Part the First: Retrospective Notes on a Pandemic. BMJ, formerly known as the British Medical Journal, has recently published two interesting pieces on COVID-19. The first is an analysis by Anthony Costello, who was previously Director of Maternal, Child, and Adolescent Health at the World Heath Organization: UK decision not to suppress covid raises questions about medical and scientific advice. Dr. Costello focuses on the United Kingdom, but his analysis applies to all countries that had the means to suppress the pandemic but did not. In the aftermath of a deadly pandemic, reasoned discussion of what was done and more importantly, not done, has been rare. I am not an infectious disease expert or an epidemiologist, but I have been adjacent to both disciplines for my entire career in biomedical science. I was asked in the spring of 2020 how long I thought COVID-19 would last. My answer was “three years, if we suppress spread of SARS-CoV-2.” I was dead wrong, but suppression might have worked. As Costello begins:
Early in the covid pandemic, evidence emerged from several East Asian countries that suppression could lead to successful control. Yet the UK did not adopt the approach. Suppression aims to avoid national lockdowns and maintain economic activity for most of the population by introducing surveillance systems to bring new outbreaks under control quickly, thus reducing the reproductive rate of infection (R0) to below 1 and causing the epidemic to wither. In May 2020, Jeremy Hunt, then chair of the health and social care select committee, criticised UK government advisers for failing to recommend a response focused on suppression of the SARS-CoV-2 virus from early in the pandemic, calling it “One of the biggest failures of scientific advice to ministers in our lifetimes.” Why was suppression not recommended, and what can be done to improve advice in future? (emphasis added here and below)
In my view, which is similar to the conclusion here, the response to COVID-19 failed to recognize SARS-CoV-2 as something “new,” although SARS and MERS were clear messages from 2002 and 2012, respectively (and as noted in Links yesterday, nine cases of MERS have recently appeared, with two deaths). In the UK strategy followed what might be done during an influenza epidemic (as we whistle past the graveyard about bird flu). From the article:
All pandemics are different, but SARS CoV-2 had an R0 value more similar to the coronavirus SARS-CoV-1 than to influenza. Influenza spreads too fast to be controlled by testing and contact tracing, but coronaviruses have longer incubation periods and potentially can be suppressed, as evidence from early in the pandemic showed. Several East Asian states avoided prolonged national lockdowns with responses focused on suppression initiated early in the pandemic.
Experts had dealt with two previous coronavirus epidemics: severe acute respiratory syndrome (SARS) in 2002-04 and Middle East respiratory syndrome (MERS), first reported in 2012. Two papers after the SARS outbreak showed that coronavirus infections, with slower transmission rates and longer incubation periods than influenza, could be suppressed.
One paper… showed that isolation and contact tracing could bring about control even if asymptomatic transmission was as high as 40% of all transmission. At the start of the epidemic in Wuhan, R0 for SARs-CoV-2 was estimated to be close to 3, similar to that seen in the SARS outbreak, indicating that similar suppression measures might have worked. (Another) paper, concluded that coronavirus epidemics require a different approach (using isolation and quarantine measures) to control than pandemic influenza.
In the early days of COVID-19, community health workers, including physicians, were called upon to respond in China, Japan, and Korea. They held the line for as long as they could in a world where most of the “Global North” thought of other things. This was also a teachable moment for the medical students in my tutorial groups in February and March of 2020. They learned very quickly they had signed up to be those who run toward a pandemic instead of away. A few were recalcitrant, which is worrying. According to this article, in the UK “750,000 people, many with health skills, responded to a call for volunteers. Most were never used in any capacity and none to support case finding. The government could have redeployed environmental health officers, sexual health contact tracers, or medical students to case finding and contact tracing but did not do so.” The result was that:
Over the next three years, death rates in China, Japan, and South Korea were five times lower than in the UK (fig 2). Demographics seem insufficient to explain these huge differences: Japan and South Korea had similar gross domestic products (GDP), life expectancy, and age profiles to the UK. Had the UK followed the same strategy and achieved the same excess cumulative death rate by March 2024 as South Korea, 69 instead of 344 deaths per 100,000, it might have prevented up to 180,000 UK deaths.
