Journal: Respiratory Research

Article Title: SARS coronavirus 2: from genome to infectome

doi: 10.1186/s12931-020-01581-z

Figure Lengend Snippet: The transmission cycle of SARS-CoV-2. The SARS-CoV-2 originated from bats and pangolins are presumed to be their intermediate amplifying hosts. The virus transmits from animal-to-human to human-to-human. The infected person transmits the virus through cough and sneeze. In the population, there are asymptomatic carrier which spread the virus without any signs or symptoms

Article Snippet: 14. , Human Anti-SARS-CoV-2 (Covid-19) IgG/IgM Rapid Test , KRISHGEN BioSystems , CE-IVD , [ ] .

Techniques: Transmission Assay, Infection

Journal: Respiratory Research

Article Title: SARS coronavirus 2: from genome to infectome

doi: 10.1186/s12931-020-01581-z

Figure Lengend Snippet: Schematic presentation of the SARS-CoV-2 genome Structure. SARS-CoV-2 has a spherical structure. The virus has an outer lipid envelope, covered with spike glycoprotein. The SARS-CoV-2 represents a typical Betacoronavirus genome organisation. The full-length RNA genome comprises of approximately 29,903 nucleotides and has a replicase complex (comprised of ORF1a and ORF1b) at the 5′UTR. The ORF1a encodes for nsp1–nsp10, while ORF1b encodes for nsp1–nsp16. Four genes that encode for the Structural proteins: Spike gene, Envelope gene, Membrane gene, Nucleocapsid gene and a poly (A) tail at the 3′UTR. The accessory genes are distributed in between the structural genes

Article Snippet: 14. , Human Anti-SARS-CoV-2 (Covid-19) IgG/IgM Rapid Test , KRISHGEN BioSystems , CE-IVD , [ ] .

Techniques:

Journal: Respiratory Research

Article Title: SARS coronavirus 2: from genome to infectome

doi: 10.1186/s12931-020-01581-z

Figure Lengend Snippet: The SARS-CoV-2 replication and pathogenesis. a The SARS-CoV-2 infects upper and lower respiratory tract. b The virus replication from 1 to 12 has been described as, (1) The virus identifies the ACE-2 receptor. (2) The binding is initiated by the Spike (S) glycoprotein of SARS-CoV-2 by receptor binding domain (RBD) to the ACE-2 receptor binding motif (RBM). (3, 4) The virus-receptor internalization occurs and a membrane fusion is carried out by S2 subunit of S glycoprotein followed by the uncoating of +ssRNA inside cytoplasm. (5–7) The +ssRNA directly translate into non-structural proteins for initiating the viral replication through RNA-dependent RNA polymerase (RdRp/nsp12) and forms -ssRNA which act as template for synthesizing various copies of +ssRNA. (8–10) The +ssRNA along with the structural protein are trafficked to ER-Golgi complex for assembly and maturation. (11–12) The vesicles-encapsulated virion fuses with the cell membrane and through exocytosis release outside the cell to infect nearby cell. The immune response: the cellular RNA receptors like, RIG-I and MDA-5 recognized the dsRNAs in cytoplasm, activating the pro-inflammatory response and antiviral response inside cells. The cytokines activate the macrophages and lymphocytes to kick start both cellular and humoral response. c The virus disseminates to the other part of body through blood affecting the brain, heart, liver spleen, large intestine, kidneys

Article Snippet: 14. , Human Anti-SARS-CoV-2 (Covid-19) IgG/IgM Rapid Test , KRISHGEN BioSystems , CE-IVD , [ ] .

Techniques: Binding Assay

Journal: Respiratory Research

Article Title: SARS coronavirus 2: from genome to infectome

doi: 10.1186/s12931-020-01581-z

Figure Lengend Snippet: Diagnostic kits for COVID-19

Article Snippet: 14. , Human Anti-SARS-CoV-2 (Covid-19) IgG/IgM Rapid Test , KRISHGEN BioSystems , CE-IVD , [ ] .

