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COVID-19 / SARS-CoV-2

The coronavirus, SARS-CoV-2, has by now reached every aspect and even the most remote corner of our daily lives. We therefore have decided to compile a list of relevant news and announcements, developments, and useful links in relation to this viral outbreak on this active “COVID-19 / SARS-CoV-2” news page. We will update and add to this page on a regular basis. This page is not a compilation of all relevant information but rather contains some key highlights that we consider to be of importance to share with the community.

Feel free to contact us either via email at info@enlightenbio.com or via twitter at @enlightenbio with additions that we missed and should be included in this compilation.

Helpful resources

COVID-19 risk level dashboard – displays risk levels for each county/state in the U.S.

Mortality Tracker

COVID-19 Module Data Dashboard – Patient Impact and Hospital Capacity Pathway – Statistical methods were used to generate estimates of patient impact and hospital capacity measures that are representative at the state level. The estimates are based on data submitted by acute care hospitals to the NHSN COVID-19 Module. The statistical methods include weighting (to account for non-response), multiple imputation (to account for missing data), and a running 7-day smoothing technique (to account for daily fluctuations and updated responses in reporting to NHSN). This dashboard is automatically updated by 12:00 pm ET on Tuesday, Wednesday, and Friday.

WHO embraces plan for Covid-19 intellectual property pool (May 15) – In response to the global race to combat the Covid-19 pandemic, the World Health Organization embraced a proposal to create a voluntary pool to collect patent rights, regulatory test data, and other information that could be shared for developing drugs, vaccines, and diagnostics.

How we reopen safely – Tracking states as they make progress towards gating criteria.

STAT COVID-19 Drugs & Treatment tracker (April 27) – A guide to some of the most talked-about efforts to treat or prevent coronavirus infection, with details on the science, history, and timeline for each endeavor. This tracker tracks novel medicines, not repurposed drugs.

Coronavirus tracked: the latest figures as the pandemic spreads – The Financial Times analyses of the scale of outbreaks and the number of deaths in countries around the world (free to read).

Corona Daily – Provides you an overview of relevant articles on the COVID-19 pandemic which crosses science, public policy, psychology and philosophy – curated daily.

Coronavirus Disease (COVID-19) – Statistics and Research – This article covers the developing situation which is updated daily by the Our World in Data team.

CDC’ Coronavirus Disease 2019 (COVID-19) guidelines

Johns Hopkins Covid-19 interactive map – Provides up-to-date counts of total confirmed Covid-19 coronavirus cases worldwide, country-by-country breakdowns, with death and recovery rates.

COVID-19 in US and Canada – Real time updates with credible sources.

World Health Organization’s COVID-19 information resource – Includes tracking of countries, areas or territories with cases, confirmed cases, and deaths.

COVID-19 U.S. Molecular Equipment Locations by Manufacturer – This map represents national and local hospitals and medical facility locations with installed molecular equipment by manufacturer.

Handbook of COVID-19 Prevention and Resources – This program was established to facilitate online communication and collaboration across borders, as well as to provide frontline medical teams around the world with the necessary communication channels to share practical experience about fighting the pandemic. Provides comprehensive guidelines and best practices by China’s top experts for coping with COVID-19.

COVIDbase – A useful resource with a work-in-progress curated list of projects, news, and data related to COVID-19.

COVID-19 Open Research Dataset (CORD-19) – The Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 44,000 scholarly articles, including over 29,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

Information Collection Platform for COVID-19 Epidemic Prevention – This project aims at collecting and gathering information of hospitals, hotels, factories, logistics, donations, contributions, prevention, treatment and any live information regarding national epidemic prevention from reliable sources to help all affected people, organizations better communicate and coordinate with each other to efficiently and effectively fight against the Novel Coronavirus (COVID-19) outbreak that started in Wuhan, Hubei, China. All of the code will be open-source and the data collected will be carefully reviewed/validated and available to the public.

The COVID Tracking Project – The COVID Tracking Project collects information from 50 US states, the District of Columbia, and 5 other US territories to provide the most comprehensive testing data we can collect for the novel coronavirus, SARS-CoV-2. We attempt to include positive and negative resultspending tests, and total people tested for each state or district currently reporting that data.

