Corona-zona

  Welp, there's a newer, worser COVID-19 strain in the wild, y'all. I've been wondering why it's been so long since we've seen news of a threatening new variant.  They are calling this one "Arcturus." The name, according to Wikipedia , means "guardian of the bear." That doesn't make a whole lot of sense to me, but then again I'm not a Greek mythology nerd.  Anyway, this variant is another of the Sons of Omicron. It descended from XBB, and has the designation XBB.1.16.  Another such descendant, XBB.1.5, is currently the king of the hill in Arizona, according to Lim Lab . XBB and its descendants are dominant nationwide, according to BioBot . According to The Independent , Arcturus was first detected in January. It is now spreading in like wildfire in India.  Like all the Sons of Omicron, this variant is "the most contagious yet," but has relatively low disease severity. One point of concern is that officials believe an "infa...

  The public health community is wringing its hands over a new variant. New variants take over periodically because they evolve better fitness and this allows them to supplant older variants. We've learned by now what trouble this can cause.  Delta took hold in summer/fall 2021. It was more infectious and caused more serious disease, and it killed a whole bunch of people. Then about a year ago Omicron started up. It caused less serious disease but was more contagious so it also caused a big surge that killed a lot of people. Since the Omicron wave died down, people who worry about these things have been waiting for a new variant to pop up and renew our misery.  First it was BA.4 and BA.5. Then it was BA.2.75.2 . When that didn't cause the expected problems, attention shifted to BQ.1 and BQ.1.1 . The new boogeyman is another son-of-omicron dubbed XBB.1.5. This one is concerning because of how quickly it is taking over. According to a guy at Northwestern University who tra...

This appears to be cave-in weekend for authoritarians around the world. First, Iran's attorney general announced it would abolish its "morality police." Then China announced it was going to back off its zero-COVID policy. It doesn't appear that all restrictions are being lifted everywhere. Instead the plan is to make the policy "more targeted and less onerous." Still the reversal seems significant, with restrictions—including the requirement to test negative before venturing anywhere in public—being lifted in most major cities. The authorities are spinning this as evidence of a "win" of sorts. The idea is that China weathered the Delta storm and can now relax because the Omicron variant is less deadly.  That is pretty much hogwash, a ccording to Linda Bauld , professor of public health at Edinburgh University: “With Omicron, certainly from the studies [so far], there may be some small reduction in disease severity but not a huge one.” It's g...

  Today my news feed contained this story about a couple of new variants called BQ.1 and BQ.1.1. These variants were previously lumped-in with BA.5, from which they descended.  They were broken out separately a month ago, and officials worry about them because of how fast they're increasing—growing to 10% of U.S. cases in one month. The article claims they are rapidly spreading in Europe too, though I can't find any mention of them on the EU Dashboard . Lim Lab lists these two variants as accounting for about 4% of Arizona cases as of October 3. Most recent data from October 10 shows only BA.5, but there are very few sequences involved in that calculation. As with the other variants, the worry is that these variants are increasing because they are better at  evading immunity from previous infections and vaccinations. There is also concern that monoclonal antibody treatments may not be as effective against them.  That's the same thing they said about BA.2.75 which I...

  Today's geek-out post is inspired by an NPR Morning Edition   story  yesterday about what is likely a new infection wave gathering steam in Europe. Here is a chart from Our World in Data: The story notes that we don't know yet whether this increase is associated with new variants, such as BA.2.75.2 that I was fretting about a week ago. I checked the EU Dashboard and indeed it looks like the OG Omicron is still dominant in France, Germany, and Italy (99.8% - 100% of sequences).  That's odd because BA.5 is dominant here, with BA.4.6 close behind, and zero percent cases of OG Omicron (BA.1.1 or BA.1.1.529) according to the CDC : I won't be losing any sleep over a new wave just yet. Current modeling shows that even in a scenario where there is a new variant it shouldn't get too bad depending on how many people get the new bivalent booster: The dotted line is the actual observations, and we have been beating the expected numbers for the last couple of months. The so...