The US response was different, but not better. The US medical establishment was not particularly useful from the beginning of the pandemic. But in my view the conclusions are inescapable. Suppression of SARS-CoV-2 could have worked, but that very notion has been flushed down the memory hole. Finally:
The UK was once rated the second-best country (after the US) in the world for pandemic preparedness. Covid-19 caused over 230,000 civilian deaths, three times the number during the Blitz. The root failure of the UK response to covid was a strategy devised in January and February 2020. Yet the four chief medical officers in their 2023 technical report for future advisers maintain that their recommendation to “contain, delay, research, and mitigate” was broadly correct, and the report does not recognise suppression successes that led to much better survival rates and lower economic damage in other states.
Five years on, many of the people who developed the UK’s flawed response are still in post; they have not changed their views on suppression, and little has been done to improve government pandemic advice committees or to introduce detailed governance rules for the UK’s future pandemic response and resilience. The covid inquiry and the UK medical establishment should properly critique this public health failure.
Ditto for the United States. In the US, one of the chief advocates of the “Let ‘er rip!” strategy, so that in a matter of months herd immunity would be reached and the pandemic would become a thing of the past, is now Director of the National Institutes of Health. Jay Bhattacharya, MD-PhD (MD but never a physician and the PhD is in Economics), is a principal author of the Great Barrington Declaration (GBD). The GBD still seems to be policy, even though, and I repeat myself to the point of irritation, durable immunity to coronaviruses, either through prior infection or vaccination remains a noble but unattained goal for at least eighty years. Thus, based on the settled science of coronavirus pathobiology, herd immunity to SARS-CoV-2 was an unlikely possibility. One may well wonder if this continuing asininity has deeper political and economic roots. And contrary to what Matt Taibbi seems to believe, Jay Bhattacharya was never “censored.” His “Merchant of Doubt” libertarianism was skewered by scientists paying attention, though.
Part the Second: The People’s Attitudes to Government and Healthcare Administrators Changed During the Pandemic. This report (paywall) is also from the UK, but the message travels well:
News reports about politicians and government officials ignoring guidelines during the pandemic was a turning point for many people, the UK covid inquiry heard.
The underlying document is here. The following is a good summary:
- Many contributors (to the survey) felt the guidelines around testing were initially clear, but confusion grew over time due to changing rules and lack of awareness about contact tracing.
- People were left confused by changes to official government guidance about when to test and self-isolate. Uncertainty about the rules in place at any one time meant that some people decided to do what they thought was appropriate regardless of whether or not it aligned with the rules.
- Some contributors described how their awareness and confidence in knowing when to test grew over time as a result of having symptoms and experiencing the virus or hearing about the experiences of others with Covid-19. However, some contributors also told us that they were confused about knowing the difference between symptoms of Covid-19 and other similar illnesses, such as colds and the flu.
- Contributors described difficulties accessing or keeping up with information about testing. This included people who did not use the internet and people whose first language was not English.
- Some contributors explained how they had found contact tracing information unclear, that it was hard to understand the purpose of it and to follow the guidance correctly.
- Few people seemed aware of the financial and practical support that was available when self-isolating.
The US responses to COVID-19 were different but the results of a US Covid Inquiry would be similar. From the beginning according to our healthcare leaders, COVID-19 was nothing more than a cold from which recovery was just a matter of time. No, not really. I don’t know how many colds I have had in this long life, but I never lost my sense of smell because of one (after the nasal congestion went away). Neither I nor any friends of family ever suffered from “Long Cold” for years after. No one ever died of Long Cold as far as I know, but I had two friends who died of COVID-19 sequelae. I received two COVID-19 shots (Pfizer/BioNTech) and so far I have not had COVID-19, as far as I know. But I have avoided crowded indoor spaces to the extent possible while remaining perfectly happy. Several coworkers have gotten multiple booster shots and have had COVID-19 multiple times. And contrary to President Biden, the COVID-19 vaccines did not work as he said they would.
Through all this, scientists, including many friends and colleagues, marvel that they are losing respect they have not already squandered? Can my colleagues and I get it back? Only if we start telling the disinterested “truth” as we understand it. Stranger things have happened, perhaps.
