Updated Wednesday, Nov 13, 2020

This resource was first created by me in response to what I saw as growing demand for reliable information. I continue to update the page with new links and resources keeping up with the rapidly changing knowledge we have on the SARS-CoV-2 infection and the disease COVID19.

I will continue to post insights about the disease on an ongoing based on the emerging data and science. I have highlighted at the top some of the key resources that you can access that are being updated by teams of people.

Key Online Resources

 

From Internet Book of Critical Care: COVID-19 details diagnosis and treatments

CDC COVID19 Page: CDC Coronavirus Page

NHS COVID19 Page: The National Health Service (NHS) Guidance Page (with some good FAQ’s and advice) and their guidance for clinical Professionals The NHS Guidance for Clinical Professionals

USCF COVID-19 Resources – including their list of resources and Decision Tree Graphic: COVID-19 Adult Clinical Evaluation Guide

Center for Infectious Disease Research and Policy (CIDRAP) – Univ Minnesota – COVID-19 Resources and References/Bibliography

WHO Database of publication on Coronavirus

COVID-19 Open Research Dataset (CORD-19) – an opportunity for data scientists to pitch in

Handbook for COVID19 prevention and Treatment from China

Coronavirus Tech Handbook – sort of assembly of “Guide of guides”

COVID Scholar Papers

Ebsco: COVID Portal

Wiley Covid-19: Novel Coronavirus Content Free to Access

Cochrane Library Resources on COVID19 – evidence relevant to critical care and infection control and prevention measures

LitCovid – curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus

Open Safely Resources – and a link to our Website Resources SafeHealthyWork.com

Nature Study demonstrating the effectiveness of Surgical Masks in preventing the spread of virus particles

COVID-19 Event Risk Assessment Planning tool

Cerner’s Reopening and Social Distancing Projections Tool

Test Analysis Tool

What We Learned From Smallpox, Measles, Cholera, and Other Health Crises

CDC Guidance for Higher Education

How we Reopen Safely

College Opening Tracker

NY Times: Latest Map and Case Count

Drill down Social Distancing Scoreboard by State and County

COVID-19 Planning Guide and Self-Assessment for Higher Education

Visualizing the effectiveness of face masks in obstructing respiratory jets – the key finding here, bandannas are ineffective, cloth masks are good, surgical masks are better

An aggregated dashboard of the Individual State Guidelines

Guidance for Health and Fitness Centers including State Level legislation

Pan American Health Resources

COVID-19 Event Risk Assessment Planning Tool

Esri COVID19 Pulse Trend Lines by States

COVID-19 Decision Support Dashboard

Simulations/Modelling of Covid-19/Spread of Diseases in the Built Environment

Harvard Public Health Dashboard: Key Metrics for COVID Suppression

Excellent living document on Aersol Transmission and Mitigation

Dashboard of COVID19 Infection rates in your Area and Worldwide

College Cases Tracking Dashboard

COVID-19 Test Calculator – how to interpret Test Results

An interactive visualization of the exponential spread of COVID-19

 

Wishing everyone well through these challenging times

 

Ongoing Updates on COVID-19

By the very nature of this “Coronavirus” (more on this later) that it is “novel” (in other words an unknown infective agent that has not been seen in humans before) the data, guidance and our understanding is fast-moving, making keeping up to date challenging for everyone.

Assembled below is a collection of resources that I have found, read, used, digested and otherwise shared through the various platforms online. I get asked a lot for my thoughts on the virus, its spread, people’s risk and suggestions on how to protect yourself which I try and answer to the best of my ability each time. So rather than starting afresh, I decided to assemble this into a single post that I will keep updated as new information arises, as new data is captured and understood and as the situation develops and changes.

I am always happy to take suggestions for inclusion and constructive comments. My bar for inclusion and dissemination remains founded on science and facts (as best as we understand them at the time). Remember that as we learn more these facts will change. For example, the mortality rate (that is the rate at which people who are infected die of the disease) will change. This is not fake science nor errors but rather a normal part of the scientific process of understanding. You can look back at the discovery of HTLV-III as it was known aka as HIV and AIDS for an example of another changing story and data.

