Corona-zona

  Here are the Arizona pandemic numbers and graph of statewide cases for the seven day period ending yesterday, as well as the most recent update of Tempe wastewater surveillance: The most concerning aspects of the table and first graph is a rather large uptick in cases at the state level. Could this be the start of a new wave?  There is reason to worry because epidemiologists have warned that it is just a matter of time until the current wave in Europe makes its way over here. JP  Weiland, a scientist who does modeling of disease spread, tweeted a graph predicting that the decline in cases would bottom out this week and be followed by another period of increasing cases. I thought we were getting an early start on a new wave until I saw this tweet from Garret Archer, a data journalist who works for ABC 15. He was informed by AzDHS prior to this week's data dump that cases would go up due to a testing provider just now reporting some data that should have been reported i...

  The United States—and to be fair the rest of the world, but I will focus on here—whiffed the pandemic. We ignored warnings and abandoned programs designed to give us what little preparedness that we had. We couldn't make enough PPE or medical equipment, or ramp-up testing when we needed it most. Our reward is almost a million people dead, and around 11 million people with "long COVID." There were plenty of people warning us that we were unprepared for this. Back in 2005, Bush wanted to invest in preparedness  (for a replay of the Spanish Flu), but Congress wouldn't listen. In 2014, Obama asked for money to prepare for an Ebola epidemic, cut Congress wouldn't listen. In 2015 Bill Gates did a TED talk about how we weren't ready for a pandemic, nobody listened. Then just months before the SARS-CoV-2 pandemic started, the Trump administration undermined a federal-level pandemic unit that had been established. Now it's looking like deja vu all over again...

Walter Reed Army Institute of Research  People who study the evolution of viruses published an op-ed in yesterday's New York Times about the likely future evolution of SARS-CoV-2. Here are some high-points of the essay. First, viruses evolve to survive and reproduce better. That is just what they do. There is no reason to think SARS-CoV-2 will stop evolving. Second, there are still plenty of pathways available for further evolution. The writers reckon there are "nearly 2000 other ways the 201 targeted amino acids could could mutate and still be able to attach to human cells." Third, the evolutionary pressure on the virus is to become better at spreading. It can do this by becoming more contagious and/or better at evading the immune system. They say it is "remarkable" how good this virus has been at responding to that pressure. Fourth, how much more transmissible the virus could become is unknown. There is not an infinite capacity: "a cheetah can’t evolve t...

  Here are the Arizona pandemic numbers and graph of statewide cases for the seven day period ending yesterday: Everything continues on the downtrend, though cases are declining by smaller amounts every week (as we'd expect). Deaths are going down now, and hospital beds continue decreasing. Maricopa county now lists the community level as "low." Looking at the graph, it's hard to believe how bad things were just two months ago. Wastewater Fail As noted in Sunday's post , I had intended to add wastewater numbers to the table, and I did put the one-week and four-week values in there. However, the Pima county numbers have vanished from the CDC site , including historical ones. It's odd because they were there just four days ago. I've sent an email to the dataset owner about this, but have not received a response.   It's not clear to me when Tempe updates their dashboard . It's currently showing data from two weeks ago, just like it was doing on Sunday...

Reports have come out before suggesting that Arizona has a poor record when it comes to pandemic deaths. A couple weeks ago I blogged about how state officials were trying to obfuscate this fact by raising questions about the validity of comparisons among states. This week the Arizona Public Health Association released an analysis detailing Arizona's dismal performance in terms of pandemic deaths. It looks across the whole pandemic, undermining criticisms that reporting differences between states make comparisons invalid; it also compares numbers before and after the pandemic and compares them to other diseases which should control for any between-state differences. As detailed in the report, compared to other states, Arizona: Had the second-highest number of COVID-19 deaths per 100,000 residents (second only to Mississippi) Had the greatest increase in deaths from all causes compared to the "before times" in both 2020 and 2021 Had COVID-19 as the number one cause of de...