World Health Organization’s COVID-19 information resource – Includes tracking of countries, areas or territories with cases, confirmed cases, and deaths.

Coronavirus Tracker – The SF Chronicle is compiling an exhaustive list of every coronavirus case in California.

DNAstack Launches COVID-19 Beacon to Accelerate Sharing Genomic Data in the Fight Against Novel Coronavirus – The beacon for SARS-CoV-2 will be available at covid-19.dnastack.com and will enable the scientific and medical communities to share and discover knowledge about the genetics of the virus in real time.

COVID-19 public dataset program: Making data freely accessible for better public outcomes – To aid researchers, data scientists, and analysts in the effort to combat COVID-19, Google Cloudis making a hosted repository of public datasets, like Johns Hopkins Center for Systems Science and Engineering (JHU CSSE), the Global Health Data from the World Bank, and OpenStreetMap data, free to access and query through the COVID-19 Public Dataset Program.

The spreading / transmission / tracking of COVID-19

Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong (September 17) – Discusses several superspreader events traced back to severals bars and weddings.

COVID-19: All the wrong moves in all the wrong places (September 15) – As the world continues to be ravaged by Covid-19, three major systemic failures appear to have coalesced to block progress in disease control, containment, and treatment. These failures reflect a “perfect storm” of governmental ineptitude, scientific ignorance/misprioritization, and the abdication of medical training to market-driven forces. This editorial highlight the shortcomings in our collective response to the COVID-19 pandemic and underscore the need for more basic research into this new disease.

COVID-19 herd immunity: where are we? (September 9) – A great article on what it takes to achieve herd immunity, and this in relation to COVID-19.

The emergence of SARS-CoV-2 in Europe and North America (September 10) – It seems SARS-CoV-2 was circulating under the radar in Washington State for weeks, though it is noct clear for how long and where the introduction came from. It is still necessary to resolve where the virus first initiated substantial community outbreaks, and whether the earliest coast-to-coast spread of the virus within the US was from west-to-east or east-to-west.

Two metres or one: what is the evidence for physical distancing in covid-19? (August 25) – Rigid safe distancing rules are an oversimplification based on outdated science and experiences of past viruses.

The pandemic appears to have spared Africa so far. Scientists are struggling to explain why (August 11) – Although Africa reported its millionth official COVID-19 case last week, it seems to have weathered the pandemic relatively well so far, with fewer than one confirmed case for every thousand people and just 23,000 deaths so far. Yet several antibody surveys suggest far more Africans have been infected with the coronavirus—a discrepancy that is puzzling scientists around the continent. “We do not have an answer,” says immunologist Sophie Uyoga at the Kenya Medical Research Institute–Wellcome Trust Research Programme.

Gene study shows how coronavirus swept through cruise ship Diamond Princess (August 5) – A genetic retracing of events shows the outbreak on the Diamond Princess likely stemmed from just one infected person, according to Japanese researchers.

Archived news – The spreading / transmission of COVID-19

Decoding SARS-CoV-2

The lasting misery of coronavirus long-haulers (September 14) – Months after infection with SARS-CoV-2, some people are still battling crushing fatigue, lung damage and other symptoms of ‘long COVID’.

Citizen Scientists Take on the Challenge of Long-Haul COVID-19 (September 3) – Interesting survey summary by a group of citizen scientists, the online Body Politic COVID-19 Support Group , who decided to take matter in their own hands to better understand COVID-19 symptoms, recovery and testing details, etc.

The coronavirus may shut down the immune system’s vital classrooms (August 25) – Autopsied people who died from COVID-19 lack so-called germinal centers, classrooms in the spleen and lymph nodes in which immune cells learn to mount a long-lasting antibody response to a pathogen.

Coronavirus re-infections raise concerns about immunity (August 24) – Two European patients are confirmed to have been re-infected with COVID-19, raising concerns about people’s immunity to the coronavirus as the world struggles to tame the pandemic.

Scientists reveal structural details of spike protein used in leading COVID-19 vaccine (August 7) – Electron microscopy techniques showed that the coronavirus spikes maintained the desired shape in the vaccine, which should help stimulate an appropriate immune response.

