SARS-CoV-2 infects T cells, the power of N protein

And more useless vaccine news

In between writing my last 2 posts, very interesting papers came out, and meaningful ones. As often, this will often be linked to older posts and a broader hypothesis… well, theory by now, let us just face it. The first one is the most of most significance. Here is a good lymphocyte one, and here you have a post commenting on a paper stating the same as the paper below.

ACE2-independent infection of T lymphocytes by SARS-CoV-2

SARS-CoV-2 induced marked lymphopenia in severe patients with COVID-19. However, whether lymphocytes are targets of viral infection is yet to be determined, although SARS-CoV-2 RNA or antigen has been identified in T cells from patients. Here, we confirmed that SARS-CoV-2 viral antigen could be detected in patient peripheral blood cells (PBCs) or postmortem lung T cells, and the infectious virus could also be detected from viral antigen-positive PBCs. We next prove that SARS-CoV-2 infects T lymphocytes, preferably activated CD4 + T cells in vitro. Upon infection, viral RNA, subgenomic RNA, viral protein or viral particle can be detected in the T cells. Furthermore, we show that the infection is spike-ACE2/TMPRSS2-independent through using ACE2 knockdown or receptor blocking experiments. Next, we demonstrate that viral antigen-positive T cells from patient undergone pronounced apoptosis. In vitro infection of T cells induced cell death that is likely in mitochondria ROS-HIF-1a-dependent pathways. Finally, we demonstrated that LFA-1, the protein exclusively expresses in multiple leukocytes, is more likely the entry molecule that mediated SARS-CoV-2 infection in T cells, compared to a list of other known receptors. Collectively, this work confirmed a SARS-CoV-2 infection of T cells, in a spike-ACE2-independent manner, which shed novel insights into the underlying mechanisms of SARS-CoV-2-induced lymphopenia in COVID-19 patients.

This paper is rather complex, but the abstract is fairly easier to understand. Authors tested and found one of the causes of lymphopenia (in a crude way, immune suppression) in severe patients, that frequently leads to death. They found virus antigen (parts) and infectious viral particles in lung T cells and peripheral blood cells (cells that can go anywhere, other blood cells go to the lymphatic system, spleen, liver, or bone marrow).

Following it they prove the virus infects CD4+ Lymphocytes, and uses a spike-ACE2/TMPRSS2-independent manner to infect them, and propose a pathway. A important pathway.

Notably, lymphopenia was observed in 83.2% of the patients on admission, and fatal infections were associated with more severe lymphopenia over time.

Lymphocytes (particularly T cells) play a central role in the human immune system, a decrease of which would result in immune suppression and serious complications.

Similarly, SARS-CoV-2 particles or proteins were also found in the spleen and lymph nodes from a study of 91 deceased COVID-19 cases, suggesting an infection of lymphocytes.

It has been shown that SARS-CoV-2-infected human monocytes, monocyte-derived macrophages, and dendritic cells in vitro, which potentially plays a major role in COVID-19 pathogenesis

Just a portion of 2 paragraphs you should keep in mind, how much the lymphopenia contributes to death, the immune suppression that comes from it, previous evidence for infection of lymphocytes.

But the last part, I would disagree with the authors. It is not just in vitro, but in vivo too, at least for dendritic cells, I was working in another part of the Reverse AIDS hypothesis, before, well, everything started cascading.

To determine whether SARS-CoV-2 infects lymphocytes, we analyzed peripheral blood cells (PBCs) collected from COVID-19 patients. PBCs were prepared from 22 patients, who were all at severe condition during the study along with 15 healthy donors. We first analyzed major lymphocyte cell types including T (CD4 + helper T and CD8 + cytotoxic T), B, and natural killer (NK) cells for their population changes or the presence of viral antigen upon infection. For all patients tested, the ratios of blood T lymphocytes declined significantly compared to those in healthy donors, whereas B and NK cells appeared to be unaffected . Notably, CD4 + and CD8 + T lymphocytes almost declined to zero in some patients . The results suggested that lymphopenia in these patients is likely attributed to a decline of T lymphocytes.

