DataSheet_1_Case Report: Evolution of Humoral and Cellular Immunity in Two COVID-19 Breakthrough Infections After BNT162b2 Vaccine.docx

BackgroundSARS-CoV-2 breakthrough infections after complete vaccination are increasing whereas their determinants remain uncharacterized.MethodsWe analyzed two cases of post-vaccination SARS-CoV-2 infections by α and β variants, respectively. For each participant both humoral (binding and neutralizing antibodies) and cellular (activation markers and cytokine expression) immune responses were characterized longitudinally.ResultsThe first participant (P1) was infected by an α variant and displayed an extended and short period of viral excretion and symptom. Analysis of cellular and humoral response 72 h post-symptom onset revealed that P1 failed at developing neutralizing antibodies and a potent CD4 memory response (lack of SARS-CoV-2 specific CD4+IL-2+ cells) and CD8 effector response (CD8+IFNγ+ cells). The second participant (P2) developed post-vaccination SARS-CoV-2 infection by a β variant, associated with a short period of viral excretion and symptoms. Despite displaying initially high levels and polyfunctional T cell responses, P2 lacked initial β-directed neutralizing antibodies. Both participants developed and/or increased their neutralization activity and cellular responses against all variants, namely, β and δ variants that lasts up to 3 months after breakthrough infection.ConclusionsAn analysis of cellular and humoral response suggests two possible mechanisms of breakthrough infection: a poor immune response to vaccine and viral evasion to neutralizing antibodies.</p

An unusually high substitution rate in transplant-associated BK polyomavirus <i>in vivo</i> is further concentrated in HLA-C-bound viral peptides - Fig 4

Fraction of amino acid substitutions within and outside of predicted epitopes presented by HLA-A, -B and -C molecules across individuals. The detected amino acid substitutions of a viral population were mapped onto reference proteins and the fraction of mutated amino acids within and outside of predicted epitopes of each viral protein and hosts HLA allele were calculated for each viral population found in patient and donor respectively. The fraction of substituted amino acids within HLA-A and -B presented epitopes (yellow) is significantly lower compared with the fraction outside (blue), while the fraction of amino acid substitutions in HLA-C binding epitopes is significantly higher compared with the fraction outside.</p

Image_1_Assessment of plasma Catestatin in COVID-19 reveals a hitherto unknown inflammatory activity with impact on morbidity-mortality.tif

IntroductionNeuroendocrine cells release Catestatin (CST) from Chromogranin A (CgA) to regulate stress responses. As regards COVID-19 patients (COVID+) requiring oxygen supply, to date nobody has studied CST as a potential mediator in the regulation of immunity.Patients & MethodsAdmission plasma CST and CgA - its precursor - concentrations were measured (ELISA test) in 73 COVID+ and 27 controls. Relationships with demographics, comorbidities, disease severity and outcomes were analysed (Mann-Whitney, Spearman correlation tests, ROC curves).ResultsAmong COVID+, 49 required ICU-admission (COVID+ICU+) and 24 standard hospitalization (COVID+ICU-). Controls were either healthy staff (COVID-ICU-, n=11) or COVID-ICU+ patients (n=16). Median plasma CST were higher in COVID+ than in controls (1.6 [1.02; 3.79] vs 0.87 [0.59; 2.21] ng/mL, pConclusionRespiratory COVID patients release significant amounts of CST in the plasma making this protein widely available for the neural regulation of immunity. If confirmed prospectively, plasma CST will reliably help in predicting in-hospital mortality, whereas CgA will facilitate the detection of patients prone to care-related infections.</p

Distribution of the normalized dN-dS per codon among proteins.

The six proteins are represented (Agnoprotein, VP1 to VP3, large T antigen “LTA” and small t antigen “stA”). Non-significant values are shown in blue, and significant values in red (positive values for positive selection and negative values for purifying selection, two-tailed binomial distribution). P-values correspond to the Nei-Gojobori test of neutrality for each gene.</p

Maximum likelihood phylogenetic trees of BK polyomavirus.

