Toby Rogers is a political economist who is also strongly …

Comment on Natural vs. Vaccine-derived Immunity by Sean Pitman.

Toby Rogers is a political economist who is also strongly anti-vax. He is not a medical scientist or physician.

In any case, this particular article, by Rogers, distorts the data regarding vaccines and the position of Dr. Peter Aaby – who is a strong supporter of vaccines in general (although, when it comes to COVID-19 vaccines, he seems to favor the adenovirus-based vaccines, such as Johnson and Johnson, AstraZeneca/Oxford or the one produced by China’s CanSino Biologics, over the mRNA-based vaccines – since the adenovirus-based vaccines may have more benefit on reducing “overall mortality – Link). Note, however, that this study found that of the 31 deaths that occured in mRNA-vaccinated individuals, only two were from COVID-19. The rest were due to other causes. For the adenovirus-vaccinated group, two of the 16 deaths were from COVID-19. It’s very difficult, then, to determine a clear relationship here between the different types of vaccines and deaths not related to COVID-19.

“The study isn’t about the effectiveness of mRNA vaccines against COVID,” said Amesh Adalja, a senior scholar at the Johns Hopkins Center for Health and Security. “The study is aimed to determine if COVID vaccines have non-specific mortality impacts that extend beyond the incontrovertible mortality benefit they confer with COVID-19. Certain vaccines have effects that extend beyond the target infection and decrease mortality from other causes (e.g. measles vaccine).”

Dr. Monica Gandhi, an infectious disease specialist at the University of California, San Francisco, also said the question of the paper isn’t about COVID-19, but whether the vaccines had a beneficial effect on other causes of mortality. The research reinforced that both types of vaccines significantly prevented COVID-19 deaths, “which is not surprising as both types of vaccines generate cellular immunity against SARS-CoV-2, protecting us against severe disease.”

“However, to be fair,” Gandhi said, “the number of non-COVID and COVID deaths were rare in all of the pooled analyses and the causes of non-COVID deaths not well adjudicated, so this analysis needs to be taken as preliminary and hypothesis generating at best.”

(Link)

What’s interesting here is that studies have shown that the “all cause” mortality rate is also reduced for those who have been vaccinated against COVID-19 – to include those who’ve been vaccinated via the mRNA-based vaccines (Link).

Anyway, here’s a more balanced view of Dr. Aaby’s position on vaccines (Link). Note also that Dr. Aaby supported the vaccines against COVID-19 for adults (Link), but not necessarily for children since children have significantly reduced risk (compared to adults) for COVID-19 infections (Link). Dr. Aaby did publish some interesting results, however, suggesting that the polio vaccine, as well as the BCG and MMR vaccines, may also reduce childhood risk from COVID-19 as well (Link, Link).

“We would not be surprised if MMR could provide some protection against severe COVID-19,” said researcher Peter Aaby, of Bandim Health Project in Guinea-Bissau and Research Centre for Vitamins and Vaccines (CVIVA), Statens Serum Institut, a governmental public health and research institution under the Danish Ministry of Health in Copenhagen, Denmark and a pioneer in the field. “Together with my partner Dr. Christine Stabell Benn, we’ve been reporting on mortality reductions from live-attenuated vaccines such as polio, BCG and measles vaccine/MMR for multiple decades now, and arguing for optimized vaccine schedules. With the COVID-19 crisis adding urgency, it’s good to see the potential of non-specific immune effects being taken seriously.” (Link)

Overall, I do find Dr. Aaby’s main concern to be well-supported that vaccines may produce unforseen beneficial as well as detrimental side effects. In the case of COVID-19, however, it was very clear to me that the potential unknown risks were clearly outweighed when compared to the known risks of getting infected by COVID-19 as well as the very clear known benefits of being vaccinated – particularly for adults over the age of 50 and those with various medical conditions that put them at great risk. Even healthy children seemed to be far more at risk from a live COVID-19 infection than from the vaccines – particularly regarding long-term effects. Of course, this was all before the current less severe Omicron variant took over and the predominant variant worldwide. At this current point in time, vaccines against COVID-19 don’t seem to me to have as significant of an advantage compared to earlier on in the pandemic.

Hope this helps,

Sean

Sean Pitman Also Commented

Natural vs. Vaccine-derived Immunity
I’m biased here since I’m a physician myself. While I personally do not favor vaccine mandates for the general public since I think that they are largely counterproductive, I personally feel that medical providers are in a different category and that medical providers (like doctors and nurses and nursing home workers) should be required to be vaccinated since they deal directly with those who are sick and most vulnerable to serious infection. Timely boosters should also be required for medical personnel since boosters have clearly been shown to improve immunity after 6 months since the previous vaccine was given.

As far as “Long-COVID”, it is a real risk following a COVID-19 infection, but isn’t a risk following vaccination. The vaccines have not been associated with the symptoms of Long-COVID since vaccines are not based on the use of a live virus that invades the entire body. In fact, there are some research studies that suggest that many Long-COVID cases are likely related to persistent COVID-19 infections (Link). This is probably why many of those who have Long-COVID improve following vaccination.


Recent Comments by Sean Pitman

Back to Square One…
I’m not sure what “teachings” you have in mind here that need amending?


Mandates vs. Religious Exemptions
I’m just saying is that if you think that what you say on blog sites like this one doesn’t really affect people, especially when you present yourself as an MD, you’re mistaken. I know that people have been influenced against taking the mRNA vaccines by what you’ve said here in this forum. You’re not simply being neutral in what you’ve posted. You do, in fact, come across as being opposed to the mRNA vaccines – also noting that you didn’t get vaccinated yourself and chose to get infected by the live COVID-19 virus without pre-established vaccine-based immunity. You’ve also come across as being strongly against any response by me to the articles that you’ve referenced where I point out how these papers really do not actually undermine the efficacy and/or the relative safety of the mRNA vaccines. Clearly, you don’t come across as being neutral on the topic.