By comparing the blood of 22 infected and 15 non-infected they found a significant drop in T lymphocytes, but B and NK cells were unaffected, in some patients both CD4 and CD8 declined to almost 0.

Authors go into great lengths to demonstrate all of their points, I would like to add that they use a Caco2 cells, a intestinal epithelial cell line, cancerous one btw, this can affect the overall results (similar to the ridiculous DNA integration paper, but this one is fairly well designed).

As a side note, know what infects CD4+ cells, usually in the intestinal epithelium? HIV…. haha.

Finally, to corroborate the findings from T-cell lines, we tested the infectivity of primary T cells isolated from healthy donors. In the three donors, SARS-CoV-2 showed time-dependent infection of T cells that is peaked at 8 h, probably because of extensive cell death induced by the virus at this time point. Taken together, our data clearly show that SARS-CoV-2 could infect T cells in vitro, although at a lower efficiency compared to tissue cells.

SARS-CoV-2 infection of T cells is ACE2 and TMPRSS2-independent

It is generally believed that ACE2 is the entry receptor for SARS-CoV-2. However, major cell populations in PBCs express extremely low levels of ACE2, raising the question whether ACE2 also mediates SARS-CoV-2 virus entry of T cells. We first tested whether an ACE2 knockdown could dampen SARS-CoV-2 infection of T cells.

SARS-CoV-2 under the settings of this paper started infecting T ells at 8h, probably because it achieves enough cell death. At least in vitro, even under the specific design of the study, the virus didn’t infect T cells as efficiently as tissue cells, a form of good news.

They go to try and find exactly the pathway the virus uses to infect T cells, won’t bother you with the details, but they did a proper design, unlike the DNA paper, were the knocked out (eliminated) ACE2 from the cell line they were testing, and showed the results.

It is known that severe patients with COVID-19 showed marked decreased lymphocyte populations.

y. T lymphocytes from COVID-19 patients underwent pronounced apoptosis compared to those from the healthy donors, showing a more than tenfold increase of apoptotic cells. In some patients, most of the apoptotic cells were also viral antigen-positive (e.g., 65% in patient 1), suggesting viral infection played a role in peripheral blood T lymphocytes death in these patients

Compared to the 24 h group, the hypoxia-related GO pathways are significantly upregulated in 48 h group, including “PID HIF1 TF pathway”, “response to hypoxia”, “positive regulation of cell death”, and “intrinsic apoptotic signaling pathway”. It has been shown that SARS-CoV-2 infection triggers mitochondrial ROS production, which induces stabilization of hypoxia-inducible factor-1a (HIF-1a) in monocytes.

In summary, SARS-CoV-2 infection induced pronounced T-cell death, which is probably dependent on mitochondria ROS-hypoxia pathways.

Here we have the pathway, which is independent of all the main ones you read about. It is worth mentioning, that I and the other person (Reverse AIDS) had this pathway in mind, HIF-1a is very important in SARS-CoV-2 infection, but we couldn’t piece it together in a fitting manner, that made sense. And now we do.

You should go back and read the mitochondria papers I commented on, Mit-ROS pathways are indeed one of the most significant aspects of this disease, and its after-effects and consequent damage. They go to mention all the upregulated proteins, etc, and they mention LFA-1 as a very influential one for this pathway.

Care to guess which type of immune response LFA-1 is critical in. (I am smirking while typing this).

Here, we showed that SARS-CoV-2 infected T lymphocytes, mainly CD4 + T cells, in an ACE2-independent manner. SARS-CoV-2 infection triggered pronounced T-cell death, which potentially contributed to lymphopenia in patients with COVID-19. T-cell infection may also pose profound influences on patients. Infected T lymphocytes not only lost the ability to control viral infection but may also carry viruses to other parts of the body through blood circulation. In addition, this ACE2-independent infection mode may compromise the therapeutic effect of neutralizing antibodies targeting at spike-ACE2 binding. These may synergistically result in more severe infection outcomes in patients with COVID-19.

It has been debated whether SARS-CoV-2 impaired the functionality of immune cell populations through direct infection. Our results provided evidence to show that SARS-CoV-2-infected T cells, as viral RNA, viral sgRNA, viral protein, and the infectious virus could be detected from T cell upon infection or from patient PBCs, although the production of infectious virus particles may stay at a low level.