In the context of the “Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” as it is known currently, the virus causing the disease as COVID19 we can be sure that estimates of mortality, infection rates, etc will change over the coming days, weeks and months. There are lots of reasons but one simple one is the change to the total number of cases. This is the denominator or lower number in fractions and as this changes so too does the % of the disease.

Dashboards

The Johns Hopkins Tracker that is prepared and updated by the CSSE team at Johns Hopkins (link) (This GitHub project is tied to this data source and presents it here)

And this from Wordometer (link). For a sense of how granular this could be, take a look at the live tracking page from Singapore, and of course the dashboard of dashboards of COVID19 trackers

And this crowdsourced mapping project:

This Jvion map is interesting as it looks at Community Vulnerability

This county-based map for COVID19 incidence is helpful

Pan American Health Dashboards (World, US)

COVID-19 Event Risk Assessment Planning Tool

College Campus Re-Opening Dashboard

Harvard Public Health Dashboard: Key Metrics for COVID Suppression

Deep Dive into Corona Virus

Recognizing some will be like me and want to dive into the detail of the science, research and latest developments these are the pages that will help satiate that hunger

SARS-CoV-2 and the lessons we have to learn from it

COVID-19 details diagnosis and treatments

CDC Guides for Prevention of Spread

Public Health Goal is to Limit the Spread as detailed in Twitter Here or Thread reader Page

Crystal Structure of the Virus Receptors: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV

Dispelling the notion that COVID is not ARDS – COVID-19 Lung Injury is Not High Altitude Pulmonary Edema

How the Disease Spreads

The virus particles are transmitted from infected individuals either directly (direct spread) or indirectly via surfaces such as your hands or inanimate objects such as doorknobs.

Direct Spread

The virus is produced by infected individuals who spread the virus particles through breathing, coughing, and sneezing. There is also evidence of fecal spread. Particles are typically aerosolized in droplets that are suspended in the air and come to rest on surfaces as well as on the infected individual especially on hands that can transmit the particles to others through direct touch. These stats from a presentation at Conference on Retroviruses and Opportunistic Infections 2020 (CROI) ( from twitter) offers some useful statistics form the experience in Wuhan

 

Indirect Spread

Data from China contained in a CDC Research Letter (Indirect Virus Transmission in Cluster of COVID-19 Cases, Wenzhou, China, 2020) suggests transmission can occur through contamination of objects and surfaces. Not definitive evidence but certainly suggestive and potentially for an extended period of time

Transmission study of 3 patients in Singapore suggests widespread contamination with virus particles and this study of 13 patients in Nebraska

The latest evidence suggests that airborne transmission is the most significant fo the spread of the disease: Identifying airborne transmission as the dominant route for the spread of COVID-19, and the CDC guidelines: Clusters of Coronavirus Disease in Communities, Japan, January–April 2020.

 

Flatten the Curve

Much has been written on “Flatten the Curve”. It boils down to reducing the rate at which people are infected by the SARS-CoV-2 virus. Our healthcare system has a limited capacity to treat people. If everyone got the disease there are not enough healthcare facilities, beds and clinicians to treat everyone. Anything we can do to reduce the spread and numbers of people catching the disease help both by reducing the potential total number of people infected and hence needing treatment AND reducing the number of people needing admission to the limited supply of available hospital beds

If you want to read more about this article by Siouxsie Wiles: The three phases of Covid-19 – and how we can make it manageable, contains some great charts and explanation of why this is so important

 

Who is at Risk

We are still learning who is at risk and the story is changing based on new data but what we know today appears to be the following

You are at higher risk if

• You have a pre-existing clinical condition or Chronic Disease (for example, Diabetes, Heart Disease or lung disease) from CDC
• You are older (increase in risk starts at ~50 yrs of age)
• You work on the front line of dealing with this response – this includes first responders, healthcare workers and others

Children appear to get infected but don’t show any major symptoms. This is significant since this makes them potential spreaders of the disease and makes the need for social distancing and limiting the spread as much as possible as we “Flatten the curve”.

