Friday, May 29, 2020

MAC Watch: Voluminous Web Articles from Noridian

I've written several blogs this month on high impact web articles from Noridian.  The sheer volume of web articles is daunting.

See their Latest Updates page here:

Recent articles are clipped below.  (See link above for hotlinks.)  It's about 75 for the month of May so far.  Some of high impact, such as breaking off the MolDx system and deleting MolDx LCDs in effect elsewhere.  

Continuing Education Units (CEUs) Only Provided When Logged Into Webinar May 29, 2020
Comprehensive Error Rate Testing (CERT) Clinic Webinar - June 24, 2020 May 29, 2020
Billing and Coding: Guardant360 May 28, 2020
Implement Operating Rules - Phase III ERA EFT: CORE 360 Uniform Use of CARC, RARC and CAGC Rule - Update from CAQH CORECR11709May 28, 2020
International Classification of Diseases, 10th Revision (ICD-10) and Other Coding Revisions to National Coverage Determination (NCDs) - October 2020 Update - RescindedCR11749May 28, 2020
Billing and Coding: Routine Foot Care - R1 May 28, 2020
Flow Cytometry Coverage Clarification Retirement - Effective May 20, 2020 May 28, 2020
MLN Connects - May 28, 2020 May 28, 2020
Overpayment Results for Part A and Part B Users Now Available May 27, 2020
RARC, CARC, MREP and PC Print UpdateCR11708May 27, 2020
Claim Status Category Codes and Claim Status Codes UpdateCR11699May 27, 2020
Therapy Codes Update - RevisedCR11791May 27, 2020
Summary of Policies in the CY 2020 MPFS PHE Interim Final RulesCR11805May 27, 2020
MolDX: Combinatorial Pharmacogenomics Limited Coverage Proposed LCD and Billing and Coding: MolDX: Combinatorial Pharmacogenomics Limited Coverage Retirement - Effective August 16, 2020 May 27, 2020
Billing and Coding: Percutaneous Vertebral Augmentation (PVA) for Osteoporotic Vertebral Compression Fracture (VCF) - R3 May 27, 2020
Outpatient Therapy - A/B Physical, Occupational, and Speech Language Pathology Webinar - June 3, 2020 May 26, 2020
Billing and Coding: MRI and CT Scans of the Head and Neck - R1 May 26, 2020
Drugs and Biologics Outpatient Documentation and Post Pay Review - Part 2 of 2 Webinar - July 9, 2020 May 26, 2020
Drugs and Biologics Outpatient Overview and Billing - Part 1 of 2 Webinar - July 8, 2020 May 26, 2020
Duplicate Claims Webinar - June 25, 2020 May 22, 2020
CMS Open-Door Forum: Prior Authorization Process and Requirements for Certain Outpatient Hospital Department Services Special Open-Door Forum - May 28 May 22, 2020
Open Meeting Announcement - June 10, 2020 May 21, 2020
Open Meeting Announcement - June 10, 2020 May 21, 2020
Open Meeting Announcement - June 03, 2020 May 21, 2020
Quarterly Medicare Updates - A/B - After Hours Webinar - July 14, 2020 May 21, 2020

Open Meeting Announcement - June 04, 2020 May 21, 2020
Quarterly Medicare Updates - A/B Webinar - July 7, 2020 May 21, 2020
Proposed LCDs - Published for Review and Comments May 21, 2020
Open Meeting Announcement - June 17, 2020 May 21, 2020
Proposed LCD and Associated Billing and Coding Article: Implantable Continuous Glucose Monitor (I-CGM) - Published for Review and Comments May 21, 2020
Billing and Coding: Prospera May 21, 2020
MLN Connects - May 21, 2020 May 21, 2020
Medicare Continues to Modernize Payment SoftwareSE20019May 20, 2020
MLN Connects Special Edition - May 19, 2020 - COVID-19: Payment for Lab Tests, Safely Reopening Nursing Homes, Lab & Ambulance Claims May 19, 2020
Billing and Coding: MolDX: BRCA1 and BRCA2 Genetic Testing - R2 May 19, 2020
Manual Update to Pub. 100-04, Chapter 38, to Remove Identification of Items or Services Related to the 2010 Oil Spill in the Gulf of Mexico SectionCR11778May 18, 2020
MLN Connects Special Edition - May 15, 2020 - COVID-19: Deadlines, New Releases, and Important Calls May 15, 2020
Medicare Secondary Payer (MSP) Payer Type Corrections via Noridian Medicare Portal (NMP) May 15, 2020
MolDX: Prospera Proposed LCD Retirement - Effective May 14, 2020 May 15, 2020
MolDX: Guardant360 Plasma-Based Comprehensive Genomic Profiling in Solid Tumors Proposed LCD Retirement - Effective May 13, 2020 May 15, 2020
National Coverage Determination (NCD 30.3.3): Acupuncture for Chronic Low Back Pain (cLBP)CR11755May 14, 2020
Billing and Coding: Routine Foot Care May 14, 2020
Billing and Coding: Hydration Services - R2 May 14, 2020
MLN Connects - May 14, 2020 May 14, 2020
Quarterly Update to the MPFSDB - July 2020 UpdateCR11788May 13, 2020
National Coverage Determination (NCD) 20.19 Ambulatory Blood Pressure Monitoring (ABPM)CR11650May 13, 2020
MLN Connects Special Edition - May 12, 2020 - COVID-19: Additional Waivers, Price Transparency, and CMS Letter to Nursing Homes May 12, 2020
New Physician Specialty Code for Micrographic Dermatologic Surgery (MDS) and Adult Congenital Heart Disease (ACHD) and a New Supplier Specialty Code for Home Infusion Therapy ServicesCR11750May 12, 2020
Medicare Pharmacies and Other Suppliers May Temporarily Enroll as Independent Clinical Diagnostic Laboratories to Help Address COVID-19 TestingSE20017May 12, 2020
Prior Authorization for Certain Hospital Outpatient Department (OPD) Services Webinars May 12, 2020

Reminder: 340B Hospital Survey Closes 5/15 May 11, 2020
Billing and Coding: MolDX: Testing of Multiple Genes May 11, 2020
Guardant360 and Prospera May 11, 2020
Positron Emission Tomography Scans Coverage - R19 May 08, 2020
MLN Connects Special Edition - May 8, 2020 - COVID-19: Nursing Home Reporting, Updated Telehealth Video, Pharmacies & Other Suppliers Can Enroll as Labs, IRF Flexibilities May 08, 2020
Billing and Coding: Mometasone Furoate Sinus Implant (Sinuva, Propel family of Implants) May 08, 2020
Proposed LCD and Associated Billing and Coding Article: Non-Invasive Fractional Flow Reserve (FFR) for Stable Ischemic Heart Disease - Published for Review and Comments May 07, 2020
MLN Connects - May 7, 2020 May 07, 2020
Sleep Lab Credentialing: Polysomnography and Other Sleep Studies Retirement - Effective May 14, 2020 May 06, 2020
Billing and Coding: MolDX: Multiplex Nucleic Acid Amplified Tests for Respiratory Viral Panels- R4 May 06, 2020
Polysomnography and Other Sleep Studies Retirement - Effective May 14, 2020 May 06, 2020
Quarterly Update to the MPFSDB - April 2020 - RevisedCR11661May 06, 2020
Medicare Clarifies Recognition of Interstate License CompactsSE20008May 06, 2020
Medicare Physician Fee Schedule (MPFS) Webinar - June 17, 2020 May 04, 2020
Claim Submission: Paper and Electronic Webinar - June 2, 2020 May 04, 2020
MLN Connects Special Edition - April 30, 2020 - COVID-19: Second Round of Sweeping Changes, RHC & FQHC Flexibilities, EMTALA Apr 30, 2020

News Flash: Noridian Deletes Another MOLDX LCD (Combinatorial PGx Panels in Psychiatry)

On May 11, 2020, the Noridian MAC rocked the MolDx world by announcing suddenly that it was deleting two major LCDs that had been finalized in other parts of the MolDx system - something that had never happened before in the ten-year history of MolDx.  Story here.   At a meeting of the California Clinical Laboratory Association with Noridian on May 26, Noridian management staff gave non-specific answers as to why this had happened or as to next steps.

