Thursday, April 23, 2020

Some COVID Data Sources: Johns Hopkins, NYT, NIH Guidelines, CDC Data, Clin Chem Guidelines, Coinfections

Johns Hopkins

The Johns Hopkins website for elaborately mapped COVID data has gotten attention for over a month - here Data is both national and international.

New York Times

NYT also provides an elaborate COVID data and map website - here.
Scroll for multiple maps, for example, hotspots where COVID is doubling every 7 days versus every 14 days.

NIH New Clinical Guidelines - Expert Panel

On April 21, NIH launched a Clinical Guidelines for COVID effort.  Announcement here, actual webpage here.

CDC COVID Epidemiology

While the data may be extractable from Johns Hopkins, simple tables, by the week, at CDC are interesting too.  Find them here.  

For example., the week of April 4, CDC tallies 6,955 COVID deaths, out of 59,246 deaths, obviously just over 10% of all deaths in the US attributed to COVID.   Of 7854 pneumonia deaths, 3,378 were COVID-Pneumonia deaths.  Influenza deaths were only around 5% of COVID deahts (400 vs 6,955).  80% of COVID deaths were in people over 65.

Milken Institute COVID-19 Treatment and Vaccine Tracker

Stating, "the Santa Monica-based Milken Institute has launched a publicly accessible spreadsheet to help the public and policymakers track progress of possible treatments and vaccines. It is developed and maintained by FasterCures, a division of Milken, along with an advisory council..."   News here, tracker here.

COVID-19 Data Portal; Host Genetics Initiative

There will probably be too many bioinformatics sources for this webpage to track, but one is the COVID 19 Data Portal - here.

See also the international Host Genetics Initiative, here.  Coverage in Genomeweb, here.

COVID-19 Healthcare Coalition

Quoting, "The COVID-19 Healthcare Coalition is a private-sector led response that brings together healthcare organizations, technology firms, nonprofits, academia, and startups to preserve the healthcare delivery system and help protect U.S. populations. Together, we’re coordinating our collective expertise, capabilities, and data and insights to provide data-driven, real-time insights to improve clinical outcomes."  Industry coalition.  Here.

IFCC Clin Chem Guidelines

The International Federation of Clinical Chemistry has a long webpage on the role of lab analyses (including COVID testing itself) in managing and diagnosing COVID patients.  Here.


Vitalware has a nice online listing of all the CMS and AMA COVID codes - hereThere are 9.

Coinfections in Severe COVID Disease

Sepsis and co-infections are a major part of severe COVID disease and COVID mortality, but get less attention.  See a paper by Zhang (here, here).  In patients with severe COVID disease, they report 29% with other viruses, 25% with bacterial infection, 11% with fungal infection.


See also my earlier blog on an interesting COVID projections website developed at Leavitt Partners, here.


Some more numbers from the CDC data.

Of 52M people over age 65, 489,000 died in this period (1%) and of that, 18,400 died of COVID.  COVID deaths in this age range exceed flu deaths by about 5:1.

In this age group, COVID deaths were 4% of all deaths (18K/489K).

If I read this right, your chance of dying of COVID - during this interval - was 1:6000 if age 65-74, 1:2400 if age 75-84, and 1:950 if age 85 plus.    (For example, about 7000 deaths in 7M people is 1:1000.) 

Of course national averages are off the point here.  Your odds are much better in Minnesota, far worse in New York.

"Missing Deaths" Theme... 
I first heard in early April that Madrid had 7000 deaths in March - normal being 2000 - and 3000 attributed to COVID.  That quickly suggested that as many as 2000 additional COVID deaths were below the radar.  Final counts remain contested
NYT makes the same point on April 22 - headlined, "28,000 missing deaths." Here.