This will be short again because of the amount of time needed still early this past week to finish creating all of the US state graphs. Next weeks should be back to normal. The only thing that might change that is if the variant data I use is broken down further, which requires an overhaul once again.
Hawaii is a good indicator of what is coming. They are affected much earlier than the rest of the US with the FLiRT variants because of vacation travel from Oceania and SE Asia. Wastewater readings (brown line) are quite high.
The TLDR: It’s back. You really should be wearing a respirator indoors. Sadly, there won’t be vaccine in time for these variants and much of the population hasn’t been boosted this year.
H5N1
This is a graph of wastewater readings for H5N1 in California. The burnt umber squares are detections of H5N1. I’m mostly concerned about it in Palo Alto and San Francisco. I truly hope this is a signal from cattle or wild bird runoff. Cattle seems unlikely though because of the locations.
Wild birds are a possibility, but do they really excrete enough to create a sufficient signal in wastewater (except Canadian geese, they have super-pooper superpowers).
I really hope this isn’t evidence of movement of H5N1 into a human population in a high-density area. That could easily spell the start of a major global disaster.
SCOTUS
The Supreme Court struck down the Chevron deference. In essence, it has been the administrative practice of allowing regulatory agencies with expertise to take the lead in policy. Now, any of those decisions are up for litigation.
This matters because without the Chevron deference in practice, dangerous drugs and medical products could enter the marketplace more easily (FDA), companies could pollute the environment and provide products that cause harm (asbestos is a good example), workers will have less protection (OSHA), food could become more dangerous (FDA and USDA), public health measures could be limited (CDC), and healthcare could become more dangerous (CMS). That’s all just the tip of the iceberg.
An article in JAMA warned of the implications in March, stating it “threatens to roll back the very regulations that have advanced medicine and public health through medical product regulation, reduced disparities in health care access and coverage, and allowed for deliberate and informed responses to public health crises. The analogous disempowerment of agencies tasked with safeguarding the environment, housing, civil rights, and workers’ rights will similarly threaten regulations directly implicating social determinants of health.”
The entire country is going backwards in time, and not in a good way.
Since a new variant wave is starting to hit the US, I spent a lot of time trying to find data that could help paint a larger picture of what is happening in a particular state given that much of the CDC data has gone extinct. I’ve stayed off social media to get this done. It was far more work than expected. In the past, it was possible to download 3-4 national data sets and then pull from them locally. Now, the way the data is configured online, I have to download individual data sets for each state each week. It’s frustrating.
Here’s a breakdown of the visualizations on the US page. Given the changes in data for many of these metrics, the most important thing is to look at the change over the last couple of months as opposed to comparing one particular point to one a few years prior. This example is California.
Early Indicators Tab
The background is the percentage of each variant colored using the same color scheme as can be found on covariants.org.
The black line is the PCR positivity rate which is on the right axis.
The brown line is wastewater and is really more of a relative scale, especially how the baseline that the CDC uses isn’t constant.
The hollow black line is COVID emergency department visits.
Google Searches – This is the newest set of data I’ve added to the site. It’s been available for a long time, but given that there was plenty of hospitalization data until recently, it seemed a bit superfluous. The search terms are listed in parentheses. This data comes from the Delphi Group at Carnegie Mellon University.
Control (type 2 diabetes, urinary tract infection, hair loss, candidiasis, and weight gain) – These are medical search terms that have nothing to do with COVID, although one could argue that searches for diabetes will be increasing over time as a result of COVID infections.
Nasal (nasal congestion, postnasal drip, rhinorrhea, sinusitis, rhinitis, and common cold)
Oral (cough, phlegm, sputum, and upper respiratory tract infection)
Fever (fever, hyperthermia, chills, shivering, and low grade fever)
Throat (laryngitis, sore throat, and throat irritation)
Lung (shortness of breath, wheeze, croup, pneumonia, asthma, crackles, acute bronchitis, and bronchitis)
Senses (anosmia, dysgeusia, and ageusia – these are the proper terms for the loss of smell, foul taste, and loss of taste, respectively). The Delphi Group made a particular point that “The symptoms in this set showed positive correlation with cases, especially after Omicron was declared a variant of concern by the WHO.”
Medical Care – these are the percentages of diagnosed COVID patients in each of these settings.
Outpatient
Emergency Department
Hospital admissions – this is a particularly lagging indicator because it is coming from claims data.
The most common cause of GAS is Streptococcus pyogenes. They look like clusters of grapes, here seen being attacked by a neutrophil, an immune system cell.