The other troubling feature of the disease suggests that health care workers who are on the front lines appear to be more susceptible to infection and get a more severe form of the disease even taking account of pre-existing risks fo conditions and age

Some good news relative to this from this one case study out of Changi General Hospital, Singapore (COVID-19 and the Risk to Health Care Workers: A Case Report) where 41 front line healthcare workers were exposed to a single patient over the course of 4 days but *none* developed COVID19

Lethality

How dangerous is this virus if you are infected. This chart from NY Times is helpful in comparing different diseases and how lethal they are

 

Preventative Steps for You to Take

Listing below various things you can and should do for your part in reducing the spread and help flatten the curve to reduce the overload on your healthcare system

 

Hand Washing

Dare I say the silver lining here is that this is now a “thing” (although as someone said, pretty sad it took the spread of a worldwide disease for it to be a thing!)

• Hand washing Science: Original Twitter Here or the Handy Thread reader Page (great deep dive into the science of Hand Washing and why it is so important)
• Hand washing Science: Science of Why it Works (lighter read)
• Hand washing guidelines from the CDC

This video from Japan will give you an idea of how long and how much you should be washing

From a timing perspective singing “Happy birthday” 2 (or it could even be 3 times to get to the required 20 seconds), but as Jen Monnier offered – that can get boring so she compiled a list of songs that have equivalent 20-second choruses (twitter link, thread reader page). It seems like a repeating loop of songs that are 20 seconds long (or their chorus lines played in all public restrooms would be a good incremental step!)

Guidance from WHO on proper handwashing technique

 

Keep Your Distance

Shaking hands is not a good idea unless you have both just washed your hands for the prescribed 20+ seconds. In which case you can go with my suggestion of Namaste (originally for the now-canceled HIMSS 2020 Conference), or perhaps an air hug.

Don’t Touch Your Face

This is probably the hardest task of all. We all touch our faces and for many different reasons and it is a habit especially hard to break. You could try this training at DoNotTouchYourFace. There are guidelines from all sorts of places like Today and, The Huffington Post. Or here are some of my suggested incremental steps to helping break that habit:

• Keep your Hands in your Pocket (sorry Dad I know how you feel about this)
• Wearing Gloves as a reminder
• Keep Something in your Hands – “Worry beads” for example
• Wear Glasses to make it difficult to Touch Your Face
• Enlist Others to Remind You and Help them Too

Or perhaps you just borrow your dog’s cone and put that around your neck!

Stay at Home if Sick

This might be harder than it seems especially given the status of “sick leave” in the United States and perhaps in other countries. Perhaps this might be a watershed moment for sick leave and the sadly named “Sick bank” policies in place in the US. For those in positions of authority and control a great opportunity not just to send out emails about employee safety insisting people who feel sick take time off and don’t come into work. Back this up with a policy that offers real sick time that doesn’t leave employees using already limited vacation days or worse yet unpaid leave.

Quarantine recommendations based on experiences with SARS and MERS are for 14 days self-quarantine in the event of possible exposure (per CDC guidelines)

Cover your Mouth and Face

This is guidance when you cough or sneeze. The classic elbow over the mouth and nose seems to work best but given this my personal view is bumping elbows is probably not optimal as a replacement to the handshake greeting.

Mythbusters

Hoping Jaimie and Adam don’t mind hijacking the term but thinking it captures the principle in one word. Lots of bad and incorrect information out there. Some resources that can help you determine fact from fiction:

The WHO Advice and Fact-Checking Page

Debunking the Myths of Coronavirus by Federation of American Scientists (FAS)

COVID-19 Facts from Dettol and Lysol

Masks

This day has been updated in light of new evidence. We still have a major need for those working at the frontline of the healthcare response and for people to prevent them from spreading it. We have a shortage so preserving those masks for those that need is essential.

