Corona-zona

  Here are the Arizona pandemic numbers for the week just ended: Slight increases last week in the infection-related numbers.  The new case increases are less than 1 per 100K, so probably nothing to get too excited about.  Still we'd rather see them keep heading in the other direction.  Positive test rates went up by a half-percent and remain stuck at about 10%.  That's something else it would be nice to see going down. Here is the vaccination accelerometer: It's nice to see a little acceleration after weeks of decline! Presumably this is the result of kids getting their jabs. Top Image by  Shutterbug75  from  Pixabay

  On one hand, Governor and Florida Man in Chief Ron DeSantis badly wants cruise ships to resume service in Florida. On the other hand, he has done the one thing that would allow that to happen.  He banned cruise lines from requiring passengers to be vaccinated.  As pointed out in a Washington Post article on the subject (paywall link), the second part is all for show.  A lawyer quoted in the article called it  Political grandstanding 100 percent.  This is not driven from a motivation of safety.  If the motivation were safety, you would say, "of course everyone has to be vaccinated." It's kowtowing to a small minority that are really a vocal base for him. Specifically it's the base whose members call the disease fake and are free-riding off the rest of us who have gotten our vaccinations. God forbid there should be any consequence that would threaten their God-given right to be stupid.  DeSantis likes poking the federal government, in this case t...

 For some time, public health officials have fretted about whether immunity to COVID-19, acquired via infection or vaccination would stick.  Studies showed rapid declines in antibodies during recovery from infection and thereafter . It turns out that this concern was overblown. A study just released says bone marrow plasma cells are a persistent source of protective antibodies, and that "circulating resting memory B cells directed against the S protein were detected in the convalescent individuals."   Another study , yet to be reviewed, suggests that vaccines boost this effect. In fact, some are suggesting this situation this could actually mean  lifetime immunity .   Whether the same thing happens with vaccination is not clear. Most estimates suggest that vaccine immunity will last about a year . More pessimistic estimates putting the protection period at six months .  The possible shorter time frame, plus the appearance of the new variants, ha...

  On Monday I did a post worrying about Arizona's falling vaccination rate.  I showed a curve suggesting that if things keep going the way they are now, the percent fully vaccinated might level-off well before we get to 50% of the population. In a conversation about that with some public health people I know, it was pointed out that we also have to take previous cases into account when considering the percent who make have some level of immunity.  Having had and recovered from COVID-19 give you some immunity, but not as much as if you're fully vaccinated.  The thinking seems to be that having a case is somewhat similar to one dose of a two-vaccine regimen. But there are problems with rolling infection-based immunity together with vaccinations to estimate what percent of the population is protected.  For one thing, many people who have had COVID-19 have also gotten vaccinated.  Some researchers I know who recently completed a nationwide study told me that ...

A paper just published in the journal Science  shows, once again, that masks are effective at mitigating SARS-CoV-2 transmission.  The twist on this study was that they looked at masks' effectiveness as a function of how virus-rich an environment is. They found that "surgical masking achieves large reductions in infection probability when the maskless infection probability is low, but increasingly smaller reductions when the maskless infection probability is high."   So in other words, masks work extremely well when the viral load is low, and less well when the viral load is high, as you'd expect. They found similar results for N95 masks, which are about an order of magnitude better at preventing infection.   They also considered different combinations of who is wearing a mask. Again, as you'd expect, the found that effectiveness was highest when there is "universal masking," next highest when someone emitting the virus is masked, and next highest when ...

  Every Sunday, Corona-zona posts a weekly summary of pandemic numbers, including the percent vaccinated. So I have been consulting the JHU dashboard every week for months now to get the latest number of doses and number fully vaccinated. There was a time, I think back in early March, where Arizona rated in the top ten (or so) states for percentage vaccinated (I can't find the exact number because there is no historical data). I was stunned. Arizona is never in the top ten states in any list .   We're 30th in livability , 31st in health , 46th in education , and 34th in quality of life . Even in an area where I thought we would "excel"— gun ownership —we are in the middle of the pack at 24th (46.3% of Arizonans have guns at home). Here is a look a the weekly fully-vaccinated numbers since January: From January to late March, you can see that there is an upward curve to the line, meaning every week we were increasing more than the previous week.  But then starting in...

  Here are the Arizona pandemic numbers for the week just ended: There are continued small improvements everywhere except s-gene dropouts.  However, that should be taken with a grain of salt because there were questionable entries in the last week's data, with one day at zero percent and another day at 100 percent.   Here is the vaccination accelerometer: We see a continued drop-off in the rate of additional vaccinations given over the last week.  That is concerning for reasons I will address in tomorrow's post. Top Image by  Shutterbug75  from  Pixabay

  I have heard this week, in multiple media reports, that infection rates are falling everywhere in the U.S., and that it's because of vaccines. I've not seen any data on the latter claim. The data are available, so I decided to geek out and see for myself. Let's start with the first claim, that infection rates are falling everywhere.  That is easy to check with data from CDC's Socrata API.  I queried it to get the new cases for the seven days ending May 18 (CDC data are a few days behind) and the same for the seven days ending April 19.  I converted these to cases per 100K using population numbers , got an average for the current week and the week one month ago, and subtracted the two values.  Here are the results: Case rates have not declined in every state, but close.  They have increased in Alabama by 7.35 and in Wyoming by 2.36.  There is essentially no change in Arkansas, Mississippi, Hawaii, Arizona and Missouri.   In every other stat...

