Monday, February 1, 2021

Daily Pandemic Diary for February 2021

What aerosol leakage looks like.
by Brian T. Lynch, MSW

Welcome to the Daily Pandemic Diary for FEBRUARY 2021. The purpose here is to provide a global context to how our nation is coping with the pandemic and to supply information about COVID-19 that might be helpful to the readers. This blog continues the daily collection of data begun in the Daily Update blog and the monthly Daily Pandemic Diaries linked below. The raw data comes from the independent, international non-profit data reporting organization called Worldometer.info. Test Positivity data comes from Johns Hopkins University. Data in red are calculated values. The hyperlinks below take you to prior months.

APRIL - JULY, 2020  

AUGUST 2020 
SEPTEMBER 2020  
OCTOBER 2020  
NOVEMBER 2020  
DECEMBER 2020 
JANUARY 2021

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NATIONAL HEALTH EMERGENCY
DAY 330 - FEBRUARY 28, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, Louisiana, Kansas, Connecticut,  Rhode Island, Alaska, Wyoming, and Missouri.
An additional 3 states did not report any COVID deaths from yesterday: Vermont, Delaware, Washington, and Pennslyvania. An estimate of the undercount of reported COVID-related death is about 126 individuals. 
COMMENTS
The statistical undercount this weekend is significant. The apparent declines in case counts and deaths are unreliable. 
Being the end of the month, a review of progress is in order. Of special note is that the U.S. test positivity rate has fallen below 5%, which is the World Health Organizations' benchmark for easing COVID restrictions. Almost all of the rest of the news is very good as well. Our global share of both COVID cases and COVID deaths declined slightly, although we are still the global outliers. And there are these bits of mostly good news: 
  • Our 7-day average of daily new infections declined by 115% in February
  • Our 7-day average of daily new deaths declined by 64%
  • Daily vaccinations numbers began and ended the month roughly equal but peaked during the month
  • COVID testing remained low and the U.S. dropped in rank from 19th to 21st in tests per million
  • We reached the half-million mark in COVID deaths this month. We stand at almost 525,000 deaths
  • There was a 9.5% decline in active COVID-19 case in February
  • The number of people who have recovered from COVID-19 rose nearly 20% in February
  • U.S. test positivity declined from 8.24% to 4.58%

NATIONAL HEALTH EMERGENCY
DAY 329 - FEBRUARY 27, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska and Missouri.
An additional 3 states did not report any COVID deaths from yesterday: Wyoming, Alaska, and Maine. An estimate of the undercount of reported COVID-related death is about 58 individuals. 

COMMENTS
The 7-day average of new infections and deaths both declined slightly today as did the test positivity rate. With the weekend upon us and our higher under-reporting that comes with it, the significance of these data is unknowable at this time.  
As I have mentioned recently, we are in a race against the new variants of the virus. It may be worthwhile to introduce ourselves to them to help make more sense of media stories to follow over the next month.  The three main variants under investigation, and active in the U.S., are called variant B.1.1.7 originating in the UK, variant B.1.351 originating in South Africa, and variant P.1 originating in Brazil. A good summary of these three variants was published on February 7th in Global Health, and a screenshot of the executive summary appears below. 
The CDC has a good, more detailed summary of these three variants as well. These are the variants that appear to be most widespread in the United States as well as their countries of origin. Are there other new variants in the U.S.? 

Yes, there are. There is a New York City variant called B.1.526 on which vaccines may be less effective. There are also two new variant strains in California that appear to make the virus more transmissible. They are called B.1.427 and B.1.1429. Together they now make up about half of all COVID-19 cases in 44 counties in California. You can read more about these variants in an article in CIDRAP out of Minnesota University. And, of course, as long as the virus is running rampant around the globe, new variants will continue to emerge. We need to bring U.S. and global infection rates down as quickly as possible. 

Virtually all of the emerging variants have one thing in common - they all easily spread from one person's breath to another. The good news is that they are therefore controllable using the same good quality masks, social distancing protocols, and social contact limitations that most of us are already practicing. So, while we are waiting to get more than 60% of the global population vaccinated, we can limit the impact of these new variants and buy the time we need for the current vaccines to work. 






NATIONAL HEALTH EMERGENCY
DAY 328 - FEBRUARY 26, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, Missouri, and Kansas.

An additional 3 states did not report any COVID deaths from yesterday: Wyoming, Alaska, and Hawaii.

COMMENTS
There are only nominal changes in the numbers between yesterday's table and today's. Vaccinations are down again slightly. It was suggested on MSNBC yesterday that the current decline is weather-related, and the slump does align with the situation in Texas. But does it account for the slight up-tic in new infections? The answer is no.

The slow and steady decline in the number of new infections in Texas has continued apace and did start trending up again since the weather crisis, as did the trends in all the Gulf states but for Florida. Contrasting this with average mask usage would be useful. Mask usage is determined by polling questionnaires, which in turn ask slightly different questions. Therefore no polling data is consistent with other polls. For example, the percentage of people who say they usually wear a mask in public is much higher than those who say they always wear a mask in public. The table I made here is of the percentage of mask-wearing in each of the 50 states and D.C. It's divided into the states that are above average nationally, and those that are at or below average. In information is from Worldometer.info, however, they obtain it. what it does show is that we have a long way to go to achieve even 90% mask usage nationally. But also, most of the states that are reluctant to submit their COVID statistics to the government are also the most reluctant to wear masks. 

This is all the more relevant for today as the NY Times just published an article amplifying what I have recently emphasized here; That we are in a race against the new COVID variants. A fourth peak is very likely unless we redouble our efforts to wear masks, socially distance, and take all the other precautions. Here is the Times article: 







NATIONAL HEALTH EMERGENCY
DAY 327 - FEBRUARY 25, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska.

An additional 3 states did not report any COVID deaths from yesterday: Wyoming, Alaska, and Idaho. Together an estimated 24 deaths were underreported.