On May 27, 2020, Noridian dropped another bombshell in announcing they were deleting a proposed MolDx LCD - which had undergone public comment at Noridian.   See the Noridian article here.  

Noridian states that draft LCDs DL36323 and draft article DA57410 are being retired (without ever having been made effective LCDs).   

Then there is an ambiguity.  There is a single sentence that states:  "This is a limited coverage policy for GeneSight®, NeuroIDGenetix, and other combinatorial pharmacogenomics panels in the treatment of psychiatric illness when ordered by a psychiatrist. GeneSight® and NeuroIDGenetix are covered for patients in whom a two gene panel consisting of CYP2C19 and CYP2D6 is reasonable and necessary."   Basically, that means that coverage requires a psychiatrist (not any other kind of clinician) to state he/she is considering at least one psychiatric drug metabolized by CYPC219 and at least one psychiatric drug metabolized by CYP2D6.   At that point, when 2 genes must be testing, Noridian will cover a panel of genes (not limited to 2 genes).   

Since this is only a web article, it contains to feedback regarding public comments on the policy (Congress requires MACs to post feedback on LCDs) and it contains no rationale for the decision, or Genesight and NeuroIDGenetix were called out and not other panels or brands.   (Congress requires LCD coverage decisions to post rationales.)   

The article refers the refer to Draft LCD DL38335, as having additional requirements, but it is unusual for a "draft" and unfinished document to be listed as holding the necessary legal requirements.   

Finally, three important points:

1) A reader pointed out to me, it's ambiguous whether the statement "This is a limited coverage policy..." applies solely as a  description to the reader of the LCD being deleted, or, if it represents the new  coverage position adopted by this article.  I read the statement about psychiatrists as being the coverage policy positioned by THIS article, but it may be mereley descriptive of the prior thing being deleted.  

2)  Myriad/Genesight bills  from Ohio, not under a west coast policy of any kind.  Though there are west coast genetics labs the Noridian decisions, whatever they are, apply to.

3) The article has an effective date of "August 20, 2020" which is weird (neither 30 nor 45 days nor immediate, the more likely effective dates.)  It's not related to the one-year rule for draft LCDs, since the draft appeared 10/19/2019.

There is also a legacy, several year old Genesight LCD; not clear what is happening to that, or when.

Friday, May 22, 2020

Very Brief Blogs: CMS Publishes Final Medicare Advantage and Part D Rules for Contract Year 2021

CMS has published the final rules, and a fact sheet, for the Medicare Advantage and Medicare Part D contract year 2021.

See the fact sheet here.   See the final rule (inspection version) here.   Fed Reg version to appear June 2.

Note that CMS made a range of proposals in proposed rulemaking in February 2022; only those with the tightest deadlines are published here.  Additional proposals will be finalized in a "part two" final rulemaking in coming weeks.  

Wednesday, May 20, 2020

Very Very Brief Blog: CMS Prices COVID Serology Tests at About $45

On May 14, I wrote a blog about the different ways that CMS could potentially price new serology tests for COVID - here.

I'm leaving the original blog from May 14 intact, but on May 19, CMS released pricing for the single-strip and the liquid phase COVID SEROLOGY tests (86328, 86769).  The are priced at $45.23 and $42.13 respectively.
  • See a trade journal article at MedTechDive here.  
  • See ACLA favorable press release here.
  • See Medicare's two-page, May 19, 2020 document online here  CMS published uniform, but contractor (MAC)-established prices for both COVID PCR codes and COVID Serology codes.

Note that the MAC-set prices for U0001 and U0002 (non-high-throughput COVID diagnosis) and the newly announced prices for 86328, 86769 serology - are technically, temporary local MAC prices.  These codes are ALSO going to be discussed for price-setting at the summer Clin Lab Fee Schedule pricing meetings.  This will result in nationally-endorsed pricing on 1/1/2021 for these four codes.   Details here.


A lot has been written over the pro's and con's of serology tests, focusing on either (1) absolute acurracy of tests, and (2) value of tests - what does a positive result mean.  For a pro-serology Op Ed in WSJ, see the May 19 article by Manish Butte and Andrew Bogan; Butte is chief of pediatric immunology at UCLA.


ACLA has a white paper on testing in the battle against COVID, here.

Monday, May 18, 2020

Medicare Stumps Me x 3: #1, CMS NCD for NGS in Oncology - New Tests


At least one of the erroneous documents from CMS has been deleted since my post on May 18.

My original May 18 blog is preserved below.

Summary:  CMS has a national coverage determination controlling FDA-authorized cancer tests using Next Gen technology.   

They've added some tests to the public, officially-covered test list - some of which I understand, and some of which I don't.


Two years ago, in March 2018, CMS finalized a new National Coverage Determination policy on the topic of NGS testing in patients with cancer, especially advanced cancer.   The NCD authorized automatic, nationally-endorsed coverage for patients with "advanced cancer" (such as metastatic or relapsed), if the NGS test was FDA cleared or approved, if it was a "companion diagnostic," and if it had an indication matching the patient's need.

See the text of this NCD, NCD 90.2, here.

By a separate publication to the public and its MAC contractors, CMS quickly authorized (1) the Foundation Medicine test in all solid cancers and (2) the Thermo Fisher Oncomine Dx-Target test in lung cancer.   

This made sense since both are approved for at least several genes as "companion diagnostics" (see FDA CDx web page here).   

The Thermo test is approved for lung cancer patients; the Foundation Medicine test is approved for several genes/cancers, and cleared, more broadly, to assist physicians by tumor gene profiling in all solid cancers.   

In a recent transmittal, document CR11655, February 21, 2020, CMS has added NGS companion diagnostic test Illumina Praxis RAS (0111U).   This is easy; it's an FDA approved companion diagnostic test for colon cancer RAS family genes.  The coverage is effective on the same date as its PLA code, which was October 1, 2019.