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity (August 19) – Annotation analysis looks at variants in SARS-CoV-2 genomes from first phase of pandemic.

AI: Cracking Covid-19’s Code – STAT News discussion scheduled for August 18. AI experts talk about how AI is accelerating a worldwide effort to crack Covid-19’s molecular code. With individuals from Microsoft and Adaptive Biotechnologies

The Coronavirus May Mess With Thyroid Levels, Too (August 10) – To the many organs affected by COVID-19, the thyroid is now added to the list as well.

Archived news – Decoding SARS-CoV-2

COVID-19 testing

FDA Compares Performance of COVID-19 Diagnostic Tests (September 17) – The FDA revealed comparative performance data for 55 molecular diagnostic COVID-19 tests that the agency approved under an Emergency Use Authorization protocol. Patients, physicians, and laboratories can use the online data to get a better understanding of how each authorized commercial assay compares with a reference panel the FDA developed.

Abbott’s Fast, $5, 15-Minute, Easy-to-Use COVID-19 Antigen Test Receives FDA Emergency Use Authorization (August 26) – Mobile App Displays Test Results to Help Our Return to Daily Life; Ramping Production to 50 Million Tests a Month.

Verily Life Sciences has established a CLIA-certified lab at the South San Francisco headquarters to create additional lab capacity in support of programs in the COVID-19 testing space, including their own return-to-work efforts for their employees (August 10)

COVID-19 spurs wave of innovative diagnostics (July 8) – The next wave in diagnostics will necessarily emerge from the intersection of physical and engineering sciences and biology.

Safer reopening will require millions more Covid-19 tests per day. One solution: ‘pool testing (June 26) – If the country wants to crank up its Covid-19 testing capacity into the millions — the range that could be required for safer reopenings of businesses and universities — it’s time to ramp up a technique known as “pool testing.” It’s a simple construct: combine — or pool — samples from multiple people and test them as a group for the coronavirus. It’s a way to dramatically and efficiently increase volume, to churn through what you expect to be a lot of negative samples at a fast clip.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Geneva, Switzerland (SEROCoV-POP): a population-based study (June 11) – The results suggest that most of the population of Geneva remained uninfected during this wave of the pandemic, despite the high prevalence of COVID-19 in the region (5000 reported clinical cases over <2·5 months in the population of half a million people). Assuming that the presence of IgG antibodies is associated with immunity, these results highlight that the epidemic is far from coming to an end by means of fewer susceptible people in the population. Further, a significantly lower seroprevalence was observed for children aged 5–9 years and adults older than 65 years, compared with those aged 10–64 years. These results will inform countries considering the easing of restrictions aimed at curbing transmission.

EUA Authorized Serology Test Performance – This is an incomplete representation of the performance of these tests. FDA also is providing a calculator that will allow users to see the estimated performance of a single test or two independent tests based on their performance characteristics and the estimated prevalence of SARS-CoV-2 antibodies in the target population.

Scientists baffled by decision to stop a pioneering coronavirus testing project (May 22) – The first and most progressive US program with 20,000 home COVID-19 tests in 10 weeks has been asked to stop testing for the disease. The decision by the US Food and Drug Administration (FDA) to prevent the SCAN project from analysing nose swabs sent from people’s homes—and reporting the results— is likely to be temporary. But it deflates local and national public-health initiatives.

First CRISPR test for the coronavirus approved in the United States (May 8) – The CRISPR-based diagnostic kit has been developed by Sherlock Biosciences. It works by programming the CRISPR machinery to detect a snippet of SARS-CoV-2 genetic material in a nose, mouth or throat swab, or in fluid from the lungs. If the virus’s genetic material is found, a CRISPR enzyme generates a fluorescent glow. The test can return results in about an hour.

The US has no idea how to manage all the testing data it’s collecting (May 7) – In the US, each state decides how it reports findings from covid-19 tests. The result is a chaotic system that’s hurting our response to the pandemic.

