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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

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.

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

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 of COVID-19

National coronavirus response: A road map to reopening (March 29) – This report, by former FDA commissioner Scott Gottlieb, provides a road map for navigating through the current COVID-19 pandemic in the United States. It outlines specific directions for adapting our public-health approach away from sweeping mitigation strategies as we limit the epidemic spread of COVID-19, such that we can transition to new tools and approaches to prevent further spread of the disease.

Iceland’s testing suggests 50% of COVID-19 cases are asymptomatic (March 26) – Iceland’s population puts it in the unique position of having very high testing capabilities with help from the Icelandic medical research company deCode Genetics, who are offering to perform large scale testing. With 50% testing positive, this would suggest that, on one hand, the virus is not as dangerous as we thought, but on the other hand, it would also suggest that it has spread far more than we are currently aware of.

UK launches whole genome sequence alliance to map spread of coronavirus (March 23) – The COVID-19 Genomics UK Consortium – comprised of the NHS , Public Health Agencies, Wellcome Sanger Institute , and numerous academic institutions – will deliver large scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the government.

Covert coronavirus infections could be seeding new outbreaks (March 20) – Scientists are rushing to estimate the proportion of people with mild or no symptoms who could be spreading the pathogen.

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2) (March 16) – A modeling of a synthetic outbreak: A high proportion of undocumented infections, many of whom were likely not severely symptomatic, appears to have facilitated the rapid spread of the virus throughout China. The best-fitting model used has a reporting delay of 9 days from initial infectiousness to confirmation; in contrast line-list data for the same 10–23 January period indicates an average 6.6 day delay from initial manifestation of symptoms to confirmation The findings also indicate that a radical increase in the identification and isolation of currently undocumented infections would be needed to fully control SARS-CoV2. These findings underscore the seriousness and the pandemic potential of SARS-CoV2 with populations without symptoms potentially spreading COVID-19.

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak (March 6) – Since travel limitations could be instrumental to national and international agencies for public health response planning, this study shows that by 23 January 2020, the epidemic had already spread to other cities within Mainland China. While the Wuhan travel ban was initially effective at reducing international case importations, the number of cases observed outside Mainland China will resume its growth after 2-3 weeks from cases that originated elsewhere. Furthermore, the modeling study shows that additional travel limitations up to 90% of the traffic have a modest effect unless paired with public health interventions and behavioral changes that achieve a considerable reduction in the disease transmissibility. The model also indicates that even in the presence of the strong travel restrictions in place to and from Mainland China since 23 January 2020, a large number of individuals exposed to the SARS-CoV-2 have been traveling internationally without being detected.

Estimating the clinical severity of COVID-19 from the transmission dynamics in Wuhan, China (February 13) – Discusses death rate estimates for the coronavirus and fatality rate in people who have symptoms of the disease which is about 1.4% (compared to 0.1% for the seasonal flu).

Decoding SARS-CoV-2

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (March 23) – 26 of the 29 viral proteins were cloned, tagged and expressed in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs).

Adaptive Biotechnologies and Microsoft expand partnership to decode COVID-19 immune response and provide open data access (March 20)

SARS-CoV-2_Sequencing (March 19) – The CDC has started a collection of SARS-CoV-2 sequencing and bioinformatic protocols, metadata guidance, scripts/workflows, links and best practices.

The proximal origin of SARS-CoV-2 (March 17) – Demonstrates that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

Over 24,000 coronavirus research papers are now available in one place (March 16) – A database with over 24,000 research papers related to the coronavirus pandemic is now live. The database not only helps scientists consolidate existing research but also makes the body of literature easier to mine for insights with artificial intelligence.

The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis (March 13) – The SARS-CoV-2 reference sequence could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future.

Why does the coronavirus spread so easily between people? (March 6) – To infect a cell, the coronaviruses use a ‘spike’ protein that binds to the cell membrane. Its spike protein differs from those of close relatives, and suggest that the protein has a site on it which is activated by a host-cell enzyme called furin. Furin is found in liver, lung, and small intestines which explains the symptoms associated with coronavirus infection – still little is know whether this is exactly what is happening and the importance of these activation sites.

Two genome sequences of coronavirus (COVID-19) show possible internal transmission (March 4) – Scientists have published two genome sequences for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Coronavirus disease (COVID-19) is an infectious disease caused by SARS-CoV-2.

Coronavirus Method Development Community – This group is for the support of researchers working on coronavirus methods, intended to facilitate method-centered collaboration and sharing.