However, CMS has also added two other tests that puzzle me.  
In CR11655, also added the much older code 0048U for the MSK IMPACT test. MSK IMPACT is a large FDA cleared gene panel test that is not a companion diagnostic.   The coverage isn't related to the recent germline-focused revision of the NCD, since the coverage now in February 2020 is retroactive to July 2018.   So I'm stumped.  IMPACT does look at both tumor and normal tissue DNA, so it might be covered as a 510(k) test under the recently revised NCD, for germline testing, but that germline-based coverage would seem to start with the germline revision date, January 27, 2020, not July 2018.
IMPACT is payable under the NCD, now, for ICD10 codes in lung cancer or colon cancer (see code 0048U in the CMS NCD coding spreadsheet inside a CMS zip file: here). 
In another document, CR11749, released May 1, 2020 and effective October 2020, CMS adds the test, Lab for Personalized Medicine (LPM), MyMRD NGS Panel for AML, myelodysplastic syndrome, 23 genes.  It's code 0171U.  I don't think I have found that this test is either FDA cleared or approved (I may be missing something).   If it's not an FDA approved test, and it's under the national coverage part of the NCD,  I'm stumped. Coverage for 0171U is effective April 1, 2020.  Note - Invivoscribe does have a PCR-based single gene test, LeukoStrat CDx FLT3 (PMA P160040B).  The CMS coverage seemed to be for the NGS 23 Gene Panel 0171U which isn't the same as their FDA PCR single gene test.  (Again, I may be missing something.)

If anybody knows the solution, I'm all ears.


As far as I can tell, the Myriad MyChoice CDx test (for BRCA and other genes, NGS based,  yielding genomic instability scores) could be added to NCD 90.2, since it's NGS test for advanced cancer, and it is an FDA approved companion diagnostic.   


Find CR11655 (February 21, 2020) here.
Find CR11497 (May 1, 2020) here.
Find both in one zip file in the cloud here.


There was an August 2018 news article that MSK IMPACT was going to seek FDA CDx status, but I haven't read that it happened.

Medicare Stumps Me x 3: #3, One MolDx MACs Deletes LCDs from Other MolDx MACs

Smmary - The MolDx policy system, with uniform LCDs, Z-codes, and pricing, spans almost 30 states and pays circa 80% of Medicare MoPath services.   For the first time since 2011, one of the MACs has deleted MolDx LCDs that are in force elsewhere.  

"Rationales" are provided for this action, but to me, they don't make sense.  I explain why it is... Puzzling!

The MolDx program was founded in 2011.  According to the Noridian website as of 5/17/2020, MolDx "establishes coverage and reimbursement for diagnostic tests."   Here.  The webpage just quoted was revised 3/24/2020, although there's no change-release record of what was revised on March 24.

According to a table on the Noridian MolDx webpage, the MolDx Contractor makes "determinations regarding coverage."  Then, according to the webpage, Noridian "implement[s] MolDx guidelines" and "process[es] claims using MolDx guidelines."   

The MolDx program is very large, spanning about 30 states.  So far, the MolDx program is active in the Palmetto jurisdictions (2), the Noridian jurisdictions (2), the WPS jurisdictions (2), and the CGS jurisdiction (1).  Based on 2018 data I reviewed previously, MolDx states or MACs process about 80% of molecular pathology dollar volume for Medicare Part B, and MolDx MACs have nearly 100% of the Medicare use of unlisted code 81479.

The week of May 11, 2020, marks the first break I am aware of where a MolDx-participating MAC declined to finalize MolDx national system LCDs.  In this case, there is little impact on the tests and patients involved, since Noridian elected to immediately replace the two LCDs with web articles conveying the same coverage content.  However, it's still a first-ever event for those who are closely watching the MolDx system.

What Happened?

In spring 2019, all the MolDx MACs posted drafted LCDs for the Natera Prospera test (detecting donor graft origin DNA and identifying renal transplant rejection) and for the Guardant G360 oncogene liquid biopsy test.  The draft LCDs reflected new coverage for Prospera, and expanded coverage for G360 (from lung cancer, to all solid tumors).  During summer 2019, the various MACs collected public comments on the LCDs.   By winter 2019/2020, the MolDx MACs had formulated a common response to all collated comments, which began appearing along with final versions of the Prospera and G360 LCDs.

By May 10, 2020, the two LCDs were still in "draft" form on the Noridian website, as they had been for nearly a year.   

Then, in rapid succession, Noridian put up 3 articles on its website.  

The first was on May 11, and was titled simply, "Guardant360 and Prospera."  This article stated coverage criteria (exactly as had been proposed in May 2019) for Guardant G360 and then Prospera.  The article also states that "In order to provide a more generic, non-proprietary coverage for plasma based genomic profiling and cell free DNA rejection technology, Noridian is retiring" the corresponding draft policies..."until such time a more comprehensive non-proprietary local coverage determination can be developed."

On May 15, Noridian put up a separate posting that G360 LCD  (DL38127) was being retired with the rational, "In order to provide a more generic, non-proprietary coverage for plasma based genomic profiling, Noridian is retiring this proposed LCD."   A separate but very similar article was also posted on May 15 for Prospera draft LCD DL38131. 

I've collated the three quoted articles in one cloud web document here.

Why It's Puzzling!

Noridian writes on the May 11 article, "Noridian will work with the CMS MolDX contractor to facilitate the future comprehensive LCD."   But Palmetto and other MACs, had already produced a "more generic, non-proprietary coverage" for plasma based cancer gene profiling, which did cover G360 and other tests on a rolling basis with similar performance.   It's LCD L38043 and represents the natural finalization of LCD DL38127 in other MACs.  In short, I don't understand the rationale as stated.  Why note finalize the future comprehensive oncogene liquid biopsy LCD that 's already written, and why not do it now?  I'd be happy if anyone has an idea.

MolDx has already proposed a future, non-proprietary or "umbrella" LCD for donor DNA tumor rejection tests.   This was first proposed a few weeks ago -  Here.  However, it could take about a year to circulate and be finaled in all the MolDx MACs.   See DL38568, liquid biopsies in solid organ transplant.   (Associated article DL58019 lists coverage for Prospera and KSORT).  

 I can't see why Noridian couldn't have finaled the DL38131 LCD at this time, and finaled the future LCD DL38568 in a year (or not, depending on the final decision and public comment and evolving science.)   MACs can always retire an LCD when an NCD or a different future LCD supercedes it.  In short -again - I don't understand the rationale as stated.  I'd be happy if anyone has an idea.

Update - On May 28, Noridian released for comment draft LCD DL38629, DA58168 (here) which is equivalent to Palmetto earlier draft LCDs DL38568.  Article A5818 includes coverage for KSORT and PROSPERA as an attachment to the umbrella LCD DL38568.  

LCDs Have Hard-Won and Statutory Process Controls

Based on CMS rules and recent lawmaking in the 21st Century Cures Act, there are a number of controls on the LCD process.  There is a process for requesting new LCDs, and a process for requesting revised LCDs.  These are logged and documented by MACs, following CMS rules.  There must be posted LCDs, with rationales and citations, there must be a public comment meeting, there must be a final Q&A document responding to public comment.  College of American Pathologist (CAP) made securing these legislative protections a major policy goal several years ago.

None of these rules apply to web articles posted by MACs.   

In addition, based on older lawmaking, there is an LCD appeals process to the administrative judge system, which is not available to articles.  (Although in a case or two, judges have ruled that an article performed the same function "in locus LCD" and therefore the stakeholder had the same legal rights as if the article were in fact an LCD pro forma.)

Stakeholders may also wonder if they should follow the published MolDx rules and processes for MolDx meetings, MolDx dossier submissions, etc, if the LCD resulting may or may not be finalized in one or another participating MAC.  

What Went Different Here?