Archived news – COVDI-19 testing

SARS-CoV-2 treatment development

Scientists Find An Avenue To Attack The Coronavirus, Aided By Cloud Imaging (September 22) – Findings discussed may let doctors one day administer drugs to COVID-19 patients that interact with the spike protein at the site where it captures linoleic acid, one of the body’s essential fatty acids that’s absorbed through food. See the original Science paper published this week.

F.D.A. ‘Grossly Misrepresented’ Blood Plasma Data, Scientists Say (August 28) – Dr. Stephen M. Hahn, the F.D.A. commissioner, erroneously stated that convalescent plasma would have saved 35 percent of coronavirus patients this year. Scientists were taken aback by the way the administration framed this data, which appeared to have been calculated based on a small subgroup of hospitalized Covid-19 patients in a Mayo Clinic study: those who were under 80 years old, not on ventilators and received plasma known to contain high levels of virus-fighting antibodies within three days of diagnosis. Many experts — including a scientist who worked on the Mayo Clinic study — were bewildered about where the statistic came from.

Protein Interactions Point the Way to Drugs Against COVID-19 (August 4) – A recent Cell report details findings on how SARS-CoV-2 modifies proteins within infected host cells to enhance the virus’s ability to invade neighboring cells. These viral modifications involve a route of infection not previously seen in the family of coronaviruses. The report also specifies at least half a dozen existing drugs that — with further testing and official approval — could be pressed into service against the virus.

Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2 (August 4) – A stable dimeric variant shows potent SARS-CoV-2 and -1 neutralization in vitro. The engineered receptor is catalytically active and its close similarity with the native receptor may limit the potential for viral escape.

Data show panic and disorganization dominate the study of Covid-19 drugs (July 6) – 1,200 clinical trials aimed at testing treatment and prevention strategies. Analysis found many of the studies are so small — 39% are enrolling or plan to enroll fewer than 100 patients — that they are unlikely to yield clear results. About 38% of the studies have not actually begun enrolling patients.

Gilead announces price for Covid-19 drug remdesivir (June 29) – The vast majority of patients are expected to receive a 5-day treatment course using 6 vials of remdesivir, which equates to $2,340 per patient.

Gilead to Test Inhaled Form of Remdesivir in COVID-19 Starting in August (June 22) – The company expects to begin screening healthy volunteers for the Phase I trial this week with plans to begin clinical studies in August. If it works, the drug could be given to patients using a nebulizer, which would allow for easier dosing outside the hospital and potentially in earlier stages of the disease.

Inexpensive, Widely Available Steroid Saved Lives in Large COVID-19 Clinical Trial (June 17) – A large clinical trial in the U.K. has found that dexamethasone, a cheap and widely available steroid, decreased the risk of death in severely ill COVID-19 patients. The preliminary results, which have not been peer-reviewed, suggest the drug could become standard care in COVID-19 severe patients.

Collecting Genomic Data to Accelerate COVID-19 Drug Discovery (June 9) – Mount Sinai researchers have developed the COVID-19 Gene Set and Drug Library to leverage genomic data and facilitate collaborative drug discovery.

Rules for Clinical Trials in a Pandemic (June 21) – A new study finds that adding a simple steroid to the treatment of severe Covid-19 cases can significantly reduce deaths. That’s another milestone in the battle against the virus. It shows a path for reducing Covid deaths faster through medical innovation and for keeping the health-care system from being overwhelmed as the epidemic spreads. Discussing also that the US case-death dissociation is primary due to more young people infected and better protection of the older age groups. An Oped piece by Scott Gottlieb and Mark McClellan.

NIH launches analytics platform to harness nationwide COVID-19 patient data to speed treatments (June 15) – The National Institutes of Health has launched a centralized, secure enclave to store and study vast amounts of medical record data from people diagnosed with coronavirus disease across the country. It is part of an effort, called the National COVID Cohort Collaborative (N3C), to  help scientists analyze these data to understand the disease and develop treatments. This effort aims to transform clinical information into knowledge urgently needed to study COVID-19, including health risk factors that indicate better or worse outcomes of the disease, and identify potentially effective treatments.

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies (June 15) – The spike protein is a key mediator of viral infectivity required for attachment and entry into target cells by binding the ACE2 receptor. Success of combination therapy for HIV demonstrated that requiring the virus to simultaneously mutate at multiple genetic positions may be the most effective way to avoid drug resistance. This study describes a parallel effort.

