Thursday, April 30, 2020

CMS Blows Open The Rules for COVID Testing; Treating Physician Order Not Required. Serology Covered.

On April 30, 2020, CMS issued a press release covering a range of new (new-new) easier rules for Medicare/Medicaid services, including new easier rules for lab test payment and access. It's paired with the release of a new 279-page interim final rule (IFR).  The activities are justified by Social Security Act §1135, emergency policymaking.

UPDATE:  The Federal Register version of the rule appeared Friday, May 8, 2020.  See 85 FR 27550-27629 (80pp) here.   I have updated pagination in this blog, to the five-digit pagination in the Fed Reg version.

Here's the top line of what's new for the lab industry:

  • On pages 27557-8, "Modified requirements for ordering OCIVD-19 diagnostic laboratory tests," broadens rules for who can "order" test - no longer the "treating physician" but any "healthcare personnel" (within state law).
    • CMS released a 2-page online PDF of all codes containing influenza or RSV or COVID testing, to which this rule is applicable.
    • This is more historic than it looks; they changed a decades-old regulation that only a treating MD can order diagnostic tests, at 42 CFR 410.32.
  • On pages 27598ff, coverage for serology testing is added to CMS regulations.
    • This one test - serology - is now baked into regulations of what is reasonable and necessary under 1861(a)(1)(A), something that CMS admits is normally done via NCD.
    • Serology testing defined as "reasonable and necessary" under broad conditions.
    • To my knowledge, CMS hasn't announced any national price for serology testing.
  • On pages 27602ff, CMS allows 99211 coding and payment for physician office specimen collection for COVID in some cases (circa $20).
CMS also has a six page summary sheet regarding COVID new rules, here.

See trade journal MedTechDive on the new rules here.

See the April 30 press release in full here.  I also cut/paste the lab section of the press release after the break.

For the new collection of COVID rule waivers, see the new April 30/May 8 rules online at Federal Register here.

(Not to be confused with the prior IFR, issued around March 30 and finaled as 85 FR 19230-92, April 6, 2020).

At the CMS homepage for emergency COVID rules and guidance here, see "List of Lab Test Codes for COVID, Influenza, RSV" - diagnoses that could clinically overlap - a wide range of codes "that can be conducted without a practitioner order."  HereThis code list includes the familiar codes U0001-U004 (CMS COVID PCR codes) but also broad CPT codes like "Infectious agent, respiratory, 12-25 targets," 87633.

See also 6-page CMS PDF on emergency lab rules here.

See also 36 page PDF on CMS emergency rulemaking, here.

COVID and related tests; new easier ordering rules; full list is 2pp; sample shown here

In the Fed Reg rule, see Serology in Section V, page 27598ff.  Serology covered as reasonable and necessary "for beneficiaries with current or known prior COVID infection or suspected current or suspected past infection."  Regarding cost justification (part of federal rulemaking), CMS states page 233, "its is unclear" what the costs will be.  Relief from "treating physician" order is codified at 42 CFR 410.32 (page 27620).

NB - I haven't seen a price for serology testing at Medicare.  COVID PCR codes are $50 (U0001-2) and $100 (U0003-4).

Ordering Requirements
Modification of ordering requirements at page 27557ff.  Writing, "We anticipate needing to test many Medicare beneficiaries quickly as part of the rapid expansion of COVID testing capacity to combat the epidemic.  Therefore, the need for a patient to first have a visit with a [treating] physician or practitioner to obtain an order for COVID testing to meet Medicare requirements could present a significant barrier to patients who might otherwise seek a test."  The relaxation applies also to tests for influenza and respiratory syncytial virus (RSV): "because the symptoms...might present the same way."

The rules seem to be that any "healthcare professional" e.g. a "professional" in a pharmacy or drive-by setting can "order" the COVID tests (including up to an 86733 25 pathogen Biofire type test, $416).

Except that it must be "clinically necessary," (not further defined), but claims require only listing of the NPI of the "ordering professional" e.g. professional or pharmacy (pharmacist or pharmacy?).

Regarding CMS's statement that test "must be clinically necessary" -  what kind of records on that "patient" would the pharmacy or for that matter a drive-thru place keep?  So there are still some puzzles.

Other features; CMS allows physician offices to bill 99211 in some circumstances for COVID specimen collection (27602ff).

CMS loosens certain rules pertaining to the DME LCD for continuous glucose monitors (27595ff).

Most features of the 80-page rulemaking emerge from authority at SSA 1135, allowing CMS to waive statutes, regulations, and policies during an emergency.  The waivers would stop the day the emergency stops.

Humor: Tech Meets Healthcare

First, be aware of the Hype Cycle Disillusionment Curve - here.
Second, be aware of healthtech social media guru Nikhil Krishnan, @nikillinit.

Here's from Nikhil on April 29:

(click to enlarge)

(My LOL started at, "Let's go to self-ensured employers...")

See also a similar graphic, not related to healthcare, but illuminating (particularly "bear trap' and "bull trap" mini inflections).  Comes from David Janny, Morgan Stanley:

click to enlarge
>> Note the slow, low dashed line, rising slowly from left to right near the bottom, representing the real value, which the hyperactive curvy line inevitably converges to.

