20 July 2023 Episode 340 Asymptomatic SARS-CoV-2, long COVID and vaccination revisited: genetics and evidence for “Long Vax”?

Thu, 07/20/2023 - 16:12

Episode 340: Asymptomatic SARS-CoV-2, long COVID and vaccination revisited: genetics and evidence for “Long Vax”?

Dear colleagues,

Similar to some other viral infections, SARS-CoV-2 is characterized by a poorly understood clinical spectrum from asymptomatic to severe multi-organ life threatening acute disease as well as protracted polymorphic complaints, known as long COVID, which can occur both after severe and after mild disease.

Some genetic and auto-immune factors, leading to a deficient type 1 IFN activity have been discovered in relation to acute severe disease, but what about genetic influences on asymptomatic SARS-CoV-2 infection and long COVID?

Vaccination has been clearly shown to protect against severe disease, while its potential to prevent infection (and asymptomatic disease) is decreasing with the emergence of immune-escaping variants, but what about the precise relation between vaccination and long COVID?


Par 1 Introduction on Long COVID

Long COVID is a “container concept”, with an heterogeneous clinical picture: complaints can be very specific (e.g. loss of smell or dyspnea) or more vague/complex (fatigue, brain fog). This lack of precision may explain why figures on incidence vary widely: 10-30 % in non-hospitalized patients and 50-70 % in those who have been hospitalized.

Ep 340-1: Davis Nature Rev Microbiol March 2023: Long COVID: major findings, mechanisms and recommendations


Long COVID symptoms and the impacts on numerous organs with differing pathology.




The impacts of long COVID on numerous organs with a wide variety of pathology are shown. The presentation of pathologies is often overlapping, which can exacerbate management challenges.


MCAS, mast cell activation syndrome; ME/CFS, myalgic encephalomyelitis/chronic fatigue syndrome; POTS, postural orthostatic tachycardia syndrome; SFN small fiber neuropathy.


Hypothesized mechanisms of long COVID pathogenesis.

There are several hypothesized mechanisms, related to the heterogeneity of long COVID, including

  • viral persistence of SARS-CoV-2 or reactivation of chronic infections by Herpes viruses EBV, Epstein–Barr virus; HHV-6, human herpesvirus 6),
  • ensuing immune dysregulation, autoimmunity
  • microbiota disruption,
  • clotting and endothelial abnormality,
  • and dysfunctional neurological signaling.


It is quite possible, even likely, that there is not a single pathogenic mechanism e.g.

  • some cardiovascular symptoms may be due to clotting and endothelial abnormalities;
  • some neurological symptoms may be due to auto-immunity;
  • gastro-intestinal symptoms could relate to dysbiosis.

EBV, Epstein–Barr virus; HHV-6, human herpesvirus 6e

The various mostly symptomatic treatments (most of which have not really been validated) reflect again the heterogeneity of the syndrome and the uncertainty on the pathogenesis.


Fortunately, in most cases, these “long COVID” complaints gradually diminish.  

Nevertheless, a recent meta-analysis of hospitalized patients, shows up to 75 % keep at least one symptom up to 1 year after the acute phase (Ep 340-2 Kelly Eur Resp Rev June 2023).  Clearly, fatigue, dyspnea, arthralgia and myalgia are dominant here, which may be rather similar to other patients with a prolonged hospital stay.


A large retrospective analysis in patients with originally mild disease  shows a decreasing trend, with persistent elevation of only a few symptoms after 6-12 months, with a slightly different picture: although respiratory disorders, dyspnea and weakness are also present in the top-five, taste and smell disorders as well as concentration and memory problems (brain fog) are more prominent here (Ep 340-3 Mizrahi BMJ 2023).  


Ep 340-4: Dhawan Lancet June 2022): It is generally accepted that Omicron infections bear a lower, but still significant risk on long-COVID.  A large UK study found a  50-75 % lower risk of long COVID in omicron versus delta infected subjects (


Par 2 Recent findings on COVID genetics

2.1. With regard to asymptomatic infection and cross-reactivity with seasonal beta-coronaviruses

Ep 340-5: Langton HLA 2021: HLA-DRB1*04:01 associated with ASYMP infection in a small UK cohort ( n= 147)

Allele frequency of HLA-DRB1*04:01 in severe patients (5.1 %) versus asymptomatic staff group (16.7 %, P = .003). after adjustment for age and sex



The positive association between disease severity and age, high BMI and male sex is expected, but the negative association with DRB1*04:01 is a new finding.