FDA Warns of Newly Discovered Potential Drug Interaction That May Reduce Effectiveness of a COVID-19 Treatment Authorized for Emergency Use (June 15) – Based on a recently completed non-clinical laboratory study, the FDA is revising the fact sheet for health care providers that accompanies the drug to state that co-administration of remdesivir and chloroquine phosphate or hydroxychloroquine sulfate is not recommended as it may result in reduced antiviral activity of remdesivir.

Eli Lilly starts trial of rheumatoid arthritis drug in COVID-19 patients (June 15) – The trial began dosing patients last week and plans to enroll around 400 patients globally. Lilly could potentially obtain U.S. regulatory approval for the drug as soon as August.

Covid-19 Patient Gets Double Lung Transplant, Offering Hope for Others (June 11) – The operation is believed to be the first of its kind in the U.S. The patient, a woman in her 20s, had been healthy, but the coronavirus devastated her lungs.

WHO Resumes Study of Hydroxychloroquine for Treating COVID-19 (June 4) – On June 3, the World Health Organization (WHO) resumed a study looking into whether the malaria drug hydroxychloroquine could be effective in treating COVID-19.

Lancet, New England Journal retract Covid-19 studies, including one that raised safety concerns about malaria drugs (June 4) – The retracted influential study that raised alarms about the safety of the experimental Covid-19 treatments chloroquine and hydroxychloroquine amid scrutiny of the data underlying the paper. Just over an hour later, the New England Journal of Medicine retracted a separate study, focused on blood pressure medications in Covid-19, that relied on data from the same company. The retractions came at the request of the authors of the studies, published last month, who were not directly involved with the data collection and sources, the journals said.

Gilead’s remdesivir shows some benefit in patients with moderate Covid-19, new data show (June 1) – The new data, from a study conducted by the company, add to the evidence that the medicine is at least somewhat effective treatment for Covid-19. But they will also likely add to the debate of exactly how effective the remdesivir is, and in what patients.

Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis (May 22) – There is no evidence of benefit for chloroquine and hydroxychloroquine in COVID- 19 patients: finding from a large observational study of nearly 14,888 patients with COVID-19 & 81,000 controls.

Dozens of coronavirus drugs are in development — what happens next? (May 14) – Drug manufacturers face supply-chain weaknesses and sourcing issues as they ramp up complex production processes to meet global demand.

NIH begins clinical trial of hydroxychloroquine and azithromycin to treat COVID-19 (May 14) – A clinical trial has begun to evaluate whether the malaria drug hydroxychloroquine, given together with the antibiotic azithromycin, can prevent hospitalization and death from coronavirus disease 2019 (COVID-19).

As We Wait For a Vaccine, Scientists Eye Antibodies (May 12) – As new information emerges about the effectiveness of the antibody response in people infected with the SARS-CoV-2 virus — including a study showing that most people who tested positive produced antibodies — a monoclonal antibody treatment for this pandemic is growing more appealing. In theory, it could even be given prophylactically to high-risk individuals to create short-term protection against future infection.

Archived news – SARS-CoV-2 treatment development

SARS-CoV-2 vaccine development

Moderna Shares the Blueprint for Its Coronavirus Vaccine Trial (September 17) – Moderna released a 135-page document spells out the details of how it is conducting the late-stage trial of its coronavirus vaccine, and how safety and efficacy will be determined. The document suggests that the first analysis of the trial data may not be conducted until late December, and that there may not be enough information then to determine whether the vaccine works. Subsequent analyses, scheduled for March and May, are more likely to provide an answer.

Moderna’s clinical study protocol with efficacy assumpations and analysis plans (September 17)

Drugmaker Pauses Covid-19 Vaccine Trial for Safety Review (September 8) – AstraZeneca halts a vaccine trial to investigate a participant’s illness. A volunteer in the U.K. trial had been found to have transverse myelitis, an inflammatory syndrome that affects the spinal cord and is often sparked by viral infections. 