  For previous waves, the pattern has been that just as a wave crests and starts dissipating, a new variant comes along to take up the slack. It happened with beta, delta, omicron and sons of omicron.  I foolishly thought this time might be different, because the current BA.4/5 wave is bottoming out. To date I have not heard about any new variants coming along that would spoil the party. Until today, that is, when I saw this article in the NY Times. They describe a new Omicron subvariant called BA.2.75.2.  As with other sons of Omicron it has tricks for avoiding natural and vaccine-induced immune response, including from the current bivalent booster.  In lab tests it evaded all but one of 13 monoclonal antibodies currently in use. It also did much better at evading antibodies derived from recent Swedish blood donors than did previous Omicron sub-variants. This from a preprint study  entitled "Omicron sublineage BA.2.75.2 exhibits extensive escape from neut...

A story out of the UK reveals an irony about the Omicron variant. It is less deadly , but has killed more people than Delta. How can both things be true? It's a numbers game.  Delta was more likely to put you in the hospital or kill you. But Omicron is a lot more contagious, with more ability to evade antibodies from vaccinations or previous infection.  So Omicron and its sub-variants are causing more infections. About a month ago I blogged about how seemingly all of my friends were getting it. That has continued. Because it is causing more infections, it is causing more deaths even though it is less pathogenic. A virologist in the article put it this way:  “To use a shooting analogy, Delta is like a sniper rifle and Omicron is more like someone with an Uzi (machine gun). So each individual shot might be less likely to kill someone but there’s a lot more bullets." In the U.S., it has been especially bad in rural areas. Experts attribute that to low vaccination rates. M...

In an earlier blog , I summarized some information on why so many vaxxed people were getting infected and what immunity was doing to those at-home antigen texts.  In that post I said: "Omicron cousins are less likely to cause severe disease, even if they are more contagious." In response to that @SuziSuperKitn on Twitter sent me this link to a Reuters article about a month ago, that reported on a preprint study looking at the question of whether Omicron in its various flavors is really less pathogenic. Note that this is a preprint, which means it has still not been reviewed. It is not unusual for the peer review process to turn-up issues with the study methodology that invalidate the study or require modifications. But this one includes authors from Massachusetts General Hospital and Harvard Med School. Such researchers don't usually do shoddy studies so it's a good bet it does not have fatal flaws. What they found, in a nutshell, is that if you just compare mortali...

  For today's bite-sized post here's a cheerful thought: What if you could get COVID-19 not once, or not twice, but over and over again—even several times in the same year? That's the depressing prospect that is being considered now, according to an article in the New York Times . The problem is that the virus is continuing to mutate, and is currently doing so from a base of the Omicron variant, which was good at evading antibodies from vaccinations and previous infections to begin with. As it continues to spin off new sub-variants, these can be expected to evolve in the direction of acq uiring mutations that make it  more contagious and/or even better at evading immune responses. Juliet Pulliam, an epidemiologist at Stellenbosch University in South Africa was quoted in the article as saying It seems likely to me that that’s going to sort of be a long-term pattern. The virus is going to keep evolving and there are probably going to be a lot of people getting many, many rei...

  A recent piece in The Atlantic suggests we could be in the middle of an "invisible" wave . It puts me in mind of the tree-fall-in-the-forest conundrum.   In the U.S. our case surveillance systems have always been crappy because they rely on self-selected participation rather than random sampling. The two approaches can give very different pictures of infection rates.  Worse, now we are not even getting an accurate count of the self-selected tests. This is for two reasons . First, people are having milder cases and they may not even recognize they have COVID-19, or may not be seeing physicians if they do.  Second, people have ready access to in-home antigen tests. I have noted before that those are of questionable accuracy , especially for asymptomatic infections. So people could have a false negative test and go about their business unknowingly spreading the disease.   But even if they get a positive test there is (as far as I know) no way to repor...

