The Immunology of Long COVID

I have written many times previously on my blog about Long COVID or PASC (post-acute sequelae of COVID-19 infection), its manifestations and potential pathogenesis. Now, a new paper looks at the immunology of Long COVID: https://www.nature.com/articles/s41577-023-00904-7. In my discussion below, I will include parts of this paper, as well as some other recent information about Long COVID.

Although post-viral syndromes have been known to occur for many decades now, it was surprising early on in the pandemic to see the large number of people who continued to be plagued by persistent symptoms following the apparent recovery from the acute SARS-CoV-2 infection, including those with mild illness, and even including some children.

There is no diagnostic test for Long COVID, and for a long time, there was no widely accepted case definition for the condition. Therefore, there were widely varying estimates of the disease burden, ranging from a low end of around 10% of COVID-19 patients to a high of around 30%.

The World Health Organization definition of Long COVID is:

A condition that occurs in individuals with a history of probable or confirmed SARS-CoV-2 infection, usually 3 months from the onset of COVID-19, with symptoms that last for at least 2 months and cannot be explained by an alternative diagnosis. Common symptoms include fatigue, shortness of breath, cognitive dysfunction and others, which generally have an impact on everyday functioning. Symptoms may be new onset, following initial recovery from an acute COVID-19 episode, or persist from the initial illness. Symptoms may also fluctuate or relapse over time. A separate definition may be applicable to children.

The CDC provides the following additional information about Long COVID:

• Long COVID can include a wide range of ongoing health problems; these conditions can last weeks, months, or years.
• Long COVID occurs more often in people who had severe COVID-19 illness, but anyone who has been infected with the virus that causes COVID-19 can experience it.
• People who are not vaccinated against COVID-19 and become infected may have a higher risk of developing Long COVID compared to people who have been vaccinated.
• People can be reinfected with SARS-CoV-2, the virus that causes COVID-19, multiple times. Each time a person is infected or reinfected with SARS-CoV-2, they have a risk of developing Long COVID.

We did see some differences relative to Long COVID with different variants. For example, comparing long COVID cases from the first wave to those from the Alpha wave, a change in symptomology was observed, with increased muscle aches, brain fog and anxiety, but decreased frequency in loss of smell and altered sense of taste. Despite these minor variations, the fact that a set of common symptoms endures across the different variants and even in vaccinated populations and, thus, across patients with differing viral loads, points to the presence of determinants of pathology that are intrinsic to the SARS-CoV-2 virus.

There are varying hypotheses as to the pathogenesis of Long COVID: (again, I have written about most of these in prior blog posts if you want to dig deeper into these)

