SARS-CoV-2 Omicron variant escapes neutralizing antibodies and T cell responses more efficiently than other variants in mild COVID-19 convalescents

Version published to 10.1016/j.xcrm.2022.100651

Jun 1, 2022

SciScore for 10.1101/2021.11.08.21266035: (What is this?)

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

Table 1: Rigor

Ethics	IRB: Study protocols were approved by the Central Adelaide Clinical Human Research Ethics Committee (#13050) and the Women’s and Children’s Health Network Human research ethics (protocol HREC/19/WCHN/65), Adelaide, Australia. Consent: All participants provided written informed consent in accordance with the Declaration of Helsinki and procedures were carried out following the approved guidelines.
Sex as a biological variable	In this study, whole blood specimens from 43 participants (19 male, 24 female) of (95% CI, 44.8-55.4) years of age (figure S1) who presented mild COVID-19 symptoms according to NIH guidelines (https://www.covid19treatmentguidelines.nih.gov/overview/clinical-spectrum/) were sampled and processed at two time points 6 months apart after PCR positive test.
Randomization	Randomisation: Since all samples that were available in South Australia were used in the study, no randomisation was performed in the experiments.
Blinding	Blinding: No experiments were blinded in this study.
Power Analysis	Statistics, replicates and sample-size estimation: All mild-COVID-19 patient samples available at the time points reported in the study from the South Australian cohort (n=43) were used in this study and, therefore, no pre hoc power calculations were carried out to determine the sample size.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Secondary antibodies were diluted in 5% skim milk in PBST as follows: Goat anti-Human IgG (H+L) Secondary Antibody, HRP (1:30,000;	anti-Human IgG suggested: None
Goat anti-human IgA HRP antibody (1:5,000; Sigma) and incubated for 1 hour at room temperature, followed by four washes with PBS-T.	anti-human IgA suggested: None
Cells were pre-treated with 0.555 µg/mL of anti-CD40 blocking antibody (HB14, Miltenyi Biotec) for 15 min.	anti-CD40 suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Recombinant proteins were overexpressed in Expi293 cells (Thermo Fisher) and 72 hrs later purified by Ni-NTA affinity and size-exclusion chromatography.	Expi293 suggested: RRID:CVCL_D615)
36 In brief, SARS-CoV-2 pseudo-particles were generated by co-transfecting expression plasmids containing SARS-CoV-2 Spike (kindly provided by Dr Markus Hoffmann)37 and the MLV gag/pol and luciferase vectors (kindly provided by Prof. Francois-Loic Cosset)38,39 in CD81KO 293T cells (kindly provided by Dr Joe Grove),40 using mammalian Calphos transfection kit (Takara Bio)	293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
41 293T-ACE2 cells were seeded 24 h earlier at 1.5 × 104 cells per well in 96-well white flat-bottom plates (Sigma-Aldrich).	293T-ACE2 suggested: None
Software and Algorithms
Sentences	Resources
Cells were washed, resuspended in FACS wash buffer and the data acquired on BD FACSAria™ III.	BD FACSAria™ suggested: (BD FACSAria II Cell Sorter, RRID:SCR_018934)
Data analysis was performed using FlowJo version 10.7.1 (TreeStar).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
36 ID50 for serum was calculated using a non-linear regression model (GraphPad Prism).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
All statistical analyses were performed using GraphPad Prism 9.0.0 (San Diego, CA, US).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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:

One caveat of these studies is that high rates of transmission of SARS-CoV-2 in the communities where the studies were conducted (e.g. Italy, UK or USA) increased the likelihood of virus re-exposure in that cohort, precluding the ability to draw firm conclusions on the duration and protective effects of primary SARS-CoV-2 immunity. Controlled, in-depth studies in convalescents have also been conducted, but vaccination and almost ubiquitous high SARS-CoV-2 infection rates have reduced the opportunities to recruit convalescents long after COVID-19 disease, and importantly, in the absence of re-infection. Conversely, vaccination programs allow for more controlled studies and deeper immune analysis and facilitate conducting experimental procedures to test immune fitness against VoC. However, to date, the majority of vaccinees have received Spike-based vaccines, which are not well-suited as a proxy for what SARS-CoV-2 immunity may look like in the long-term, or its adaptability to VoC. Here, we have taken advantage of the relatively unique situation in South Australia, where local transmission of SARS-CoV-2 was eliminated early on in the pandemic in 2020, enabling us to conduct a 12-month longitudinal study of SARS-CoV-2 immunity in mild-COVID-19 convalescents and test their immune fitness against the current VoC. Total RBD IgG titers and other circulating Ig isotypes against SARS-CoV-2 Spike and RBD antigens decrease over the months following COVID-19 disease, with the strongest ...

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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SARS-CoV-2 Omicron variant escapes neutralizing antibodies and T cell responses more efficiently than other variants in mild COVID-19 convalescents

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