MolDx medical directors, at various public conferences, have presented the MolDx 11-step process as shown below.  In fact, I've personally seen companies try to jump this process and work directly with Noridian in past years, and they were deflected and pointed to MolDx.  
  1. MolDx provides a central point of contact for new tests.
  2. MolDx provides non-binding advice during preliminary meetings.
  3. Stakeholder submits Formal LCD Request -- to MolDx.
  4. MolDx then coordinates technology assessment and review.  If appropriate, MolDx develops draft LCD.
  5. MolDx circulates the draft LCD to participating MACs and MAC medical directors.
  6. With consensus, the final draft LCD is released in uniform format across MACs.
  7. Release of draft LCD means Medicare has proposed and taken the coverage position stated, at the time of release.   
  8. Public comment follows at each MAC.
  9. Public comments are collated and a consensus Q&A document is produced.
  10. MolDx leads any required LCD revisions and then circulates with participating MACs for buy-in.
  11. Buy-in on the final LCD having been achieved, the final LCDs are rolled out, uniformly, at each MAC.
The final step #11 may drag on for up to six months, which is puzzling if a consensus final LCD was already agreed on at steps #9, #10, and therefore only required the formal act of posting in step #11.  

Medicare Stumps Me x 3: #2, Gene Panel Coding Guidances Breed Like Rabbits

As of May 2020, there are at least FOUR different official CMS guidances you are supposed to follow, at least if you live in some MolDx states.   And there's not the same.  Puzzling!

Medicare Panel Coding Guidance #1

The oldest is the MolDx Molecular Test Panel Alert, currently in V5 updated October 2019, but dating back at least five or six years.  Find it here.  I also include at the bottom of this blog as "Exhibit A."  

Presumably, this article applies to MolDx regions up until the publication of A57503 on 10/21/2019 and revised 1/1/2020, since the currently online article now states it applies up until the publication of such a title. 

Medicare Panel Coding Guidance #2

The-next oldest, and longest, is the MolDx CMS Article Database article, MolDX: Testing of Multiple Genes (A57503).  Find it here.  I also include at the bottom of this blog as "Exhibit B."  Published 10/21/2019 and revised 1/1/2020.

See also coverage of this when it was new, October 18, 2019 here.

Medicare Panel Coding Guidance #3

The newest, and shortest, is the Noridian online article published May 11, 2020, effective June 7, 2020.  It shares some text with A57503, but appears on the Noridian website rather than the CMS article database.  The text of this Noridian article (#3) is truncated quite quickly, related to A57503 at Palmetto (#2), and may not, entirely, mean the same thing.  Find it here.  And see it at bottom of blog as "Exhibit C."

And...Medicare Panel Coding Guidance #4

Finally, there is a nationally binding rulebook of correct coding guidance called National Correct Coding Inititative Policy Manual (NCCI-PM).  Find it here.  Download "Policy Manual for Medicare Services."  This is national guidance for all 50 states, not just MolDx.  It's confusing in context of guidances #1,#2, #3 above.  The national NCCI guidance is also distinctive in being directly self-contradictory within the space of just four sentences.   See at bottom of blog as "Exhibit D."

Note that CMS publishes separate, but identical, NCCI policy manuals for Medicare and Medicaid.  The Medicaid one is here.


One of the problems with web-based contractor articles (see #1, #3) is that they are added, revised, and deleted at irregular intervals with no archival record of when which version was effective, making law enforcement and medical review very difficult. 

 In addition, here, there seems to be a lack of consistency between the national ruling (#4), which should be "enough guidance" and "national guidance" and the differing articles #1 and #2 and #3.   

National guidance #4 clearly seems to allow different billing schemes at different prices for the same thing.  It states that a party "may" bill one way or "may" bill another.  This is the opposite of correct coding guidance.  To borrow a phrase I've heard and try to apply in other contexts, if a correct coding guidance doesn't lead to one clear coding solution, the correct coding guidance isn't done yet.  

In case CMS links change - I've put all four documents in a cloud file here.


For an article by attorney David Glaser on the problems when Medicare definitions accumulate and collide, here.

Exhibit A.  MolDx Molecular Test Panel Alert 

(Abridged; see full text on website.)

Molecular Test Panel Edit Alert (M00101, V5)

The guidance below only applies to MolDX jurisdictions for which the article "Billing and Coding: MolDX: Testing of Multiple Genes" has not been published by the local MAC to whom a provider or supplier submits claims. 

Palmetto GBA has published the article "Billing and Coding: MolDX: Testing of Multiple Genes external link " for Jurisdictions J and M on the Medicare Coverage Database.

MolDX CPT code range affected: 81161-81408

Test Panel Definition: A predetermined set of medical tests composed of individual laboratory tests, related by medical condition, specimen type, frequency ordered, methodology or types of components to aid in the diagnosis/treatment of disease.

Palmetto considers the performance of multiple molecular biomarkers, regardless of whether the test requisition lists the tests as a panel or individually, and completed on a single sample to be a "panel" of tests. Therefore, each panel should be registered and billed with a single CPT code and a unique MolDX identifier. Based on data analysis of MolDX claims, labs are submitting multiple biomarker 'panels' as individual tests similar to the submission of the previous stacking codes.

Example: A lab receives a patient specimen and performs the following tests:

CPT code 81225-CYP2C19, cv
CPT code 81240-F2, 20210G>A
CPT code 81241-F5, Leiden

The panel of three tests listed above should be registered and claims submitted with CPT code 81479 and a single MolDX ID. 


Exhibit B.  MolDx Testing of Multiple Genes Article A57503 (CMS Database)

Billing and Coding: MolDX: Testing of Multiple Genes (A57503)

The following information will be effective 10/21/2019 for dates of service on or after 10/15/2019 [sic??].

A panel of genes is a distinct procedural service from a series of individual genes. All services billed to Medicare must be reasonable and necessary. As such, if a provider or supplier submits a claim for a panel, then the patient’s medical record must reflect that the panel was reasonable and necessary. Alternatively, if a provider or supplier bills for a number of individual genes, then the patient’s medical record must reflect that each individual gene is reasonable and necessary.

For ease of reading the term “gene” when used in this document will be used to indicate a gene, region of a gene, and / or variant(s) of a gene.

Genes can be assayed serially or in parallel. Genes assayed on the same date of service are considered to be assayed in parallel if the result of one assay does not affect the decision to complete the assay on another gene, and the two genes are being tested for the same indication. Genes assayed on the same date of service are considered to be assayed serially when there is a reflexive decision component where the results of the analysis of one or more genes determines whether the results of additional analyses are reasonable and necessary.

If a laboratory assays two or more genes in a patient in parallel, then those two or more genes will be considered part of the same panel. A panel constitutes a single procedural service, so one HCPCS codes must be submitted for the panel. If the laboratory assays genes in serial, then the laboratory must submit claims for genes individually. The order by the treating clinician must reflect whether the treating clinician is ordering a panel or single genes, and additionally, the patient’s medical record must reflect that the service billed was reasonable and necessary.

Two examples:

Single Service Example: A clinician orders 5 specific genes associated with breast cancer. The laboratory analyzes the 5 genes for common mutations using polymerase chain reaction. All 5 PCR procedures are started prior to the results of any one PCR procedure being known. The results are signed off on simultaneously, and all 5 results are sent to a clinician.