COVID-19 testing

FDA grants emergency use authorization for fastest available molecular point-of-care test for novel coronavirus (March 27) – Abbott has received emergency use authorization (EUA) for the fastest available molecular point-of-care test for the detection of COVID-19, delivering positive results in as little as five minutes and negative results in 13 minutes. The new Abbott ID NOW COVID-19 test runs on Abbott’s ID NOWTM platform—a lightweight box (6.6 pounds and the size of a small toaster). The plan is to ramp up production to deliver 50,000 ID NOW COVID-19 tests per day, beginning next week, to the U.S. healthcare system.

Coronavirus SARS CoV-2 testing in the US (March 27) – CDC site

Number of specimens tested for SARS CoV-2 by CDC labs (N=4,654) and U.S. public health laboratories* (N=107,928)†

Mystery In Wuhan: Recovered Coronavirus Patients Test Negative … Then Positive (March 27) – Some of those who retested positive appear to be asymptomatic carriers — those who carry the virus and are possibly infectious but do not exhibit any of the illness’s associated symptoms — suggesting that the outbreak in Wuhan is not close to being over.

Real-Time Fluorescent RT-PCR Kit for Detecting SARS-2019-nCoV (March 26) – The U.S. FDA issued an Emergency Use Authorization (EUA) for BGI’s Real-Time Fluorescent RT-PCR Kit for Detecting SARS-2019-nCoV. It is intended for the qualitative detection of SARS-CoV-2 which can return results within three hours.

How many tests for COVID-19 are being performed around the world? (March 20)

COVID-19 data as of 20 March: Total tests performed by country

The First U.S. Company Has Announced an Upcoming Home COVID-19 Test (March 18) – Everlywell, a home testing company that offers dozens of lab tests to consumers, is adding a COVID-19 test beginning on March 23.

LabCorp Launches Test for Coronavirus Disease 2019 (COVID-19) (March 9) – The LabCorp 2019 Novel Coronavirus (COVID-19), NAA Test is for Use by Clinicians with Patients Who Meet COVID-19 Evaluation Criteria. LabCorp does not currently collect specimens for the test. Patients for whom testing has been ordered should not be sent to a LabCorp location to have a specimen collected. Instead, an appropriate specimen should be collected at the healthcare facility where the patient was seen and the test was ordered. The specimen should be sent to LabCorp using standard procedures. Test results will be available in 3-4 days. More information about the test, including specimen collection and packaging requirements, is available on their website.

SARS-CoV-2 treatment development

‘This is insane!’ Many scientists lament Trump’s embrace of risky malaria drugs for coronavirus (March 26) – Many scientists have criticized the French trial as riddled with enough methodological flaws to render its findings unreliable or misleading. Biostatisticians from the United Kingdom and Ireland cited a basic failure: Investigators didn’t randomize the groups – essential to ensuring dependable comparisons. They also noted that six of the treated patients were lost to the study, five of whom fared badly—one died, three entered intensive care, and one stopped treatment because of nausea. Yet they were dropped from the analysis, potentially skewing the outcome. Among the immediate consequences: Shortages of the drug are endangering patients who need it for lupus or rheumatoid arthritis.

Gilead asks FDA to take back lucrative orphan drug status on possible coronavirus treatment (March 25)

WHO launches global megatrial of the four most promising coronavirus treatments (March 22) – The large global trial is called SOLIDARITY. When a person with a confirmed case of COVID-19 is deemed eligible, the physician can enter the patient’s data into a WHO website, including any underlying condition that could change the course of the disease, such as diabetes or HIV infection. The participant has to sign an informed consent form that is scanned and sent to WHO electronically. After the physician states which drugs are available at his or her hospital, the website will randomize the patient to one of the drugs available or to the local standard care for COVID-19. The design is not double-blind, the gold standard in medical research, so there could be placebo effects from patients knowing they received a candidate drug. But WHO says it had to balance scientific rigor against speed.

As the coronavirus spreads, a drug that once raised the world’s hopes is given a second shot (March 16) – Remdesivir, in the spotlight as scientists and governments scramble to find a treatment for the disease, took a circuitous route to center stage. Born as a general antiviral candidate, researchers threw it at an array of viruses and saw where it stuck. For years, Gilead was primarily focused on ushering remdesivir into trials and toward approval for a different kind of infection: Ebola. Remdesivir is now being tested in five Covid-19 clinical trials that have been set up at breakneck speed.

NIH clinical trial of remdesivir to treat COVID-19 begins (Feb 25) – Remdesivir, developed by Gilead Sciences Inc., is an investigational broad-spectrum antiviral treatment. It was previously tested in humans with Ebola virus disease and has shown promise in animal models for treating Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS), which are caused by other coronaviruses. Clinicians will regularly monitor participants and will assign them daily scores based on a predefined scale of clinical outcomes that considers factors such as temperature, blood pressure and use of supplemental oxygen, among others. Participants also will be asked to provide blood samples and nose and throat swabs approximately every two days. Researchers will test these specimens for SARS-CoV-2.