  Today's post is by Corona-zona Senior Canada Correspondent Salishsailor. Many countries have set hard border closures as a way to block the spread of COVID-19. Canada is one of them. All “nonessential” travel across the U.S.-Canada border has been blocked since mid-March 2020. What’s “nonessential” and what’s “essential,” though, depends on where you stand.   Literally. At the national level, “essential” means “ any nondiscretionary travel ,” which is equivalent to saying that essential means . . . what, obligatory? Mandatory? Who knows? The hard closures might better allow people to comply if authorities circulated behavioral descriptions of the terms. At the national level it remains murky . British Columbia—the province I’m most focused on, because I’m moving to BC when I can get access—has made a stab at defining cross-border “essential” travel. Included are such reasons as fleeing the risk of abuse or violence; working, both paid and volunteer; getting healthcare;...

  Earlier this week, NPR Morning Edition aired a story about the AIDS epidemic. The first news that a mysterious disease was killing gays appeared forty years ago.  The reaction at the time was similar to the reaction to COVID-19 today. People preferred not to have their lives impacted so they pretended like the disease wasn't real. Government officials and world leaders questioned the facts.  So did medical experts. One, interviewed for the story, published an op-ed saying rumors of a gay plague were unfounded.  Another published an article in a well-respected scholarly journal saying there was no evidence that HIV causes AIDS. Sound familiar? The story raises the question of whether events forty years ago set the stage for the anti-science discourse and disease denialism we have seen over the past year.   It's an excellent piece, well worth 11 minutes of your time.  You can listen here .

As you probably know, the FDA has approved the Pfizer vaccine for kids aged 12-15. Presumably approvals for other vaccines will not be far behind. But just because they can get the vaccine, we can't be sure they will .  They need parental permission, and parents are being influenced by scumbag anti-vaxxers who are spreading misinformation to make money off of their fake preventatives and cures. SurveyMonkey and Boston Children's Hospital recently surveyed 6,619 parents with children under 18 about their intentions to get their kids vaccinated.  The good news is that overall 53% said they would get their kids aged 16-17 vaccinated, and 43% said they would do so for their 12-15 year-olds. But 26% and 29%, respectively, said they would not, and 21% and 27%, respectively, said they are not sure.  Things get interesting when you break things down by the parents' vaccination status.  Here is a screenshot from SurveyMonkey's Tableau site (which you can access and play ...

  In the past few days, I have been seeing stories like this one from CNN reporting on a COVID-19 outbreak in Taiwan. Yesterday they reported 335 new cases.  Its health minister has said "we are in critical condition now, and this is not a joke." The CNN story has a picture of two guys in hazmat suits sitting in the back of a truck, going down the street spraying disinfectant in the air. There is another picture showing bare shelves in stores where toilet paper should be. This struck me as mighty strange, given that Taiwan has been a model of pandemic management. They nipped the infection curve in the bud about a year ago. I remember seeing pictures last summer of Taiwanese attending a soccer match with full stands. So I decided to have a look at the infection rates, and compare them to the U.S. and other countries in that region using the  right numbers . Here is a chart from Our World in Data: As of one day ago, their outbreak amounts to 4.91 cases per 100K on a seven...

  The CDC and its director Rochelle Walensky are taking a lot of flack over their announcement last week that vaccinated people no longer need to wear masks in most settings. This is something everyone has been wanting, so why the uproar? Just a couple of days before the announcement, Walensky was defending CDCs mask policies at a Senate hearing. She got an earful from Sen. Susan Collins, who said "I always considered the CDC to be the gold standard. I don't anymore." She continued: So, here we have unnecessary barriers to reopening schools, exaggerating the risks of outdoor transmission, and unworkable restrictions on summer camps. Why does this matter? It matters because it undermines public confidence in your recommendation, in the recommendations that do make sense, in the recommendations that Americans should be following.  Ouch.  So you would think Collins and people like her would be overjoyed when the mask guidance changed. Perhaps she was, but others, not s...

  Here are the AZ pandemic numbers for the week just ended: All the numbers are headed in the right direction, including S-gene dropouts. As a reminder, that is the number of tests done by ASU's lab that have a marker associated with the UK variant.  Last week there was a problem with the numbers reported on their dashboard. It was reporting greater than 100 dropouts per 100 tests, which is obviously not possible.  They have fixed the problem so I recalculated last week's number in the table. Here is the vaccine accelerator this week: The any shot and both shot lines continue to decelerate.  We picked up only about 1.5% more people for both last week. This may pick up now that adolescents are eligible for the shots. Top Image by  Shutterbug75  from  Pixabay

Yesterday Wired magazine released an excellent  long-form article on how WHO and CDC were dragged kicking and screaming into an admission that they had been wrong about the main transmission mechanism for SARS-CoV-2, and why it took so long to get it right. You may recall that about a year ago, we were being told to keep 6 feet away from other people and wash hands frequently. That's because they thought the main way the virus spread was through respiratory droplets, a.k.a. fomites .  The theory was that an infected person would cough or sneeze, this would release large respiratory droplets that if you were too close, could land in your mouth or nose or eyes—the origin of the six foot rule. They could also land and persist for some time on surfaces, which you could touch and transfer the virus to those same openings.   Believing this was the main infection route, people were washing packages and vegetables from the grocery store in bleach.  There were shortage...