COMMENTS
According to CDC data, vaccine administration peaked on February 12th with nearly 2.3 million injections given. It has declined since then. This is a 24% decline in the 7-day average over the past 12 days. What's behind this decline and why haven't we read more about it in the press? Is it a failure of vaccine providers to accurately report data to the CDC? (I suspect all the private pharmacies and physicians may not be reporting.) Is there a shortage of vaccines? Is it a logistical issue or are people declining to get vaccinated? Whatever the reason, it is surely a temporary regression, yet we can ill-afford any slack at a time when the more infectious variants are gaining ground at a rate of about 10% per week. 

Herein are two graphs depicting our vaccination status in the United States. The first is the CDC daily doses administered graph and the second is a national picture of the percentages of vaccinations given in the States. The darker the color the higher percentage of people getting vaccinated. 


https://wtop.com/coronavirus/2021/02/latest-vaccination-numbers-in-dc-maryland-and-virginia/  








                  

NATIONAL HEALTH EMERGENCY
DAY 326 - FEBRUARY 24, 2021


UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska and Tennessee.
An additional 3 states did not report any COVID deaths from yesterday: Hawaii, Alaska, and South Dakota. Together an estimated 16 deaths were underreported.
COMMENTS
A bump in the road? The 7-day average for both new infections and deaths rose again from yesterday's numbers. The test positivity rate remains at about 5.2%, still above the World Health Organization's guideline for opening up the economy. The 7-day average for vaccinations given also declined over the past two days while the United States slipped to 22nd in the world for the number of COVID tests given per million population. So, testing is down, vaccinations are down, infections and deaths are up. It's too soon to say if this is a blip or a slump. Watch this space, as Rachael Maddow says. 
Three days ago I mentioned the dire situation in Ireland. Since then, the Irish Prime Minister, Michael Martin, gave an address to the people of Ireland that is worth hearing. It is in such contrast to the messaging we have been subjected to over the past year. It's good to have a broader international perspective. 









NATIONAL HEALTH EMERGENCY
DAY 325 - FEBRUARY 23, 2021

UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska.
The following 12 states did not report any COVID deaths from yesterday: North Dakota, South Dakota, Montana, Hawaii, Maine, D.C., Mississippi, New Hampshire, Oregon, Idaho, Wyoming, Wisconsin, and Alabama. Together an estimated 208 deaths were underreported.



COMMENTS
It seems we are at another inflection point in the daily data. With significant underreporting yet to be added back into the daily data this week, we reversed direction in the daily averages for new cases and new deaths, both showing slight upward movements. The U.S. test positivity rate is essentially stable at 5.2% in the past three days with COVID testing rates averaging well below 2,000 per day. The 7-day average for vaccinations also declined slightly. This may all be a bump in the road. One day's numbers do not a trend make. 
We marked the occasion of surpassing half a million deaths yesterday in media accounts and, more importantly, by our President's heartfelt remarks and a memorial service at the White House. You can watch it here. The New York Times put this number in perspective by creating a full-page bar graph with 500,000 dots on a timeline, each dot representing someone who died. It was very effective. Prior to September 22, 2020 we averaged 50,000 deaths every 53 days. Since that day we reached 50,000 deaths in 26 days, then 19 days, 17 days 15 day, and now 18 days. Despite the recent climb-down from our January peak, we are still nowhere near the lower level of infections we experienced last summer. Yet, our pandemic fatigue and political pressures are causing state governors to open up public spaces well before it is justified by our numbers. Just look again at the New York Times graph. Those very dark bars at the bottom are telling us we are at a deadly phase in the pandemic and we should not be relaxing restriction right now. 


NATIONAL HEALTH EMERGENCY
DAY 324 - FEBRUARY 22, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, Kansas, Missouri, Michigan, Idaho, Connecticut, Rhode Island, and Alaska. 
The following states did not report any COVID deaths from yesterday: Wyoming, Washington, Maine, Mississippi, Wisconsin, and Iowa. Together an estimated 200 deaths were underreported.
COMMENTS
If you add in the undercount of deaths from yesterday, the U.S. share of global deaths would be closer to 22%. This is still over the 20.6% share of total deaths globally, so the disparity is still growing. We should know towards the end of the week if the downward trends in infections and deaths are still declining. The test positivity rate hasn't been updated yet. I will update my table when that comes in. 

The good news is that research to update and improve the current vaccines is starting to accelerate and there are promising new avenues being explored to extend both the durability of vaccinations and better protect us from the variants. This may lead to a second-generation of vaccines following the clinical trials that would be necessary beforehand. 

Finally, allow me to point you to a very good article in the Atlantic today titled, "We're Just Rediscovering a 19th-Century Pandemic Strategy". We forget that our modern germ theory was preceded by the "miasma" theory of illness. People believed that "bad air" caused diseases. It led to a novel treatment - Fresh Air. Houses, hospitals, and other buildings were built with elaborate detail to exchanging bad air in confined spaces with fresh air to prevent illnesses. We have stopped thinking in these terms, so the idea that our breath aerosols might build up indoors and make us sick is alien to us. I remember a social media discussion thread I had with the owner of a gym early on in the pandemic. She was looking to reopen after wiping down all the equipment, etc., in her facility. I tried to explain the steps she should consider taking to prevent aerosol build-up. Her response was, "If you are suggesting I also have to scrub the air I may never be able to reopen."  But, that is exactly what has to happen in gyms, restaurants, bars, schools, and businesses in the absence of vaccination-induced herd immunity. So, good, tightly fitted N95 masks, humidified air, fresh air exchanges, and HEPA filtration are the tools against biotoxic "bad air."