This would be considered a single procedural service, a single 5 gene panel, and it must be billed as such. This single panel must be reasonable and necessary to be billed to Medicare.

Multiple Distinct Procedural Services Example: A clinician requests that genes associated with early onset colorectal cancer be analyzed in a patient. The clinician orders stepwise reflex testing where a negative or positive result in one gene determines whether additional analysis on other genes will be performed or what that will be.

Each gene assayed represents one procedural service, so if more than one gene is analyzed, then multiple procedural services may be billed in some patients for whom reflex testing goes beyond the first gene. Each gene billed to Medicare must be individually reasonable and necessary. A clinician’s order is not by itself sufficient to indicate that a test was reasonable and necessary. The record must reflect that the test is used in the management of the beneficiary's specific medical problem in accordance with CFR §410.32.

Labs must register a test with the Diagnostics Exchange as it reflected on the order form and is run in the laboratory. If a gene / variant is tested as part of a panel, then the lab must register the panel and must submit the correct z-code and CPT code for the panel. If a lab has a panel but sometimes also analyzes individual genes from the panel, the lab must register both the panel and the individual genes that are analyzed.

In general two or more codes describing a genetic test billed on the same beneficiary on the same date may constitute a panel, and if so the service must be billed as a single procedural service. We would generally expect that a provider or supplier would not bill for more than two distinct laboratory genetic testing procedural services on a single beneficiary on a single date of service. If providers or suppliers do bill for more than two distinct laboratory genetic testing procedural services on a single beneficiary on a single date of service, the provider or supplier must attest that each additional service billed is a distinct procedural service using the 59 modifier.

The use of the 59 modifier will be considered an attestation that distinct procedural services are being performed rather than a panel. Providers and suppliers must use the 59 modifier in conjunction with other modifiers where appropriate. When providers and suppliers bill for multiple distinct procedural services, each service must be reasonable and necessary.

Laboratories that are billing for many individual genes using the 59 modifier rather than panels may be subject to medical review as outliers.

Exhibit C.  Noridian (Local Website) "Testing of Multiple Genes."

Billing and Coding: MolDx: Testing of Multiple Genes.

This coverage article has been published for notice under contract numbers: 01112 (NCA), 01182 (SCA), 01212 (AS, GU, HI, NMI), and 01312 (NV).

Effective Date: June 07, 2020

Summary of Article: A panel of genes is a distinct procedural service from a series of individual genes. All services billed to Medicare must be reasonable and necessary. As such, if a provider or supplier submits a claim for a panel, then the patient's medical record must reflect that the panel was reasonable and necessary. Alternatively, if a provider or supplier bills for a number of individual genes, then the patient's medical record must reflect that each individual gene was reasonable and necessary.

For ease of reading the term "gene" when used in this document will be used to indicate a gene, region of a gene, and/or variant(s) of a gene.

Exhibit D.  CMS National Correct Code Edits:  Paragraph 8, Gene Panels

Note:  CMS publishes separate, but usually identical, correct coding manuals for Medicare and Medicaid. 

Correct Coding Edits, Medicare, Final 103119.docx, Laboratory Services, Chapter X.

8. If one laboratory procedure evaluates multiple genes 
using a next generation sequencing procedure, the laboratory 
shall report only one unit of service of one genomic sequencing 
procedure, molecular multianalyte assay, multianalyte assay with 
algorithmic analysis, or proprietary laboratory analysis CPT 

If no CPT code accurately describes the procedure 
performed, the laboratory may report CPT code 81479 (Unlisted 
molecular pathology procedure) with one unit of service or may 
report multiple individual CPT codes  describing the component 
test results when medically reasonable and necessary. 

Procedures reported together must be both medically reasonable and 
necessary (e.g., sequencing of procedures) and ordered by the 
physician who is treating the beneficiary and using the results 
in the management of the beneficiary's specific medical 

If a single procedure is performed, only one HCPCS/CPT 
code with one unit of service may be reported for the procedure. 

Sunday, May 17, 2020

Washington Post Highlights Really Smart, Logical Plan for Pandemic Recovery - With Diagnostics

We've seen a huge amount of interest in pandemic recovery, with diagnostics and tracing, but too often some huge number is thrown out ($1B, $10B, $50B, $100B of tests) without a clear rationale.   

Washington Post this weekend highlights an important, logical report with a lot of thought capital produced by a consortium of experts and institutes, found on the Harvard website.

Here are the entry points:
  • WaPo article by Tabarrok and Ohlhaver here.
  • Harvard webpage for master document here.
  • Actual 66 page PDF here.
They divide the US into green, yellow, and red zones by COVID prevalence.  In a green zone, "fewer than 1 resident in 36,000 is infected...requires 1 test per day per 10,000 people and 5 contact tracers per 100,000 people."   Until 2 weeks ago, there were a number of green zones in the U.S. (there are none today).   Most Americans (circa 85%) live in yellow zones today, with disease prevalence between .002% and 1%.   "Yellow zones require 2500 tests for every daily death."  

Just 30M Americans live today in red zones - such as Detroit, New Jersey, New Orleans, New York City.  These zones require full social closures and stay-at-home orders.  The article and white paper outline steps to reduce red zones to yellow zones within weeks.

They note that Congress has authorized $3T in corona relief with a (disputed) additional $3T on the table, and that large multi-trillion dollar economic losses are coming.  They suggest the tracing and testing program outlined in their report tallies $75B.  

Note that the budgetary distribution includes $25B for (mega) labs and kits, $30B for isolation financial support, and $9B for contact tracing.

Like any plan, this one can probably be disputed or even shot down.  To my eye, there was a level of "thought capital" in this one that I haven't seen before.


Did We Drop Ball on Partial Tracing A Month Ago?

From news articles, you have the impression that the U.S. will be ramping up contact tracing "now" and in the future, with reopening.  But shouldn't we have done partial or as-possible contact tracing the past six weeks?   If there were 2000 cases somewhere per week, and capacity to sample-trace 50, 1 in 40, weren't we doing that?   I ask because around May 8 New York announced that 66% of new cases were coming from "home" - meaning NOT essential workers but at-home workers, unemployed, or retired.  And this was treated as a really big surprise (for example, by Gov. Cuomo.)  It seemed to me that kind of data - including from sparse sampling if necessary - was crucial to know. 


ProPublica Compares New York, California

News source ProPublica compares COVID responses in New York and California, May 16, here.

Friday, May 15, 2020

Very Very Brief Blog: WSJ and Weekly Death Data, March to April

WSJ publishes data (through week of April 11) on weekly deaths from all causes in the US.

All deaths per week are normally about 58,000 per week (yellow line).  2020 deaths by week were flat to March 21, just elevated March 28, and then spiked over the next two weeks to April 11.  

The raw death rate per week rose from about 1 per 6000 to 1 per 4500.  That's an a raw death rate per year rising from 1:115 to 1:88.

Note that death rate is a lagging indicator to COVID infection events; many of the people people dying April 1-11 were likely infected in mid-March (say, March 25).  Known death certificates and public health data directly attribute about 2/3 of the increase to COVID-19.   To me, this shows the speed of essentially uncontrolled COVID spread up to the 3rd week of March.   With states "reopening" (which often means restaurants at 50% seating or less, theaters closed, etc) the increase over 5-6 weeks would be much less than the uncontrolled rate shown here.   It will be interesting to have weekly death rate data for the weeks in 2H April, which will come out closer to June 1 and which would be reflective of new COVID events under pretty generalized lockdown (closed theaters, most shopping closed, etc).   