• tissue and organ damage caused directly by the viral infection,
  • heart
  • lungs
  • brain
  • kidneys
• persistence or lack of clearance of SARS-CoV-2 and ongoing antigenic stimulation,
  • gastrointestinal tract,
  • testis,
  • a space between the skull and the brain
• an abnormal immune response to acute COVID-19,
  • an overactive immune response resulting in organ damage either in response to a very high viral load or a dysregulated immune response,
  • an inadequate immune response that allows the virus to wreak more havoc or may result in failure to clear the virus
• reactivation of other viruses,
  • Epstein–Barr virus (EBV) reactivation has been the leading candidate (most people have been infected with this virus that causes infectious mononucleosis or sometimes colloquially referred to as the kissing disease), though human herpes virus – 6 has been implicated.
• altered systemic immune responses,
  • We know that we can see various abnormal or exaggerated immune responses during acute infection and in the several months following (e.g., MIS-C, MIS-A – see prior blog posts where I have discussed these if interested).
  • There is intense debate surrounding whether there is potential longer term immune dysfunction and if so, whether it is relevant to the development of Long COVID or apparent susceptibility to other infections following COVID-19 (e.g., RSV, invasive group A strep, etc.). There are other viruses known to cause either temporary (e.g., a temporary loss of humoral immune memory following measles) or permanent immune dysfunction following infection (e.g., HIV). And, of course, there is the confounding factor that not all of the immune disturbance may be the direct effect of SARS-CoV-2 infection, but rather may be in part related to the indirect effect of reactivation of other viruses, such as Epstein-Barr virus, in those patients in which this occurs. One area of intense disagreement is whether COVID-19 results in significant and persistent T-cell exhaustion in some persons. (You can also read about T-cell exhaustion in some of my posts from last year).
• auto-immunity,
  • Many studies have demonstrated that acute SARS-CoV-2 infection can result in the production of a diverse population of autoantibodies, likely a result of viral mimicry (in other words, the virus contains antigens to which the body produces antibodies that are sufficiently similar to other self-antigens that the antibodies not only attack the virus, but the person’s own cells with that similar antigen on their cell surface.
  • Recent studies have identified increasing accounts of antibodies produced against interferon, which is a critical part of the body’s innate immune response in that interferon serves as a cellular warning system that an invading virus has been identified, which in turn, allows nearby cells to take some precautions that make viral entry more difficult.
  • Just a year ago, we concluded that Epstein-Barr virus (EBV) infection can cause multiple sclerosis decades later following infection, likely through an autoimmune mechanism. It is not yet clear whether EBV reactivation during COVID-19 might also contribute to the development of autoimmunity.
  • Of particular concern are autoantibodies that may target various cells of the brain potentially causing or contributing to the wide array of neurological complications seen during and following COVID-19.
• micro-blood clots, and
  • Some autoantibodies are of the type seen in a syndrome characterized by abnormal clotting.
  • Some antibodies may stimulate endothelial cell (the cells that line the inner walls of blood vessels) activation, which itself can promote clotting.
  • There have also been reports of an amyloid-like protein within these micro-clots that may make them more resistant to the body’s normal mechanisms for dissolving clots.
• microbiome dysbiosis (disruption of the normal gut microbiome).

Now we examine what evidence we have at this point in time to correlate immune responses with Long COVID.

As I mentioned, as of yet, we do not have a diagnostic test for Long COVID (in contrast to other diseases such as blood pressure measures for the diagnosis of hypertension or blood sugars for the diagnosis of diabetes). On the other hand, there have been studies that have found biomarkers (these are not diagnostic of Long COVID, but rather predictive of higher risk for the development of Long COVID such as the persistence of abnormal levels of certain cytokines and chemokines (these are chemical messengers of the immune system that may boost or calm the immune response) such as certain interferons or interleukins. One of the chemokines found to be persistently increased in some patients with Long COVID is CCL11, which interestingly and concerningly, has been identified as a mediator of the neurocognitive decline seen with aging.

Recall from my earlier blog posts that the spike protein is referred to as “S” or the S protein, and people will develop antibodies to the S protein with either vaccination or infection. There are other important proteins in the SARS-CoV-2 virus, and one of those is the nucleocapsid protein, which is referred to as N. Antibodies against the N protein are referred to as anti-N antibodies, and we generally only see anti-N antibodies in the case of infection, because U.S. vaccines only include the S protein and not the N protein.

A study looking at the initial anti-N antibody response during acute infection found an inverse correlation between antibody level and likelihood of symptoms at 3 months or beyond, supporting the view that an inadequate initial antibody response may predispose to Long COVID. [If you are having trouble following that, think about high antibody levels as a vigorous immune response and low antibody levels as a potentially inadequate immune response, but only use this framework early on in an infection, as antibody levels normally decline over time.]

An analysis of a cohort of hospitalized patients of whom roughly 20% would go on to experience Long COVID symptoms at 1-year post-infection found that the Long COVID group showed significantly lower antibody levels to S, with no difference in T cell response. [In this case, the lower antibody levels are to the Spike protein]. Together with the study mentioned directly above, with an association of low anti-N and low anti-S antibody levels with Long COVID, this would naturally cause us to query whether an underwhelming humoral immune response might predispose to the development of Long COVID.