Three major groups are found: genotype I in blue, a single group including genotypes II/III in red, and genotype IV in green. (A) Unrooted ML phylogenetic tree with 309 complete genome published sequences retrieved from NCBI. (B) Unrooted ML phylogenetic tree with 309 VP1 gene sequences retrieved from NCBI. (C) Unrooted ML phylogenetic tree with 225 complete genome consensus sequences obtained in this study by next-generation sequencing and one reference strain of each genotype and subtype. Reference strains are marked with dots (Ia, Ib1, Ib2, Ic, II, III, IVa1, IVa2, IVb1, IVb2, IVc1, IVc2).</p

Genomic evolutionary rates for the major Baltimore groups and BKV.

Substitution rates are given as substitutions per nucleotide site per year (s/s/y). For the major groups (dsDNA: double-stranded DNA viruses—BKV [5, 7, 28] (time span of sequences (TSS) of 29 years (y), 25 y, and 32 y, respectively), JC polyomavirus [27, 31] (TSS 33 y and 13 y, respectively), herpes simplex virus 1 [32, 33] (TSS not available and 21 y, respectively), human papillomavirus 18 [34] (TSS not available), monkeypox virus [35] (TSS 7 y), variola virus [5] (TSS 31 y), varicella zoster virus [5] (TSS 37 y); ssDNA: single-stranded DNA viruses—African cassava mosaic virus [25] (TSS 5 y), banana bunchy top virus [36] (TSS 2 months), human bocavirus [37] (TSS 1 y), human parvovirus B19 [38, 39] (TSS 14 y and 28 y, respectively), porcine circovirus 2 [40] (TSS 27 y), tomato yellow leaf curl virus [41] (TSS 29 y); RT: retroviruses—avian hepatitis B virus [42] (TSS 22 y), human hepatitis B virus [42–44] (TSS 22 y, 25 y and 35 y, respectively); human immunodeficiency virus 1 [45] (TSS 2 y), primate T-cell lymphotropic virus [45] (TSS 2 y); dsRNA: double-stranded RNA viruses—bluetongue virus [46] (TSS 48 y), human rotavirus [47] (TSS 16 y), homalodisca vitripennis virus [48] (TSS 2 y); ss(-)RNA: single-stranded RNA viruses with negative polarity–Ebola virus [49] (TSS 4 months), fever, thrombocytopenia and leukocytopenia syndrome virus [50] (TSS 4 y), influenza A virus [51, 52] (TSS 28 y and 1 y, respectively), hepatitis delta virus [53] (TSS 3 y), human respiratory syncytial virus [54] (TSS 10 y), rabies virus [55] (TSS 30 y), rift valley fever virus [56] (TSS 10 y); and ss(+)RNA: single-stranded RNA viruses with positive polarity—avian coronavirus [57] (TSS 41 y), barley yellow dwarf virus [58] (TSS 2 y), dengue virus [59](TSS 29 y), foot-and-mouth disease virus [60] (TSS 75 y), hepatitis A virus [61] (TSS 13 y), hepatitis C virus [62] (TSS 20 y), Japanese encephalitis virus [63] (TSS 60 y), Middle East respiratory syndrome coronavirus [64](TSS 4 months), porcine reproductive and respiratory syndrome virus [65] (TSS 3 y), rubella virus [66] (TSS not available), severe acute respiratory syndrome coronavirus [67] (TSS 4 months), St. Louis encephalitis virus [68] (TSS 46 y), Venezuelan equine encephalitis virus [69] (TSS 54 y)). Each point represents the value of a previously published genomic evolutionary rate (note that for some references, more than one substitution rate is represented in the caption). Red circles represent short time span estimates ( 5 years). Medians with interquartile ranges are indicated. In the case of the inter- and intra-host genomic evolutionary rates of BKV, the values are represented as a range of values obtained in this study.</p