GAO Report on National Antibiotics Crisis: 20 Pages on Role of Diagnostics

GAO has released a massive 135-page report on the state of antibiotics development, resistance, and the health of antibiotics R&D in the United States and internationally.

See the GAO report here.  See coverage at Endpoints here.

Much emphasis on the poor economics of antibiotics development, the growing need, and the lack of "postmarket" actions (in addition to depositing money in startups to help R&D.)

I noted there are nearly 20 pages devoted to diagnostics (pages 35-53.)

The high-level bullet point for diagnostics is:
  • "Clarify roles and responsibilities to assess the clinical outcomes of diagnostic testing"
The Diagnostics chapter lists these more specific takeaways:
  • Challenges in Addressing Diagnostic Test Gaps 
According to federal documents and literature, challenges to diagnostic test development include:
• Lengthy and costly regulatory requirements, including additional regulatory hurdles in other countries
• Limitations in technical feasibility assessments due to intellectual property protection and conflict of interest requirements
• Differences in expertise between manufacturers and regulatory bodies
• Limited evidence on cost-effectiveness and clinical outcomes for using tests
• Limited resources in some settings to transport specimens, conduct, and maintain tests 

Note that GAO had done an earlier report in 2017, "Challenges and Capabilities to Enable Rapid Diagnoses of Infectious Disease," (64pp) here.

Very Brief Blog: Vinay Prasad Publishes Book on Oncology "Hype"; See Also New Book on Pharma Price Inflation

For several years, Vinay Prasad has been one of the most outspoken voices that oncology trials lack enough data before FDA approval and prices are too high (the issues being related - Prasad asserts, too often a high price for a thinly-validated drug).  In large part, he's skeptical on accelerated approvals.

Social Media
See his webpage here.  Follow him on Twitter here.

See a 2018 profile of Dr. Prasad at NPR, here.  (See also NPR on accelerated approvals, 2019, here.)

In 2017, he received a $2M  donation from the Arnold Foundation to research ineffective healthcare (here).  Concurrently, Arnold Foundation donated $14M to ICER.

For some recent PubMed citations, pairing "Prasad V" with keyword "oncology," click here.  For example, see "The Evidence Landscape in Precision Medicine," Sci Transl Med April 22, 2020, here.

Precision Medicine Horizon Scan: Prasad's New Book

As of April 21, 2020, he has a new book out, "Malignant: How Bad Policy and Bad Evidence Harm People with Cancer" - Johns Hopkins University Press.  JHU here, Amazon here.

Some soundbites include: "This is a book about how the actions of human beings—our policies, our standards of evidence, and our drug regulation—incentivize the pursuit of marginal or unproven therapies at lofty and unsustainable prices. [And Prasad] critiques the financial conflicts of interest that pervade the oncology field, the pharmaceutical industry, and the US Food and Drug administration."


This is Prasad's second book; see also "Ending Medical Reversal," Prasad & Cifu, Johns Hopkins, 2015.  Here.


Feldman on Biopharma Price Inflation

On similar themes, see 2019, Robin Feldman, "Drugs, Money, Secret Handshakes: The Unstoppable Growth of Prescription Drug Prices," [Cambridge University Press], here.  Focus includes PBMs.

Feldman also produced 2017, "Drug Wars: How Big Pharma Raises Prices and Keeps Generics Off the Market," [Cambridge University Press, Feldman & Frondorf] here.

Feldman is a Professor of Law at Hastings Law School / Berkeley.  She also published "Rethinking Patent Law," in 2012 (Harvard University Press), on patent litigation, patent trolling, and possible improvements.

Wednesday, April 29, 2020

Very Brief Blog: United Healthcare Stock; Private Payers in Richardson et al.

Richardson et al., 2020, is the JAMA paper that made headlines for finding that 88% of COVID patients placed on a respirator in NYC died.

I had the paper out for another purpose today and noted the distribution of payers, included in Table 1.  The distribution was 33% commercial insurance, 21% Medicaid, 42% Medicare, and 4% other.  In other words, about 70% of NYC COVID patients were not on commercial insurance.

I don't want to draw a direct line, but I looked up performance of United Healthcare stock over six months.   It ran around $280 last fall and through January.  It hit a nadir of $195 on March 23.  It's running about $290 today.

Just as hospitals (outside of NYC and a few places) have empty elective operating suites and often two-thirds empty ERs, and just as many non-essential clinics are closed and doctors face serious financial unknowns (here) - all of that missing revenue on the hospital and clinic side represents revenue not migrating out of payers' balance sheets.

Medicare Nerd Note: CMS Spreadsheet for Lab Tests Exempted from Outpatient Bundling

Medicare's date of service rule is painfully complex, and has been complexified over the years since it was first promulgated.

In a nutshell, all tests on inpatient specimens are bundled, unless ordered by the physician 14 days after the day of hospital discharge.

Tests on outpatient specimens are also bundled, EXCEPT FOR exceptions.  The exceptions are "molecular pathology tests" and ADLT tests.*   These tests are billed to Medicare by the lab that performed them, be it hospital or freestanding lab.

Tests on non-hospital-associated tests are billed by the performing lab.

What's New 

The point of this blog is to flag that CMS has a webpage devoted to the 14 day rule, with a number of links.  Here.