Very Brief Blog: CMS Updates FFS COVID Billing Guidance, May 15

CMS regularly updates a lengthy guidance on Fee for Service (FFS) Medicare billing under COVID.

See the May 15 update here.  

CMS has a separate file for MAC COVID test pricing, but it doesn't yet include serology codes (here).  

Thursday, May 14, 2020

Webinar May 21: Transformation of Healthcare After COVID (Glorikian et al; Foley Lardner LLP)

On Thursday, May 21, 3 ET, 2 CT, 12 PT, Foley Lardner LLP is hosting a webinar on "Post Pandemic Transformation in Health Care and Life Sciences." 

Harry Glorikian and I will be the two guest panelists. Harry Glorikian is a noted entrepreneur, biotech strategist, book author, futurist, and venture capitalist. (I'm one of those things). 

For the event website and full description (registration is free), click here.

Announcement continues:

While the health care and life sciences communities have been intently focused on responding to the COVID-19 pandemic, we have seen a number of major changes in care delivery and product development emerge that promise to become permanent — for example, a significant increase in telemedicine and greater reliance on telehealth technologies, regulatory shifts impacting care delivery sites and reimbursement models, and the application of AI and location data for disease tracking and contact tracing, to name a few. 

These changes will undoubtedly drive industry transformation, presenting both challenges and opportunities for businesses to consider in a new post-pandemic ecosystem.

As we continue to address today’s immediate and unprecedented public health crisis, it is important we also look to address tomorrow’s critical questions of what the “new normal” might look like for health care and life sciences development moving forward, as well as how to thrive in that changed environment.

Please join Foley presenters and featured industry guests on Thursday, May 21, for a webinar focused on navigating this “new normal.” Core discussion topics will include:
Top emerging changes and how they are expected to impact the future of health care and life sciences
How to prepare for and adapt to these changes to keep your company competitive and positioned for continued success
Potential opportunities for business development and growth stemming from industry transformation, including when to pursue them and associated risks to avoid

Very Brief Blog: How Will Medicare Price the Two COVID Serology Codes?


I'm leaving the original blog from May 14 intact, but on May 19, CMS released pricing for the single-strip and the liquid phase COVID SEROLOGY tests (86328, 86769).  The are priced at $45.23 and $42.13 respectively.


My most-frequently-asked question in the past week or two has been, How will CMS price the codes for COVID-19 serology?   This has a lot of implications for the lab industry, because the services will potentially be used millions of times.

Necessary Background

Let's work up to that question with some background.   On February 13, 2020, CMS created two codes for COVID-19 virus detection, e.g. PCR.   These were codes U0001 and U0002, for  CDC kits and commercial kits, respectively.  (I believe CMS assumed the CDC kits were free, leading to a lower CMS price for U0001 to labs).   Within a couple weeks, CMS announced that their MACs had collectively issued uniform "local" prices (at about $35 and $50, respectively).    That is, the pricing was a "MAC" local decision (where all MACs happened to match each other), not a "federal" decision.   On April 15, CMS created two new COVID detection codes, for "high throughput" detection, defined as >200 cases per platform.   CMS created codes U0003/U0004 by an "Administrator's Ruling," a rare type of action, and concurrently priced codes U0003/U0004 federally at exactly $100 each.   Details here.

Creation of Serology Codes; CMS Silent on Pricing

Meanwhile, on April 10, AMA CPT created two codes for COVID serology (antibodies).  
  • 86328 describes a reagent strip or similar method, 
  • 86769 describes a more complex method (e.g. the Electrosys Roche test).  
  • AMA info here, here.  
These are AMA codes; AMA does not set prices.   CMS has been silent on how these codes are priced.  While AMA created the codes on April 10 and "effective April 10," but I'm not sure if CMS has made these codes active in CMS claims processing computers yet.   CMS set its software to accept codes May 1; see CMS PDF online here.

I haven't seen any CMS news on how they are priced.  CMS could have issued pricing for these serology codes in interim federal rulemaking on April 30; CMS was silent on pricing then, although they did issue a ruling that the serology codes were covered by Medicare.  (Here.)  (See footnote). 

What We Know:  86328/86769 Set for CMS's Summer/Fall Lab Test Pricing Process

Here's what we do know.   

For all new lab codes (except for U0003/U0004, set by direct federal decision-making, see above), CMS by law holds summertime public meetings and issues final prices in late fall.   

That's the process that 86328/86769 are currently tracked into, although nothing prevents CMS from issuing provisional MAC prices as they did for U0001/U0002 in April.

See the codes on the June 2020 meeting agenda here:

click to enlarge, agenda items 95/96

I discussed the normal CMS pricing process in a prior blog here.  
  • If no higher decision intervenes, the codes will be MAC-priced locally all year.   
  • CMS will take public comment on correct pricing for 86328/86769 on June 22 in a virtual public meeting, then...
  • Hold a professional advisory panel on July 29/30 to discuss correct pricing.  
  • Taking this input, CMS will issue proposed pricing in early September
  • Take public comment for 30 days, and 
  • Issue final pricing for 86328/86769 in November, which will be...
  • Nationally effective on the clin lab fee schedule on 1/1/2021.     
Other events, in no preferred order, include:
  • CMS asks MACs to decide on local prices, and CMS makes them public, as it did for U0001/U0002.  CMS doesn't have to do this.
  • CMS issues pricing in the next Interim Final Rulemaking, assuming there is one.
  • Congress sets CMS serology pricing in the next COVID bill, assuming there is one.
  • CMS issues pricing for serology codes by Administrator's Ruling (unlikely; A.R.'s are very rare).
Absent one of these events, the CLFS pricing process will creep along til November.   The lab industry may advocate for quicker and more public pricing news before that. 

Update: In a 5/15/2020 PDF, CMS notes that the serology tests are currently locally priced until a CMS national price is announced - here.

AMA/CPT Antigen Testing

There is no code yet for COVID antigen testing; either AMA CPT or CMS could create such a code through the urgent channels used for the other COVID codes.

Historically, CMS has been pretty frugal when pricing infectious disease assays (current prices reflect PAMA survey prices, not the prices originally set administratively by CMS).  For example, 87880 is immunoassay, visual observation of result (like a strep throat laminar flow assay), $16.53.  Tests for both HIV antigen and HIV antibodies are circa $33 (87804).  CMS showed it was willing to go to more robust pricing for U0003/U0004 due to the COVID emergency.   


Note regarding scope of this article. 

I should point out I'm only considering the Medicare price.  

An expert pointed out that commercial insurance, per the CARES Act, H.R. 748, Section 3202, must cover COVID testing without copay and at one of two prices.  Either the negotiated (contracted) rate with the lab, or else, the lab's public cash price on the lab's website which it shall post.   


In April 30 rulemaking published May 8 (here, 85 Fed Reg 27550), p. 27598, CMS announced that serology tests were covered, noting it normally makes coverage decisions through NCDs, but here, through emergency rulemaking.  

CMS sort of danced around the medical usefulness of serology testing with the following text:

Having COVID–19 serology test
results is useful to individual patients,
their practitioners, and their
communities because it could change
the decisions Medicare beneficiaries
make for themselves and influences
practitioner management of the
beneficiaries’ medical treatment.