NATIONAL HEALTH EMERGENCY
DAY 323 - FEBRUARY 21, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, Kansas, Missouri, Louisiana, Connecticut, Rhode Island, Alaska, and Wyoming. 
The following states did not report any COVID deaths from yesterday: Idaho, Iowa, Hawaii, and Washington. Together an estimated 132 deaths were underreported. 
COMMENTS
Chris Hayes on MSNBC expressed cautious optimism yesterday on his show that we may be near the tipping point in the fight against the virus as the very positive numbers are falling so quickly. Let's hope this is true. Part of the cause for optimism is the very good news that people who are fully vaccinated do not appear to be spreading any virus themselves, and that the degree of protection is very strong. Part of that optimism also rests on estimates that far more people have been exposed to the SARS-CoV-2 virus than reported, thus more people have natural anti-bodies and herd immunity is closer than we think. Let's hope this proves true, but don't unmask yourselves too soon. 
Keep in mind that while all this progress seems to be happening, the new and more infectious variant has been gaining ground at a rate of about 10% per week. We are in a race against its encroachment and have taken the lead, but the race isn't over. If our weekend underreporting was not such a big problem we might already know whether or not our progress is still slowing the community spread. We will know for sure by the end of the week when all of the backlogs are added up. 
Ireland presents a cautionary tale. My relatives there told me this past week that the new variant makes up over 90% of the new cases and they are in lockdown, unable to travel more than six kilometers from their home. A friend of theirs died of it a few weeks ago and six of the seven people who attended his small funeral caught the virus. So, not to be a downer, but don't let up on the precautions you need to stay safe and to be safe around those in contact with you. Masks and social distancing work - Well-fitting masks and fewer social contacts work better. We are almost at the promised land. Stay safe so that we arrive there together. 


NATIONAL HEALTH EMERGENCY
DAY 322 - FEBRUARY 20, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, Kansas, and Missouri. 
The following states did not report any COVID deaths from yesterday: Wyoming and Alaska, Vermont, North Dakota, Idaho, and Oregon.
COMMENTS
The drop in new infections and deaths continues. The positivity rate went up a fraction ending weeks of steady decline. COVID testing rates remain sluggish. the 7-day average rate of vaccinations just 2.5% from yesterday's report, which is double what the daily rise has been. 
On January 21st the Biden administration began outlining the beginnings of an actual national pandemic policy and that effort took another big step forward yesterday with the release of the text of the 500+ page rescue plan entitled, ‘‘American Rescue Plan Act of 2021." A link is provided herein if you wish to peruse through it. The vote on it is expected next week. I prepared the following summary of the rescue plan from a CNN article:  


NATIONAL HEALTH EMERGENCY
DAY 321 - FEBRUARY 19, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska.
The following states did not report any COVID deaths from yesterday: Wyoming and Alaska.
COMMENTS
The U.S. is still by far the top hotspot in the world, and the status of cases is still higher than in the prior peak. Globally, our new daily infections are declining faster than in the rest of the world, but our COVID deaths are declining slower. U.S. test positivity continues to decline while the 7-day average of new vaccines inches upwards by about 1.1% a day (or 7.6%/week). This isn't yet an acceptable growth rate in vaccinations. The New York Times has a story today that reports: "Millions of doses of coronavirus vaccine are still sitting in freezers, allocated in excess to nursing homes or stockpiled for later use. Now states are claiming them." There are also media reports today that France is giving up some of its doses to send to poorer nations in Africa, and that other countries are calling for more vaccines to be sent to poor nations. This is an enlightened view. None of us are safe until all of us are safe and the pandemic is well under control everywhere. Of course, the U.S. is the world's largest incubator of the virus, so the rest of the world needs us to focus on healing ourselves first. 







NATIONAL HEALTH EMERGENCY
DAY 320 - FEBRUARY 18, 2021
UNDERCOUNT
The following states did not report any COVID statistics from yesterday: Nebraska, of course.
The following states did not report any COVID deaths from yesterday: Vermont, North Dakota, South Dakota, and Wyoming.
COMMENTS
New infections continue to decline. Today's 7-day average was last this low on Oct. 29th but still higher than the second peak on July 25th. The number of new deaths is declining more slowly. The 7-day average was last this low on Dec. 4th, but it is lower than the initial peak of 2,262 back on April 21st. Test positivity is also still in decline (see more on this subject on Day 318). 

It is still too soon to say for sure that the decline in cases is the result of vaccines. A more recent study on mask usage suggests the trend in wearing masks is growing, but mask use is still inconsistent. The study identifies who is more, or less likely to wear a mask, and is a good read. I was unable to find reliable information on shifts in the quality of masks being worn or sales figures for N95 masks in the U.S. but haven't found any yet. 


NATIONAL HEALTH EMERGENCY
DAY 319 - FEBRUARY 17, 2021
UNDERCOUNT
The following states did not report their COVID statistics from yesterday: Nebraska and Louisiana. Hawaii, North Dakota, and South Dakota reported no deaths. 

COMMENTS
No comments today. 





NATIONAL HEALTH EMERGENCY

DAY 318 - FEBRUARY 16, 2021
UNDERCOUNT
The following states did not report their COVID statistics from yesterday: Nebraska, Idaho, Alaska, and Wyoming. 
The following states reported new cases but not new deaths: Hawaii, North Dakota, South Dakota, Maine, Arizona, Washington, Oregon, Delaware, and Missouri. The death toll from yesterday is undercounted by at least 250 people. 

COMMENTS
Global pandemic numbers are in sharp decline from the number of new cases that peaked on January 8th and the peak new COVID deaths two weeks later. Community spread and COVID deaths are declining in the U.S. as well, perhaps slightly faster than they are globally. It's difficult to tell for sure with our undercounts, and not just the significant non-report delays mentioned above.  

HIDDEN SOURCE OF UNDERCOUNTS
The U.S. test positivity rate is within 1/2 point of meeting the W.H.O. target of under 5%. That's counted as a good thing, but it seems a bit odd. Daily COVID test numbers are also declining, perhaps more sharply than they are globally. The decline in both test being administered and test positivity rates can mean that doctor's are diagnosing more patients based on symptoms and antigen screening test without ordering the definitive PCR test for confirmations. Diagnosing cases by symptom presentation and a positive screening test represents a reporting category called a "Probable" case. Because almost half the States don't report "probable" COVID-19 cases as required by the CDC reporting protocols, this scenario would reduce both test positivity results and suppress reported numbers of new cases. 