What's new to me, CMS offers, via a Zip file, an Excel spreadsheet listing by code and name all of the 349 lab codes that are EXEMPTED from outpatient bundling rules.   Get the most current version at the CMS webpage under "lab codes exception" zip file.  I've also put the April 2020 version in the cloud here.   Note it has two tabs, one a CPT code tab and one a Notes tab.  The date of decision is listed for each code.  Newest codes are at the bottom in red.

What's Bundled, What's Not - CMS Lists Differ

Most of the codes exempted are in the CPT 812xx 813xx 814xx 815xx code series - human DNA/RNA tests.   81479 and 81599 (unlisted codes) are on this list. 

Interestingly, if you go to the April 2020 file of all CPT codes in the outpatient setting, a few additional codes are "Status A" that are not on the list of excepted lab codes offered on the DOS page.  For example, 86631 86632, chlamydia antibody tests, are status A, whereas the hundreds of microbiology codes around them are bundled status Q4.  Mystery to me.  But these 86631/86632 lab tests codes that are excepted from bundling are not on the special CMS listing of lab codes excepted from bundling.

Also, I saw elsewhere (probably a transmittal) that novel COVID codes U0001, U0002, U0003, U0004 are unbundled (Status A), but they aren't listed on the special list of excepted codes

U0001 U0002 are listed on the general outpatient list of all codes, as unbundled, Status A, however.

ADLT tests are a tiny group of tests designated as Advanced Diagnostic Laboratory Tests by CMS.  They are always sole source tests and are covered by Medicare and are either MAAA tests or FDA approved sole source tests.  Rules.

Very Very Brief Blog: Database for COVID Pre Prints

Very briefly, this came through my inbox overnight:

I've copied the link here to be sure it works for you:

click to enlarge


COVID-19 preprints. 

Preprints — academic papers published online before they’ve gone through traditional peer review — have become a common way for scientists to disseminate their coronavirus-related findings. So researchers Nicholas Fraser and Bianca Kramer have begun compiling a dataset of more than 6,000 COVID-19 preprints. For each paper, the dataset includes the title, abstract, DOI, date posted, and the hosting repository (such as medRxiv, the most common so far).

Tuesday, April 28, 2020

April 28: Bonanza of COVID Testing Articles

On a normal day, it's impossible to keep track of the flood of COVID news, but maybe even less so today.

I'm providing a listing from the deluge that came just in my morning horizon scan.

  • President Releases COVID Testing Plan for Reopening America
    • See 11 page White House white paper here.
    • See MedPage Today here.
    • CNN here.
    • Re expanded testing: CVS press here, Walgreens allies with Labcorp, press here.\
    • Plan, like Gottlieb's (next), depends on "state based contact tracing" which suggests alot of replication of processes and knowledge across the 50 states.  See Johns Hopkins white paper on contact tracing (April 10) here.
    • Flaws of antibody testing highlighted in yet another article, Atlantic, here.
  • Separately a four-page "Bipartisan Letter" - from former FDA Republican Scott Gottlieb and former CMS Democrat Andrew Slavitt and a dozen co-authors - recommends a $45B testing and contact tracing plan.
    • See news coverage at Healthcare Dive here.
    • See original four page PDF letter to Hill, here.
    • Separately: STAT article urges public-private partnerships for contact tracing, here.
  • WSJ publishes 17 page report to White House from "a secret group of scientists" connected to among others, Goldman Sachs and Pence advisors.
    • WSJ here.
    • Similar coverage followed quickly at Business Insider, here.
    • Original PDF letter here.
  • Contact Tracing Technology: Next Big Thing...
    • Are apps effective?  Digital Health article here.
    • WaPo says apps may be effective, but raise privacy issues, here.
    • See a full length article by Kim and Paul at MedRxiv, here.  "Contact Tracing: A Game of Big Numbers in the Time of COVID."
    • See an April 24 update on the ongoing role of Apple/Google - here.
    • See an April 23 article in MobiHealthNews on an app from CarePredict - here.
    • Lawfare (new to me) runs article on April 17 Senate "virtual hearing" on contact tracing best practices and problems - hereExcellent article by Elliott Selzer.
    • NYT highlights the diversity of tracking apps, April 29, here.
    • Contact tracing in UK/NHS highlighted in Guardian, here.
    • See Park et al. in JAMA on contact tracing and digital deployment in South Korea, here.

  • NYT - Shoddy Testing!
    • NYT publishes a particularly hostile Op Ed on the "shoddy" state of US COVID testing. Here.    
    • See also LA Times April 28 on serology by Aleccia here, and LA Times same day on a novel but uncertain saliva PCR test by Lau, here
    • Flaws of antibody testing for public health needs and reopening, highlighted in yet another article, Atlantic, here.
    • BGI inks $260M contract for PCR COVID in Saudi Arabia, here.
  • LA Times - LA Reliant On Uncertain, VC-Backed Test.
  • Should we consider COVID sequencing rather than PCR?
    • Articles argue the point while showing tech approaches - at BioRxiv by Munnink here, by St Hilaire here.
    • Prof. Bert Ely (Univ South Carolina) at Discover argues that "the coronavirus genome is like a shipping label," with beautiful graphics, here.
    • WSJ has lead article on how coronavirus mutations map the global outbreak (April 30), here.
    • NYT has a similar lead article on the same thing (also April 30), here.
    • NYT has article that CDC will launch national effort to track COVID strains and mutations (also April 30), here.
    • See a global website for COVID SEQ data here.
    • (National Geographic had a very early article, in March already, here, quoting Phil Febbo, Chief Medical Officer at Illumina.  NYT reported NYC cases came from Europe on April 8, here.   NYT on spread of cases eastward from Seattle, April 22, here.)