The infection of CD4 + T lymphocytes by SARS-CoV-2 virus may be a major contributor of virus induced pathogenesis. Armed T cells play a pivotal role against pathogen infection.

The mechanism underlying SARS-CoV-2 infection-induced CD8 + T lymphocytes depletion is currently unknown.

Did you catch it, in the first paragraph ? No ? Here, “In addition, this ACE2-independent infection mode may compromise the therapeutic effect of neutralizing antibodies targeting at spike-ACE2 binding.”

Tell me, what happens when you have NON-neutralizing antibodies to the spike-ACE2 binding ? We now have a pathway, and explanation on why, after being vaccinated and suffering a breakthrough infection, people are in a quasi-everlasting state of immune dysfunction, and some go-to immune exhaustion.

At some level, this must happen in every infection, and under certain circumstances, a person develops a secondary infection and any other of the myriad of after-effects. Which is terrifying if you think about the vaccinated individuals.

There are many other important angles to this paper, which I won’t cover, for multiple reasons, but, we already know how and why I think the virus causes a decline in CD8+ cells. This is a very significant paper, with huge implications.

Nucleocapsid-specific humoral responses improve the control of SARS-CoV-2

The spike protein of SARS-CoV-2 is a critical antigen present in all approved SARS-CoV-2 vaccines. This surface viral protein is also the target for all monoclonal antibody therapies, but it is unclear whether antibodies targeting other viral proteins can also improve protection against COVID-19. Here, we interrogate whether nucleocapsid-specific antibodies can improve protection against SARS-CoV-2. We first immunized mice with a nucleocapsid-based vaccine, and then transferred sera from th ese mice into naïve mice. On the next day, the recipient mice were challenged in tranasally with SARS-CoV-2 to evaluate whether nucleocapsid-specific humoral responses affect viral control.

Interestingly, mice that received nucleocapsid-specific sera exhibited enhanced control of a SARS-CoV-2 infection.

In post from the Reverse Marek series, you can find a screenshot from the UK government, talking about how the vaccinated can create an immune response to the N protein of the virus. In this one, how a CD8+ response to the N protein helps clear the infection. And here, how they use plasma from recovered people to help sick ones, and it, you guessed, helped with the N protein.

These findings suggest that even though nucleocapsid-specific antibodies do not exert any antiviral effect in vitro, they can exert antiviral effects in vivo.

I decided to insert this quote here for the sole purpose to remind everyone, from doctors who read me, to laymen. Sometimes whatever works in vitro, might not work in vivo, and the contrary is true. The design of studies also matters, especially when the claim is extraordinary (reverse transcription paper, badly designed).

Short-term drop in antibody titer after the third dose of SARS-CoV-2 BNT162b2 vaccine in adults

As it usually happens with these papers, especially lately, they find X and they will tell you, insist on something that is not working, so ignoring whatever the reason authors spew bullshit (take more useless vaccines), here we another one, of many papers, showing the rapid drop in (non-neutralizing, useless, perhaps dangerous) antibodies in adults.

Both this paper, and the N are just to reinforce points I made for almost 2 years on Twitter, and here in numerous posts.

The concerning trends about BA. 2 in Honk Kong, and other places keep growing, there are also many signals in social media, like Twitter and Reddit, specially the last one.

On a personal note, I know for a fact a few people who had a BA. 1 infection in January, are now infected with BA. 2, and some who had BA. 1, now, weeks after infection, have some of these after-effects. Now is NOT the time to let your guard down.

Keep taking whatever chosen supplement stack you came up with, and keep your immune system primed, at peak performance, ready, fueled with nutrient-dense foods and supplements.

Regardless if Omicron was a lab leak, a white hat, a devil’s bargain, you can’t math biology, and you can’t predict the evolutionary direction (called evolutionary molecular clock). Before someone asks, “how you can”, that is because I created my own way of doing it, and it ain’t precise enough for therapeutic development, just risk mitigation at a big scale.

Just because most people stopped paying attention, and mimic the behavior of the herd to focus on the new things, doesn’t mean the virus stopped evolving. Stay safe, stay healthy people.

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