  These last few weeks have been a relief. I've reduced masking a lot and have felt better about going out to eat (though still only outside).   Still, I've been waiting for the BA.2/"stealh" Omicron shoe to drop and force me back into January-style behavior again. Yesterday the CDC said it makes up almost three quarters of the variants detected in infected people in the U.S.  It is spreading rapidly in China , but that is different from the U.S. because so few people in China have been infected or vaccinated with an effective vaccine. On the other hand it is spreading like wildfire in Europe, which is not so different from the U.S.  Experts are thinking it probably won't cause a severe wave here in the U.S. I sure hope they are right. Unfortunately there are other variants brewing. They are recombinant strains, produced when two variants infect the same person and share generic material. One is called XE. It is a combo of BA.1 and its cousin BA.2, and i...

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 is the Arizona pandemic numbers summary and graph of seven-day average of new cases for the week just ended*: Case rates are in the green both statewide and in Maricopa County. The graph shows we topped out on January 24 and are coming down. That's almost exactly when the modelers predicted  it would happen. The only cautionary note is that during the Delta wave there was a false peak at the end of August after which  things seemed to be coming down, only to ramp back up and surpass that rate a little in early December.  Let's hope that doesn't happen again because of the "stealth" Omicron . It has been detected in Arizona and is estimated by Danish researchers to be 50% more transmissible. If we have passed the peak, it was some peak. Previously, the worst seven-day average for Arizona was in January 12, 2021 at 9,808 cases. The peak on January 24, 2022 was 20,778, more than two times higher! Deaths are in the red. The media are freaking out about it. B...

  There is a new variant spreading that people are calling "stealth" Omicron. It is a variant of of the existing Omicron variant. According to the Washington Post  the variant has been detected in many countries, and this includes India, Britain, and Denmark. Three U.S. cases have been detected at a hospital in Houston. The virus is similar to Omicron, labeled BA.1 by researchers, but contains some mutations that make it different. The reason is it called "stealth" is that,  according to the UK Health Services Agency: Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously.    This is also known as an "s-gene dropout" and you have seen it referred to in this blog before. Variants that have this feature can be quickly identified in the course of processing PCR tests. If a variant does not have the fea...

  Schools have been under stress due to the pandemic, but now Omicron is making things worse. A lot worse. Here in Arizona, staffing company Educational Services Inc. says they have seen a 10%-20% increase in absences, depending on the district. Phoenix Union district is reporting "between 10% and 15% staff absences and around 15% to 16% student absences." Some substitutes are staying away too, in no small part because of our governor's public illness campaign . One substitute teacher on  reddit  said: I just saw that Peoria Unified was contemplating having kids sick with covid, back at school after 5 days.... Masks are optional. I'm a substitute, and this is why I will not substitute anymore. It's not only happening here. The situation is similar  in Florida , where they are also experiencing a shortage of bus drivers.   My sister, who is a high school teacher in Illinois, tells me that her district is so desperate for substitutes they are trying t...

  As I noted on Sunda y, Omicron has finally started doing its dirty work in State 48. As of then, case rates had doubled over the week.   Yesterday AzDHS put out a chart that is getting a lot of attention in the media that shows the same thing: Then also yesterday, AzDHS reported 14,192 new cases. Some outlets, like usnews.com couldn't resist sensationalizing it, claiming it was the highest new number of cases in a year. I heard the same claim in a radio report on KJZZ. Well yeah it was, but the number was high because of holiday reporting snafus. The usnews.com story said this, but it was in one sentence in the third paragraph.  More responsible outlets presented the number in context. For example,  azfamily.com  reported the number but immediately and extensively quoted health officials who explained that the number was an anomaly. But even they couldn't resist a headline with that huge number. Everybody knows those daily counts are not reliable.  ...

  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...