NedNotes (not blog): 05feb21 COVIData Sweep

Dédié à cinq Américains morts de la pandémie covidieuse: dos inmigrantes hispan@s; deux nègres et infirmières en établissements de soins aux; del este al medio oeste; ages ranging from forty to ninety-one years old; average age of seventy, median of seventy-five.

B.L.U.F. (bottom-line up-front). The season of jolly follies is working itself through the health-care system. Fifth week in a row with 22,000+ deaths; next week looking for a 25-50% decrease in weekly fatalities. Also this week, the variable virus.

INTRODUCTION
Summary. Improvements across the board led by Colorado, Illinois, and Maryland. Only three states under review deteriorated this week: Alabama, Missouri, and Tennessee. The emergence of three new strains create several concerns as discussed below. This essay serves as a data supplement to the 05feb21 cluster analysis.

Again another week of mixed results reflecting an up-tick in lethality of three strains from Brazil, Britain, and South Africa already detected in the United States. The British strain, hopefully, will predominate by late March according to Dr Fauci. As matters stand now, "Her Majesty's Mutation" looks to be the least lethal of the three and may well be no more potent than the current coronavirus.

Nevertheless, the worst of the surge has occurred, despite the higher than expected level of deaths. The vaccination efforts across the country are gaining traction, even as supplies may be short. As those inoculations accelerate over the next month, one can expect the weekly death toll to decline rapidly. The short-term forecast is 15-17,000 deaths this upcoming week, followed by a return to pre-Thanksgiving totals of 9-11,000 total fatalities every seven-days by month's end.

OVERVIEW of COLLECTED DATA
Summary. Improvements across more than 90% of the country in mortality rates and positivity with modest improvements in the availability of Intensive Care Unit (I.C.U.) capacity as well general hospital facilities. Unfortunately, leading indicators point toward increasing mortality run rates concurrent with the reduced number of cases.

During the week under review, fatalities have increased by 5% from 440,342 last week to 462,933 this week (i.e., 22,591 new deaths). This result is disappointing and is attributable to slower than hoped for -- and hyped -- vaccine roll-out. The deployment of vaccines is slowed by three factors, two to be expected and one from an unforced error.

1. Any massive project like this one poses steep challenges in the initial stages due to learning curves (e.g., the Obama-Care web-site and program) and unanticipated constraints (e.g., the time consumed in tracking down the stragglers within targeted demographics).
2. When there is a crisis, the solution of which is perceived to be dependent upon a scarce resource (i.e., the vaccines), rival countries -- at least those rich in resources -- practice a nationalism in bidding up prices on the market plus an autarky of keeping domestically produced supplies.
3. The unforced error is the Trump Administration apparently checking out in mid-to-late October, leaving the U.S. less and less prepared relative to other well-to-do countries as well as leaving states and municipalities to scramble for insufficient resources in the absence of any financial, planning, or logistical support from D.C.  

Nevertheless, grim as this news sounds, it is largely in the rear-view mirror, albeit hogging up that mirror; time to look forward. States are getting their footing on scheduling and administering vaccines while inoculations already top one million per day (i.e., the implicit goal set out by President Biden during the campaign and transition). The supply shortages should ease as two or three vaccines come on line over the next month or two. 

Two American companies -- Johnson & Johnson and Novavax -- are leading the development of vaccines imminently to be used. The third, from AstraZeneca, is a British product and may well be on its way to staying in its 'captive' market as the U.K. remains grudging in her release of vaccines contractually obligated for the European Union. An extra incentive for the Brits is the effectiveness of this Oxford-created vaccine against the highly contagious London variant.

In any case, despite the stubbornly high level of fatalities during the week, the country made some significant progress in the following areas:

• hospitalizations falling by 13% -- remember: in one week -- to 86,373;
• patients requiring critical care declining by 9% to 22,559;
• average daily new cases dropping by 21% to 121,286;
• I.C.U. availability increasing by 10%, or two percentage points, to 27%; as well as,
• the positivity rate dropping 18%, or a point and a half, to 7.0% with at least seventeen states reporting test results at or below the containment threshold of 5% set by the World Health Organization.