Viral infections of the upper respiratory tract (including Influenza, RSV, and COVID-19) are associated with increased susceptibility to invasive diseases caused by Streptococcus pyogenes (group A streptococcus), including pneumonia, necrotizing fasciitis, toxic shock syndrome, and bacteremia.
There has been a sharp rise in non-invasive GAS in children in the last couple of years, such as this study involving pediatric clinics in France.
Of course, none of this really should be surprising when we know that COVID causes immune system damage. In addition, the virus likes to hang out in places like the tonsils.
This is a brief account of necrotizing fasciitis in a 55-yo male who had a mastectomy for breast cancer (yes, men do get breast cancer) as a means to provide just how damaging this can be. It can be much worse than this.
Three months after his mastectomy, “the patient revisited, presenting symptoms of swelling of the entire left arm which started from the axilla 2 weeks ago, high-grade fever for 5 days, severe pain, multiple wounds on the lateral aspect of his elbow with bloody discharge.”
He had to undergo surgical debridement of the wounds on his elbow. That’s a procedure to cut away dead, diseased, or infected tissue to give healthy tissue a chance to recover. This is how is elbow looked a two weeks (a) and six weeks (b) after surgery.
After cleaning out the wounds, it was apparent that the bacteria had eaten completely though his scalp leaving the skull exposed.
Here you can see the extent of damage to his face and scalp ad the debride the tissue in the affected area, including enucleating (removing) the left eye.
He will carry the scars of this for the rest of his life. (A, B) are images at six months after surgery, (C, D) are images at one year after surgery.
Fortunately, GAS is relatively rare. What doesn’t make sense is increasing the risk of it and other diseases by getting infected with COVID.
Just a picture from my trip almost exactly 5 years ago so people who didn’t want to see those in the GAS section have a buffer.
“Strikingly, sC5b9 levels [a biomarker for microthrombi] were abnormal even in children with minimal disease or an incidental finding of SARS-CoV-2 infection, suggesting that any exposure to SARS-CoV-2 may be sufficient to induce elevations in this biomarker. In addition, schistocytes were prevalent in blood smears of patients with minimal COVID-19, severe COVID-19, and MIS-C. IL-8, a marker of endothelial damage, was also significantly higher in patients with MIS-C and severe COVID-19 compared with the minimal COVID-19 group [ie, even in mild infections, COVID causes blood clots and vessel damage].
The presence of elevated sC5b9 even in children with minimal symptoms of COVID-19 disease is particularly striking. This finding implies that SARS-CoV-2 clinical syndromes are associated with robust complement activation, even when symptoms are minimal.”
“In the main and replication cohorts, individuals with SARS-CoV-2 infection had a higher adjusted hazard ratio (HR) for post-acute respiratory sequelae compared to the general population (main: HR, 1.68 [95% confidence interval (CI), 1.62–1.75]; replication: HR, 3.32 [95% CI, 3.27–3.37]) in Table 2. Furthermore, patients with SARS-CoV-2 infection had an increased risk for acute respiratory complication compared to non-infected controls (main: HR, 8.06 [95% CI, 6.92–9.38]; replication: HR, 4.17 [95% CI, 3.90–4.45]). When directly comparing the risk for acute respiratory complication between SARS-CoV-2 and influenza infections, SARS-CoV-2 infection was significantly associated with an increased risk (main: HR, 4.32 [95% CI, 2.73–6.83]; replication: HR, 6.51 [95% CI, 5.38–7.87])”
H5N1
The current situation in the US can be captured in two screen grabs. The higher these number go, the greater the chance of a nightmare beyond most people’s comprehension.
Well, I wrote a book about the psychological underpinnings explaining how it’s possible that one could work in the area of health promotion & disease prevention, yet discount an ongoing pandemic for an omnipresent…
No big updates this week because I took a much needed weekend away. However, I will point out that two of the FLiRT variants are both at about 25% each of samples in the US.
With other variants, hospitalizations increase when we are around the 50% mark. I would estimate that would be sometime around the end of July.
The biggest news this week was of a third farm worker with H5N1. The most concerning part is that “The patient reported upper respiratory tract symptoms, including cough without fever, and eye discomfort with watery discharge.” The question then becomes one of if the virus has adapted more to the human respiratory tract. That poses obvious challenges, particularly around gaining easier respiratory spread, thus leading to higher chances of mutations that make spread easier or make the virus more damaging. It seems like we have crossed a threshold though and the only thing ahead is for this to get worse, especially in a culture of pushback against any mitigation efforts. The costs and suffering will be far worse the less that is done. It will be particularly interesting to see how COVID-damaged immune systems respond. I think we are heading into a very bleak period.
