Corona-zona

  Two updates on testing. Antigen Tests Less Sensitive to Omicron On Wednesday I blogged about the challenges the new Omicron variant is posing for testing. Essentially, you can have antigen tests that are fast and inaccurate or PCR tests that are slow and accurate.  Antigen tests are just barely satisfactory for symptomatic cases (false negatives in 1 of 4 to 1 of 8 tests), and they are basically useless for asymptomatic cases (false negatives in 1 of 2 to 1 of 3 tests). Even that assumes the tests work for Omicron. Well yesterday the FDA announced that antigen tests are less sensitive to Omicron than other variants. They don't have information on how much less sensitive they are but are working to get that info. They are also trying to learn why and think the tests can be adjusted to compensate once they know. Dr. Fauci is quoted in this article: "What the FDA is saying today is that when you look at Omicron and its ability to detect Omicron, some of the tests have a dimin...

  Yesterday my sinuses felt somewhat irritated, my nose was running a little, and I had a little pang that could have been the beginning of a headache. I am fully vaxxed and boosted, so I wondered: Could I have a breakthrough case of the Omicon variant? There is growing evidence that Omicron produces less severe disease. Some people are claiming that it has different symptoms than "classic" COVID-19 too, ones more like a common cold.  Experts warn  that it's too soon to tell if the symptoms are fundamentally different from those associated with Delta. But this doesn't stop people like me from wondering whether any respiratory symptom might be COVID-19. At least four people I know—someone I work with, a friend, and two toddlers of another friend—have  symptoms of mild respiratory illness. They are all worried that they could have COVID-19 and have gotten or are seeking tests. There are many other people in the same boat. Public health practitioners are saying that th...

  On Sunday I noted that Arizona had not yet seen an explosion of cases due to the Omicron, like elsewhere. On Monday I thought there may have been detonation, with AzDHS reporting over 7000 new cases.  But today they're reporting just 1,976 new cases. So it looks like once again we have unreliability due to  delays in reporting cases . Anyway, ASU reported over 70% of tests with s-gene dropouts (explainer here ) yesterday. That means Omicron is definitely taking over in Arizona. So what should you do about testing if you think you're infected? The current choices are antigen tests and PCR tests. Antigen Tests Antigen tests are the kind you can buy (if you're lucky) at the drug store and that you can administer yourself. The tests produce results in 15-30 minutes. That's great if you're trying to catch an Omicron infection because it spreads quickly and you want to stay away from other people if you have it. The problem is that these tests are not very accurate. ...

  Here is the Arizona pandemic numbers summary for the week just ended: Most of the numbers are looking good, except Maricopa County over the last week. As noted on Friday , it's a little surprising we are not yet seeing a surge in cases due to Omicron.  That variant has been present in the state since early December. In other locations its infections have been doubling every couple of days. It is hammering New York right now.   Not so here. Since that time we've been in a downtrend. The curve has flattened out, but is not looking anything like an exponential increase (yet): I'm starting to feel like a broken record, but another week with no progress since August on the vaccine front:

Today seemed like a good time for an update on the Omicron variant.   Ramping Up in Arizona? So it's not totally clear what the Omicron situation is in State 48. Strangely, the  GISAID database  lists only one sequence for B.1.1.529 (the number assigned to Omicron) in Arizona over the last month. Next we have the  tgen dashboard . That catalogs all the sequences done in the state. As of December 21 they say Omicron represented 1.44% of samples. Since they display results for each month, I assume that is for samples taken between November 23 and December 23. The rest were various flavors of Delta. Then there is ASU dashboard . For unknown reasons, it hasn't had its circulating variants widget updated since Dec 6. At that time they said 3.16% of sequences were Omicron. But they also have a chart for "s-gene dropouts."  That is a feature of PCR tests where they fail to detect a particular bit of genetic material.  It is indicative of only some variants, a...

  In my news feed today there appeared an article in Defense One saying that the Walter Reed Army Institute of Research (WRAIR) has developed a new coronavirus vaccine. This one, the article claimed, "is effective against COVID-19 and all its variants, even Omicron, as well as previous SARS-origin" viruses. It is also stable at non-freezing temperatures. According to the article, the vaccine uses something called a spike ferritin nanoparticle. It was described as something like a tiny soccer ball, with different coronavirus spike proteins attached to its panels. It sounds, then, like this is not an mRNA vaccine but something more akin to traditional vaccines.  The unique formulation means that it can theoretically elicit a broad immune response against all kinds of coronaviruses, including SARS-CoV-2 and its variants. Initial tests in animals showed positive results , as have Phase 1 clinical trials in humans. Phase 2 & 3 trials are pending. Walter Reed put out a correct...

  Arizona has earned a few ignoble distinctions lately. They relate to deaths, stressed care systems, and abysmal leadership. On the deaths front, we have two marks of shame. First, Becker's Hospital Review lists Arizona  as having the second highest death rate in the country. Over the course of the pandemic we've had 0.94 deaths per 100K residents, and averaged 68.4 deaths daily. We're exceeded only by Michigan (1.17 & 117.3). Second, over the last year COVID-19 was the leading cause of death in Arizona. It has killed more people than heart disease or cancer. Dr. Joshua LaBaer, executive director of Arizona State University’s Biodesign Institute, pointed out that this doesn't even include people who had conditions that went untreated because our medical system was overwhelmed by COVID-19 patients. Speaking of overwhelmed systems, the Arizona Public Health Association says our hospitals are now in "crisis standards of care." That's because they are f...