Techniques: Diagnostic Assay, Quantitative RT-PCR

Journal: Respiratory Research

Article Title: SARS coronavirus 2: from genome to infectome

doi: 10.1186/s12931-020-01581-z

Figure Lengend Snippet: List of candidate vaccines against COVID-19. This table has been taken with permission from the WHO website (Draft landscape of COVID19 candidate vaccine) with slight modifications [ 169 ]

Article Snippet: 14. , Human Anti-SARS-CoV-2 (Covid-19) IgG/IgM Rapid Test , KRISHGEN BioSystems , CE-IVD , [ ] .

Techniques: Plasmid Preparation, Recombinant, Electroporation, Produced, Derivative Assay

Journal: medRxiv

Article Title: Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses

doi: 10.1101/2022.11.07.22282030

Figure Lengend Snippet: (A) Heatmap indicating antibody functions (antibody-dependent complement deposition, ADCD; cellular phagocytosis, ADCP; neutrophil phagocytosis, ADNP; NK activation with production of CD107a, IFNγ and MIP1β), capacity to bind Fcγ receptors (FcγR 2A, 2B, 3A, 3B) and total IgG of different SARS-CoV-2 specific antigens (Spike, S1, S2, RBD and NC) in individuals who did not develop (no PASC) or developed neurological PASC (neuroPASC). Each row corresponds to a single individual. Z-scores, positive (i.e. higher than the mean) in purple, negative (i.e. lower than the mean) in blue. NC= nucleocapsid, RBD=receptor binding domain (B) Bar dot plots show the level of IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA, FcγR binding capacity ( , , , ) and functions (ADCD, ADNP, ADNKA with production of CD107a) of Spike-specific antibodies in individuals who did not develop (no PASC, in blue) or developed neurological PASC (neuroPASC, in purple). MFI=Median Fluorescence Intensity. Mann-Whitney, *p<0.05, **p<0.01, ***p<0.001 ****p<0.0001. (C) Radial plots indicate the levels of IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM, IgA1, IgA2, binding capacity to FcγR ( , , , ), FcαR, and functions (ADCD, ADCP, ADNP, ADNKA with production of CD107a, IFNγ and MIP1β) of Spike-specific antibodies in individuals who did not develop (noPASC) or developed neurological PASC (neuroPASC). Each sector represents a z-scored antibody feature. (D) Heatmap indicating the average difference (%) of Spike-specific functions (ADCD, ADCP, ADNP, ADNKA with production of CD107a, IFNγ and MIP1β), binding capacity to FcγR (2A, 2B, 3A, 3B), FcαR, IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA between individuals with no PASC and with neuroPASC. Each column represents an antibody feature. Positive values indicate features enriched in no PASC, null values indicate features equally present in both no PASC and neuroPASC. None of the features were enriched in neuroPASC.

Article Snippet: The antibody responses were assessed against 5 different SARS-CoV-2 antigens, including Spike WT (Sino Biological 40589-V08H4), RBD WT (Sino Biological 40592-V08H), S1 WT (Sino Biological 40591-V08H), S2 WT (Sino Biological 40590-V08B) and Nucleocapsid (Sino Biological 40588-V08B), as well as 4 non-SARS-CoV-2 coronaviruses, including HCoV-OC43 (Sino Biological 40607-V08B), -HKU1 (Sino Biological 40606-V08B), -NL63 (Sino Biological 40604-V08B), -229E (Sino Biological 40605-V08B).