This guidance may be changing as we look at the results from other countries especially Singapore and Hong Kong where they have seen positive effects of more widespread mask usage. This was covered in Atul Gawande’s article (Keeping the Coronavirus from Infecting Health-Care Workers). Recently published article in Nature Medicine: Respiratory virus shedding in exhaled breath and efficacy of face masks suggesting that the use of surgical masks is effective in reducing transmission. This article in the Atlantic “Everyone Thinks They’re Right About Masks” offers some good insights and links to original data and studies with the upshot being the answer for you individually should you wear a mask is it depends. That said the guidance is likely to change to recommend everyone wear a mask when out

This paper published in Jun 2020: Visualizing the effectiveness of face masks in obstructing respiratory jets offers some important insights

Bandannas are ineffective, cloth masks are good, surgical masks are better

 

 

Testing

I will detail what information I can find on testing here. Currently, the testing capacity in the US has been insufficient for our needs (and behind other countries). The CDC has a page detailing testing carried out in the US here.  There are commitments to ramp this up and reports of various testing options that may be available from other countries and suppliers. Until we have the capacity the clinical guidelines determine who should be tested.

To test someone specimens are collected from your nose and mouth and sputum and or lungs – the test uses a technique called PCR (Polymerase chain reaction). A long-standing technique used in science and genomics and testing that essentially amplifies the cells in the sample to allow for the detection of a signal. In this case, the PCR amplifies specific genetic material that is unique to the from the SARS-CoV-2 virus to confirm it is present. There is also a blood test that looks for antibodies to the virus in the blood – this is less common (in the US currently).

All tests have some errors, which we call false positives and negatives. The current test has demonstrated false negatives (patients that have the disease but the test says they don’t) as detailed in this paper: Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing an in the press).

 

Testing will remain relevant long past the outbreak as we will need to identify patients who have been infected, recovered, and are neither susceptible nor capable of infecting others which will be important since these individuals could be cleared to work early even if they might be exposed to infected individuals. This will help us return to some more “normal” state and work is already in progress on this.

This article Must we wait for the perfect COVID immunity test is an excellent deep dive into the importance of getting serological testing right

Testing accuracy remains an ongoing problem and is not just based on sensitivity and specificity but also on the prevalence of the disease in the population being tested. As seen in the chart form the NEJM article False Negative Tests for SARS-CoV-2 Infection — Challenges and Implications the pre-test probability can be as high at 30% in the population for a more accurate test (which based on current data the tests we have available are substantially lower sensitivity and more likely at 70% – the blue line).

What if You get it

To borrow from the Hitchhikers Guide to the Galaxy (and Dad’s Army):

Don’t Panic

80% of people who get the SARS-CoV-2 infection have a mild version and recover on their own

How the remaining 20% breakdown is still unclear but for people that are admitted to hospital we currently know based on data from China

• 10-20% Admitted to the Intensive Care Unit (ICU)
• 3-10% require intubation (a breathing tube)
• 2-5% die

The Risk profile currently suggests that

• If you are <50 risk is low (this includes children but may not include the very young)
• Over 50 and your risk rises with age and specifically with other conditions that exacerbate the infection – these include lung and heart disease, diabetes and even cerebrovascular (think brain, stroke, etc) disease.

What does our current treatment look like – this article of 3 cases in China (and video) explains this in detailed clinical terms

Symptoms

The symptoms of COVID19 infection are similar to the Flu – the predominant symptoms being

• Fever
• Cough
• Shortness of Breath

 

 

 

 

 

 

What You Should Do in Case of Possible Exposure

Home isolation (this includes having a separate room and bathroom) for the majority so as not to spread the disease with careful monitoring is the primary method. Engaging with your healthcare professional using one of the many telehealth applications (which one will depend on where you are in the world and in the US on your healthcare coverage which may specific one). At its most basic a video chat can work. Some good resources on self-isolation from the NHS here.