Part the Third. Pathogenic Bacteria Can Eat Plastic and Form Stronger Biofilms. To which one can only reply, what took them so long? As Ian Malcolm/Jeff Goldblum put it, “Life, uh, finds a way.” As an aside, I generally do not read much science fiction, but Michael Crichton had a way with the biological form of the genre, beginning with The Andromeda Strain. Jurassic Park was a good read and better movie (to me) but required even more suspension of disbelief than The Da Vinci Code (I would nevertheless recommend in the illustrated version, which I picked up from a Remainder Table).
Actually, it has been known for some time that bacteria will “learn” to eat plastic. They are versatile organisms and given time they will evolve to eat what is available. They like sugar, starch, fat, and protein just like us, but they can get by on little and are very patient. A current paper is Cell Reports tells us that Pseudomonas aeruginosa clinical isolates can encode plastic-degrading enzymes that allow survival on plastic and augment biofilm formation (open access but very technical). From the Summary/Abstract:
Multiple bacteria encoding plastic-degrading enzymes have been isolated from the environment. Given the widespread use of plastic in healthcare, we hypothesized that bacterial clinical isolates may also degrade plastic. This could render plastic-containing medical devices susceptible to degradation and failure and potentially offer these pathogens a growth-sustaining substrate, enabling them to persist in the hospital-built environment. Here, we mined the genomes of prevalent pathogens and identified several species encoding enzymes with homology to known plastic-degrading enzymes. We identify a clinical isolate of Pseudomonas aeruginosa that encodes an enzyme that enables it to degrade a medically relevant plastic, polycaprolactone (PCL), by 78% in 7 days. Furthermore, this degradation enables the bacterium to utilize PCL as its sole carbon source. We also demonstrate that encoding plastic-degrading enzymes can enhance biofilm formation and pathogenicity. Given the central role of plastic in healthcare, screening nosocomial bacteria for plastic-degrading capacity should be an important future consideration.
Or in bullet points:
- Clinical isolate of Pseudomonas aeruginosa PA-W23 can degrade a medically relevant plastic
- Encodes novel polyesterase Pap1, which is responsible for plastic-degrading activity
- aeruginosa PA-W23 can use plastic as a carbon source to grow
- Pap1 can influence virulence phenotypes, such as biofilm formation, in the presence of plastic
Why is this important? P. aeruginosa infections typically occur in healthcare settings and are often resistant to antibiotics. From CDC:
Some types are resistant to nearly all antibiotics, including carbapenems, known as multidrug-resistant (MDR) P. aeruginosa. In 2017, MDR P. aeruginosa caused an estimated 32,600 infections among hospitalized patients and 2,700 estimated deaths in the United States.
Pathogenic bacteria are also very good at building their environment in the form of biofilms, where they can effectively hide from antibiotics. Biofilms form on surgical implants and catheters, making chronic infections difficult to treat. P. aeruginosa is often the culprit.
Will these latest “superbugs” eventually cause widespread problems? Probably not, but it is important that biomedical science stays ahead of them. Sixty years ago, it was generally believed (but not by disinterested microbiologists) that infectious diseases were becoming a thing of the past. Our misuse of antibiotics proved that notion false with the development of antibiotic-resistant bacteria. Sir Alexander Fleming predicted this would happen if penicillin were misused, especially as it was in the United States beginning in the 1950s. In the 1960s the standard of care for viral infections of my very good group of family doctors included oral penicillin. I went to the library and looked up the pill in the Physician’s Desk Reference, now available online. The budding biologist in me was puzzled at this practice. Except for secondary bacterial infections during a viral infection (which may have contributed to the virulence of the 1918 flu pandemic), antibiotics are not recommended for the common cold and similar illnesses. But they were (over)used. Now they are an essential ingredient in animal feed used in CAFOs. To the unthinking technologist, can implies ought and often leads to novel problems.