Note that probable infections are a standard reporting practice for all other infectious diseases. This category is adds to the total count of flu cases, to give one example. Doctors diagnose and treat you for the flu based on your symptoms and maybe a throat swab or similar screening test without ordering expensive labs to confirm the diagnosis. That flu diagnosis is counted as a flu case in our national statistics. This is true for most other infectious diseases. Confirmatory lab tests are not always required. And what is true for living patients is also true for the dead. Medical examiners who can readily determine a SARS-CoV-2 related death might save their county or parish money by not ordering an expensive lab test to confirm it. But these autopsy reports are also labeled as probable COVID-19 deaths and therefore not counted as COVID-19 deaths in many states. This is one of several ways that SARS-CoV-2 is still being grossly under-reported in the United States.



NATIONAL HEALTH EMERGENCY
DAY 317 - FEBRUARY 15, 2021

UNDERCOUNT
The following states did not report their COVID statistics from yesterday: Nebraska, Missouri, Michigan, Kansas, Connecticut, Rhode Island, Idaho, Alaska. The following states had no deaths or reported no deaths from yesterday: Wyoming, North Dakota, Vermont, Montana, D.C., Oregon, Iowa, and Alabama. The estimated number of missing death reports today is 198 deaths. 
COMMENTS
The statistical counts today are significantly undercounted due to the number of states not reporting over the weekend. Sixteen states did not report Sunday's statistics fully over the weekends, which makes it more difficult to spot early upward trends should they begin.  From CNN: 

What you need to know

The US has administered nearly 53 million vaccine doses, and more states are loosening Covid-19 restrictions – but experts warn the country is not yet in the clear.
More than 600,000 Americans will have died of the virus by June 1, according to the latest prediction by a prominent forecast model.
More evidence suggests the UK variant is linked to more severe disease researchers say.
Pfizer-BioNTech vaccine sharply reduces symptomatic Covid-19 in the real world, according to an Israeli study.
Addendum: I just ran across these pictures of surgical masks as they leak aerosols, depicted here by smoke. This is why we double mask (which helps plug the leaks) or wear N95 masks. Scary, right? 



















NATIONAL HEALTH EMERGENCY
DAY 316 - FEBRUARY 14, 2021
UNDERCOUNT
The following states did not report their COVID statistics from yesterday: Nebraska, Missouri, Louisiana, Kansas, Connecticut, Rhode Island, Alaska, and Wyoming. The following states had no deaths or reported no deaths from yesterday: Hawaii, North Dakota, Vermont, and Washington. The estimated number of missing death reports today is 145 deaths. 

COMMENTS
No Comments today







NATIONAL HEALTH EMERGENCY
DAY 315 - FEBRUARY 13, 2021
UNDERCOUNT
Nebraska and Missouri statistics for yesterday are missing. Wyoming either had no deaths or didn't report any. The estimated undercount of deaths yesterday is 66 people. 

COMMENTS
Hooray for us! After 315 days of our National Health Emergency, we finally reached the point where the total number of COVID tests given to date equals the U.S. population. As recently as September experts were saying we needed about 6.4 million tests per day to safely open schools and businesses. At that rate, we should have conducted over 2 billion COVID tests by now. The number of tests needed is based on the rate of community spread and not just the population size. Media accounts of testing never understood this, so we can be forgiven if we thought we were doing well on this measure. Actually, it is one of our biggest failings, and for reasons yet unknown, testing rates are continuing to decline when they should still be ramping up. I don't recall a day when we ever reached even half the daily recommended number of tests. When the pandemic is behind us, and we look back to see how we can do better in the future, the area of testing and test availability needs to be a major focus. 

On a side note: I notice that in calculating percentages based on U.S. population size during this pandemic diary the denominator, the population size, was larger every day. Our nation is still growing in population despite the excess pandemic deaths. From a macro-perspectives, population overgrowth is the world's most serious underlying conditions. It is the driver behind every environmental stress factor, including global warming. It impacts every economic stress factor and nearly every geopolitical conundrum as well from migration movements, global refugee problems, and political conflicts. It even plays a role in how frequently, and how badly we are affected by pandemics. We have one of the lower population growth rates in the world, yet in the past 211 days, our national population rose by 1.23 million people. That means more mouths to feed, more housing to build, more traffic, more job competition and more plastic and garbage going into landfills. 

NATIONAL HEALTH EMERGENCY

DAY 314 - FEBRUARY 12, 2021
UNDERCOUNT
There are no statistical reports today from Nebraska, Missouri, or Kansas and not death or death reports from Alaska, Wyoming, Maine, Montana, or Idaho.

COMMENTS
The Biden Administration has obtained a contract to purchase 200 million doses of vaccine that will be manufactured and delivered in full by July or sooner. This is in addition to any vaccines that might be approved in the meantime. If the inoculation logistics can be worked out, this would mean that the vast majority of us will have immunity by late summer. 

This time period would likely be long enough for the pharmaceutical companies to develop a booster shot if one is required. It would also mean that America's children can safely start a new school year, businesses can fully reopen, and people can return to work safely. 

But we must remember, this is a global pandemic. The U.S. alone getting control of the outbreak here reduces by about 25% the size of the global pandemic. However, if the rest of the world doesn't get enough vaccine the emergence of new variations of the virus will continue apace threatening progress everywhere. So, as we begin to pull ourselves out of this pandemic dumpster, let's not forget to look around and see who else we can help up. 








NATIONAL HEALTH EMERGENCY
DAY 313 - FEBRUARY 11, 2021
UNDERCOUNT
No reports from Nebraska. Wyoming and Alaska had no deaths or reported none.

