Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants
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SciScore for 10.1101/2022.01.13.475409: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Use of clinical specimen for virus isolation and use of human serum samples for micro-neutralization assays were approved by the University of Saskatchewan’s Biomedical Research Ethics Board (REB# 2591)
Consent: Cohort participants provided informed consent for sharing of serum, and studies were approved by the Sunnybrook Research Institute (REB# 149-1994) and/or the Mount Sinai Hospital (REB# 02-0118-U, 20-0339-E, and 21-0069-E) Research Ethics Board 13.Sex as a biological variable not detected. Randomization Contexual sequences were incorporated into the phylogenetic analysis by using Nexstrain’s ingested GISAID metadata and pandas to randomly sample a representative subset of sequences … SciScore for 10.1101/2022.01.13.475409: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Use of clinical specimen for virus isolation and use of human serum samples for micro-neutralization assays were approved by the University of Saskatchewan’s Biomedical Research Ethics Board (REB# 2591)
Consent: Cohort participants provided informed consent for sharing of serum, and studies were approved by the Sunnybrook Research Institute (REB# 149-1994) and/or the Mount Sinai Hospital (REB# 02-0118-U, 20-0339-E, and 21-0069-E) Research Ethics Board 13.Sex as a biological variable not detected. Randomization Contexual sequences were incorporated into the phylogenetic analysis by using Nexstrain’s ingested GISAID metadata and pandas to randomly sample a representative subset of sequences (jointly deposited in NCBI and GISAID) that belonged to lineages observed in Canada (see also Supplemental Tables S1 and S2 for metadata). Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources For samples from each cohort, samples were selected to have a representative range of anti-spike trimer and anti-RBD antibodies as measured by enzyme-linked immunosorbent assay 14. anti-RBDsuggested: NoneExperimental Models: Cell Lines Sentences Resources EXPERIMENTAL MODEL: Cells and viruses: Vero’76 cells (CRL-1587, ATCC) were used to isolate and/or propagate all virus isolates using a previously published protocol 8. Vero’76suggested: NoneSoftware and Algorithms Sentences Resources Full sequences of the viral isolates have been deposited to NCBI BioProject PRJNA794206. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Paired-end (2×150 bp) sequencing was performed on a MiniSeq with a 300–cycle reagent kit (Illumina, USA) with a negative control library with no input SARS-CoV-2 RNA extract. MiniSeqsuggested: NoneRaw reads underwent adapter/quality trimming (trim-galore v0.6.5) 15, host filtering and read mapping to reference [bwa v0.7.17 16, samtools v.1.7 17,18] trimming of primers (iVar v1.3 19) and variant/consensus calling (freebayes v1.3.2 20) using the SIGNAL workflow (https://github.com/jaleezyy/covid-19-signal) v1.4.4dev (#60dd466) with the ARTICv4 amplicon scheme (from https://github.com/artic-network/artic-ncov2019) and the MN908947.3 SARS-CoV-2 reference genome and annotations. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Additional quality control and variant effect annotation (SnpEff v5.0-0 21) was performed using the ncov-tools v1.8.0 (https://github.com/jts/ncov-tools/). SnpEffsuggested: (SnpEff, RRID:SCR_005191)Variants were summarised using PyVCF v0.6.8 [citation: https://github.com/jamescasbon/PyVCF] and pandas v1.2.4 24. PyVCFsuggested: NoneResults from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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