Ep 340-6: Katie Immunity 2021: Immunodominant SARS-CoV-2 epitope

A single Nucleocapside-encoded epitope (SPR-LPR) that was highly conserved across circulating beta coronaviruses drives an immunodominant CD8 T cell response.


In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity toward seasonal circulating OC43 and HKU-1 beta-coronaviruses but not 229E or NL63 alphacoronaviruses because of different peptide conformations.


CD8+ T cell responses toward N peptides derived from seasonal and pandemic coronaviruses



PBMCs from unexposed and COVID-19-recovered donors were stimulated with SPR (SARS-CoV-2), LPR (OC43/HKU-1 betacoronavirus), SPK (229E alphacoronavirus), or PPK (NL63 alphacoronavirus) peptides, cultured for 2 weeks in the presence of IL-2, and then assessed for IFN-g production following recall with their cognate peptide or each of the homologous peptides listed above.


There is clear cross-reactivity between the SPR and LPR peptides: they activate both SPR and LPR specific T cells.

No cross-reactivity with SPK or PPK peptides or T cells



T cell receptor (TCR) sequencing indicated that cross-reactivity between SARS-CoV-2 and seasonal beta CoV (OC43 and HKU-1) was driven by private TCR repertoires with a bias for TRBV27 and a long CDR3b loop


This preliminary evidence suggests genetically defined T cell mediated cross-reactivity between seasonal beta Cov as a factor in asymptomatic infection. It is nicely confirmed in a very recent paper


Ep 340-7: Danillo Augusto Nature 19 July 2023: HLA-B15 associated with ASY SARS-COV-2 Nature 19 July 2023

The strong association between HLA-B15 was observed in two independent cohorts




Remarkably, HLA-B15 is associated (in linkage disequilibrium) with HLA-DRB1*04:01 (see Ep 340-5).


T cells from pre-pandemic samples (not exposed to SARS-CoV-2) from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 Spike-derived peptide NQKLIANQF (further referred to as NQK-Q8).   These T cells have a “memory” phenotype, suggesting that they have been stimulated before by another virus.




In fact, these T cells cross-react with the homologous peptide NQKLIANAF (hereafter, NQK-A8) from seasonal beta CoV OC43 and HKU-1 and they are highly polyfunctional.




Both cross-reacting peptides bind with high affinity to HLA-B15.01


CD8+ T cells able to bind both peptides presented by HLA-B15.01 tetramers NQK-Q8 (tet-Q8) NQK-A8 (tet-A8) primarily expressed a particular set of public T clonotypes

  • TRBV7-2/7-8 (42%) paired with TRAV21 (54%);
  • TRBV9 (36%, pairing unknown); or
  • TRBV5-4/5-8 (12%) paired with TRAV41 (36%)


2.1 Genetic factor in long COVID?


Ep 340-8: Vilma Lammi medRxiv 1 July 2023: A large compilation of several “genome-wide association studies” (GWAS with over 6000  long COVID and over 1 million controls) shows a weak, but significant association between long COVID (both in a “strict” and a “large” definition) with a particular allelic variant rs9367106-C at the FOXP4 locus on chromosome 6  in a population of European descendance.



While FOXP4 has a wide distribution, it is certainly present in several lung cell populations and it is also linked to immune development and T regulatory function.  Hence multiple pathogenic mechanisms could be suggested.


Interestingly, the same variant is also associated with lung cancer and COVID severity in the acute phase, but the relation with long COVID is not only dependent on disease severity.



Par 3 Complex relation of long COVID and vaccination

In this episode we will try to answer the following  questions:

  1. Can vaccination protect against long COVID after breakthrough infection (despite vaccination)?
  2. Is vaccination still useful during long COVID: i.e. if given to originally unvaccinated but SARS-CoV-2 infected subjects, who have developed long COVID?
  3. Can vaccination itself elicit long COVID symptoms without infection, a condition labelled as “Long Vax” ?

Ep 340-9: UKSHA Feb 2022 Effectiveness of vaccination against long COVID

In this meta-analysis, the former two questions are addressed:

  1. Vaccination with 2 doses of any vaccine protects against long COVID in 6 out of 7 studies.  The degree of protection is variable: from 13 to over 80 %, but:
  • Definitions of long COVID vary
  • The total protective effect is an underestimation, since the vaccine prevents at least a proportion of breakthrough infections

An example is shown as Ep 340-10

  1. The effect of vaccination on already established long COVID is usually, but not always, beneficial and less pronounced than vaccination before infection.


An example is shown as Ep 340-11


Ep 340-10: Zyad Al Ali Nat Med June 2022 in a very large Veterans Administration cohort

Risk and 6-month excess burden of post-acute sequelae in people with breakthrough infection (BTI) compared to those with SARS-CoV-2 infection without prior vaccination.



