I will be using SARS-CoV-2 and COVID interchangeably, but SARS-CoV-2 is the virus that causes COVID, which is the disease.
An interesting study came to my attention this week that has me thinking much more about the dynamics of the interaction between influenza A virus (IAV) and the SARS-CoV-2 virus in a way that hadn’t occurred to me before.
The investigators infected a cell culture with IAV and then used spike protein from SARS-CoV-2 attached to a marker to study uptake of the spike protein. They found that “cells became highly sensitive (up to 10,000-fold) to the pseudo-SARS-CoV-2 virus after infection with IAV at different doses.”
They proceeded to repeat the experiment, but instead using live SARS-CoV-2 virus and then measured some of the genetic sequences that were produced as a metric for viral replication. They found that “cells that are inherently susceptible to SARS-CoV-2, IAV preinfection further increased SARS-CoV-2 infectivity by > 5-fold.” This suggests the production of far more of the COVID virus if they are already infected with influenza A, meaning that they will be much sicker but also much more likely to spread COVID because of the higher viral load.
They continued their study in mice. “A significant increase in SARS-CoV-2 viral load was observed in lung homogenates from coinfected mice compared to homogenates from SARS-CoV-2 single-infected mice…The lung histological data further illustrate that IAV and SARS-CoV-2 coinfection induced more severe lung pathologic changes, with massive cell infiltration and obvious alveolar necrosis, compared to SARS-CoV-2 single infection or mock infection.”
They went on to test a few other respiratory viruses to see if the same COVID virus amplification would occur, and it didn’t. This suggests that there is something unique about IAV that enhances COVID infection. In addition, they studied ACE-2 receptor (the binding site for COVID) expression and found that cell cultures infected with IAV expressed THREE TIMES as many ACE-2 receptors. In coinfection of the two viruses, ACE-2 expression increased 5-28x based on the cell culture line used.
My interpretation of the increased ACE-2 expression is that it suggests that someone who is coinfected with both IAV and COVID is MORE susceptible to infections that use the ACE-2 receptor to infect cells.
At this point, you might be wondering why this grabbed my attention since it seems obvious that getting infected with two different viruses simultaneously is bad for someone.
H5N1 is a type of an influenza A virus.
If a H5N1 pandemic starts with rapid human to human transmission, we can expect a massive surge in COVID cases as well based on this evidence. The big problem is that hospitals wouldn’t be able to handle that increased demand. Early in the COVID pandemic, we saw the need for the use of BiPAP and CPAP machines in some areas to help reduce ventilator demand, which I had alluded to in an interview in 2006 (no paywall here). If we have a concurrent H5N1 and COVID pandemic, I don’t think we will be able to stumble through the demand anywhere as easily, and those who were on the front lines at the start of COVID would tell you it wasn’t easy at all.
Caregivers for Future Chronic Disease Pandemics Due to COVID
A really good review of the literature on respiratory protection was just published, prompting me to update two pages on this site. You can read about it and two other review articles in the first link. The second link addresses some of the misinformation about respiratory protection, particularly calling out the Brownstone Institute as well as the Cochrane Review that is often mischaracterized.
There is enough to cover with two topics this week. There wasn’t much new on H5N1 other than it is showing up in more places and continued resistance by big agriculture to allow public health to conduct surveillance monitoring. That seems to be an analogy to the “Goodbye Data” section related to COVID this week.
Worse, the CDC had pulled the plug on mandatory reporting of COVID data by hospitals on May 1st. I simply had thought that the consequences of this would be having a smaller sample size from which to draw inferences. I had been using two large data tables as important sources for the visualizations on this site.
Last June, the CDC had dropped the reporting requirements for suspected cases. I had developed a methodology to still visualize data adjusted for these changes and had thought that I could use the same approach for when some hospitals stopped reporting. The data from the CDC lags the reporting dates by two weeks, so this current weekend was when I expected to see just how that was starting to impact data. May 1st was on a Wed, so there would have been full reporting for the first half of the week and then voluntary for the last.
Unfortunately, that’s not how things played out. Instead, CDC just stopped updating the data tables altogether. This was unnecessary because many sites continued to report. I still continued to report daily for my hospital, even on weekends and did so this morning (Saturday). I can see what hospitals are reporting in my region of the state I’m currently in and saw that hospitals that represent 84% of beds in the region are still reporting. This makes me think that the CDC is still getting a lot of data but is not making it available under political pressure. Sometimes I honestly wonder if this site put enough pressure on the CDC or embarrassed them enough to drive the change. I know that many had tweeted out some of my tweets using it to @cdcdirector and @cdcgov.
I have been doing MORE to make this data readily understandable by the public which is part of the reason I created this site since nobody had been doing so. I hoped that a university might do something as well, but it didn’t happen. Early on we knew the need for data for making public health decisions.
In the article, they state “Persons can use information about the current level of COVID-19 impact on their community to decide which prevention behaviors to use and when (at all times or at specific times), based on their own risk for severe illness and that of members of their household, their risk tolerance, and setting-specific factors.”
Unfortunately, this is pretty much impossible to do now. In May 2022, the CDC dropped their “Community Levels” tool, which really had been efficient at minimizing COVID compared to their prior tool, but at least it was something. Even so, this data lagged quite a bit because of the 7-10 days it takes to develop symptoms after an infection. Forbes stated it nicely. “Relying on hospitalizations and deaths to determine what to do can be sort of like saying that you are going to wait until you’re fired or the company is bankrupt before determining whether you need to improve your job performance. Or waiting until the divorce papers arrived before saying, ‘Hmm, maybe I should start doing the dishes and not do all that that cheating stuff?’ Hospitalizations tend to occur about one to two weeks after people have gotten infected.”