The structure appears to be nearly in place for a rapid reduction of cases and fatalities. As stated earlier, the following three states have seen their performance sag noticeably this week:

• Alabama, clearly out of control, now, with an 11% growth rate in deaths, insufficient release of I.C.U. beds, and one of two states under review confronting a growing positivity rate to 35.7%;
• Missouri with fatalities up 5% during the week on slowing case-loads almost to double the weekly mortality run rate to 5.3% exacerbated by tight hospital availability ; as well as,
• Tennessee with a 10% increase in fatalities and declining testing capacity.

Among the bellwether states, Arizona and California continue to face challenges with the growth rates in deaths doubling or trebling the increases of confirmed cases. Lag-times in fatalities relative infections should be spent by now. Georgia still faces her own challenges with a 6.3% weekly growth in mortality compounded by a double-digit positivity rate (i.e., 13.4%) and a strained I.C.U. capacity. The watch-list remains the same despite improvements registered by California and Pennsylvania. 

Each of the Golden and Keystone State stays on the watch-list for different reasons since one week does not a trend make and, and, in any case, neither have turned the corner. Both states are re-opening their economies with a strong possibility of doing so too soon in view of their recently losing control of the coronavirus contagions within their borders. The invasion of highly contagious variants with their population pools will likely provoke up-ticks in lethality to make the timing of a proposed re-opening tricky for any state. 

Pennsylvania and California also have unique challenges open to exacerbating the effects imposed by the new strains. California still contends with a large COVID epicenter in the San Diego / Tijuana (México) cross-border mega-region to accelerate the transmission of the new and improved bug. Pennsylvania faces very low vaccination rates in Philadelphia plus a poor week for the Western half of the Commonwealth. Both Governors Newsome (CA) and Wolf (PA) function in the midst of political pressures (e.g., a growing electoral movement to remove a Governor or fighting COVID with an depleted treasury).

FEATURE: STRAINing to KEEP ONE's HEAD above WATER
Summary. This section reviews only four of the four thousand mutations floating around. These four likely make the coronavirus more contagious, more deadly, perhaps both. At the end of this section are data para mi querido México and pour ma chère Tunisie. Unfortunately, the data are not available to give the reader a trend. A snap-shot will simply have to do. 

Only three of the variants are identified by the Centers for Disease Control and Prevention (C.D.C.) and their counterparts in Europe, Africa, and South America; the fourth (i.e., Italy in the Winter of 2020) is my personal view. Early indications point toward a fifth malicious mutation emerging in California, but the data are insufficient for any actionable conclusions. Each mutation will be treated in the order it has become known to U.S. epidemiologists through communications and an up-lift in genomic surveillance:

• Italy, March 2020;
• South Africa, October 2020;
• Great Britain (see three-minute vid.), December 2020; and,
• Brazil, early January 2021 (perhaps the most lethal).

What these mutations have in common are accelerated transmission rates and their predominance in the viral space after a month or two. The Italian mutation, with the virus morphing as the original coronavirus migrated west from China, overwhelmed one of the more advanced health systems across the world in Italy. It then hurt France, Spain, the BeNeLux countries, and, especially, the Northeast U.S. 

There is little mention of the Brazil mutation. Another defining characteristic of these ‘little buggers’ remains their constant evolutionary change, threatening the efficacy of vaccines already in the market and possibly making re-infection more likely. One final point: these variants will keep coming, likely becoming more resistant to anti-bodies. The idea of ‘vacci-nationalism’ at the expense of poorer nations may lock humanity into a self-fulfilling nightmare.

FIRST, Italy (population of 62,390,364): 2.6 million cases (14 million re-stated for U.S. population versus 27 million cases incurred by the United States herself); 90,136 deaths (496,345 deaths re-stated for U.S. population versus 463,933 for the United States); 3.5% mortality run rate; 3.5% of population inoculated with at least one vaccine; 6.5% estimated positivity rate; 51% estimated I.C.U. bed availability.

Who does not recall the shocking news from ten-to-eleven months ago when the coronavirus from China swiftly overwhelmed one of the world’s premier health-care systems? True, China was almost certainly under-reporting her data, a practice later alleged against Italy herself. Within a month, however, Italy’s fatalities overtook those of China. Once the virus made its way to New York, the Empire State’s fatalities exceeded Italy’s in another month. 