Techniques: Activation Assay, Binding Assay, Fluorescence, MANN-WHITNEY

Journal: medRxiv

Article Title: Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses

doi: 10.1101/2022.11.07.22282030

Figure Lengend Snippet: (A) Bar dot plots show the level of IgG1 antibodies against non-coronaviruses (EBV, Flu, HSV1) in individuals who did not develop (no PASC, in blue) or developed neurological PASC (neuroPASC, in purple). MFI=Median Fluorescence Intensity. Mann-Whitney, ns= statistically not significant. (B) Heatmap indicates the average difference (%) of SARS-CoV-2 -specific (Spike, S1, S2, RBD and NC) and common Coronaviruses-specific (229E, OC43, NL63, HKU1) IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA1, IgA2, binding capacity to FcγRs (2A, 2B, 3A, 3B), FcαR, between individuals with no PASC and with neuroPASC. Each column represents an antibody feature. Positive values (purple) indicate features enriched in no PASC, negative values (blue) indicate features enriched in neuroPASC, null values (white) indicate features equally present in both no PASC and neuroPASC. Common CoVs = other non-SARS-CoV-2 common Coronaviruses; NC= SARS-CoV-2 nucleocapsid; RBD= SARS-CoV-2 receptor binding domain. Mann-Whitney was used to define statistically significant differences at a univariate level between no PASC and neuroPASC, *p<0.01 or less. ( C-D ) Multivariate analysis of antibody signatures in individuals with neuroPASC and no PASC. Partial least square discriminant analysis (PLSDA) on LASSO-selected features was used to resolve antibody profiles in neuroPASC and no PASC. Dots represent individual samples (no PASC, blue; neuroPASC, red) across SARS-CoV-2 specific (Spike, S1, S2, RBD, NC), and common Coronaviruses (229E, OC43, NL63, HKU1) specific antibody features. Bar graph shows LV1 loadings of LASSO-selected features ranked by their Variable Importance in Projection (VIP). Features enriched in no PASC are in blue, features enriched in neuroPASC are in red. Ten-fold cross validation was performed, resulting in 84% cross validation accuracy (p<0.01). (E) Chord plots indicate the Spearman correlation coefficients between the LASSO-selected features enriched in no PASC (left) and in neuroPASC (right), and the non-LASSO selected antibody features across SARS-CoV-2 antigens (Spike, S1, S2, RBD, NC), and other common Coronaviruses antigens (229E, OC43, NL63, HKU1). Only coefficients >0.5 are plotted, p<0.01 after Benjamini-Hochberg correction for multiple comparisons. Positive values represent direct correlations, negative values represent inverse correlations (none of the features were inversely correlated with any other feature).

Article Snippet: The antibody responses were assessed against 5 different SARS-CoV-2 antigens, including Spike WT (Sino Biological 40589-V08H4), RBD WT (Sino Biological 40592-V08H), S1 WT (Sino Biological 40591-V08H), S2 WT (Sino Biological 40590-V08B) and Nucleocapsid (Sino Biological 40588-V08B), as well as 4 non-SARS-CoV-2 coronaviruses, including HCoV-OC43 (Sino Biological 40607-V08B), -HKU1 (Sino Biological 40606-V08B), -NL63 (Sino Biological 40604-V08B), -229E (Sino Biological 40605-V08B).