Right panel: Risk and 6-month excess burden of death, at least one post-acute sequela and post-acute sequelae by organ system are plotted. Incident outcomes were assessed from 30 days after the positive SARS-CoV-2 infection test to the end of follow-up. Results are in comparison of BTI (n = 33,940) to those with SARS-CoV-2 infection without prior vaccination (n = 113,474).


Left panel:  Adjusted HRs (dots) and 95% CIs (error bars) are presented, as are estimated

excess burden (bars) and 95% CIs (error bars). Burdens are presented per 1,000 persons at 6 months of follow-up.

Ep 340-11: Ayoubkhani BMJ 2022 Trajectory of long covid symptoms after covid-19 vaccination

Modelled probabilities of long covid for a hypothetical study participant who received a first covid-19 vaccine dose 24 weeks after SARS -CoV-2 infection and a second dose 12 weeks later.



A first vaccine dose was associated with an initial 12.8% decrease (95% CI -18.6% to -6.6%) of symptoms, a second vaccine by a 8.8 % decrease (-14.1 to -3.1%).


Ep 340-12: Gretchen Vogel and Jennifer Couzin-Frankel in Science Insider 3 July call attention for a rare COVID-like illness following vaccination (without infection).  The paper is mainly based on two publications Ep 340-13 and -14

Ep 340-13: Farinaz Safavi medRxiv May 2022 reports on peripheral neuropathy in 23 mainly female subjects.


  • Within 3 weeks after 1st or 2nd vaccine (1 Astra-Zeneca; 1 Janssen, 9 Moderna, 12 Pfizer
  • All had paresthesia in limbs and/or face; 60 % had autonomous symptoms (tachycardia, heat intolerance, Raynaud’s syndrome)
  • 58 % diagnosis of “small fiber neuropathy” (SFN) and 50 % “postural orthostatic tachycardia syndrome” (POTS).
  • Most (18/23) partly or fully recovered within 12 weeks.  Immune therapy (either corticosteroids or IV immunoglobulins) seemed to promote recovery.


Ep 340-14: Alan Kwan Nat Cardiovasc Res Oct 2022 investigates in a large US cohort (over 289,000)  

the risk on several conditions after COVID vaccination or infection by comparing

  • the “spontaneous” incidence in the 90 days before vaccination or infection
  • with the incidence in the 90 days following Vacc/infect.




CPC = common primary care diagnoses.



From this very complicated study, it can be seen that for instance

  • POTS is 5 X more common after infection than after vaccination
  • Also myocarditis, diabetes, depression, anxiety etc are more prevalent after infection than vaccination.


Potential mechanism of these rare post-vaccination effect?

An unproven hypothesis suggests that the anti-Spike Ab (elicited by vaccination or infection) could induce “anti-idiotypic Ab”, which are Ab reacting with the variable part of the Spike specific Ab, that would resemble the antigen (= Spike) and therefore could bind and trigger the ACE-2, which is know to have a role in blood pressure and pulse frequency as well as in neurological tissue.



= Spike







  1. Genetic factors related to asymptomatic infection point to HLA molecules and T cell receptor (TCR) clonotypes.  Both CD4 T cells (through HLA-DRB1) and CD8 T cells (through HLA-B15) may be involved and cross-reactivity with seasonal coronaviruses (CoV) may have an important role as an explanation. Nevertheless, the literature on the influence of protection against SARS-CoV-2 and cross-reaction to seasonal CoV is not very consistent.  In fact this apparent inconsistency is not so surprising: only a minority of subjects may carry HLA molecules and TCR types that can lead to truly protective cross-reactive immune responses.
  2. The genetics of long COVID is even more complex, as it is a very heterogeneous set of syndromes, wherein very different pathogenic mechanisms, with different genetic associations may be involved. Until now only a weak association has been found with FOXP4, which, interestingly, has an immune regulatory role.
  3. While the protective effect of vaccination on severe COVID is very strong, its effect on long COVID is much less evident. Most studies point to a clear, but moderate positive effect of vaccination to prevent COVID, if applied in uninfected subjects.  A “therapeutic” effect of vaccination on long COVID after infection is more doubtful and there is evidence that vaccination itself (in the absence of infection) can elicit some syndromes that have been associated with long COVID, such as neuropathy and POTS, in the popular press referred to as “long Vax”. But then again, on a population level, the occurrence of these and other side effects of vaccination (such as myocarditis) are much less frequent after vaccination than after infection.