  • MedCity News ran a report on "easy the bottlenecks of COVID testing" - here.
  • Retail executives promise to "ramp up testing" - here.

  • Healthcare Dive published an article on "reimbursement portal" for testing and treating the uninsured - here.
  • Scientific American publishes article, "How the Pandemic Might End," here.
    • With their own bonanza of articles, Sci Am also ran:
    • Beware of COVID immunity passports - here.
    • Will America allow COVID Tracking Apps? here.
  • WSJ ran an article on airlines and new mask requirements, here.
    • WSJ also ran an article (April 29) the whole spectrum of faults in US pre-pandemic status and supply chains, here.
    • WaPo ran an article on deadly contagions on airplanes, here.
    • Guardian ran a deep dive article on contagiousness of COVID in early April, still relevant, here(Highlights include Gangelt, Germany crisis).
    • WaPo says, further proof that COVID is 10X deadlier than flu, here.

Trio of Articles about Confusion:

Thomas Wilckens has an article on Linked In - What if much of what we know about COVID is wrong?  Here.
Peter Bach has a piece in NYT, science is messy, very messy, get used to it - here.
Ed Yong has an article in The Atlantic on why COVID is so confusing - here.
Another "big think" on COVID piece - lots of signs we are heading into a depression - Harvard Business Review on why we "are not" heading into a depression - here.


Separately, and on a more medical note, BMJ publishes a weekly medical news reoundup by the horizon-scanning Richard Lehman - always a good collection - here.

National Academy of Medicine / US, broadcasts two hour update on COVID, April 26, YouTube, here.

Tenner at Atlantic argues that lean hospitals with 95% occupancy and lean staff left us exposed to crisis - here.

And unrelated to COVID, Exponents published an interesting article by Chris Dobro, "Beyond Single Payer," here.

President Trump to sign order to keep meat plants open; potentially aids both consumers and farmers who are respectively late and early in the supply chain (here).  20 meat workers have died.  (In earlier news, a few weeks ago, already 50 NYC transit workers had died).  House will not return to session in DC next week (here).

NYT also profiles life in Sweden under light restrictions, here.


An early version of this post included "White House Reverses..." by error.  That was based on an April 9 article.   The article at Business Insider primarily tracked back to an NPR article here.
  • APRIL 9: Also from the White House:  "White House Reverses Decision re Federal Funding for Test Sites" - at Business Insider, here.

Monday, April 27, 2020

Very Brief Blog: Cloth and Better Masks and Viral Transmission

There was a lot of debate about whether the public should wear masks or not during the COVID pandemic.   There's some somewhat ominous data about how far COVID nanodroplets (from talking, for example) can travel.  On the other hand, COVID isn't infinitely transmissable.  In a Chinese restaurant, about half the people in the room for an hour with a COVID positive person caught it, about half didn't (here).

Today, WSJ had an interesting article about a group of scientists who allied with some major politicos (or Goldman Sachs types) and have access to the White House staff (here).    WSJ also posted a 17-page report from the group (online here.)   Their white paper is a well-written document about key features and watch-outs in vaccine trials, drug development, etc.   It's not a lightning bolt from heaven; it is organized and assembled common sense on a wide range of COVID topics.

But their references 13 and 14 provide some original research reports on viral transmissions and different types of masks/.   These are Jefferson et al. 2008, and MacIntyre et al. 2015. 

As the white paper authors summarize,

  • Surgical style masks have an odds ratio of 0.32 of transmission.
  • N95 masks are better, but have an odds ratio close to 0.1 (10% of un-masked transmission).
    • N95 odds ratio as low as 0.03 (3%) when used perfectly.
  • Controlled studies of surgical masks and N95 masks in "real world settings" have found them similarly effective.
  • Cloth masks were "63% as effective in preventing symptoms" but "8% as effective in preventing influenza-like illness."
  • Coronavirus has a limited lifetime on paper and masks (not otherwise sterilizing) might be reused after 5-7 days of storage.

I've seem bits of these data in news articles but hadn't found the original citations.  Note that all these studies quoted are about protecting the mask user.  We've all seen reports that cloth masks are good at preventing transmission outward (e.g. coughing particles), so the mask protects people around the wearer.  So if everyone was wearing a cloth mask, everyone would be protected from everyone else.

As far as protecting the mask wearer himself from COVID, you can still wonder.  In the MacIntyre cloth mask study, it wasn't clear if the "cloth masks" used were very thick or had a very close fit.  You see people wearing surgical blue paper masks (surgical masks being more highly recommended) with a lot of open space on the sides, which does not seem that protective against nanoparticle viruses in free air.  Luthra makes this point at Kaiser Health News here.

Jefferson 2008 - Open access
Physical interventions to interrupt or reduce the spread of respiratory viruses: systematic review.

MacIntyre 2015 - Open access
A cluster randomised trial of cloth masks compared with medical masks in healthcare workers


Saturday, April 25, 2020

Palmetto MolDx Posts Five New Molecular LCDs - Plus Urine Drug Testing

On April 23, 2020, Palmetto Jurisdiction M, the home jurisdiction for MolDx, published five new MolDx-branded LCDs, plus a sixth LCD of interest to the lab community, on urine drug testing.