COMMENTS
The United States remains the #1 hotspot on planet Earth. That said, not only is the number of new infections in the United States continuing to decline, but our infection rate is also starting to decline relative to the rest of the world, from a high of 31.8% of global new cases on February 2nd. As long as our daily percentages stay below our total percentages we are heading in the right direction. New deaths are declining at a slower rate. They are a lagging indicator so, a similar decline in daily new deaths should follow. U.S. test positivity rates are continuing to do decline as well, but the number of COVID tests is also declining, and it shouldn't be. We just slipped into a global 21st ranking on tests given per million population. The milestone here is the point where we have given the equivalent of one test per person since the pandemic started. We should be closing in on three-times that number at least. The other note for today is a change in recording total vaccines administered. It is apparent that the CDC is collecting vaccine data from the date of administration and continuously updates daily totals as data comes in. They, therefore, use a 5-day lag time before considering the 7-day averages substantially accurate. Starting today that number will be what is reported here. For anyone who wishes to see the CDC vaccine Trends, you may follow the hyperlink provided here.  Below is the CDC graphic depicting the daily numbers of new cases. Note the sharp decline and congratulate yourselves. The progress is mostly due to those of us who are taking greater precautions. 






















NATIONAL HEALTH EMERGENCY

DAY 312 - FEBRUARY 10, 2021

UNDERCOUNT
Nebraska no longer provides accessible data. North Dakota, Hawaii, South Dakota, and Kansas provided no death statistics or had no deaths yesterday. The estimate of unreported deaths is 84 people. 
COMMENTS
While 84 is my estimate of the undercount deaths from yesterday, based solely on states not recording their statistics. According to a recent study, the actual undercount of deaths has been estimated at 35% nationally for all other causes. Likewise, a more accurate estimate of the number of infections is much higher as well, but still far less than needed for natural herd immunity. Regarding today's statistics, our PCR testing rates continue to decline, as do our test positivity rates (which is a good thing). By way of a correction to the table above, our global rank in testing as a nation slipped to 20th about a week ago. Our global status as a pandemic response failure is unchanged. We still have about a quarter of the new cases and daily deaths with just 4% of the global population, but at least our numbers are still moving in the right direction. Also, I added the 7-day average for daily vaccinations to the table but the reliability and consistency of the data seem in question. I built in a two-day delay in reporting the average to give the CDC time to update their counts. 







NATIONAL HEALTH EMERGENCY
DAY 311 - FEBRUARY 9, 2021
UNDERCOUNT
Nebraska's daily COVID data is no longer accessible. Alaska, Delaware, Wyoming, Vermont, Montana, South Dakota, North Dakota, and Hawaii either had no deaths or did not provide data on new deaths from yesterday. Based on active cases, there were about 180 unreported deaths from yesterday or 19.7% of the global death toll. 

COMMENTS
As of this morning, 22.8 million people have their first vaccination shot and 9.5 million have had their second dose. That means that 2.9% of the population are at or near full immunity while another 6.8% have partial vaccination immunity. This is a good start, but these numbers do not account for the continuing decline in community spread, COVID deaths, or declining positivity rates. What does account for the decline in the spread of the virus is greater compliance with mask use and social distancing. A recent poll found that over 80% of us are wearing masks most of the time in public. That's up from 72% about a month ago. Also, more people are wearing better grade masks as supplies have increased and more people are wearing them properly as public education on mask use has increased. These changes can't come too soon. Not only are we facing an up-tic in cases from the Super Bowl superspreader events over the weekend, but more ominously, CDC is projecting that the new, more contagious variant of the virus will become the dominant strain by sometime next month. 

There is a good NPR story from two days ago regarding recent mask research. John Volckens, professor of mechanical engineering and the director of the Center for Energy Development and Health at Colorado State University discusses his work on developing conformity standards for medical masks. He believes we should all be transitioning to N95 masks as they become more available because they allow for much less leakage than even KN95 masks. As the new variants continue to gain a foothold, we need to adapt better habits and PPE to fight community spread and keep everyone safe.











NATIONAL HEALTH EMERGENCY
DAY 310 - FEBRUARY 8, 2021
UNDERCOUNT
No statistics, new cases, or deaths, reported here from Nebraska, Michigan, Missouri, Kansas, Connecticut, Idaho, Rhode Island, or Alaska. No deaths or reports of deaths from Wyoming, Iowa, or North Dakota. The estimate of the undercount of those who died yesterday is 1,700 additional people. 

COMMENTS
No comments. Just a really good NPR  story explaining mask research and proper use.   

https://www.wnyc.org/story/face-mask-best-practices/ 


NATIONAL HEALTH EMERGENCY
DAY 309 - FEBRUARY 7, 2021
UNDERCOUNT
No data from Nebraska (of course) but also no new cases or deaths were reported by Louisiana, Missouri, Kansas, Connecticut, Rhode Island, or Alaska. There is also no deaths or death statistics from Wyoming or Hawaii. The estimated number of deaths not reported today is 1,500 people suggesting that the actual death toll from yesterday is well over 4,000. 

COMMENT
There has been a steady and steep decline in new COVID cases since the peak on January 8th. The 7-day average of new cases has not been this low since November 7th, 2020.  Deaths have also declined since the peak on January 12th, but not as steeply. The 7-day average number of daily deaths is about where it was on January 9th. The U.S. test positivity rate has continued to steadily decline for weeks now, but so has the number of PCR tests given every day. The reason for this decline in testing is a bit of a mystery. What isn't a mystery is the fact that the total number of tests given in the past year is still 100,000 less than our total population. This is an anemic rate of testing. 

Against the backdrop of mostly good news are two less positive trends. According to media reports, the rate of variant transmissions is doubling every ten days. Also, the rate of vaccine administration numbers had been steadily declining since January 29th, from a 7-day daily average peak of 1,384,775 on that day to an average daily number of 807,098 yesterday. So, the race between declining and growing community spread is tightening. Starting tomorrow the 7-day average of vaccines administered will be included on the daily table above. 







