WHERE IS THE DELTA VARIANT SURGING?
Low vaccination rates, loosened pandemic restrictions and a highly contagious variant make for a coming storm.
11 July 2021/Sunday/800pm PDT
"We have a lot of [COVID-]susceptible people out there yet that have been not vaccinated, that, for example, should this Delta variant take over, we’re going to see local and regional surges that are substantial."
-Michael Osterholm PhD/MPH, epidemiologist and director of CIDRAP (Center for Infectious Disease Research and Policy) at the University of Minnesota, 18 June 2021
High resolution version of today's pandemic graphic: https://drive.google.com/file/d/1chcKaZAdYduR6mwmwi2aa8OKRkhsNOnu/view?usp=sharing
BACKGROUND
The increase in COVID cases and hospitalizations almost exclusively among the unvaccinated that started in southwestern Missouri has now spread to adjacent states to now involve Kansas, Oklahoma and Arkansas. The challenges of this late summer surge hinge largely along vaccination rates, particularly among the high risk populations- and keep in mind that 60% of American adults have at least one medical condition that qualifies as a high risk factor for significant COVID disease that can result in death.
Think about that for a second- the *majority* of the US adult population is a high risk population for significant COVID morbidity and mortality. A
And that's even before get on the subject of the increasing pediatric hospitalization rates from COVID as B.1.617.2, the Delta variant, has now become the dominant US variant, displacing B.1.1.7 Alpha as of mid-June according to genomic surveillance data. Back when I started keeping on eye on genomic surveillance data in February, there were barely 200,000 viral samples in the GISAID database. This evening when I checked on some data for tonight's post, there's about 607,000 samples from US patients.
A REFRESHER ON TEST POSITIVE RATES
The test positive rate is the percentage of COVID tests done that are positive for the virus. While not truly durable (independent of testing rates), it still offers some useful information on the pandemic burden in a given community.
A test positive rate of 10% or higher is concerning because it indicates that testing numbers are insufficient to catch all possible infected individuals and test their close contacts. The COVID Policy Lab of Children's Hospital of Philadelphia (CHOP) considers a test positive rate of 9% or higher concerning.
If you are testing for all potentially infected individuals and their close contacts, then the test positive rate goes down- more tests done, the more likely you will catch those who do not have COVID at all. The lower the test positive rate, the better. Not testing doesn't reward you- you'll just have more positive tests and higher positive rate. Test more people, catch more that are negative. The test positive rate (TPR) "rewards" expanding testing.
By most accepted measures, a test positive rate less than 5% is considered to be the goal. If the pandemic spread in the community is slowing and testing is increased, then the test positive rate goes down. The CHOP Policy Lab, however, is more stringent (understandable given they are viewing this pandemic through the lens of the pediatric population, most of whom are not eligible for vaccination yet) in that they consider a TPR of 3% or less better.
TEST POSITIVE RATES BY US COUNTY
The main map in today's graphic I stitched together from the CHOP Policy Lab so it was easier to view in full without losing the county level details. California, Washington, Connecticut and Rhode Island are not part of CHOP's research, so that it why those four states are blank. But checking on their overall pandemic environment at the state level, it's better than most places in the United States. I'll be taking a look at those states in a later post.
You can clearly see where the Delta surge is taking place in Missouri, Kansas, Arkansas and Oklahoma. What I've done is taken the nine states with the highest test positive rates and they have their own databox that shows the following:
Percentage of population fully vaccinated (green italics)
State level (overall) test positive rate
Percentage of genomic samples in the last 60 days that were the Delta variant
You can see from that data that Kansas is at 49% Delta variant, Missouri is 53% Delta, Arkansas is at 39% Delta and Oklahoma is at 32%- not as high but the overall trends in Oklahoma will likely put them in the same critical care resource crunch as Missouri and Arkansas well before the end of this month.
With Kansas, Oklahoma, Missouri and Arkansas as the current ground zero of the US Delta variant surge, let's take a look at the other states I've highlighted in this graphic.
UTAH, NEVADA, AND IDAHO
These three western states are a great example of how B.1.1.7 Alpha is still a threat even with the Delta variant as the new dominant variant in the United States. In these three states, their TPRs are over 10% yet in every single one, the dominant variant is not Delta but B.1.1.7 Alpha.
Utah and Idaho are in the bottom third of US states in terms of vaccination rates but Nevada is slightly higher.
ALABAMA AND MISSISSIPPI
These two states are in dead last for overall vaccination rates in the United States and the TPR data concurs with that assessment. Just over one out of every four COVID tests done in Alabama is positive. One out of every five tests in Mississippi is positive. They are dealing with not only poor vaccination uptake but an overwhelmed testing infrastructure combined with extensive community spread suggested by the TPRs.
What is going on right now in Missouri and Arkansas has the potential to be greatly overshadowed by what is coming for Alabama and Mississippi given their poor vaccination rates. Kansas is nearly ten percentage points better than these two states and Kansas is *still* seeing one in four COVID tests as positive which is highly concerning.