A reasonable explanation for the massive failure involves two factors: lack of experience and information, exacerbated by Chinese opacity in the beginning, as well as a deadlier mutation as the virus migrated west. Please note that this assertion of a mutation remains my personal view – my conjecture – only. These days, life with COVID remains difficult for Italy as she veers toward 100,000 deaths due, at least in part, to a phenomenon witnessed in the United States: spread of the U.K. and South African variants to the rural areas in Southern Italy.

SECOND, The United Kingdom (population of 66,052,076): 3.9 million cases (19 million cases restated for U.S. population); 110,303 deaths (555,520 fatalities restated for U.S. population); 2.8% mortality run rate; 15.9% of population with at least one vaccine; estimated 21% I.C.U. availability; 3.3% current positivity rate.

First detected in late 2020, this variant became most evident in mid-January with hospitalizations up by two-thirds from the Spring 2020 peak. Prime Minister Johnson had to order a second lock-down in early January 2021. This variant is expected to predominate in the United States sometime next month. This new strain may well be more deadly since more of the virus invades the human body. (That is to say: the ‘viral load’ is multiplied; think of it as packing more into a punch.) 

This more contagious coronavirus may mutate enough to render vaccines ineffective, though the government expert leading the corona charge believes vaccines can be modified into effectiveness in four-to-six weeks.  As described in a COVIData Sweep for 29jan21, the Brits have also to contend with the same specious arguments against vaccination circulating throughout the United States.

THIRD, South Africa (population of 56,978,635): 1.4 million cases (8.5 million cases re-stated for U.S. population); 45,605 fatalities (266,110 deaths restated for U.S. population); 3.1% mortality run rate; 0% vaccinated; estimated positivity rate of 16%; 83% estimated I.C.U. availability.

The danger of this variant has been covered in an earlier COVIData Sweep and the “The Los Angeles Times”. The threat of this mutation is the doubling of its binding on the cell attacked. It is also more contagious than the virus addressed by the vaccines. In four months since the South African variant has appeared, it has proven to be far more adaptable than the U.K. strain, lt dominates 90% of the infections in the country. Additionally, the variant has leapt across borders to choke off a rapidly increasing portion of the southern half of sub-Saharan Africa.

Inevitably, spreading will seep into Europe and the United States. America has already suffered at least one fatality from this South African variant. Britain is preparing for the onslaught; the outlook for vaccines remains unclear, with conflicting results for vaccine durability. Generally, the strain reduces vaccine efficacy by 20-30%, eliminating much of the redundancy of a second dose. The U.K. is trying out a vaccine tag-team approach of mixing formulae to off-set this impairment.

FOURTH: Brasil (population of 213,445,417); 9.4 million cases (14.6 million restated for U.S. population); 228,817 deaths (356,629 restated for U.S. population); 2.4% mortality run rate; 1.2% vaccination rate; 32.9% positivity (limited testing); unknown I.C.U. availability; Manaus, as the epicenter, a city of two million people in the heart of the Amazon region.

This newest of the known threats is likely to prove more lethal for five reasons. First is an accelerating contagion overwhelming the regional health-care system for the northern ‘Amazon’ population of 24 million people by breaking down the herd immunity nearly or recently attained at the renewed epicenter. Second the virus can ‘ally’ with, or evade the antibodies from a previous infection of, the older COVID-19 coronavirus to attack a weaker immune system with enhanced toxicity. 

Third, the variant appears to be more debilitating for younger people than other strains. Much of the current epidemic in Brazil lies at the feet of now-unpopular Presidente Bolsonaro, a populist, who took a defiant disregard of the consequences of an epidemic from day-1. Fourth, the grinding inequality pervasive in Brazil is facilitating an epidemic of unaddressed lethality despite economic intervention early on. 

Lastly, in addition to a failed vaccination response, Brazil is administering the less than reliable products of China and Russia as well as an untested British formula. Though only around for a month and, like the U.K. variant (i.e., originating in a rural setting), the Brazilian variant has found its way, at least, to Minnesota and California.

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México (population of 130,207,371); 1.9 million cases (4.8 million cases restated for U.S. population); 161,661 deaths (412,967 restated for U.S. population; would rank 21st in common-sized deaths, or below average); 8.6% mortality run rate; 0.5% vaccination rate; estimated 39.5% positivity rate; data on I.C.U. capacity unavailable. 