In my view, the likelihood that we will stay ahead of bacteria during the current attack on American science is small. The common answer to the contrary is that Big Pharma will do the work. No, probably not. A good friend and colleague who left academia to work in Biotech eventually took his research to Big Pharma. He was never able to talk to me in detail about his work, but it was on the development of a completely new approach to antibiotics. This was an exciting time for him. He was working with some of the best scientists and scientific workers with no constraints on resources. The Big Pharma corporation that had bought the “intellectual property” and lured him in nevertheless pulled the plug, because they apparently decided there was no upside to their “investment.” If the drugs cured intractable bacterial infections, no matter how much they cost per course they would be a financial loss. My friend retired to a house with a view in the mountains. Is this a true story? Undoubtedly. Granted, it is only one story. But has it happened before, and will it happen again? Undoubtedly.
Part the Fourth. The Secretary of Health and Human Services Speaks. Or as STAT+ puts it, In combative hearings, Kennedy defends HHS cuts, backtracks – and lashes out (paywall, but you can get the photograph at the link; I do not know if it was taken during the May 14 hearing). The gist:
In hours of combative congressional hearings Wednesday, health secretary Robert F. Kennedy Jr. swung between defending sweeping changes at his agency and backtracking on aspects of a reorganization he nevertheless said would be “painful.”
He repeatedly cast doubts on reports about negative impacts of the changes, often calling them a “canard.” For instance, he claimed that amid sweeping cuts to his agency, “we did not fire any working scientists.”
His statement before the Senate HELP Committee seems to contradict news reports and former agency staff, who say deep funding cuts have halted scientific research and clinical trials across the country.
One employee at the National Institutes of Health told STAT they were “100% sure” Kennedy’s assertion was false. Another person recently employed at the agency said they knew of “plenty of scientific staff” who had been among the nearly 20,000 employees HHS is shedding. FDA food scientists were fired, though some were later rehired, and support staff let go. Scientists who relied on nearly $2 billion in NIH grants have lost that money.
I would point out here that “working scientists” do not get much done when those who staff their laboratories and provide institutional and administrative support that make research possible go missing.
Senator Tim Scott (R-South Carolina) asked the Secretary about the “continuation of minority health programs (and) Kennedy pointed to a program that was terminated because it had elements of DEI — though he committed to supporting other kinds of minority health programs.” As they say in these parts, “Yeah, right.” The largest blemishes on American healthcare are the wide disparities in outcomes depending on socioeconomic factors. If noticing the obvious is “DEI,” then there is no dealing with these people.
Regarding Senator Bill Cassidy (R-Louisiana), the former practicing physician who clinched the nomination of RFKJr as Secretary of Health and Human Services:
And after Kennedy misrepresented vaccine safety testing standards, Cassidy fact-checked him, pointing out that rotavirus, measles and HPV vaccines were evaluated against placebos, and others were tested against previous versions of the vaccine.
And:
In some cases, Kennedy told lawmakers that what appeared to be cuts were actually shifts of agency functions into the new Administration for a Healthy America — an explanation several Democrats found unsatisfying. (HHS hasn’t laid out official plans for AHA, and its funding level isn’t yet clear.)
For instance, he told senators that the CDC branch that worked on Alzheimer’s disease would be folded into the AHA. “A lot of the reports that whole divisions have been liquidated were just wrong,” Kennedy said.
Will the Administration for a Healthy America become another very powerful but faux government department like DOGE? If so, perhaps they can use the book written by our future Surgeon General as a guide to make America healthy again, while recommending glucose monitors from Levels, the company founded by her and her brother, and cookbooks that require organic radishes and certified free-range, pasture-raised chicken and wild Atlantic salmon. It will be difficult to find and pay for these in the food deserts of America, where health outcomes are “problematic.”
Anyway, regarding the Secretary’s dissembling, a 50% budget cut forced on the largest and most productive biomedical science organization in the world, albeit one that could use several improvements, necessarily pushes thousands of our scientists into the outer darkness. Mostly, it seems, because their research does not align with Administration “priorities.” This is a new thing in American biomedical science. The same thing is happening to the National Science Foundation, the other crown jewel of American science. Trofim Lysenko has been mentioned here before and in Links on Wednesday, May 14th. History rhymes yet again? It would seem so.
See you next week, with good things about current science, if all goes according to plan.