NATIONAL HEALTH EMERGENCY
DAY 308 - FEBRUARY 6, 2021
UNDERCOUNT
Missouri joins Nebraska today in not publishing new cases or COVID deaths. Additionally, Hawaii, Alaska, Wyoming, Vermont, and Montana have not reported any deaths. Together, today's death count is missing about 100 people who died yesterday.

COMMENTS A virus is an otherwise inanimate strand of DNA that replicates under the right conditions. It shares none of the other characteristics of a life-form. Yet the first life it took in this country a year ago today presents a great irony. 
Patricia Dowd of California died of a heart attack a year ago after contracting the virus about a week earlier. She was well under 65 years old. She had no underlying health conditions. She was not obese. She exercised regularly and kept herself fit. She had only moderate flu-like symptoms. She didn’t see a doctor. She was never hospitalized. She died at home of a heart attack. She didn’t know she was dying from COVID-19 and no one else would have ever known if her cause of death hadn’t raised curiosity and concern in a dedicated coroner in Santa Clara County.

The completely atypical presentations in Ms. Dowd’s case highlights many fault lines in a year-long debate that defines our dueling perceptions about the pandemic. The Jekyll and Hyde way that the virus can attack the human body has brought out the Jekyll and Hyde’s in our body politic.

One year since the first U.S. American died of COVID-19 and there is no definitive count of those who have fallen ill or died of the virus since then. It seems that there is no national consensus on anything. Different sources will offer different sets of data. Every aspect of the pandemic in this country, tracking, tracing, treating, preventing its spread, counting the dead, all of it has fallen into the vortex of a social upheaval we continue to mislabel as politics. Even our great scientific institutions sustained injuries in the media stoked melee unfolding around us. This pandemic arrived at a time in America when every fact generates an anti-fact that cannot be merged without annihilation. Growing uncertainty is the product, if not the purpose, of the disinformation plague that rendered our great nation incapable of mustering a great response.

On a global scale, this country's response to the pandemic is the most spectacular failure in history. With just over 4% of the earth’s human population, we had 26% of all the infections and over 20% of all the deaths. The difference between those proportions represents the suffering and death that could have, and should have been avoided.

By any source, the number of people who have fallen ill or died in the U.S. is staggering. The Worldometer.info source used here caps the year's death toll at 470,705 U.S. Americans. For context, that is more than all of the U.S. combat deaths since General Lee surrendered at the Appomattox Court House in 1865. The number of PCR confirmed cases in this country over the past year is approximately 27.4 million people, about 8% of our population. The fact that a greater percentage of us haven’t gotten ill or died is a testament to the great majority of us who wear our masks, wash our hands and keep our social distance despite counter-cultural pressures opposing these measures.

We should be united this day in memorializing our dead and acknowledging the grief of millions who lost someone they loved this past year, but we are not yet capable of accepting that shared perspective. Until we recognize and disarm the malevolent forces working to divide this great nation we cannot begin to mourn our dead.








NATIONAL HEALTH EMERGENCY
DAY 307 - FEBRUARY 5, 2021
UNDERCOUNT
Nebraska statistics are not recorded in the numbers and a look at their Dashboard reveals they have not updated their new case number on their bar graph or their death statistics in the past three days. All other states and D.C. are reporting new case numbers. North Dakota, Kansas, Alaska, Wyoming, and Idaho either had no deaths or did not record their death statistics from yesterday. 

COMMENTS
A year ago today Patricia Dowd, age 57, was working from home at her mangers job with LAM Research, a semiconductor company in Santa Claria, California. She was recovering from flu symptoms she developed less than a week before but wasn't quite feeling up to returning to work. Patricia, or Trish to her friends, called her brother Rick three days earlier to say she wasn't feeling well and wouldn't be attending a family gathering that weekend. The next day, a Thursday, the 6th of February, at about 8:00 am, she called work to check in with her colleagues. Two hours later Trish died of an apparent heart attack. She didn't have any known heart condition. She had been an athlete at St. Francis High School and kept herself fit throughout her adult life. She was healthy, she exercised regularly, watched what she ate, and didn't smoke. She liked to read and was a devoted member of a book club. She liked to travel and did a lot of international travel for her job, but hadn't traveled anywhere in months. She was an energetic, caring, generous person to her friends, a loving wife to her husband Dean, and a good mother to her daughter Kaila. 

What caused this healthy woman to suddenly have a heart attack was a mystery to the Santa Clara County coroner who performed her autopsy. The coroner had a suspicion her death had something to do with the novel coronavirus that was recently in the news, so a sample of her tissues was sent off to the CDC for further tests. Eventually, the test results came back showing that Trish had contracted SARS-CoV-2 making Patricia Dowd the first person in the U.S.A. to die of COVID-19. 

Since Trish's death, another 93,500 thousand residents of Santa Clara Country have come down with COVID-19, including her sister, Letica Macias, who works at the Valley Medical Center. Over 1,080 have died in Santa Clara in the year that followed. Nationally over 27,274,000 American's in this country have caught the virus since Trish's death and over 466,000 have died. Ten-o'clock tomorrow marks the one-year anniversary of this first pandemic casualty and we should mark this solemn occasion with a national moment of silence for all those who lost their lives in the pandemic over the past year.













NATIONAL HEALTH EMERGENCY
DAY 306 - FEBRUARY 4, 2021

UNDERCOUNT
Nebraska isn't counted in today's statistics. Their last bar graph entry on its Dashboard site is 373 new positive tests for Feb. 2nd, and the day before is now up to 715 new positive tests. Nebraska appears to be backfilling the dates of testing, a method that makes it impossible to accurately report on a daily basis.  Other states report on whatever is counted on a given day without regard for when a positive diagnosis was made. No one from Nebraska's HHS agency has returned my phone call yet. No death reports were recorded by Nebraska or North Dakota and none were reported in Wyoming or Alaska.

COMMENTS - Correction on the daily table above: The U.S. international ranking for COVID PCR tests per million slipped to 20th today.  No other comments for today.