Comment periods started April 23, run to June 6.   Palmetto will hold a public meeting, I believe, but is no longer required to hold a former Contractor Advisory Committee meeting. 

The MolDx LCDs should propagate to other MolDx contractors - CGS, WPS, Noridian. 

I'm not sure if the UDT test, which is not branded "MolDx," will be picked up by other contractors; it's possible.
  • DL38566 - Phenotypic Markers in Circulating Tumor Cells
  • DL38558 - Liquid Biopsies in Solid Organ Transplant
  • DL37264 - Endopredict Test in Breast Cancer
  • DL37794 - BCI Test in Breast Cancer
  • DL38576 - Predictive, Prognostic Tests in Bladder Cancer
  • DL38557 - Urine Drug Testing

To see the LCD proposals and check for updates, I recommend you go to the Palmetto LCD policy page (here)  and at the bottom, click on Proposed LCD Status Report.  This will send you to the CMS web page; note the relevant LCDs may be on one or more CMS web pages (click next-page).

Making Your Life Easier:

I've put the diagnostic LCDs in one open access zip file in the cloud - here.

Liquid Biopsy in Solid Transplants

MolDx already has a two-year-old LCD for CareDx AlloSure Test based on circulating donor DNA.  MolDx also produced an LCD last year for the Natera Prospera based on circulating donor DNA.  Eurofins also has a donor DNA transplant test, and there may be other companies entering this space in the future.

MolDx, since August 2019, has started to exhibit a strong preference for writing "umbrella" LCDs wherever possible, to avoid writing 2,3,4 or more individual single-brand LCDs.   That seems to be the intention with the "Liquid Biopsy Solid Transplant" test.   Typically it takes literally most of a year for a MolDx LCD to propagate among the several MolDx independent MACs and get finalized (I've got the data to back up that "almost a year" point, as long as you include the word "typically.")  It's unclear if MolDx would have concurrent brand-specific LCDs in this space a year from now, or shift to one umbrella LCD, once it is finalized and in place.

 CTC for Phenotypic Markers

This LCD has a broad title but the content is restricted to Her-2-neu CTC detection.

Friday, April 24, 2020

Breaking News: NYT Study Disses Antibody Tests; Health Affairs Reports on National COVID Hospital Costs

Two new stories on April 24, 2020.

COVID Antibody Tests

New York Times - here, Mandavilli - reports a preprint study of 14 different COVID antibody tests.  See the preprint Whitman et al. online here.   See the webpage "COVID Testing Project" here.

Researchers assert that only 3 of 14 COVID antibody tests were workably accurate.  Assert further that some test kits had as much as 16% false positive rate, making them "useless" for clinical and public health purposes. 

Meanwhile, the WHO issues a report that's very conservative on serology use and value so far (WHO here, NPR here).  And see an April 24 story on COVID and (our underdeveloped system of) enterprise risk management here

Politico piles on, April 27,  here.  While Genomeweb's Madeleine Johnson writes about the challenges of developing and validating serology tests (subscription; here.)

COVID Medical Costs - Individual and National

Healthcare Dive reports on a new online study at Health Affairs looking at patient and society medical costs for COVID.   Mensik at Healthcare Dive here.  Bartsch et al. at Health Affairs here.

Inpatient costs for an individual tallied $14,400, roughly triple the costs of a conventional influenza hospitalization. 

Meanwhile, Henry Ford health system in Detroit announced massive financial losses and laid off 2,800 (10%) of employees (here).

Per Bartsch et al., national costs could mount to between $160B and $650B over two years (from 20% to 80% national infection rate).

Mayo said it lost $3B in 1Q2020 - here.

See also a JAMA article on costs by Wadhera et al. here.

New National COVID Testing Plan: Rockefeller Foundation

On April 9, McClellan, Gottlieb, and coauthors at the Margolis Institute at Duke released a national testing plan for COVID, including the rollout of serology testing.  Here.

On April 23, another plan.  This is a 30-page plan and report from Rockefeller Foundation.  See the home page here, the 30 page PDF here.

The plan has the most dramatic expansion of testing I have seen, reaching 30M per week.

The authors summarize,
Our National Covid-19 Testing Action Plan lays out the precise steps necessary to enact robust testing, tracing, and coordination to more safely reopen our economy – starting with a dramatic expansion of testing from 1 million tests per week to initially 3 million per week and then 30 million per week, backed by an Emergency Network for Covid-19 Testing to coordinate and underwrite the testing market, a public-private testing technology accelerator, and a national initiative to rapidly expand and optimize the use of U.S., university, and local lab capacity. 
The plan also includes: launching a Covid Community Healthcare Corps so every American can easily get tested with privacy-centric contact tracing; a testing data commons and digital platform to track Covid-19 statuses, resources, and effective treatment protocols across states and be a clearinghouse for data on new technologies; and a Pandemic Testing Board, in line with other recommendations, to bridge divides across governmental jurisdictions and professional fields.
Not the main point, but it's pretty unusual in English to see a 160-word explanation divided into only two sentences, in this case by the lonely period appearing after the term "lab capacity." 

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.