  I find it hard to muster any sympathy for anti-vaxxers, and have said before that I think they are asshats .  That is not to say they are all evil.  I'm willing to believe some people are fearful and/or uninformed and/or have been  misled . But this makes them no less wrong. Like the rest of us, one of the main reasons they are alive is that vaccines have saved them from smallpox, polio, tuberculosis, tetanus, etc. But some anti-vaxxers are using their "advocacy" to line their pockets.  For example, in 2019 The Washington Post detailed (paywalled link) donations of $2.9 million to an anti-vax groups (whose name I don't want to publicize) by Joseph Mercola.  His donations accounted for about 40% of the group's funding.  Mercola's enterprises sell "natural" heath products and quack cures, some of which are marketed as alternatives to vaccines. His enterprises are estimated to bring in about $15 million annually. According to a investigation  by ...

  As if our friends in India aren't having enough problems with the COVID-19 wave there, there is a new problem. This one isn't a complication of the disease per se but a result of its treatment. India is seeing a huge spike in cases of mucormycosis, a.k.a Black Fungus, in humans. According to a  report , India has had a handful of cases over the last decade, but is suddenly seeing tens of thousands of infections. Experts think this is happening because shortages of oxygen are causing physicians to prescribe more corticosteroids to people with COVID-19 (you can also buy these drugs without a prescription in India). Experts reason that these drugs are suppressing inflammatory responses and are thereby creating opportunities for the fungus to take hold. The disease happens when people inhale spores of a mold that lives in the ground and decaying organic material. According to the CDC , infections can happen in the lungs and gastrointestinal tract, but the infections being ...

  There is a branch of complex dynamic systems theory called global cascades modeling  that tries to explain things like avalanches and sand piles. In both cases, everything is fine, and you have a coherent snow load or sand pile.  Then, suddenly and spontaneously, the structure collapses. The snow comes crashing down the mountain or the sand pile collapses for no  apparent  reason. Of course, there is a cause, but it's some very small change too small to notice in a big system of snowflakes or sand grains. Researchers in Austria are applying a different but similar approach to the COVID-19 pandemic. Borrowing ideas from fluid dynamics, normally used to study turbulence in things like pipes, they are showing why COVID-19 infection rates are either boom or bust (from the virus's point of view).  You want to avoid turbulence in pipes because it increases resistance, slowing down the flow of whatever liquid you're trying to move. As with cascades, turbulence ...

  With over 60% of its inhabitants fully vaccinated against COVID-19 you would think the Seychelles Islands would be skating to the end of the pandemic.  Yet that is not what's happening. Here is a helpful graphic Google threw up when I was researching articles on this: Why is the most vaccinated country in the world experiencing a surge of cases and re-imposition of restrictions? Nobody is sure. Officials are speculating that gatherings around Easter may be to blame. A worrisome fact is that one-third of the cases are among people who have received two doses of China's Sinopharm vaccine. The manufacturer rates  its effectiveness at 79%.  That figure would put it about 15% less effective than the Moderna and Pfizer shots. Though scientists have cautioned that it's not appropriate to compare effectiveness across vaccines that were tested under different protocols, we do have the recent statement by a Chinese official saying that the country's vaccines aren't very ...

  Here are the Arizona pandemic numbers for the week just ended: It's good to see all the one-week change numbers going in the right direction again.  The only red spot is S-gene dropouts, which indicates the prevalence of the UK variant in the state. But I think there must be something wrong with the dashboard where this data is reported, because we shouldn't be able to get more than 100 dropouts per 100 tests. I am inquiring with the publishers.   Meanwhile, speaking of getting things wrong... Major Correction I have been making an error in the vaccination percentages, and by extension the accelerator back to January when I started making these weekly reports.  I thought the JHU dashboard, where I get the vaccination data, was reporting number of people with one or more shots, and people fully vaccinated.  The other day I noticed that the first figure is the number of doses, not the number of people with at least one shot.   I regret the error a...

  Racist attacks against people of Asian descent are up, including those targeting old ladies with sneak attacks and stabbings. You may ask, why now?  It's undoubtedly because of the efforts or an orange racist (and ex-President) to label SARS-CoV-2 as the "China virus." He is so wrong about about so many things, it should come as no surprise that he's wrong about this, too.    According to a recent report , researchers are now finding evidence that the virus detected in Wuhan in December 2019 had a progenitor that had been spreading worldwide well in advance of the Wuhan event. They determined this using tracing of relations of mutations called  phylogeny . “We have found progenitor genetic fingerprint in January 2020 and later in multiple coronavirus infections in China and the USA. The progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China,” said one researcher. Another added that the timeline suggests the p...