Techniques: Fluorescence, MANN-WHITNEY, Binding Assay

Journal: medRxiv

Article Title: Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses

doi: 10.1101/2022.11.07.22282030

Figure Lengend Snippet: (A) The heatmap indicates functions (ADCD, ADCP, ADNP, ADNKA with production of CD107a, IFNγ and MIP1β), IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM, IgA, capacity to bind to Fcγ receptors (FcγR2A, 2B, 3A, 3B) and FcαR of antibodies to different SARS-CoV-2 specific antigens (Spike, S1, S2, RBD and NC) in serum and CSF from individuals with neuroPASC. Each row corresponds to a single sample. Z-scores, positive (i.e. higher than the mean) in purple, negative (i.e. lower than the mean) in blue. NC= nucleocapsid, RBD=receptor binding domain (B) Radial plots indicate levels of IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA1, IgA2, binding capacity to FcγR ( , , , ), FcαR, and functions (ADCD, ADCP, ADNP, ADNKA with production of CD107a, IFNγ and MIP1β) of Spike-specific antibodies in serum and CSF from individuals with neuroPASC. Each sector represents a z-scored antibody feature. (C) Bar dot plots show the level of IgG subclasses (IgG1, IgG2, IgG3), IgM and IgA, binding capacity to FcγR ( , , , ) and FcαR, and functions (ADCD, ADNP, ADNKA) of Spike-specific antibodies in serum (purple) and CSF (blue) from individuals with neuroPASC. MFI=Median Fluorescence Intensity. Mann-Whitney, *p<0.05, **p<0.01, ***p<0.001 ****p<0.0001. (D) The bar plots indicate the percentage of neuroPASC subjects/samples with positive Spike-specific antibody responses of each IgG subclass in serum and CSF. Positive responses were considered if MFI of each sample was 2-fold higher than the median MFI of PBS level (background). (E) Heatmap indicating the average difference (%) of Spike-specific IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA1, IgA2, binding capacity to FcγR (2A, 2B, 3A, 3B) and FcαR, between CSF and serum from individuals with neuroPASC. Each column represents an antibody feature. Positive values (purple) indicate features enriched in serum, negative values (blue) indicate features enriched in CSF, null values (white) indicate features equally present in serum and CSF. No features were enriched in CSF.

Article Snippet: The antibody responses were assessed against 5 different SARS-CoV-2 antigens, including Spike WT (Sino Biological 40589-V08H4), RBD WT (Sino Biological 40592-V08H), S1 WT (Sino Biological 40591-V08H), S2 WT (Sino Biological 40590-V08B) and Nucleocapsid (Sino Biological 40588-V08B), as well as 4 non-SARS-CoV-2 coronaviruses, including HCoV-OC43 (Sino Biological 40607-V08B), -HKU1 (Sino Biological 40606-V08B), -NL63 (Sino Biological 40604-V08B), -229E (Sino Biological 40605-V08B).

Techniques: Binding Assay, Fluorescence, MANN-WHITNEY

Journal: medRxiv

Article Title: Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses

doi: 10.1101/2022.11.07.22282030

Figure Lengend Snippet: (A) Heatmap indicating the average difference (%) of antibody responses to SARS-CoV-2 (Spike, S1, S2, RBD and NC), other common Coronaviruses (229E, OC43, NL63, HKU1) and non-coronaviruses (EBV, Flu, HHV1), including IgG subclasses (IgG1, IgG2, IgG3, IgG4), IgM and IgA, binding capacity to FcγR (2A, 2B, 3A, 3B) and FcαR, between serum and CSF from individuals with neuroPASC. Positive values (purple) indicate features enriched in serum, negative values (blue) indicate features enriched in CSF, null values (white) indicate features equally present in both serum and CSF. There were no features enriched in CSF. Common CoVs = other non-SARS-CoV-2 common Coronaviruses (229E, OC43, NL63, HKU1); NC= nucleocapsid; RBD= receptor binding domain (B-C) Multivariate analyses of antibody signatures in serum and CSF from individuals with neuroPASC. Multilevel partial least square discriminant analysis (M-PLSDA) on LASSO-selected features was used to resolve antibody profiles in serum:CSF pairs. Dots represent individual samples (serum, blue; CSF, purple) across SARS-CoV-2 antigens (Spike, S1, S2, RBD, NC), and common Coronaviruses (229E, OC43, NL63, HKU1). Bar graph shows LV1 loadings of LASSO-selected features ranked by their Variable Importance in Projection (VIP). Features enriched in serum are in purple, no features were enriched in CSF. Ten-fold cross validation was performed, resulting in 100% cross validation accuracy (p<0.01). (D-E) Bar dot plots indicate CSF to serum ratios of IgG1, FcγR (2A, 2B, 3A) and FcαR binding capacity for SARS-CoV-2 (Spike, S1, S2, RBD, NC antigens combined) and other common Coronaviruses (229E, OC43, NL63, HKU1 combined) antibodies in individuals with neuroPASC. Mann-Whitney, *p<0.05, ***p<0.001 ****p<0.0001. CoV=common Coronaviruses; NC= nucleocapsid; RBD= receptor binding domain (F) Bar dot plots show the binding capacity of antibodies to the neonatal Fc receptor (FcRn) of serum and CSF SARS-CoV-2 antibodies targeting different antigens (Spike, S1, S2, RDB, NC) in individuals with neuroPASC. Mann-Whitney, *p<0.05, **p<0.01, ***p<0.001 ****p<0.0001. MFI=Median Fluorescence Intensity; NC=nucleocapsid; RBD=receptor binding domain (G) Bar dot plots indicate the FcRn binding capacity of serum and CSF SARS-CoV-2 antibodies (Spike, S1, S2, RBD, NC, combined), compared to common Coronaviruses (229E, OC43, NL63, HKU1 combined) and non-coronaviruses (EBV, Flu, HSV1 combined). Kruskal Wallis test, Dunn’s correction for multiple comparisons. **p<0.01, ****p<0.0001. MFI=Median Fluorescence Intensity; NC= nucleocapsid; RBD= receptor binding domain