The Brazilian variant coming through southern border with Guatemala and the British strain migrating through the U.S. border, especially California, make México uniquely vulnerable in an atmosphere of willful indifference by el presidente Andrés Manuel López Obrador, despite contracting the virus himself, The attitude of 'A.M.L.O.' conjures up the image of Presidente Jair Messias Bolsonaro in Brasil. In response to a 'lazy faire' policy response, N.G.O. teams are trying to aid the poorest people in D.F.

Tunisie (population of 11,811,335); 213,526 cases (6.0 million cases restated for U.S. population); 7,026 deaths (198,020 restated for U.S. population; would rank 43rd, or the upper-most quintile; ¡very good!); 3.3% mortality run rate; 2.0% positivity rate; < 10% estimated I.C.U. availability; 0-0.5% vaccination rate. 

Little Tunisia may be short on resources but she is long on resilience. Though on the same continent as South Africa, home of one of the more lethal new and transmissible mutations, Tunisia is a European country in trade, by culture, and at heart. Thus, the likely variant to sweep through the country, if any, will be the milder British strain. One concern remains paramount: a national hesitance toward taking vaccines.

METHODOLOGY 
Since this data sweep serves as a information supplement without very little research, this week provides an opportunity to clean up the presentation through the following changes. For informational purposes, this text will follow the second table on thirty-eight states and five territories in subsequent weeks. For comprehensive explanations on methodology and purpose, please revert to Appendix I. 

1st, please remember that percentages for 'population tested' implicitly assumes that anyone taking a COVID test does so only one time. Many people are getting multiple tests. For example, for various reasons, I have had five tests. That would count as five people taking tests for the datum calculated for Maryland. My S.W.A.G. (scientifically wild-assed guess) is that a more accurate level of people actually tested is half, or less, of the percentage cited in the ‘38+ table’ above.

2nd, the two averages of weekly growth rates for the ten bellwether states are clarified in the Appendix. Essentially, the geometric or compound average growth rate is a smoothed average that allows for growth-on-growth increases (i.e., similar to compounding interest). The time weighted weekly averages are a trend-weighted average of each week's particular growth rates. While the compound rate is theoretically more defensible, comparing the two averages gives one a sense of more recent trends and volatilities.

3rd, in the '38+' table (of thirty-eight states and five territories), the risk classifications  -- of very low; low; moderate; high; and, very high -- remain the same. The parameters, however, are loosened to reflect nine months of experience. The new parameters center upon the first year base case fatality level of 335,301 souls that I forecast eight months ago, together with projections of November 2020 from the University of Washington of 470,974 deaths. On 04dec20, the old and new parameters are applied to facilitate  transition.

4th, changes in how positivity rates are presented in the '38+' table above now align the data with the original intention behind presenting them. The intent here is to show whether positivity is trending up or down and to what degree. The parameters are loosened to match the practical reporting constraints and data lags facing most states. 

States with changed positivity rates of less than 10% up (i.e., worsening) or down (i.e., improving) are deemed unchanged and the information unformatted (i.e., appearing in plain black font). The formatting differentiates deteriorations from improvements in the color of the font between 10-20%. Bold fonts indicate material deteriorations or improvements of more than 20%. 

Keep in mind that these percentage changes are based on percentages; percentages of percentages can attenuate the utility of data.

5th, a refresher on the assessment of a state’s testing capacity, again on the 38+ table. The data pivot off of the tests per million people expressed as a percentage. The symbology uses hand gestures to assessment the degree of testing capability and commitment relative to the national average for the week under review. Colors indicate whether testing is declining (red font) or improving (blue font) when a states results place its commitment to a new category of, specifically:

• 👎👎 meaning a state's testing level materially below the concurrent national benchmark (i.e., > 15 points below);
• 👎 meaning a state's testing is noticeably below the weekly national average (i.e., 5-15 points below);
• 👈 meaning a state's testing activity is slightly lower than average (i.e., < 5 points below);
• 👉👈 meaning a state's testing level is basically equal to that of the nation;
• 👉 meaning a state's testing level is < 5 points above the benchmark;
• 👍 meaning a state's testing activity is 10-15 points above the weekly national level; and,
• 👍👍 meaning a state's testing commitment is > 15 points above the concurrent average.