of HIV and strains of the Zika virus.

He has already analyzed nine samples from the more than two dozen passengers who tested positive for the coronavirus on the Grand Princess cruise ship and is close to pinpointing the origin of those cases.

Those sequences belong in the same cluster as the infection in Washington state, Chiu said. They really suggest a link between Washington state and California.

The Grand Princess, whose home port is San Francisco, departed Feb. 21 for a trip to Hawaii with more than 3,500 people aboard. It was halted off the coast of San Francisco after being called back because passengers from the ships previous cruise, to Mexico, had tested positive for the disease.

Among the passengers on the Mexico trip who tested positive was a 71-year-old Placer County man who died. Five people from Sonoma, Contra Costa and Alameda counties who were on that cruise also were infected.

Chiu has collected seven samples from passengers on the Hawaii cruise and, with help from the California Department of Public Health and the Washington State Department of Health, compared them with samples from two of the infected passengers on the Mexico cruise.

All of them were mapped to the Washington state strain, known to scientists as the WA1 strain, Chiu said. So the first cruise was basically the cause of all of those cases on the second cruise.

Chiu traced the disease back to a Mexico cruise passenger from Sonoma County who apparently transmitted the virus to the others, including crew members. They probably infected passengers on the Hawaii cruise.

Authorities are still tracing the links and validating the findings, but Chiu believes the infected Sonoma County man, who survived the disease, either visited Seattle before the cruise, came in contact with someone from Washington state or contracted it from an as-yet unidentified passenger from Washington state.

Chiu said tracking the spread of the virus through genetics is possible because coronaviruses are known to have one to two mutations per month, allowing genomic sequencing to track a particular strain back to its origin.

The rate of mutation in coronaviruses is much slower than it is with the influenza virus, which averages about eight to 10 mutations per month. The mutations are why it is impossible for humans to become immune to the flu, which comes back in a new form every year.

Chiu used genomic sequencing to identify Californias first case of community transmission a Solano County woman who was infected by an unknown source. She and a Santa Clara County woman who was subsequently diagnosed had not traveled any place where the coronavirus was known to have spread, and had not had contact with anyone who was infected.

The Solano County woman transmitted the disease to two health care workers. Chiu found that the three of them had a strain that was different from the others he has documented. In all likelihood, he said, it originated in China and was transmitted just to her by a traveler.

Perhaps by identifying that patient (and isolating her), we might have been able to stop that strain from multiplying, he said.

A separate strain seen nowhere else in the United States was also found in a San Benito County person who returned from a visit to China.

Its quite different from what is going on in Washington state, where all the cases are related to that single strain, he said about the 20 genomes that have been sequenced in that state, all of which originated in China.

With the new sequencing machine, Chiu expects to quickly analyze the 30 positive samples he has in the lab and more than 200 positive swabs he expects to receive from Santa Clara County on Monday. It will, he said, dramatically increase the amount of genetic information available about the coronavirus and its rampage.

Who knows what it will look like when we get the 200 samples, he said. Were basically scrambling to keep up. The situation changes every day.

The problem with tracking the various strains, Chiu said, is that China has not done much genomic sequencing only 50 sequences are available. Thats another reason Chius work is so important.

Im now investigating a cluster in Santa Clara, in which four people in a single building tested positive, Chiu said. A key public health question is, Are these all related, or is it just by chance that four people who had been infected separately were in the same place? Knowing this might affect how you implement public safety precautions.

Chiu is sequencing coronavirus genomes from cases in San Francisco and Berkeley, and from Sacramento, Santa Clara, San Mateo and Solano counties.

During the past week, the Washington strain has spread into California counties, he said. It means that what started out as a series of disconnected clusters of different strains is growing into a large conflagration of infection.

It concerns me that the Washington strain appears to be infiltrating California, he said. You could think of it like a fire, with sparks flying out. If all we are seeing is these sparks, the hope is that it never evolves into a fire. Are we still at the spark stage, where social distancing, quarantining, would make a difference? The question for us is, do we have the ability to contain this?

Another question is whether mutations can make the virus worse.

Its hard to answer that question, he said. I think over time we will find out if it becomes more transmissible or more deadly. Those questions take time.

One positive, he said, is that this virus mutates slowly. While the RNA changes slightly, the virus proteins and characteristics dont. The only way to tell whether the strength of the strain or the way it is transmitted has changed, he said, is to examine a lot of samples.

Even though influenza mutates every year, were not worried about it getting more deadly, Chiu said. Its unlikely that (the virus) will mutate to the point where it gets more deadly.

Chiu is also trying to solve the state and the countrys biggest problem the lack of diagnostic testing. California has the capacity to process only about 200 swab tests a day, largely as a result of the nationwide shortage in test kits, regulatory delays and a lack of equipment, he said. His lab is developing a test that will give a result in 30 minutes.

Our goal is to develop the next generation of tests, he said. Two hundred tests is not good at all. We need thousands, tens of thousands.

Soon, all outpatient samples from the Bay Area and much of the state are expected to be sent to his lab. That would allow him to sequence more genomes and find out more about the disease.