Article Snippet: The antibody responses were assessed against 5 different SARS-CoV-2 antigens, including Spike WT (Sino Biological 40589-V08H4), RBD WT (Sino Biological 40592-V08H), S1 WT (Sino Biological 40591-V08H), S2 WT (Sino Biological 40590-V08B) and Nucleocapsid (Sino Biological 40588-V08B), as well as 4 non-SARS-CoV-2 coronaviruses, including HCoV-OC43 (Sino Biological 40607-V08B), -HKU1 (Sino Biological 40606-V08B), -NL63 (Sino Biological 40604-V08B), -229E (Sino Biological 40605-V08B).

Techniques: Binding Assay, MANN-WHITNEY, Fluorescence

Journal: medRxiv

Article Title: Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses

doi: 10.1101/2022.11.07.22282030

Figure Lengend Snippet: (A) The radial plots indicate the levels of IgG1 and FcγR2A binding capacity of SARS-CoV-2 antibodies (Spike, S1, S2, RBD, upper half circle) and common Coronaviruses (229E, OC43, NL63, lower half circle) in individuals with neuroPASC, divided into those with good versus poor outcome. Each sector represents a z-scored antibody feature. RBD=receptor binding domain (B-C) Volcano plots showing the correlation of each SARS-CoV-2 and common Coronaviruses (229E, OC43, NL63, HKU1)-antibody feature with modified Rankin Scale (mRS). Spearman correlation coefficients are indicated in the x-axis (positive correlation on the right, red; negative correlation on the left, blue), and the statistical significance is indicated in the y-axis (-log10[p-values]). Values above black dashed line indicate statistically significant correlations (p adjusted value<0.01, Benjamini-Hochberg correction for multiple comparisons). Negative correlations, indicating good outcome, were identified with serum antibodies (left graph, in blue), whereas negative correlations, indicating poor outcome, were identified with CSF antibody profiles (right graph, in red).

Article Snippet: The antibody responses were assessed against 5 different SARS-CoV-2 antigens, including Spike WT (Sino Biological 40589-V08H4), RBD WT (Sino Biological 40592-V08H), S1 WT (Sino Biological 40591-V08H), S2 WT (Sino Biological 40590-V08B) and Nucleocapsid (Sino Biological 40588-V08B), as well as 4 non-SARS-CoV-2 coronaviruses, including HCoV-OC43 (Sino Biological 40607-V08B), -HKU1 (Sino Biological 40606-V08B), -NL63 (Sino Biological 40604-V08B), -229E (Sino Biological 40605-V08B).

Techniques: Binding Assay, Modification