" Double ouch, double vaccination "  by  jacco de boer  is marked with  CC BY-NC-SA 2.0 .   The CSC has added new data on the risk of hospitalizations for unvaccinated kids 5-11 years old relative to those who are vaccinated. The data are from January, when the Omicron wave was still active. Here is their chart: If you divide the unvaccinated rate by the vaccinated rate and average over the five weeks represented, the ratio is 5.23 to 1.  In other words, unvaccinated kids in this age range were, during the period covered, on average more than five times as likely to be hospitalized with COVID-19. Granted, the risk is small either way. The highest rate, on January 22, was only 3.9 per 100K. But when it's your kid I'm pretty sure you'd prefer the risk 1/3 as high for the vaccinated group.

It has been known for some time that people infected with SARS-CoV-2 can shed the virus in their feces, even if they don’t have symptoms. Wastewater can be analyzed for presence of the virus much in the same way nose swabs or spit samples are analyzed. The advantage of this kind of surveillance, according to the CDC , is that—unlike case rates that are typically reported—wastewater testing "does not depend on people having access to healthcare, people seeking healthcare when sick, or availability of COVID-19 testing." It also covers large numbers of people.  It is therefore a good early warning indicator and one epidemiologists use to get a more accurate picture of how prevalent the virus is in a community. We could use a good early warning indicator now that our leaders have eaten the marshmallow and scaled back their pandemic reporting to weekly. So I decided to take a look at wastewater surveillance in Arizona. Predictably, we are doing a half-assed job. The CDC has a das...

  Here are the Arizona pandemic numbers and graph of statewide cases for the seven day period ending yesterday: Everything continues to look good. Case rates are essentially down to levels seen last spring. Hospital beds are declining and are below ten percent. There is a slight uptick in deaths, but it's a fraction of a case per 100K and it is expected for deaths to lag case declines. However, I worry this may be an "enjoy it while you can" situation. Case rates are increasing in Europe again due to the so-called "stealth" Omicron variant .  They have seen case rates roughly double from late February to mid-March. In Arizona, just yesterday it was reported to  account for 10% of cases in Pima County. Experience shows that what happens in Europe tends to happen here about two weeks later. Now, thanks to our leaders  failing a marshmallow test  and dropping reporting frequencies to weekly, we are not going to know the increase is hitting in Arizona until it...

  A team of 53 of the of the world’s best epidemiologists, pharmacologists, virologists, immunologists, and policy experts has released a report entitled "Getting to and Sustaining the Next Normal: A Roadmap for Living with COVID." The report is 129 pages comprising a comprehensive set of topics about how to get back to normal and prepare for next pandemic. If we follow standard operating procedure, then our political system will forget all about the COVID-19 pandemic as soon as possible once the case rates go down to endemic/background levels. Then something as bad as or worse than COVID-19 will come along, we will find ourselves in a  Don't Look Up situation, and we will endure another shitshow like the one we've just been through. The report offers recommendations in twelve categories for avoiding this. Here is a quick summary of the bottom-line recommendations: Shift our public health focus from just COVID-19 to respiratory viral illnesses to include influenza a...

Mask-hole parents who disrupt and threaten violence  against school boards over mask mandates look like even bigger idiots than they did before. A new study forthcoming in the journal Pediatrics shows that masking is effective at preventing the spread of COVID-19 at school, just like the public health people have said all along. Researchers studied within-school transmission in the last six months of 2021 among over a million students and over 150,000 staff member in 61 K-12 districts in nine states. Six of the districts had optional masking policies, nine had partial masking policies (changing over time or based on conditions), and 46 had universal masking policies. The differences were big. For every 100 community-acquired infections, the universally masked districts had 7.3 cases acquired in-school, while the optionally masked districts had 26.4 cases. That is a rate 3.6 times (or 72%) higher. Districts with partial masking policies had rates 2.4 times higher. This seems obvi...

