Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

Version published to 10.1016/j.heliyon.2023.e17958

Jul 1, 2023

SciScore for 10.1101/2022.03.18.484814: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Antibodies
Sentences	Resources
Briefly, all collected plasma and saliva samples were tested for SARS-CoV-2 specific antibodies by enzyme-linked immunosorbent assay (ELISA) and pseudovirus neutralization assay (Fig. 2 and Suppl.	SARS-CoV-2 suggested: None
After 4X washing, 100 μL of 1:5000 diluted Goat anti-human secondary antibody was added into each well and incubated at 37°C for 1 hr (Goat Anti-Human IgG ɣ Chain Specific HRP conjugated, species Adsorbed (Human IgM, IgD and IgA) Polyclonal Antibody for IgG (Cat# AP504P, EMD Millipore, Burlington, MA)	IgA suggested: (Millipore Cat# AP504P, RRID:AB_805350)
Goat Anti-Human IgA, a-chain …

SciScore for 10.1101/2022.03.18.484814: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Antibodies
Sentences	Resources
Briefly, all collected plasma and saliva samples were tested for SARS-CoV-2 specific antibodies by enzyme-linked immunosorbent assay (ELISA) and pseudovirus neutralization assay (Fig. 2 and Suppl.	SARS-CoV-2 suggested: None
After 4X washing, 100 μL of 1:5000 diluted Goat anti-human secondary antibody was added into each well and incubated at 37°C for 1 hr (Goat Anti-Human IgG ɣ Chain Specific HRP conjugated, species Adsorbed (Human IgM, IgD and IgA) Polyclonal Antibody for IgG (Cat# AP504P, EMD Millipore, Burlington, MA)	IgA suggested: (Millipore Cat# AP504P, RRID:AB_805350)
Goat Anti-Human IgA, a-chain specific Peroxidase conjugate for IgA (Cat# 401132-2ML, Calbiochem, San Diego, CA) for IgA, and Goat Anti-Human IgM Fc5µ Fragment specific HRP conjugated secondary antibody for IgM (Cat# AP114P	Goat Anti-Human IgA suggested: None Anti-Human IgA suggested: None Anti-Human IgM suggested: (Millipore Cat# AP114P, RRID:AB_92449) IgM suggested: (Millipore Cat# AP114P, RRID:AB_92449)
Experimental Models: Cell Lines
Sentences	Resources
Briefly, 293T cells were transfected with pCAGGS.S (30 μg for a T75 flask) using Lipofectamine 3000 (Invitrogen, L3000015) following the manufacturer’s instruction.	293T suggested: None
Briefly, Vero cells were seeded at a density of 2.5 × 104/50 μL in a Greiner Bio-One™ CellStar™ μClear™ 96-Well, Cell Culture-Treated, Flat-Bottom, Half-Area Microplate (Thermo Fisher Scientific, Waltham, MA).	Vero suggested: RRID:CVCL_ZW93)
Recombinant DNA
Sentences	Resources
Generation of pseudo-virus (rVSV-GFPΔG*Spike): For pseudoviruses construction, spike genes from strain Wuhan-Hu-1 (GenBank: MN908947) were codon-optimized for human cells and cloned into eukaryotic expression plasmid pCAGGS to generate the envelope recombinant plasmids pCAGGS.S as described previously with slight modifications 73.	pCAGGS suggested: RRID:Addgene_127347)
Briefly, 293T cells were transfected with pCAGGS.S (30 μg for a T75 flask) using Lipofectamine 3000 (Invitrogen, L3000015) following the manufacturer’s instruction.	pCAGGS.S suggested: None
Software and Algorithms
Sentences	Resources
Positive response was determined by the area under the curve (AUC) using GraphPad Prism version 8.3.1 (GraphPad Software, Inc.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
The neutralizing activity of the plasma sample was determined as pNT50 calculated from a transformed non-linear regression curve generated by GraphPad Prism version 8.3.1.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
Significantly enriched proteins in convalescent samples (p<0.05)(Table 2) were subjected to the network analysis by STRING enrichment analysis (Cytoscape software v	STRING suggested: (STRING, RRID:SCR_005223) Cytoscape suggested: (Cytoscape, RRID:SCR_003032)
The heatmap was created using the pheatmap package in R using hierarchical distance matrix and clustering option 80.	pheatmap suggested: (pheatmap, RRID:SCR_016418)
Correlation among different parameters (antibody titers, proteomic marker expression levels, categorized demographic information, and salivary protein subgrouping) was evaluated by both Pearson’s R and simple linear regression analyses using Graphpad Prism-8 suites of software (GraphPad Software, Inc.	Pearson’s suggested: None

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitation of our study consists of selection bias of donors enrolled in our study with inclusion criteria that considered most donors that had SARS-CoV-2 RT-qPCR-positive results and not healthy donors. The control population came from a pre-COVID era, and did not include an RT-qPCR, but attempted to match most of the demographics. Since our analysis was based on convalescent samples passively collected from persons with COVID-19 in the recovery phase, our study result does not directly reflect responses during the active disease phase of the viral infection. Some parameters, such as RBD binding IgG responses, seem to be already waned and did not display significant differences from healthy. While we could detect unresolved inflammatory status lagged from the acute phase of COVID-19, our study setting was not optimal to elucidate innate immunopathogenesis. As our data set was missing critical information, such as viral load, we cannot fully exclude the confounding factors that could possibly impact the antibody and proteomic alterations. Also, the samples were collected at only a one-time point, and antibody levels or proteomic responses were not adjusted by the different baseline of each individual and it was not possible to draw predictive conclusions on our findings but instead correlations. Most importantly, this is our cross-sectional study investigating one time point comparing health vesus disease and saliva versus plasma.Future longitudinal studies should investigate...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

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Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

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