Wednesday, April 22, 2020

The Santa Clara Serology Study; Debate; John Ioannanidis with a Target on his Back

The simple story this week is that a new Stanford study of seroprevalence of COVID-19 antibodies show that past infections are far higher than most reports have indicated - Science, April 21, here.  See the paper by Bendavid et al., here, posted April 17.

The authors projected a seroprevalence of 2.5% to 4%, being 50-85X higher than the PCR confirmed cases.

For critiques, see e.g. San Jose Mercury News, here.  For some context and back story, TalkingPoints here.  There, John Marshall argues that New York City shows the lowest possible death rate is about 0.5%.  A Bloomberg article reports that the data are mixed and conclusions in either direction are hard to draw - here.  For another article on the debate with quite a bit of context, by Stephanie Lee, hereAnd Lee and others are discussed by a Columbia academician here.

John Ioannidis in NYT

What caught my attention - and my sense of humor - was today's NYT article, by Gina Kolata, with extensive quotes from John Ioannanidis.   Ioannanidis has spent over a decade as a high-profile, highly-quoted critic of other people's sciences, flaws in other people's studies, and generally finding that other people's science was not high quality enough.  One headline - "Ioannanidis, Making Science Look Bad Since 2005."

Here he's on the defensive for a change, and scrambling, and he's archived like a scrambling fly in amber in the NYT.  I couldn't help but feel he was newly in a scenario where the tables were turned.
  • “It’s not perfect, but it’s the best science can do,” said Dr. John Ioannidis, a professor of medicine at Stanford University and an author of the Santa Clara County report.
  • “We tried to look into the possibility of bias influencing the results,” Dr. Ioannidis said. 
    • Adding: "We did a very lengthy set of analyses.”  
    • (Umm...ok...lengthy data scrubbing?)
  • Nobody knows the truth — let’s be honest,” Dr. Ioannidis said of the prevalence figures. 
  • “But if I had to guess [!], I would say it is probably higher than our estimate," he summarized.
    • (Just what should lay people do while conflicting expert guesses fill up the media?)
  • For an update, an interview with Dr. Ioannidis on May 9, here.

BARDA Director Rick Bright Retains Lawyers; PrePrint Disses Chloroquine as COVID Therapy; WSJ & Azar

BARDA In Brief:

BARDA Director Rick Bright, terminated from that position yesterday, has retained lawyers and will ask OIG to investigate the conditions of his termination.

See a story at Endpoints News hereSee NYT here.
  • First, Bright asserts that his resistance to chloroquine and hydroxychloroquine therapies was the cause for his unjust termination.  
  • Second, in a statement vetted by his attorneys, he asserts that "Sidelining me in the middle of this pandemic ...stunts national efforts to safely and effectively address this urgent public health crisis."  
  • Third, he says he will formally ask for an OIG investigation.
His attorneys announced they will "request that the Office of Special Counsel seek a stay of Dr. Bright’s termination."  NYT reports that House E&C committee will investigate (here).

NYT also quotes Administration officials that Bright was "a polarizing figure" within HHS, and other critiques.  A next-day story at CNN by Diamond et al. provides more he-said, she-said quotes (here).    One HHS official said that Bright "slammed things and broke binders" but another provided an HHS job review rating of 480/500 from May 2019.

This week, BARDA netted a new $2B in yesterday's Senate bill for COVID recovery which includes $25B for diagnostics topics (here).

Negative Paper on Hydroxychloroquine Performance

An article in MedCity News focuses on a preprint article in which 368 hospitalized COVID patients had no benefit (but excess deaths) when given hydroxychloroquine.   MedCity here.  Preprint at here, by Magagnoli et al.

The study was retrospective, raising the risk that the Rx treated patients were sicker than non-Rx patients, in ways not captured by propensity adjustment.  However, the adjusted mortality hazard ratio was 2.6 for the Rx group.

Fireworks:  Alex Azar Broadsided in WSJ

WSJ publishes a highly negative story (2600 words) about HHS chief Alex Azar, citing numerous White House sources.  Here.   Similarly at Reuters, here.

Numerous media outlets headlined the news that Azar's pick for pandemic leader, Brian Harrison, was a longtime colleague and experienced Labradoodle breeder.  Sample headlines:

click to enlarge


An April 6 article in Stat Plus (subscription) gave a scorecard for BARDA's performance to date under COVID - here.

Tuesday, April 21, 2020

Senate Passes "COVID 4" Legislation: $25 Billion for Testing

On April 21, 2020, the Senate passed "COVID 4," a $500B aid bill which goes to the House for a vote in the next two days ^ and was passed on Thursday, April 23 by 388 to 5.
  • The bill contains $25B for the lab industry.
  • An online-only copy of the 25 page bill is at CNN, here.
  • It's not pretty, but I've cut/pasted the raw text of the lab portions of the bill into an online HTML file here.
Roll Call has an analysis of the full bill, by Shutt and Krawzak, and contains several paragraphs specific to the $25B for testing.  Go here and scroll to the headline, "National testing strategy."

What's In the $25B?

The test money in part is allocated to states, but they must submit information to a national testing strategic entity as well.   Democrats, who control the House, wanted enough emphasis on a "national strategy" and did not want the money to just flow as block grants to states.