If it can be determined that they are
immune, these patients would possibly
not be at risk for contracting COVID–19
and not be risking the health of their
communities if they travel outside of
their home as they would not spread

Among the biggest risks to
the community are patients with
COVID–19 infection who have not
developed symptoms or had minor 
nonspecific symptoms, yet are infectious.51

Beneficiaries who are negative for
COVID–19 antibodies through serology
testing may need to take more
preventive measures to reduce their
personal risk of infection as some
persons, based on age and other factors,
are at higher risk of serious illness or
death from the disease. Further, a
practitioner should discuss the results
of the serology test with the beneficiary
to ensure that the beneficiary
understands the results of the test and 
the results are considered in the overall
management of the patient.  

CMS then writes:

We would not expect
such tests to be performed and billed
unless clinically indicated.

We are finalizing on an interim basis,
that during the PHE for the COVID–19
pandemic, Medicare will cover FDA
authorized COVID–19 serology tests as
they are reasonable and necessary under
section 1862(a)(1)(A) of the Act for
beneficiaries with known current or
known prior COVID–19 infection or
suspected current or suspected past
COVID–19 infection.

This is a really broad coverage conclusion:  serology tests are "reasonable and necessary" if the patient has "known current or prior infection" or "suspected current or past infection."   This is a much broader use of the term "reasonable and necessary" than CMS and MACs usually employ, but it's now written into federal law at 42 CFR 410.32.   For example, the MolDx MACs had (have) a 2019 policy against viral panel testing for reasons that help the community or help patients make decisions; panels had to be useful for medically managing the individual patient's disease (e.g. LCD L37348).  CMS also describes the serology test as assisting in "preventive" methods (above) but MACs are usually loathe to consider "preventive" features of testing as grounds for Medicare coverage.  

The exact language at 42/410.32 is:

^ FDA-authorized COVID–19 serology
tests are included as covered tests
during the Public Health Emergency, as
defined in § 400.20 of this chapter, for
the COVID–19 pandemic, as they are
reasonable and necessary under section
1862(a)(1)(A) of the Act for beneficiaries
with known current or known prior
COVID–19 infection or suspected
current or suspected prior COVID–19

Very Brief Blog: More About Masks: Atul Gawande in New Yorker

In Los Angeles, on May 14, we woke up to news that we are required to wear masks when outdoors.  Prior, masks had been required when shopping (groceries, drugstores) but recommended outside when near people.   

Masks for the public in streets and parks been controversial nationally, with strong feelings on both sides.   This week there is a review by Atul Gawande in New Yorker (May 13, here.  I think this is open access if you click through enough subscription offers.)   

I have been suspicious of classic surgical-type masks (typically blue paper), because of the large spaces they usually leave at the sides.   Gawande notes these are actually specially-designed electrostatic fibers meant to try virus at high rates.   (I'm not sure if that grade of paper technology is also found in non-certified blue paper masks sold to the public, though).   

Gawande also quotes a preprint 8 page "evidence review" (not peer reviewed) by Howard et al. on mask value, here.  Howard et al. include a multi color chart which I think is actually relatively simple data modeling.    They assume that R=2.4 (transmittals per infected individual; bottom left corner), and they project transmittal rates if 0-100% of people wear masks which are 0-100% effective.   

For example, if 100% of people wore masks that were 50% effective, R=1.2, and similarly if 50% of people wore masks that were 100% effective.   
(This modeling and limit-modeling is not real data, but it can be helpful.  For example, I don't know what Anthony Fauci weighs, yet I can also be 100% sure it is more than 110 pounds and less than 180 pounds.   It would be great to know if the requirements for masks changed infection somewhere between [+20% to -20%], or alternately, somewhere between [-20% to -60%].)
Preprint Typesetting Watch

As far as I remember, a couple months ago, preprint articles at BioRxiv or MedRxiv were almost always very bare-bones affairs.   

A week ago I noticed a preprint (Kai et al) that was upping the typesetting quality of the preprint game (here).    

For my eye, the Howard et al. pre-print on mask efficiency pulls the preprint game another step higher, with quite elaborate typesetting.   See a screen shot of Howard et al., page 1, below.

Increasingly elaborate typesetting of un-reviewed preprints

Monday, May 11, 2020

Very Brief Blog: CMS Releases FY2021 Inpatient Proposed Rule

CMS typically releases the annual fiscal year proposed inpatient rule around April 20-25; this year it appeared on May 11, 2020, after market close.
  • See the CMS fact sheet here.
    • See the more P.R. oriented press release, here.
  • See the "inspection copy" or advance typescript copy here.
    • It clocks in at 1602 pages.
    • The Federal Register version typically appears about a week later.
    • Comments are taken until July 10.
    • The final rule should appear around August 1, 60 days before the October 1 fiscal year
    • Most early trade journal reactions lead with, "Hospitals slam price transparency proposals," such as:
    • At Dive Healthcare, here.  MedCity News here. Becker's, here.  
NTAP Bonanza; N=24

There is a bonanza of New Technology Add-On Payment applications - usually there are 10 to 12.  This year there are 24.   Of the 24 applications, 9 were in special pathways: 3 as inpatient FDA breakthrough devices, and 9 as QDIP or "Qualified Infectious Disease Products."  All 9 are proposed for approval (these are categorized that are fast tracked to simpler review, inclined toward approval).   

CMS has 15 additional applications besides the 9 just cited.

In addition, CMS plans to add another category to its accelerated NTAP approval for antibiotics.  In addition to the FDA QDIP pathway, they will include products under the LPAD (Limited Population Pathway for Antbacterial and Antifungal Drugs).   

The rule proposes to require increased reporting and public release of private payer rates (e.g. price transparency policy). 

Press Release (Opening)

CMS Builds on Commitment to Transform Healthcare Through Competition and Innovation

"Today, the Trump Administration proposed changes for acute care and long term care hospitals that build on the progress made over the last three years and further the agency’s priority to transform the healthcare delivery system through competition and innovation while providing patients with better value and results. 
The proposed rule would update Medicare payment policies for hospitals paid under the Inpatient Prospective Payment System (IPPS) ... for fiscal year 2021."

Very Brief Blog: PrePrint Article Circulates, Suggests Masks Could Be Very Important Against COVID Spread; PLUS Upping Your PrePrint Game

If there has been one particularly controversial point about COVID, it's been advice for and against masks, with arguments and public policies on both sides.  (From March 1 right up to the news May 11 about masks in the White House).

See healthcare journalist David Ewing Duncan writing on May 8 about a preprint article - Kai et al. - arguing that 80% mask wearing rate is practically as good as 80% herd immunity for cutting infection rates with COVID-19.   

In the graphic below, from Kai et al., red and yellow are different but high rates of masking; blue is "lockdown continues indefinitely."  Gray is conventional success of social distancing w/o masking.

I can't speak to the quality of the input data or the model in Kai et al.  I did notice, they substantially raise the stakes in terms of the sophisticated formatting of a pre print article.  See below.