NATIONAL HEALTH EMERGENCY

DAY 305  - FEBRUARY 3, 2021
UNDERCOUNT
Nebraska is the only state not reporting any COVID-19 statistics. Nebraska stopped daily reporting on January 19th and only reported partial data twice since then. North Dakota provided no death report for yesterday and Hawaii reported no deaths. 







COMMENTS
What is happening in Nebraska that its statistics are not being reported? Apparently, they are not reporting their data in an easy-to-see format. I placed a call to the Nebraska HHS office to ask about this after observing that their COVID-19 Dash Board does not give a daily count of new cases or deaths. I left a message and am awaiting a return call. It appears that deaths are reported in cumulative totals and I don't know how often it is updated. New cases are only reported via a bar graph that only gives a day's total if you scroll over a bar. I don't know if there is any buffering to assure the daily number is complete, or if the numbers are updated continuously as the results are filed. Otherwise, New positive CRP tests are only reported as county totals over a 14 day period. Based on that data I was able to calculate that Nebraska currently has an average of 494 new cases per day. Nebraska is 29th out of 50 states in PCR testing and only bases new cases on positive PRC test results, not on any clinical diagnosis of COVID absent a PCR test. Despite its low testing rates, Nebraska ranks 9th in the nation for the number of cases per million and 16th in the number of deaths per million. The bar graph does indicate that community spread is declining. 









NATIONAL HEALTH EMERGENCY
DAY 304  - FEBRUARY 2, 2021
UNDERCOUNT
Nebraska is still not reporting its statistics for some reason. There were no deaths or death statistics reported from Alabama, North Dakota, South Dakota, Alaska, Hawaii, or Wyoming.

COMMENTS
It seems like another Ground Hog Day in our pandemic world (plus 6 more weeks of winter), but there are positive changes happening. 

The New York Times put out a positive-sounding article yesterday explaining that when scientists say a vaccine is 95% or 85% effective, it means that percentage of those who took the vaccine in a trial didn't get sick at all. Scientific protocols don't count people who got minor symptoms, for example. Also, of the 75,000 people who got the vaccine in the trial, not one of them died. And that includes those who did get sick with some of the variants. 

The point is that if the vaccines aren't 100% effective, but reduce COVID-19 to something more like a common cold, we could all go back to living without having to wear masks or social distancing. The goal isn't eradication of the virus, but of getting control over it both in reducing its impact and reducing its community spread. 

Even so, this status is still in the future. We have to get there first. Until then, every day is still Ground Hogs day. The quicker we beat down the daily infections (by becoming better people with regards to staying safe), the quicker we will get there. So get your Fauci-ouchy ASAP and continue doubling down on infection precautions. 

Regarding staying safe, the NFL really took to science in a big way to keep their players safe for the season and to learn exactly what works to stay safe. The whole effort has been written up by the CDC and has changed the guidelines they are putting out. For example, they found that people can become infected even if they keep their social distance, depending on the surroundings. Here is a link.





NATIONAL HEALTH EMERGENCY

DAY 303  - February 1, 2021
UNDERCOUNT
A significant undercount from the weekend persists. The following states failed to report their statistics: Michigan, Missouri, Kansas, Connecticut, Nebraska, Idaho, Oregon, and Rhode Island. Four states either had no deaths or didn't report death statistics. They are North Dakota, Alaska, Maine, and Wyoming. The estimated missing number of COVID-19 deaths from yesterday is 1,776 souls.

COMMENTS
Our global share of COVID cases is still massively out of proportion to the rest of the world as we head into February. This will be a pivotal month for the fight against the coronavirus. On one hand, the vaccination programs will be scaled up significantly over the month and mask-wearing is at an all-time high. On the other hand, the several variants of the virus unleashed in the States last month will be racing to undo our progress. We may see a growing number of hotspots where the new variants are competing for dominance. Strategic targeting of our national resources and greater adherence to protective measures and local restrictions.






Saturday, January 30, 2021

New COVID Variants Threaten Progress and What We Can Do About That

 by Brian T. Lynch, MSW

I am highlighting today's Daily Pandemic Diary in this separate post because I believe the message is critical for everyone, and I want more people to have access to this information. To read other posts in the Daily Pandemic Diary you can click on this hyperlink

DAILY PANDEMIC DIARY 

NATIONAL HEALTH EMERGENCY
DAY 301  - JANUARY 30, 2021

UNDERCOUNT
Missouri and Nebraska have not posted their COVID data again today. Vermont, Alaska, and Wyoming either had no deaths or didn't post them. 
COMMENTS
Today, the big news is that the virus is mutating into vaccine-resistant variants faster than scientists expected. The reason is clear. According to the LA Times piece, "... the speedy evolution is largely a result of the virus’ unchecked spread." 
Whenever any cell or virus replicates, there is a slim chance that a mistake or mutation happens. The faster a virus replicates the more frequently these mistakes happen. Most mistakes do nothing, but every so often, by chance, a mistake makes the virus heartier. This new "variant" is more successful at replication. It eventually out-competes the original strain, becomes the dominant strain, and this mutation process continues. 
The number of times a virus replicates in the human body is such that the rate of mutations is low and the likelihood of a beneficial mutation occurring is extremely rare. But, multiply the speed of mutations in an individual by 26 million, which is the number of active COVID-19 cases worldwide, and you greatly speed up the rate at which more robust variants emerge. The more people who are sick with the coronavirus, the quicker the vaccine becomes less effective. The race for an effective vaccine isn't over.
What can be done to keep new resistant variants from disrupting our progress? Three ideas come to mind. We can try to speed up how quickly scientists can identify more robust variants and modify existing vaccines to counter the variants. We have seen already how slow that process can be. The speed of development for the current vaccines is already record-breaking. We can, and should, greatly pick-up the pace of getting people vaccinated all around the world. This is an enormous task and would require a level of global effort and cooperation that is unparalleled in human history. The third, most practical and effective way to slow the speed of new, more robust variants is to greatly reduce the spread of the infection. So, it all comes back to the basics of prevention. 
properly wear good quality masks and keep yourself six or more feet from everyone who is not in your immediate household. Don't go indoors to bars, restaurants, or any other place where you might have to remove your mask to eat or drink unless they are scrubbing the air in the facility. Stay away from crowds, outdoors or indoors. If you must be in a building where you are around strangers, such as a doctor's office, etc., make sure there are air scrubbers running (medical-grade HEPA air filters) or proper air exchangers operating. Make sure everyone has the ability to stay 6 feet apart. 
And remember, everyone in a hot zone everywhere on earth needs rapid access to a vaccine and all the PPE necessary to prevent the spread of the virus. A new variant anywhere in the world will make its way everywhere else on earth. We are all in this together, so PPE and vaccines must be readily available in every county for all of us to be safe here at home. 