According to Roll Call:
  • $11B for states which may include employer testing.   $4B is distributed based on COVID case density.
  • $1B for CDC for "surveillance, lab capacity, and contract tracing."
  • $2B for NIH to "develop testing, research into rapid testing, partnerships."
  • $1B for BARDA for R&D and production of tests and supplies.
  • $1B for the uninsured.
They also mention $22M for FDA.  Roll Call writes, "The testing provisions require that states, local government and other recipients of the testing dollars file plans for how they will spend the money."


Trivia: It's called the "Paycheck Protection Program and Health Care Enhancement Act," PPPHCEA.

For an April 6 (subscription) article in STAT Plus on BARDA's functioning so far under COVID, here.

The NYT writes,

At the insistence of Democrats, the measure would provide $25 billion for testing and a mandate that the Trump administration establish a national strategy to help states and localities, which are required to outline their own plans for testing. 

It is a step that public health experts and governors have said will be crucial to allowing states and sectors of the economy to safely reopen in the weeks and months to come, although economists and health researchers say the funding is a fraction of what will ultimately be necessary to deploy the kind of testing and tracing that will be needed to restart large amounts of activity by the summer.


Very Very Brief Blog: Proposed Inpatient Rule Watch (Normally April 23/24)

When will the annual CMS inpatient rulemaking come out?  For FY2021, which begins in October 2020?

In 2019, the FY2020 proposed rule came out on April 23.

In 2018, the FY2019 proposed rule came out on April 24.

It will be interesting to see if the FY2021 inpatient rule is on time, or delayed due to COVID.

Generally, CMS tries to get the rule out in late April, providing 60 days of comment until late June.

Then, the final rule appears around August 1, which in turn allows hospitals 60 days to implement new policies for the new fiscal year on October 1.

Very Brief Blog: CAP Today Reviews Billing & Denial Landscape (April 2020)

In the past several years, in the lab industry, we've heard more and more about denials and reduced payment rates.  See for example an article on Lab Benefit Managers (LBM) in Health Affairs this past fall (here).

In April 2020, CAP TODAY has a five-page article interviewing experts about the rising problems of billing and reimbursement in pathology and lab medicine.  Find it here.

Very Brief Blog: COVID Travel in Air; CDC Chinese Restaurant Article

As we go in and out of grocery stores and drug stores under COVID conditions, wearing masks, and looking ahead to lighter restrictions and more stores open - how contagious is COVID in air?

CDC published an article on April 2 which got more press in the last 24 hour news cycle.  April 2 CDC here, new at ABC here.

In a nutshell, a restuarant in China had 5 tables with 4-10 seats.  One patient (A1) at table A was COVID-positive but pre-symptomatic.   9 people in the room became positive, all in the draft line of Table A.   73 other diners on the floor, during the day, did not get sick.  Those who got sick were seated for 30-60 minutes.   There was no report of staff walking in and out of the room getting sick.

So this draws two lessons.  COVID is really, really contagious, even to people sitting 10-15 feet away for an hour (if they were in the air-flow lines). 

On the other hand, it's not infinitely contagious - not everyone in the room during that hour got sick, especially those seated further away. 

click to enlarge (CDC figure)

Monday, April 20, 2020

Important International Genomic Precision Medicine Study in COVID Is Launched; part of COVID Host Genetics Initiative

On March 1, I wrote a blog that we need a deep dive, high intensity sequencing view of COVID vulnerability - we should never just assume it is "age and comorbidity."

Instead, we should seek to discover genomic risk factors, whether it be HLA, T-cell receptors, cytokine response genetics, or other factors (March 1 blog here).

On April 20, 2020, Genomeweb reports an international study, based in Hannover, Germany, looking at genomic factors affecting COVID response - by Justin Petrone, here

Partners include Bionano Genomics, Genoos, Rescale, and Amazon.  They will study 1000 patients.  Bionano will provide its Saphyr platform, while Genoox, in Palo Alto, will provide AI.

Genomeweb writes in part,
   Participants will undergo analysis of their transcriptomes to look at gene expression, metabolomes, and a variety of immune markers such as cytokines and T-cell response.
   The goal of the study is to identify genomic variants that affect the disease, and immune or metabolic variables in the healthier participants that can protect against more severe disease, and to use this knowledge for the development of novel therapies and vaccines.
Bravo to this study.  Kudos also to Adaptive Biotechnology, which announced on March 20 a national call for volunteers to study immune receptor dynamics in COVID - here.  In other news, researchers are searching for ACE2 receptor variations that might impact COVID binding and virulence (here), and proteomics researchers set up for immuno-oncology proteomics are turning to COVID rsposnes as well (here).

COVID Host Genetics Initiative - Important to Be Aware of This One

The Hannover consortium is part of the COVID Host Genetics Initiative, with many centers spanning Europe, Asia, and North America.  See its homepage hereIt currently has 133 parterships in an easily searched database. Click to enlarge the screen shot:
See earlier articles on the CHGI at Genomeweb here (on CHGI, March 26, by Andrea Anderson) and here (April 8, in connection with 23andMe).


In other molecular COVID news today, Exact Sciences received FDA EUA for a COVID diagnostic - here.

April 19/20: A Flurry of Real News about COVID - NYT, WSJ, Testing, Symptom-Free Rates, More

Yes, every day 80% of the news is COVID news,  But for me, Sunday/Monday April 19/20, 2020, was a flurry of actual new-news about COVID.