 Here is the Arizona pandemic numbers summary for the week just ended: Everything is improved from last week, and everything is improved from a month ago except hospital beds. The seven day average of cases continues a strong downtrend: I would be optimistic if it weren't for Omicron. The ASU dashboard is reporting variants now, and as of December 6 they reported that 3.1% of sequenced samples had the variant. I don't know why they haven't updated since December 6. Vaccinations continue to increase at an anemic pace:

  The other day, a notification popped-up on my phone asking if I wanted to install this app called Covid Watch Arizona. Naturally, I accepted. This technology has been around for some time. Similar system are in place in (at least) Virginia and New York.   With this app (available from the  Play Store  or the  App Store ) your phone has anonymous Bluetooth conversations with other phones nearby so it knows what phones it has been near. When the owner of one of those phones reports an infection, others who were near it are notified. This does not involve any central repository of what phones were near other phones. Your phone keeps the list of anonymous ID numbers of the phones it was near and only alerts you when it receives word that one of those IDs has an infected owner.  It's not totally clear to me who is behind the development and deployment of the app in Arizona. As you can see from the screenshot above, it is listed as belonging to AzDHS. But ...

  If you're like me and millions of other people you have recently bought something from Amazon. You're also probably not aware that they are a major supporter and enabler of the anti-vax movement. According to the blog Popular Information , Amazon directly donated more than $40,000 to one of the nation's leading sources of vaccine misinformation, the so-called National Vaccine Information Center. The amount donated has increased each of the last three quarters. According to an article in the  The Guardian , in addition to endorsing and legitimizing the anti-vax movement with these donations, Amazon supports the movement by selling books by anti-vaxxers. It then uses its recommendation algorithm to push more anti-vax books to people who have bought them.  In September of this year NPR reported that a book by Joseph Mercola was the number one recommendation when they did a search on "COVID-19." In the spring of 2019 the American Medical Association sent  a lett...

  Here is the Arizona pandemic numbers summary for the week just ended: There are some positives this week. Statewide cases rates are down a little, as are hospital beds. On the other hand Maricopa County rates are up, though not by a lot.  The long-term 7 day average of cases is displaying a  strange pattern, oscillating over the past four weeks: No clue what could account for that unless it's reporting issues over the Thanksgiving holiday. Vaccination numbers are terrible. As I reported yesterday , Maricopa County has about half the national average in booster update.   In overall vaccination percentage we've fallen two notches in the state rankings. As usual we have a sub-one-percent increase in fully vaccinated people.  

  The other day I got curious about how many people were getting the booster shots in Arizona. So I decided to check into it. Pandemic reporting by AZDHS is basically terrible. Their dashboard says the "percent of people vaccinated" is 63.5%. There is no explanation of whether this means one shot or fully vaccinated, or what is the basis for the percentage (population? eligible?). There is a footnote that says "vaccination numbers are displayed by the county or residence" even though the number so-footnoted is for the state.  This seems like a possible attempt to make the vaccination numbers look better than what they are. According to Johns Hopkins just 57.5% of Arizonans are fully vaccinated. I comes a no surprise, then, that AZDHS does not offer data on how many people have gotten a booster statewide. Fortunately, Maricopa County (with over 60% the state's population) does a better job of reporting, and offers this data. According to to their dashboard ,  25...

For some time we have known that obesity elevates the risk of having a serious case COVID-19. The CDC says  "the risk of severe COVID-19 illness increases sharply with elevated BMI" (body mass index). New research, published in pre-print  (meaning it has not yet been reviewed), sheds light on why that is true: The virus attacks fat cells. This, in turn causes an inflammatory response. The more fat you have the bigger the response and the more severe disease you're likely to have. The relationship between fat and inflammation has been on scientists' radar for some time. They believe chronic low-grade inflammation caused by fat is responsible for the negative health outcomes associated with obesity, like heart disease, cancer, diabetes, and so on. The coronavirus seems to turbocharge this process. Scientists think  this ability to infect fat cells may also help the virus evade our immune response. In other words, fat may serve as something of a reservoir where the viru...

  A week ago I blogged about the Omicron variant, urging everybody not to panic while the experts figure out what is going on. Here are a few updates suggesting that was a good approach. Who is Getting It As of a week ago, Omicron had been detected in  24 countries . In the US it has been  detected  in California, Colorado, Connecticut, Hawaii, Maryland, Massachusetts, Minnesota, Missouri, Nebraska, New Jersey, New York, Pennsylvania, Utah, Washington and Wisconsin. Strangely, there is also  evidence that the virus is mostly infecting younger people. Data from South Africa shows that 80% of hospital admissions were among people younger than 50, a marked departure of from the picture with Delta. Experts caution that this could be because of lower vaccination rates in that age group in South Africa, however. More Contagious but Milder Disease There is pretty good evidence that Omicron spreads more easily than Delta. Cases in one South African province are ...

  Here is the Arizona pandemic numbers summary for the week just ended: Nothing too surprising here. Cases keep increasing statewide. There was a small decrease for Maricopa County, which is one small bit of good news.  The seven-day average is headed back up after dipping last week. As I suspected, that seems to have been a holiday anomaly. Hospitalizations are up but much less so than infections. That's continued evidence that the vaccines work. On the other hand, hospitals are working based on contingency standards of care  with ICU beds full of unvaccinated COVIDiots. Speaking of vaccines, Arizona had another pathetic increase in vaccinations this week. Also we have slipped one spot in the rankings among states.