Friday, January 1, 2021

Guest Blog - New COVID-19 Variant, Summary of British Research on B117

GUEST BLOG – Dr. Deepti Gurdasani tweeted out the following informational summary of the newly published Imperial Report regarding the new COVID-19 virus variant.  Her tweets are reproduced here in their entirety with attribution to its author. Dr. Gurdasani wrote a far better summary than I could on the topic and has my gratitude. - Brian T. Lynch, MSW


Dr. Deepti Gurdasani

Senior Lecturer at Queen Mary University of London

University of Cambridge

 

The Imperial report on the new UK B117 strain is out. [It is a] Very concerning findings, that highlight why we need to act on this *now*. These findings suggest that the situation within the UK is likely to get much worse than it is now. Here's why-

First, this study is perhaps one of the most comprehensive evaluations of the impact and spread of the B117 variant- combining epidemiological national evidence with genomic data from large numbers of samples across the UK. The study examines something called 'spike dropout' as a proxy indicator for the new B117 variant. The B117 variant includes a deletion in the virus genome which has been associated with a different read-out on some PCR tests, - referred to as 'spike dropout'. While 'spike dropout' (S-) does not necessarily signify the B117 variant, as this deletion can occur out with the B117 variant >97% of tests showing S- since mid-Nov have been attributed to the new variant, given its high prevalence relative to other variants.

We see a very rapid rise in frequency of the B117 variant in London, SE England & E of England - rising to 80% by mid-Dec. Looking at the distribution across England, the estimated frequency varies by region between 15% in Yorkshire to 85% in SE England.




What does this mean? While the variant is still at low levels across many parts of England, the trajectory in some regions (Oxford & Birmingham) suggests rapid recent increases in frequency - which means it will likely follow the same trajectory as other areas unless we act now.  It’s worth noting that the multiplicative increase is estimated within the current context, and many not extrapolate the same way to other contexts.

 

Distribution of the new variant compared to the previous variant by age group suggests that the ratio between S- (variant proxy)/S+ (normal strain) is highest for those in the 0-9 yr and 10-19 yr group - data till mid-Dec. This is concerning on many levels.




It's clear that the variant is more dominant (1.2x) in children aged 0-9 yrs and 0-19 yrs. There could be many reasons for this - including transmission dynamics - due to high levels of unmitigated transmission in schools during lockdown - which has favoured the variant.

It could also mean that children with the variant are more likely to develop symptoms and therefore be tested. Given these are not random samples from healthy people, but results based on pillar 2 testing, we need to interpret these cautiously. This also does not necessarily mean increased biological susceptibility in children vs adults, & shouldn't be interpreted as such.

Irrespective of the relative prominence of the variant among children the prevalence of the variant is greatest among 10-19 yrs among those tested. The data also suggests that the standard variant is still predominant among older age groups (at least among those tested) who are most susceptible to severe COVID-19.

Why is this important? This really highlights the potential impact of waiting to act. We know that virus transmission that begins in younger age groups inevitably spreads to older people, and ultimately results in severe illness & death. We've seen this pattern before. The geographical & age distribution suggests that although the UK pandemic is in a critical state now, there's real potential for it to get a *lot* worse. We know increases in R correlate strongly with the variant frequency. We can see the frequency rising in other regions. We can see it spreading outside South & East England. Given this is only at a frequency of 15% in some regions (and increasing), a rise would increase R much more than it is now, and worsen spread significantly.

Similarly, if infection in children is not curbed, the new variant will likely rapidly become dominant in adults as well, and potentially lead to an even more rapid spread of infection in older groups where the infection is more likely to be deadly & create further pressure on the NHS. The study shows that the R number associated with the variant *during* lockdown was 1.45 compared with 0.92 for other strains. This means that cases with the variant continued to rapidly grow during the last lockdown. The variant is associated with an increase in R of 0.4-0.7.

It's clear that although the situation is dire now, there is potential for it to get much worse & given the rises we're seeing in variant frequency in other regions, if we don't act now, not only with exponential rise continue, but the rate of rise will increase.

This may also mean more cases among older age groups- while the variant is currently dominant among children, the situation is likely to get much worse if this gains dominance among adults, who will be more likely to spread to other adults & older people - which means more deaths

To illustrate this with an example- Say 15% of a region has the variant now and has an overall R of 1.1 (fairly realistic given the rises we're seeing in much of England where the variant isn't dominant yet).

Assuming R of 1.7 for the VOC and 1 for the standard strain, the variant would be expected to rise to >70% frequency within a month. This would mean an increase in R to 1.5 in this period from 1.1. In terms of case numbers, it would be devastating. All the evidence is pointing in the same direction- we need to act urgently to curb spread across *all* of the UK. Letting this variant spread is not an option. And we need to close schools until we can make them safe, & prevent onward transmission. This is critical now.

[See the] Full report here: https://imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-12-31-COVID19-Report-42-Preprint-VOC.pdf

Just adding a short note here as many people have asked how the variant increases transmissibility. We don't know the exact mechanism -we know that one of the mutations changes the virus spike protein in a way that it binds to the human receptor needed for infection more strongly.

There are also studies that suggest that virus levels in the throat and nose are higher among those infected with the [new variant] virus, suggesting that this might be one of the ways in which it may make spread easier.

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