I highlight items below.

88% Symptom-Free Rates at Columbia University Medical Center

  • In the most interesting story, 15% of women coming to labor and delivery at Columbia IrvingMedical Center tested positive for COVID virus (PCR), but 88% had no symptoms.  (The math is, 13% of all of these individuals were virus positive and asymptomatic.) 
    • This hospital serves Upper Manhattan and Bronx.  S
  • See article in WaPo by Goffman and Sutton here.
  • The original medical article appeared NEJM, April 13, 2020, here.
  • The authors tested 215 women March 22-April 4, and published in NEJM on April 13.
Beyond that one, some more "new-news" stories came one after another.

NYT and WSJ Pile On Testing Crisis and Reopening
  • New York Times and Wall Street Journal concurrently ran articles about the testing crisis.
    • NYT April 19 (Eder et al.) focuses on poor antibody tests Here.
    • See similarly April 21 at LATimes (Chabria et al.) - "wild west" of antibody testing, here.
    • -- While WSJ has April 20 article that New York is gearing up for large-scale antibody testing - Dvorak et al., here.
    • WSJ April 19 (Weaver & Ballhaus) focuses on chaos and shortage in the supply chain of parts and necessities for testing. Here.
    • -- To my eye, the WSJ builds up a substantial set of unflattering quotations from Brett Giroir, the HHS official newly in charge of national testing.
    • A third newspaper, Washington Post, jumps on Giroir, asserting he was fired from a job in vaccine development not long before joining HHS. Here.
    • WSJ also features an April 20 article (Kraus) on the dynamic push at Amazon, General Motors, and other employers to ramp up employee COVID testing - here.
    • Also on the theme of workplace, Gottlieb and Ostroff in WSJ April 19 have opinion on the return to work, discussing both distancing and testing - here.
    • NYT says that the next COVID business relief bill is held up over debates regarding national vs state control of the testing fiasco, here In WaPo, Senators Alexander and Blunt propose a "shark tank" test to reboot US COVID testing, here.
    • On the theme of reopening, the Brit newspaper The Guardian April 20 has a detailed article on reopening plans in Europe, with excellent graphics and tables across the E.U. - here.

Paradoxical Bankruptcies of Physicians and Hospitals?

In the past week, I saw an article about a Colorado hospital that had had 8 COVID patients in four weeks, but had many empty beds, no elective surgeries, and an empty ER, facing financial disaster and laying off staff.  MedCity News April 17 here.  More on this theme this weekend.

  • WSJ April 19 (Editorial Board) on the economic crisis facing many healthcare institutions and individual providers - here.
  • Similarly April 20 as Axios - here.
  • HHS - Reopen Hospitals in Low-Incidence Areas
    • On Sunday, April 19: the administration issued policies for reopening hospitals in low-incidence areas.  Press release here PDF here This updates the March 18 notice against non-emergent care.
    • (I believe this is couched as HHS recommendations, since hospitals are also under state law.)

Cities - California

San Francisco County (1M people) has had 20 deaths from COVID, Los Angeles County has 600 deaths (10M people).  (Accounting for the 10X population, the death rate in LA is 3X higher, which is a lot higher, but not as graphic as the absolute numbers suggest.)
  • LA Times April 20 profiles SF mayor London Breed - here.
  • LA Times April 20 profiles speech by major Eric Garcetti forecasting grim times and many layoffs in LA government - here  Obviously, these layoffs also contribute to the financial catastrophe with more payments for unemployment, more people without health insurance, with hurdles maintaining food and shelter.

Human Interest

WaPo article April 19 by a nurse (Sakal) who left her job in an overwhelmed ER - here.   An ER doctor at Bellevue in NYC argues that we need home pulse oximeter monitoring of COVID patients to save lives, here.

From April 17 - Leavitt Partners COVID Dashboard & Projections

See the Leavitt Partners national, state, county dashboard for COVID here.

For example, they predict the national ICU cases is circa 6,000 on April 20, relatively flat (5000-6000) from April 10-20, but still, and using the best data through today, predicted to double to 12,000 ICU beds for COVID by May 3.


New Cases?
One key fact I have not seen - in places with 3-4 weeks of lockdown, Los Angeles, New York - where do we think the most new cases are coming from?  Obviously nursing home patients, and likely healthcare workers at 10-20%.  But after that?   From front line workers (fire, police, ambulance)?  Centralized workers (Amazon?)   Retail public workers (CVS?)  Seemingly random (person at home, goes to grocery store twice a week?)   We should know something about this, and feed it into reopening plans, but I don't see it written about.    

Prevalence vs Deaths
If the prevalence of COVID positivity is higher - 2%, 4%, 8% - the death rate is lower.  But the absolute death rate is the same.  I read a week or two ago, that over 50 NYC transit workers had died - not sick, not hospitalized, but dead.  That's really scary regardless of whether we think 1% or 3% of bus riders were occult positives.  And surely those dead transit workers didn't have someone walk up to their face and cough on them repeatedly.



While putting this together, I found some interesting articles at Chem & Engineering News.

  • Scaling up remdesivir production, here.
  • Best material for homemade mask, here.
  • Disinfectants and COVID, here.
  • COVID virus in sewage, here.
  • Biology of non-respiratory symptoms in COVID, here.