True, things would have been far worse under a Republican administration, and there are many studies supporting this, leaving us three bad options for president. One who minimized the pandemic from the beginning setting the stage to make it political, one who is a science denying quack infested by a brain worm, and the current one who is following the minimizing lead of the prior in the support of politics. From a public health standpoint, we are screwed.
This is incredibly bad timing with the emergence of the FLiRT strains, not that any time is good IN THE MIDDLE OF A PANDEMIC.
SHAME ON YOU CDC
Antibiotic Resistance and COVID
A massive (n=892,312) global study and metanalysis of 173 studies on antibiotic resistance was published this week. What was particularly alarming is the high prevalence of resistant organisms among COVID patients.
Part of my role in healthcare is related to antibiotic stewardship and ensuring that patients with any of these above categories of resistant organisms are properly isolated to prevent spread. It makes me wonder if we should be asking patients on admission if they have a COVID history. If they do, I wonder if we should be doing surveillance cultures given these high rates to ensure that they are placed in contact precautions.
Antibiotics are useful when indicated. Unfortunately, many of the antivax/ivermectin grifters include antibiotics in their protocols. Antibiotics do as much for viruses as hydroxychloroquine and ivermectin – absolutely nothing. They are beneficial if there is a secondary bacterial infection, but widespread use of them pushes us closer to the post-antibiotic era.
One of the organizations pushing these protocols is the Front Line COVID-19 Critical Care Alliance (FLCCC). Their protocol BEGINS with ivermectin and hydroxychloroquine. Both have been shown to be useless for COVID, but they are making a lot of money of people by selling this stuff. I’ve previously written a rebuttal to one of the websites that is often used to push ivermectin. What is written in this screenshot is simply unsubstantiated garbage used for grifting patients.
DON’T DO THIS:
If patients don’t improve within three days, then they suggest adding antibiotics.
Imagine living in a world where tending to your rose bushes causes a small scratch to your skin or a small scrape to a knuckle like I had yesterday could become fatal if an infection invades.
The last time I spoke on antibiotic resistance was about 10 years ago. I’m going to provide a few slides from that presentation many of which contain references if interested. I would also recommend the book reviewed here if this topic interests you.
There is an early indication that KP.2 is causing trouble in the UK. Here is positivity over the pandemic using PCR for the area.
The US is just slightly behind the UK in the rise of dominance of it.
As a general thumb rule, I’ve noticed that hospitalizations tend to start rising rapidly when a variant reaches about the 40% mark of all variants in a country, so it will be interesting to watch what happens when the UK crosses that threshold. Currently the downward trend in COVID hospitalizations seems to have hit a plateau, suggesting that this estimate may prove to be correct again.
One of the problems with the new variants is a distinct growth advantage over JN.1. That will be the case for each variant to become dominant. Almost by definition, it has to have a spread advantage over those before it in order for it to gain dominance.
The advantage of KP.2 and KP.3 has been worked out by the Murrell Group in comparing to the JN.1 variant.
Some preliminary data suggests that these variants may also be more immune evasive, but fortunately less infectious. However, the lower number of COVID hospitalizations in the US during the past year compared to the rest of the pandemic suggests a lower number of infections, which may be due to prior infection or vaccination.
We know that immunity from both infection and from vaccination wanes over time. Given the low uptake of the most recent booster and the large proportions of those who were infected who don’t build antibodies, we have a large proportion of the population in the US that might be considered to be immune naive, especially in the context of a more immune evasive variant.
I would still advocate for a booster if you can get one because data with influenza suggests even when there is not a good match, there is still some protection provided from vaccine. However, all of this also emphasizes the need for good respiratory protection with a respirator as well as improved ventilation.
It also doesn’t help that the CDC seems to be sweeping COVID under the rug with the lifting of the healthcare reporting requirements on May 1 as well as removing the link to those data sets right on the front page of the healthdata.gov website. It used to say “COVID-19 Datasets” in the area indicated by the red arrow. I estimate that next weekend we will start to see the drop in reporting in the data, although since it happened midweek, it will be the following weekend when the scale of this change becomes most apparent.
The big change this week is that HHS no longer requires COVID reporting from hospitals. This is very concerning based on what happened when they stopped requiring the reporting of suspected COVID admissions last June. Here’s how that influenced the data in a number of major cities. The dotted line represents the reports received. There is a very clear drop in the admission numbers at that time.
Atlanta
Boston
Chicago
Cincinatti
Cleveland
Dallas
Indianapolis
Houston
Las Vegas
Little Rock
New York
It’s also suspicious that this change had been made when we were not in a surge, just like now. That made it much easier to let this slip by, such as can be seen in Denver.
It dawned on me that not only should I organize material about myths, but also make it easy to find truths based on primary sources. The first one in this section is Vaccines reduce the risk of hospitalization and death. There is a lot here to build out.
I had written about influenza A surging in wastewater at a treatment plant in Amarillo, TX on April 22. It was odd that CNN did a story about it on April 30. As a follow up, here’s the influenza wastewater curves from across the country, with that site highlighted. It’s good that it has come back down, but I still suspect that it means that H5N1 has entered beef cattle.
Cattle Workers
We also learned more about the dairy worker in Texas that had been infected with H5N1. A neuroscientist pointed out that this is likely a very neurotropic (affinity toward nerve tissue) virus based on the condition of the eyes of the dairy worker.
Also in Texas, “The first calls that Dr. Barb Petersen received in early March were from dairy owners worried about crows, pigeons and other birds dying on their Texas farms. Then came word that barn cats — half of them on one farm — had died suddenly…
…At the same time, on almost every farm with sick animals, Petersen said she saw sick people, too.
‘We were actively checking on humans,’ Petersen said. ‘I had people who never missed work, miss work.'”