Recall that there are three main parts of the immune response – the innate, the humoral and the cellular immune responses. I liken these to three branches of our military response, e.g., ground troop responses with the Army, a sea response with the Navy and an air response with the Air Force. In the case of immunology, the innate immune response is non-specific and not targeted – continuing with my military analogy, it is like lobbing grenades or dropping bombs from B-52 airplanes like we did decades ago and hoping they get close enough to take out enemy soldiers or tanks, but also realizing there will be a lot of potential collateral damage. The innate immune response is the most immediate immune response.

The humoral and cellular immune responses take days to a week or more longer to develop than the innate immune response. The humoral immune response is your antibody response – these are like laser-guided or heat-seeking missiles that are specifically targeted to the invading enemy. The cellular immune response is incredibly complicated, but in simple terms, antibodies can only capture enemy virus before they enter and infect cells. Once inside cells, we need specialized immune cells that can recognize that a cell is harboring fugitive virus inside and then have orders to take the entire cell out and kill everything in it. [If you are totally geeking out on this and must know what these specialized cells are, these are the cytotoxic T-cells or CD8+ cells].

So far in COVID-19, our limited understanding is that neutralizing antibody levels (a subset of all antibodies, these antibodies are capable of preventing the virus from entering and infecting cells, as opposed to other antibodies that bind to the virus, but do not block cell entry, which we broadly refer to as binding antibodies) correlate with protection from infection and cellular immune responses protect against severe disease. The reason that the COVID vaccines help prevent severe disease is that they provide you with a supply of neutralizing antibodies and stimulation of the cellular immune capability prior to getting infected so that your immune system is already primed and ready, as opposed to infection in unvaccinated persons where the virus gets a 3 – 7-day head start before the immune response can catch up to the virus. Unfortunately, as we have allowed uncontrolled transmission of the virus with subsequent development of progressively more transmissible and immune evasive variants, the neutralizing antibody response from either prior infection or vaccination is less effective and shorter lasting, but fortunately, we have seen the cellular immune response be much more durable lasting in most people at least 8 months and perhaps even longer.

However, a study looking at SARS-CoV-2-specific antibodies and T cell responses at 1–2 months post-infection and 4 months post-infection showed minimal differences between individuals with persistent symptoms and those without. When I see conflicting results from studies, we either have to consider other explanations such as perhaps not all persons with Long COVID have the same immune profiles, but as of now, we cannot conclude a unifying explanation for the development of the disease such as the hypothesis that perhaps those with inadequate humoral immune responses are those that are at risk for developing Long COVID.

Still, in other patients with Long COVID, there is evidence for an enhanced immune response, which may lend support for persistent antigenic stimulation from uncleared virus or virus particles.

Frankly, while this may frustrate readers that results seem to be all over the board, this just suggests to me that Long COVID may very well be a spectrum of disease, manifesting in different ways related to a number of potential pathogenic mechanisms by which Long COVID may result (e.g., perhaps in some patients Long COVID is related to latent Epstein-Barr virus reactivation, but in others it is related to auto-immune responses).

Results of studies that might support this hypothesis include those that show that individuals who went on to report persistent respiratory symptoms showed low serum cortisol, whereas those going on to develop neurological symptoms had an elevation of proteins involved in circadian regulation of the sleep cycle. Also, evidence of Epstein-Barr virus reactivation during acute COVID-19 was a predictor for the development of persistent fatigue.

We have yet to find a unifying immune profile that can be attributed to the development of Long COVID. That could be because Long COVID is not a result of immunopathology or is only such a result in some patients, or there are various profiles involved that account for the variation in how Long COVID manifests. This requires more research because we do have a range of targeted therapies that can treat specific aspects of the immune response. We can remain hopeful that as we better understand Long COVID, we will be able to offer more options to patients.