VARIANT TRENDS IN THE UNITED STATES
The lower graph in today's graphic shows the trends since January 2021 of the major variants present in the US- B.1.1.7 Alpha, P.1 Gamma, B.1.617.2 Delta, B.1.427/429 Epsilon, and B.1.526 Iota.
Note the mid-June point when Delta surpassed Alpha as the dominant variant in the United States. Note also that Delta's increase in prevalence in genomic viral samples was much faster than that of Alpha.
Note also that the other variants have not increased to the same degree as either B.1.1.7 Alpha or B.1.617.2 Delta.
The US map on the lower right shows the prevalence in each US state of the Delta variant. What is important to note here in light of the big map in the upper half is that even though Delta is not the majority of samples in Nevada and Utah, it's rate of increase in the last 60 days has been rapid. So yes, B.1.1.7 Alpha is still the big threat in those two states but not for long.
PLACES TO WATCH
From the main map that shows the county level TPRs, note there are other areas that bear watching in the next several weeks that I did not mark out on the map:
Florida
Indiana
Louisiana
Arizona
Texas
TAKE HOME MESSAGES
1/ The current ground zero of the current Delta wave is centered on southwest Missouri and extending outward into Kansas, Oklahoma and Arkansas.
2/ I fully expect Alabama and Mississippi to experience a critical care resource crunch in the coming weeks with increasing TPRs and the lowest vaccination rates in the United States.
3/ Idaho, Utah, and Nevada are good examples of how B.1.1.7 Alpha is still a threat even when Delta has become the dominant variant.
4 / Keep in mind that no one number gives you a full picture of the pandemic environment. In today's graphic I tried to tie together vaccination rates, test positive rates, and genomic surveillance data. Even that has limitations thanks to the geographic differences, socio-economic disparities and even political affiliations in community populations.
5/ The Delta variant has genetic mutations that make it highly contagious, more so than any other variant of COVID we have dealt with so far in this pandemic. The epidemiologic data shows rapid spread that is consistent with the molecular biology of the mutations of this variant. Any variant that is more contagious cancels out any biological advantage that children had in riding out this pandemic last year. Given that those under 12 are not yet eligible for vaccination, our schools will be the new front line of the pandemic this fall whether we like it or not.
6/ The vast majority of hospitalizations and deaths are now occurring in those who are unvaccinated. In the words of Governor Jim Justice (R) of West Virginia:
"When it really boils right down to it, they're in a lottery to themselves. We have a lottery, you know, that basically says, 'if you're vaccinated, we're going to give you stuff. Well you've got another lottery going on, and it's the death lottery."
PARTING THOUGHTS
You know what our challenge now is in this pandemic? It's not boosting vaccination rates. It's not containing the new variants. It is addressing the rot that has eaten away at the moral fortitude of this nation, a multi-level cancer that has been lurking and festering for years that has been laid bare in this pandemic. From individuals not looking beyond their own wants and inconveniences to health care systems pretending to give a shit when actually giving a shit would cost money they don't want to spend for fear of losing health care market share. It's politicians using the disregard of established medicine and science as a litmus test of false patriotism.
That moral rot is worse than the virus itself.
THE MOST RECENT PANDEMIC POSTS
COVID VARIANTS TABLE UPDATE (30 June 2021): https://www.facebook.com/jp.j.santiago/posts/10219119070944604
MAYO CLINIC GRAND ROUNDS: VACCINES AND VARIANTS (14 June 2021): https://www.facebook.com/jp.j.santiago/posts/10219031846404045
THE MOLECULAR BIOLOGY OF THE E484K MUTATION (10 May 2021): https://www.facebook.com/jp.j.santiago/posts/10218832046529173
IMMUNOLOGY 101: THE IMMUNE SYSTEM- REPOST/UPDATE (05 May 2021): https://www.facebook.com/jp.j.santiago/posts/10218801066954703
COVID VARIANTS OVERVIEW AND UPDATE (22 April 2021): https://www.facebook.com/jp.j.santiago/posts/10218722676514991
NEW COVID VARIANT OF INTEREST: B.1.617 (18 April 2021): https://www.facebook.com/jp.j.santiago/posts/10218699298170547
CASE SURGES CAN RESULT IN COVID VARIANTS (12 April 2021): https://www.facebook.com/jp.j.santiago/posts/10218657527966318
THE OVERVIEW & STATUS OF COVID VARIANTS (9 April 2021): https://www.facebook.com/jp.j.santiago/posts/10218637120816152
QUICK UPDATE: THE COVID FAMILY TREE (01 February 2021): https://www.facebook.com/jp.j.santiago/posts/10218211054244754
COVID MUTANTS: VARIANTS OF CONCERN (31 January 2021): https://www.facebook.com/jp.j.santiago/posts/10218204381877949
COVID MOLECULAR BIOLOGY: THE SPIKE (6 January 2021): https://www.facebook.com/jp.j.santiago/posts/10218019683340601