Notes on Estimating Fatality Rate – WHO Report 6 Mar (3-4%) (words of Caution)

See section above on Lethality

What About Treatment

There are no antiviral therapies that have been shown to work. There are lots of teams working on finding and testing possible candidates and some existing therapies being tried as well.

Beyond specific therapies that don’t exist as yet, our treatment options are to proceed as we have been doing for years to treat severe viral pneumonia and Acute Respiratory Distress Syndrome (ARDS ). For the most part, the treatment is the same as it is for influenza (flu).

Latest details from this article in JAMA Apr 13 Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19)

Repurpose Existing Drugs

There has been some initial interest and possibilities around the following drugs that have already been developed and used for other diseases but may prove useful in treating or at least reducing the severity of COVID19

Chloroquine – used to treat malaria and may decrease the amount of virus by interfering with the pH of Lysosomes
HIV Drugs – The COVIS19 shares characteristics to the HIV virus so there is hope the established treatments for HIV might work on COVID19
Remdesivir – Developed to treat Ebola and is being tested and had some success in limited cases

Convalescent Plasma

This technique was used with success (albeit in a more raw form of whole blood) during the Spanish flu. Essentially using the immunity developed by those that get the disease but recover and giving this to patients with the disease to help their immune system cope (JCI)

Vaccine

Meanwhile, scientists and researchers are working at breakneck speed (to be clear in the world of research, drugs, vaccine and research breakneck is measured in months) to develop a vaccine. I would be happy to be proved wrong and while I know there are some novel approaches to vaccine development that might yet accelerate the development of one for COVID19 yet, the safety testing will still take months. Our best estimates suggest we are not likely to see a vaccine for 12-18 months

It is extraordinarily difficult to compress the vaccine development process – there is likely no higher bar for safety and testing of drugs than vaccines since they are given to ordinarily healthy (and not infected) individuals. We need to be as sure as we can be that any vaccine has a positive effect and limit the negative effects including a previously seen problem of immune enhancement in our attempts to develop a vaccine for Respiratory Syncytial Virus (RSV).

 

Can I Get it Twice

The short answer is we are not sure but the data suggests that this is unlikely. There have been anecdotal reports of individuals who recovered returning to hospitals and suffering the COVID19 disease again. Without a detailed analysis of these cases that would need to include a detailed assessment of their original treatment and confirming that they were successfully treated and disease-free, we can’t be sure that this is not simply a case of them not being fully cured and relapsing.

As you may have read above we have a concept of Convalescent Plasma, for this, to work the individuals must develop antibodies and hence some level of immunity for at least some period of time. There has been some work on finding markers for long term antibodies and a small study in Macaques Monkey’s developing long term immunity you can read a more detailed analysis (including the limitations) here.

You can read more about the detail of Coronavirsu immune responses in this article: Coronavirus infections and immune responses if you want to dig into the detail (TL;dr: It’s complicated!)

Our best Proxy (even tho’ they are all different) is SARS so this study of “Duration of Antibody Responses after Severe Acute Respiratory Syndrome” demonstrated average persistence of antibodies for SARS for 2 years. Suffice to say it is untested and uncertain but some of the signals appear positive if this behaves like the closest relative we have to compare SARS and other Coronaviruses then expect some level of immunity for ~2 years

Resource Pages

I am sure there are plenty more but some of the ones I have found to be useful

CDC Coronavirus Page and CDC Flu Guidance (much overlaps)

The National Health Service (NHS) Guidance Page (with some good FAQ’s and advice)

The NHS Guidance for Clinical Professionals

USCF COVID-19 Resources – including their list of resources and Decision Tree Graphic: COVID-19 Adult Clinical Evaluation Guide

Digging into the genomics of COVID19 NSR Paper and GISAID Genomic Epidemiology hCoV19 Epidemiology Tracking