Kai et al: Much more elaborate preprint formatting (click to enlarge)

Very Brief Blog: The Louisiana COVID Success Story Deserves Attention

Monday's LA Times carries a story that California has fallen in the ranking of states with a successful COVID response, with case rates still rising markedly - here.  The story quotes on Sunday talk show with Christopher Murray of University of Washington - remarking,

"“Some good-ish news coming out of New York and New Jersey and Michigan, where the death cases and death numbers are coming down faster than expected,” Murray said Sunday on CBS’ “Face the Nation.” “Some other states where cases and deaths are going up more than we expected — Illinois and then Arizona, Florida, California as examples of that.”

Louisiana as an Early Hotspot

We heard in March that Louisiana and especially New Orleans was becoming a high-COVID population, (also here), typically traced to an influx of travelers for Mardi Gras (February 25 this year).  Genetic studies suggest that New York tourists were a key factor - here.   

Sharp Drop in Cases in Most of Louisiana, Especially New Orleans

Less publicity to the fact that Louisiana and New Orleans thereafter saw a sharp drop, especially in New Orleans, in new cases.   This is less true in central and northeast Louisiana, but it is true in many districts.  See May 9 story here, see figure below.

For example, in the chart below, the overall chart for Los Angeles right now looks a lot like Louisiana-Northeast-Region 8, and nothing like New Orleans, Region 1.

Click to enlarge


LA Times also had an additional story on Monday, about California being on a prolonged plateau with a substantial death rate neither rising or falling.   See LAT story by Lin & Lee, here.   As I mentioned earlier, we look like Louisiana Region 8 above:

LA Times. May 11, Lin & Lee

Very Brief Blog: Preprint Article Highlights Host Vulnerability to COVID

There is a global host-response consortium for studying the radically different responses of different person to COVID-19 infection - see early article at Genomeweb here, see consortium website here.  See a review of human genomics relative to COVID virus in Genetic in Medicine, Murray et al., here.

May 10, trade press Tomislav Mestrovic (here) on a preprint article by Kachuri et al., "Landscape of Host Genetic Factors Involved in Infection in Common Viruses and SARS-CoV-2" (here).    

For viral response as a whole, the authors write, "We conducted a comprehensive study in the UK biobank linking germline genetic variation and gene expression with 28 antigens for 16 viruses in 7924 subjects. We discovered 7 novel loci associated with antibody response (P<5.0×10-8), including FUT2 for human polyomavirus BKV, TMEM173 for Merkel cell polyomavirus (MCV), and TBKBP1 for human herpesvirus 7."  Turning more specifically to COVID, they write, "Based on 1028 subjects tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we identify 7 class II HLA susceptibility alleles (5 [also] associated with other viruses). We also observe that genetic determinants of ACE2 expression may influence SARS- CoV-2 susceptibility. Our findings elucidate the genetic architecture of host response to viral infection, with potential implications for complex diseases and COVID-19."  Kachuri et al. are mostly UCSF-based, and used data from the UK genomes biobank.

Notably, most of the odds ratios for SNPs and likelihood of COVID-positive testing were small (0.4-1.6).  However, this is a non-clinical study, and the more important factor, the odds of COVID hospitalization or death, were not studied.  It may turn out that genetic factors play a largely role in the cascade of host response than in turning test-positive or not. 

COVID Sequencing: Is It About to Become Important for Public Health?

One of the great early victories in the COVID-19 battle was generating a complete sequence of the virus now known as SARS-CoV-2.   Soon, it was recognized that there were many emerging but clinically silent mutations.  For example, it was identified by March that most Italian cases may have come from Germany, and that most New York City cases may have come from Europe (see NYT lead story, April 8, here.)

May 10, the British newspaper The Guardian ran two articles about COVID-19 sequence mutations.   The first, by science editor Ian Sample, is an overview for the educated public on COVID mutations (here).  The second is an article by Sample on potential clinical implications of adaptive mutations of CSARS-CoV-2 (here).    He keys off what I think is one of the largest global sequence variants publications, by Phelan et al., in pre-release at - here.  They built a new phylogenetic tree with 3,958 viral SNPs from a total library of 5,349 whole genomes.  

For example, complex genetic trees can be constructed (these do not necessarily have any clinical correlate):

And mutations can be mapped to points on the COVID spike, as below (green points):

Large Companies Discussing Sequencing

Large players in the genomics industry are discussing sequencing.   Thermo Fisher announced an RUO setup for COVID sequencing on its new Genexus platform (here, here).    Illumina's investor call last week discussed the potential market for sequencing, including very high throughput sequencing for mass diagnostics (here, here).   Guardant's investor call also highlighted  a potential move into COVID sequencing for what has historically been an oncology company (at Genomeweb premium here, original transcript here).   This is just a highlight of the scientific and economic activity that is starting to pour into the U.S. and global COVID sequencing infrastructure.  

Public Health Value: Contact Tracing?

CMS currently pays $100 for COVID PCR (or any method) high throughput analysis of COVID for diagnostics (code U0004).   At scale, COVID sequencing might come into the same price range, and provide both diagnostic and sequence information.  Alternatively, if the same sample can be used twice, large-scale testing could be run for every 100 samples by PCR, with 1 in 10 or 1 in 20 samples that are positive for PCR being shunted into a secondary SEQ test.   (For example, CMS would pay $10,000 for 100 PCR samples for diagnostics under U0004.  If 10 were positive and one were sampled for SEQ, and seq cost $150, the total cost impact of the single extra $150 over the $10,000 total payment would be very tiny).   

Look at what could happen - it's highly favorable.  Public health authorities would have nearly-automated ongoing visibility in to the COVID sequence profiles in a community (assuming over an intervals tens of thousands of total COVID tests are being run, the 1 in 10 sampling will be an accurate survey.)  And this approach could also provide a quality check for whether contact tracing is actually pairing up individuals who truly were infected by the same viral strain.   This could lead to rapid quality improvement and selection of the best (and most efficient) practices in contact tracing, something that will be mission-critical to the US economy in Q2, Q3, Q4 of 2020.   Without spot checking for sequence, public health official will be flying entirely blind whether they are truly tracking and matching up real carriers and the corresponding infected persons accurately.

For an update from CDC, see the homepage for its SPHERES consortium for COVID sequencing,


The day after I wrote this, Genomeweb (Julia Karow) ran a deep dive article on the growing importance of COVID sequencing (vs PCR testing) - here.

Update 2:

A few days later, Genomeweb ran an article (Christie Rizk) on active use of COVID SEQ testing in a hospital, identifying unexpected patterns of virus in a study including patients, family members, and hospital staff.  Here.

Sunday, May 10, 2020

Very Brief Blog; CMS Releases 6-page Fact Sheet of COVID Special Lab Rules

Since March, CMS has issued new codes, rules, or other updates almost weekly.   I've covered these on a rolling basis, most recently, an 80-page new Interim Final Rulemaking (IFR) in the Federal Register (released April 30, publication May 8) - here.

CMS has a six-page online update of COVID rules through April 30: online here.

See also a two-page CMS listing of lab codes that can be ordered by any "health professional" (not just the "physician who is treating the patient") - hereNote that the listing of lab codes includes CMS and AMA CPT COVID codes, including serology, but also influenza and RSV-containing codes, as long as they are ordered along with at least one COVID test and are part of the differential diagnosis of COVID.  This list includes the circa-$400 test, 87633, respiratory panel, 12-25 targets, which includes influenza virus and respiratory syncytial virus.

screen shot only; see six page PDF at link in text