  Here are the Arizona pandemic numbers and and graph of statewide cases for the seven day period ending yesterday: Except for a fractional percent increase in deaths, everything continues to look good. The seven-day average of cases shown in the graph is comparable to levels last seen in mid-july last year when Delta was just cranking up. The curve appears to be continuing downward, so in another week we might be back to spring 2021 levels.  I take the Maricopa county numbers with a grain of salt. For one thing, the cases per 100K are reported "for the most current calendar week of data 02/27-03/05." So the numbers are lagged by five days. Second, I divide the number they list (55) by seven to get a seven-day average. It seems like an awfully big drop from last week, though not an impossible one. Third, none of their numbers line up with their "community transmission indicators." On a detail page they say total new cases per 100K in the range of 0-9 is low, 10-49 ...

  Unless you're an anti-vax moron, you already accept that vaccines are safe and effective. You also know that a booster is important to strengthening your immunity, and that this immunity is likely to be enduring . That all describes me, but even I didn't know how dramatic the effects of boosters really are. I found out last week, when AzDHS released an analysis of the effects of vaccinations on COVID-19 rates and outcomes. The bottom line (well actually top line) result is that, compared to people who are fully vaxxed and boosted, unvaccinated people have 11 times the risk of testing positive, 67 times the risk of being hospitalized, and 180 times the risk of dying.  Breaking out groups who are unvaccinated, fully vaccinated, and fully vaccinated plus booster, and looking at the Omicron period, there are few differences between the first two groups in case rates, and only a very small rate for the third. There are big differences between the first two on hospitalizations a...

  Will Humble, former AzDHS Director and current Arizona Public Health Association Director, recently  tweeted  an analysis showing that Arizona has extremely high COVID-19 death rates. It is first among states in increase in observed deaths by all causes during the pandemic for both 2020 and 2021. Earlier this week there appeared an article in the Arizona Republic  (paywalled; you can get a copy here if you don't mind a non-encrypted link) asking why this is so. It cites a CDC ranking that puts us at number three for COVID-19 deaths, but I'm unable to find it.  Here is one from the Kaiser Family Foundation that puts us second behind Mississippi. The Republic reporter asked state officials for an explanation, and they tried to create uncertainty about the comparisons. For instance, the AzDHS Assistant Director for Public Health Preparedness said:  I think it's really difficult to say whether we are third-worst in the country just based on the variability...

  Here are the Arizona pandemic numbers and and graph of statewide cases for the seven day period ending yesterday: This is my first summary since the state switched to weekly reporting of data. Before I point out changes, I note that everything is moving in the right direction, and cases are moving below the levels from last fall's Delta surge, hopefully headed for near-zero. Changes As for changes, first, I an getting data directly form the AzDHS and Maricopa County dashboards. The former now updates on Wednesday, and the latter updates case numbers a day late, which is why I'll be posting this summary on Thursdays instead of Wednesdays.  Second, obviously the new cases graph can no longer show daily values, but will include numbers from every Wednesday instead. It's not quite as smooth but otherwise no big loss. Third, you will notice that the past values and change values for vaccinations are blank. That's because in researching the mystery surge in vaccination perc...

  A discussion today over on the CoronavirusAZ subreddit about Arizona death rates got me thinking about how Indian country fared on this outcome. A little over a year ago I blogged about how the tribes in Northeast Arizona were killing it with their vaccination programs.  Even today, their vaccination rates make the state's largest county look lame. According to this recent ranking , out of 15 counties in the state Apache County is number one (95% vaccinated), Navajo County is number four (75.3%), and Maricopa County comes in at number ten (55.8%).  So how have these counties fared in terms of death rates? I got data on reported deaths from the ASU Dashboard , converted these figures to new deaths per 100K population, then took the seven-day average of that.  Here is a chart based on that data: Sadly, the tribes' excellent vaccination uptake didn't save them from higher death rates than Maricopa County, save for a few random days. Overall the latter is below the t...