And, such comments have an effect on people – they really do. While that upsets me, again, it’s more important to me to allow for those who disagree with me to also post their comments rather than to only allow what I personally think is true to be posted.

Beyond this, no one is twisting your arm to post our comments here. You can post or not post as you wish. That’s entirely up to you. But, don’t expect that I won’t push back when you post comments that I think will increase the risk of those who read what you have to say…


Mandates vs. Religious Exemptions
The difference between us is that I see people in the ICU, as does my brother-in-law Dr. Roger Seheult (a pulmonologist in S. Cal.). You might see the occasional person die from COVID-19, but those who work ICUs in larger medical centers see far too many people die from COVID-19 – to include young people (not just those in nursing homes). You might offer the vaccine to those whom you see, but if you present arguments to them like the ones you’ve presented here, such advice most certainly does result in increased injuries and even death. For me, that’s a big deal. You might call it “weird and overly dramatic” if you want, but for me the effort to save lives and reduce injuries is neither “weird” nor “overly dramatic”. I mean, that’s why I do what I do…

Now, you say, “The discussions that I have on blogs like this are my personal thoughts and concerns. They don’t reflect the way that I actually practice primary care medicine on a daily basis.”

That would be great if this were a private conversation, but it isn’t. It is a public conversation and your words have an impact on the hundreds who read this blog every day. I mean, in a very real sense, especially given that you include your title “MD” with your name, and often point out that you are a medical doctor when you post to this blog, you are, in fact, practicing medicine when you post public comments like you do. You cannot simply say, “I don’t actually follow my own advice that I post in blogs when I practice primary care medicine on a daily basis.” Your influence simply isn’t limited to what you do face-to-face with patients in your clinic. Your influence also extends to what you say and do in front of people outside of your daily medical practice.


Mandates vs. Religious Exemptions
Well, I’m glad you go at least this far… although I still think that the kinds of arguments you present here really do put people’s lives and health at increased risk. I know you don’t agree, but that’s how I see things from my own perspective.

Now, I’m fine with you, and those who think like you, having the ability to freely share your opinions – despite how mistaken and damaging I personally think these opinions may be. That’s just the nature of living in a free society – which I think is far more important than restricting the freedom of speech.


Mandates vs. Religious Exemptions
Yes, I’ve been reviewing these particular evolutionary arguments for over 20 years myself: Link, Link

Again, however, when it comes to active retrotransposons in normal human cells, naturally, the expression of LINE sequences is repressed in most cell types. Its RNA is mainly heritable during early embryogenesis because of its enrichment and high retrotransposition activity in early embryos (Grow et al., 2015). That’s why the Swedish research team used a tumor cell line where LINE-1 sequences where more strongly expressed.

On the other hand, it does seem to be true that cells infected by live SARS-COV-2 viruses do show enhancement of expression of retrotransposons:

In our study, we analyzed publicly available transcriptome data of human cells infected with coronavirus MERS-CoV, SARS-CoV, and SARS-CoV-2, and observed enhanced expression of TEs including several retrotransposons, as well as inflammation, immunity, and apoptosis related genes. We further noticed potential fusion of SARS-CoV-2 RNA with retrotransposon transcripts especially LINEs and SINEs… One of the major mechanisms for LINE-1 silencing is DNA methylation, and we examined expression of genes encoding DNA methyltransferases (DNMTs) and Ten-eleven translocation (TET) enzymes mediating active DNA demethylation. We observed that Tet genes were generally upregulated after coronavirus infection (Figure 2D), and upregulated DNA demethylation activity may lead to demethylation of retrotransposon promoters. This result supports that increased retrotransposon expression was caused by genome-wide DNA demethylation. We obtained similar results in MERS-CoV/SARS-CoV infected MRC5 cells which are noncancerous human lung fibroblast cells (Figures 2A–D)… SARS-CoV-2 infection also causes upregulation of TET gene expression (Figure 2D). Similarly, SARS-CoV-2 was identified to have the capability of infecting human intestinal organoids (Figure 2E) and increased retrotransposon expression can also be observed post infection in a time-dependent manner (Figure 2F)…

Coronaviruses are RNA viruses and are not supposed to integrate into host genome by themselves. However, it was reported that several RNA viruses have capacity to recombine with retrotransposons to invade host genome (Geuking et al., 2009)… This demonstrates high efficiency of LINE family especially LINE-1 in forming chimeric transcript with SARS-CoV-2 RNA. LINE-1 is autonomous retrotransposon with retrotransposition activity, and RNA-RNA ligation mediated by endogenous RNA ligase RtcB was previously reported for LINE-1 to carry other types of RNA for host genomic invasion (Moldovan et al., 2019), so similar mechanisms may apply for SARS-CoV-2 transcripts. Further examination of human genome from SARS-CoV-2 infected human cells or biopsies will be particularly important to identity existence of integration of coronavirus RNA into human genome.
(Link)

So, you see, if anything, infection by live SARS-COV-2 viruses puts a person at higher risk of cellular genetic modification compared to the mRNA vaccines. This only adds to the reasons to get vaccinated against COVID-19 rather than to gain “natural immunity” the hard way – i.e., via a live SARS-COV-2 infection. Yet again, the risks are simply far higher here for the natural infection vs. vaccination.