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com. Twitter: @pfimrite

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The man behind the sequencing of the coronavirus could have keys to the disease - San Francisco Chronicle

On March 10, 2020, Iranian filmmaker Nader Talebzadeh hosted a discussion about the possibility that COVID-19 is a biological weapon on this show on Ofogh TV (Iran). The discussion was preceded by an animation that explained that the assumption is that COVID-19 is a synthetic virus that was designed as a bioterrorism agent in secret American laboratories as part of America's economic conflict with China. During the show, Iranian documentarian Hamed Ezzatizadeh said that his research has led him to the conclusion that the coronavirus is being used as a weapon, even though it is not clear whether it was produced as such or whether it is a naturally occurring virus. He wondered why China and Iran, which he explained are America's economic and ideological enemies, respectively, are two of the countries hit hardest by the virus, and he questioned why Hong Kong and the many poor countries with undeveloped public health systems that are between Iran and China, such as Tibet, Mongolia, and Afghanistan, have not been as affected by the virus as Iran has been. Dr. Ali Karami, a lecturer in medicine, said that as a result of the Iranian Genome Project, which he said was performed at Stanford University in violation of international conventions and with funding from Baha'i sources, the Americans and the Zionists have completely sequenced the genome of Iranians, and he suggested that the Americans have used this information in order to develop "ethnic weapons" that are most effective against certain ethnic groups. He said that Israel has been using these kinds of weapons to target Palestinians for a long time, and that this would explain why Iran, China, and South Korea are among the countries most affected by the coronavirus. Dr. Karami also claimed that Italy has been hit hard by the virus because Italians are genetically similar to Iranians. The other guest, Ezzatizadeh, pointed out that a similar campaign of ethnic bioterrorism had been used to annihilate the Native American population in the United States.

Animation: "The main assumption is that this virus is synthetic. In recent weeks, it has been said in the media and even by certain officials that this virus was produced in bioterrorism labs.

[...]

"America is one of the countries that has carried out extensive secret military activities in this field. America's main military biological labs that can produce such viruses are BSL-4 laboratories.

[...]

"Using biological means is of such importance for the Americans that the number of these labs grew from five in 2001 to 15 in 2009. First, one should answer the following question: Why has America produced and spread this virus? The answer is not difficult, because in the past year and a half, at minimum, America and China have engaged in every form of war, with the exception of military conflict. The trade war was another dimension of America's war to rein China in. This policy has been somewhat successful in showing down China's economic growth from 10%, which it had been for over three decades, to 6.6%. The integration of China's economy in the world economy has landed several blows to America's economy. Ultimately, Trump reached a short-term trade ceasefire with China. It seems, however, that while Trump was busy signing this agreement, the American researchers were busy producing a dangerous virus in America's biological labs in the region, in order to harm China's economy."

Hamed Ezzatizadeh: "My inquiries have not led me to the conclusion that this virus was produced as a weapon, nor have I reached the conclusion that it is natural and that it was not produced as a weapon. What is certain, though, is that it is being used as a weapon.

[...]

"Some regimes are using [this virus] as a weapon in order to whitewash things that they are doing. What happened in India was a disaster, yet everybody's attention was directed at the coronavirus. What is happening now in Saudi Arabia... Once again, they are laying siege to Qatif, and apparently they are about to severely oppress the Shi'ites there.

[...]

"Among the countries that have to seriously deal with the coronavirus, two are serious enemies of the Americans. One is their economic enemy, and the other is their ideological enemy.

[...]

"The structure of the coronavirus is very similar to that of a virus called MERS. It is also known as 'Camels Corona', and it appeared in Saudi Arabia in 2012. It is also very similar to SARS. This really increases the possibility that this virus was engineered. If we put aside all these technical matters, one question arises: There are many countries between China and Iran. How did the virus fly into Iran and affect it so badly? Is it because Iran's health system is so week? No, this is not the case. Between China and Iran, there are so many poor countries with health systems that are nearly destroyed. Look at Tibet, Mongolia, and Afghanistan. Iran is much stronger than these countries. How did this virus fly to Iran all of a sudden? Hong Kong shares a border with China. Hongkongers are similar to the Chinese from a genetic perspective, as well as in their diet, lifestyle, and everything. Yet, nothing is happening there."

[...]

Dr. Ali Karami: "The mortality rate in Iran... The number of deaths in our country is somewhat strange to me, because of the type of virus I am now researching. Look at Italy. How come the mortality rate there is so high? Italy is a European country. Our analysis shows that the genetics of the Italians are very similar to those of the Iranians.

[...]

"We are talking about something that I am how suggesting exists: Ethnic weapons. These are biological weapons that cause higher mortality rates among certain races. From the molecular-biological perspective, this is not strange at all.

[...]

"The question is: Was this virus altered? Was the genome of this virus built in a way that makes it easier for it to attach itself to the receptors of a certain genetic [identity] and cause an epidemic? Iran is the third most infected country after [China and] South Korea. What are the Americans doing in their labs?

[...]

"Dear people who listen to me, look up 'Iranian Genome Project' on the internet. Who conducted this project? The American Stanford University. I've been following this project in the past five years. Three Iranians and two Americans at Stanford, who had $200,000 donated to the university by a Baha'i foundation, completely sequenced the Iranians' genome. According to the conventions on genetic diversity and on the preservation of countries' genomes, this measure is completely illegal. It violates international conventions.

[...]

"114 Iranians from various ethnic groups participated in this project. They sequenced our genome in its entirety. 25,000 of our genes are held by the Americans and Israelis. They have our proteins. Did you know that they can produce medications or special viruses with specific receptors? Dear people who refuse to listen to me don't say that I suffer from conspiracy theory-related anxieties.

[...]

"In the Zionist regime, they work on bioterrorism agents that only infect a certain ethnic group the Palestinians. Do not tell me that this is impossible."

[...]

Hamed Ezzatizadeh: "With regard to the ethnic weapon he was talking about this is how they annihilated the Indians in America."

Nader Talebzadeh: "Exactly"

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Iranian Experts: COVID-19 Is An 'Ethnic' Bioterrorism Weapon - Middle East Media Research Institute