How do the Coronavirsu Testing Kits work

Center for Infectious Disease Research and Policy (CIDRAP) – Univ Minnesota – COVID-19 Resources and References/Bibliography

WHO Database of publication on Coronovarus

The Imperial College Paper that models the impact of non-pharmaceutical interventions

COVID-19 Open Research Dataset (CORD-19) – an opportunity for data scientists to pitch in

Handbook for COVID19 prevention and Treatment from China (context for the resource)

Coronavirus Tech Handbook – sort of assembly of “Guide of guides”

COVID Scholar Papers

COVID Portal

Wiley Covid-19: Novel Coronavirus Content Free to Access

Epidemic Calculator on GitHub

A clinical guide for the management of palliative care during Pandemic (NHS)

Fascinating Testing Strategy to Look at Sewage to Understand the spread of COVID19

Google’s Site on Community Mobility Reports

The Weather Channel has a COVID19 tab that offers details of cases local to you

Need a refresher on Ventilating Patients – Here’s one from Harvard available for Free

JAMA Apr 13, 2020 – Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19)

BMJ Best Practice Guide and Treatment Algorithm

Guidance for Health and Fitness Centers including State Level legislation

Excellent living document on Aersol Transmission and Mitigation

 

History of Changes

I stopped updating this section in April and just update the latest date at the top of the page

Updated Tuesday, April 23, 2020 at 09:14
Added BMJ Best practice clinical guide (includes treatment algorithm), detailed article on importance of accuracy in serological testing

Updated Tuesday, April 14, 2020 at 16:04
Updated pharmacologic treatments, details on COVID-19 Lung Injury and why it is Not High Altitude Pulmonary Edema

Updated Wednesday April 8, 2020 at 12:21
Added ventilator course from Harvard

Updated: Sunday April 5, at  13:01
Added the Weather channel localized tracking page

Updated: Friday April 3, at  16:20
Updated information on Mask, added details on self-isolation instructions, Study on sewage to reveal the spread of disease, detailed report of crystal structure of virus receptor bindings,

Updated: Tuesday Mar 31, at 09:43
Added Palliative care guide, more details on who’s at risk with data for frontline healthcare workers,

Updated: Friday, March 27, 2020 at 16:15
Added Jvion Community risk of severity Map

Updated: Thursday, March 26, 2020 at 16:37
Added section on risks of re-infection, added Cochrane Library COVID19 Collections

Updated: Monday, March 23, 2020 at 15:32
Reducing the Frequency of updates and highlighting professionally updated sites and links managed by teams of people

Saturday March 21, 2020 at 17:50
Adding Additional references and Content

Wednesday March 18, 2020 at 17:22
Imperial college NPI paper, COVID19 Open Source Data Set, reorder and removed “latest news” – impossible to keep up, Guide of Guides (CoV Tech Handbook), an update on treatements

Sunday March 15, 2020 at11:53
Cleaned up virus spread section and details, added section on lethality and who is at risk, additional note on challenges of vaccine development

Friday March 13 2020 at 19:10
Updated the Johns Hopkins Tracker Link, updated section on disease spread, added link to clinical treatment experience of 3 patients in China, slides from COIS insights from China, details on testing, cleaned up preventative steps section and added info on flattening the curve

Wednesday 11 March 2020 at 12:21
Added ToC, Estimating Fatality and Cautionary Note, CIDRAP links, Quarantine guidelines + link, symptoms of the disease, added handwashing technique, added CDC guides on prevention of spread, crowdsourced mapping project

Tuesday 10 March at 10:06
Added additional news and details on how coronavirus testing kits work

Monday 9 March 2020 at 13:02
Added genomics links to GISAID resources

Monday 9 March 2020 at 10:16
Added UCSF list of resources including COVID-19 Clinical Evaluation Sheet

 

Retired or Old Information

You don’t need masks – really! (There are a subset of folks who may need masks)

 

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