Let’s get real. No vaccine will work as if by magic, returning us to ‘normal’ (September 6) – The “first” vaccine, or even the first generation of vaccines, will most likely not be perfect; we need to be pragmatic and transparent on that front. The first generation of Covid19 vaccines will probably be only partially effective. They might not be completely effective in all ages or appropriate in all health systems. It is very possible that they might provide immunity only for a limited period, even as short as 12 to 18 months. This might not be what we are used to from a vaccine, but there is no doubt that the first effective vaccines, even imperfect ones, can have a major impact and be a precious commodity.
#COVID19 #SARSCoV2 #coronarvirus

Twist Bioscience Announces Potent SARS-CoV-2 Neutralizing Data from COVID-19 Therapeutic Antibody Program (September 2) – Data demonstrating the potent neutralizing effects of multiple potential therapeutic antibodies, both Immunoglobulin G (IgG) antibodies and substantially smaller single domain VHH “nanobodies,” against SARS-CoV-2.

Liability risks emerge as an obstacle in Europe’s COVID-19 vaccine negotiations (August 26) – With all eyes on the hunt for #COVID19 vaccines, Europe’s supply negotiations with drugmakers have hit snags over potential liability for side effects. So far only AstraZeneca has completed an agreement—for 400 million doses.

In the race for a Covid-19 vaccine, Pfizer turns to a scientist with a history of defying skeptics — and getting results (August 24) – The company’s head of vaccine research and development, Jansen, 62, has led the development of the world’s two best-selling vaccines, against human papilloma virus and pneumococcus, at two different companies. 

Moderna Wants to Transform the Body Into a Vaccine-Making Machine (August) – The U.S. company and its German rival BioNTech plan to use RNA as a messenger inside cells to produce an immune reaction. The advance could upend vaccine development long after the pandemic.

Coronavirus Vaccine Tracker (August 14) – Allows to see the status of all the vaccines currently developed around the world – more than 165 vaccines against the coronavirus, with 31 vaccines in human trials. Vaccines typically require years of research and testing before reaching the clinic, but scientists are racing to produce a safe and effective vaccine by next year. A NYT tools.

Designer antibodies could battle COVID-19 before vaccines arrive (August 4) – Designer antibodies have the potential to be an important bridge until a vaccine is available.

Archived news – SARS-CoV-2 vaccine development

Coronavirus reading

Science Is What Determined a Successful Public Response to COVID-19 (September 22) – an article by Meredith Salisbury in Techonomy discussing why flattening the curve wasn’t an effective COVID-19 strategy, and more about the best and worst public health responses.

The Coronavirus Is Mutating, and That’s Fine (So Far) (September 11) – The real question is: Has the virus become more virulent or more infectious than it was when it was first detected in Wuhan, central China, in December? The evidence suggests that it has not.

America Is Trapped in a Pandemic Spiral (September 9) – The latest piece written by Ed Yong (The Atlantic)

No, 94 Percent of COVID-19 Deaths Were Not Caused by Something Else (September 1) – Important read! Only 6 percent of reported COVID-19 deaths have the virus as the sole cause of death listed. Thinking that 94% had additional issues is a huge misunderstanding of the statistics.

A Vaccine That Stops Covid-19 Won’t Be Enough (August 24) – Interesting Op-ed by Adam Finn (The New York Times)

The Plan That Could Give Us Our Lives Back (August 14) – An article bRobinson Meyer and Alexis C. Madrigal (The Atlantic). The U.S. has never had enough coronavirus tests. Now a group of epidemiologists, economists, and dreamers is plotting a new strategy to defeat the virus, even before a vaccine is found.

Immunology Is Where Intuition Goes to Die (August 5) – Another great article by Ed Yong (The Atlantic) delving into the immune system and how our partial understanding of it plays into our current situation. “Immunology is where intuition goes to die.”

Two decades of pandemic war games failed to account for Donald Trump (August 4) – Biosecurity researchers didn’t predict that the US would be among the hardest-hit countries. On the contrary, last year, leaders in the field ranked the US top in the Global Health Security Index in terms of how well prepared they were to fight outbreaks..

How the Pandemic Defeated America (August 4) – A virus has brought the world’s most powerful country to its knees. The latest article by Ed Yong (The Atlantic)

Archived news – Coronavirus reading

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