SARS-CoV-2 vaccine development

First Results From Moderna Covid-19 Vaccine May Take Two More Months (March 25) – Moderna announced dosing the first patient in the early stage study of mRNA-1273 on March 16. The trial in 45 healthy people is being run by the National Institutes of Health’s National Institute of Allergy and Infectious Diseases, with patients in the study getting two doses of the vaccination 28 days apart. While NIH has control over when results will be disclosed, management guided to data availability in the near-term and suggested that the first data release will likely include a full cohort (>3-5 patients) to reflect the totality of the scientific picture.

As the First Coronavirus Vaccine Human Trials Begin, Manufacturer Is Already Preparing to Scale Production to Millions (March 23) – The vaccine will be studied first in a group of 45 healthy volunteers, who have not been infected with SARS-CoV-2, the virus that causes COVID-19. In this group, scientists are looking to see if the shots are safe, and to test three different dosages to see which seems to activate the strongest immune response. Moderna uses mRNA, a genetic form of the virus’ genome, in its vaccine. When it’s injected into people, cells then process it so immune cells can recognize it and target it for destruction. Unlike the processes used to make most traditional vaccines, this method does not require growing huge amounts of the virus, which is time-consuming.

Everything You Need to Know About Coronavirus Vaccines (March 4) – As Covid-19 spreads, the pressure is on for drugmakers to get a vaccine to market. But it’s not that easy. Includes a list of companies working on a vaccine with a breakdown of the 30+ candidates in development (so far).

Coronavirus reading

The US now has more confirmed coronavirus cases than anywhere else in the world (March 26) – This marks an unhappy milestone for the United States: It’s now No. 1 in confirmed coronavirus cases. China, where the novel coronavirus originated, was the previous leader. The country reported 81,782 cases as per the Johns Hopkins interactive map. Until now, second place was held by Italy, which has reported 80,589 cases.

How the Pandemic Will End (March 25) – An overview of the likely scenarios that the world will be facing in the coming months while managing the COVID-19 pandemic – discussing the next months, the endgame, and the aftermath.

COVID-19 workers get training to protect their own health (March 23) – The National Institutes of Health launched the COVID-19 website with important educational resources for coronavirus workers dealing with the spread of COVID-19. 

Can you become immune to the coronavirus? (March 23) – A New York Times article.

How the Coronavirus Became an American Catastrophe (March 21) – The death and economic damage sweeping the United States could have been avoided – if only we had started testing for the virus sooner.

Coronavirus: The Hammer and the Dance (March 19) – What the Next 18 Months Can Look Like, if Leaders Buy Us Time

Suppression vs. Mitigation vs. Do Nothing – early on

Tracking a pandemic: Q&A with a COVID-19 detective (March 13) – What Fred Hutch expert Trevor Bedford is learning as he chases the coronavirus evolution and spread. Scientists track small changes in the virus’ genetic code as COVID-19 spreads from person to person. The changes act like fingerprints, helping researchers chart its global movements in near real time. 

America’s shamefully slow coronavirus testing threatens all of us (March 12) – The US lags just about every developed country on testing for Covid-19 disease.

Coronavirus: Why You Must Act Now (March 10) – Great, extensive article on the virus and how it’s spreads.

Trump’s mismanagement helped fuel coronavirus crisis (March 7) – Current and former administration officials blame the president for creating a no-bad-news atmosphere that stifled attempts to combat the outbreak. For six weeks behind the scenes, and now increasingly in public, Trump has undermined his administration’s own efforts to fight the coronavirus outbreak — resisting attempts to plan for worst-case scenarios, overturning a public-health plan upon request from political allies and repeating only the warnings that he chose to hear. 

China’s cases of Covid-19 are finally declining. A WHO expert explains why. (March 3) – “It’s all about speed”: the most important lessons from China’s Covid-19 response.

Cryptic transmission of novel coronavirus revealed by genomic epidemiology (March 2) – An informative piece on genomic epidemiology applied to COVID-19. It is encouraging that we can sequence, share and analyze pathogen data so quickly today.

Therapeutic and triage strategies for 2019 novel coronavirus disease in fever clinics (February 13) – Outlines the best practice strategies for diagnosing and treating Covid-19 from the point of view of hospitals and clinics, but can also be helpful for individuals experiencing symptoms.

Trump Has Sabotaged America’s Coronavirus Response (January 31) – As it improvises its way through a public health crisis, the United States has never been less prepared for a pandemic. For the United States, the answers are especially worrying because the government has intentionally rendered itself incapable. In 2018, the Trump administration fired the government’s entire pandemic response chain of command, including the White House management infrastructure. If the United States still has a clear chain of command for pandemic response, the White House urgently needs to clarify what it is – not just for the public but for the government itself, which largely finds itself in the dark.

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