key: cord-0261569-eq67buho
authors: Lee, H. K.; Knabl, L.; Walter, M.; Dai, Y.; Fussl, M.; Caf, Y.; Jeller, C.; Knabl, P.; Obermoser, M.; Baurecht, C.; Kaiser, N.; Zabernigg, A.; Wurdinger, G. M.; Furth, P. A.; Hennighausen, L.
title: Prior vaccination enables a more robust immune response to Omicron infection
date: 2022-03-30
journal: nan
DOI: 10.1101/2022.03.24.22272837
sha: 30c0643429e600cfe9aeb1adff05dd7a88e2de34
doc_id: 261569
cord_uid: eq67buho

The antibody response following Omicron infection has been reported to be less robust than to other variants. Here we compared the immune-transcriptome and antibody responses following Omicron infection in unvaccinated and vaccinated individuals who experienced mild to moderate symptoms. The unvaccinated individuals showed a quantitatively greater transcriptional response but a muted antibody response than vaccinated individuals. Prior vaccination modifies the transcriptional response to Omicron infection with a more robust antibody response.

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 30, 2022. ; https://doi.org/10.1101/2022.03.24.22272837 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. None of the study participants had reported a previous SARS-CoV-2 infection and were either asymptomatic or displayed mild to moderate symptoms after the Omicron infection.

Demographic and clinical characteristics of the study population are provided in Supplementary Table 1 .

First, we measured circulating antibody responses in serum samples obtained from the Omicron patients within the first two days of validated infection and after 13 days (Fig.   1a ). The baseline levels (Days 1-2) of anti-spike IgG levels directed against the ancestral strain (WH04) and Omicron were lowest in the naïve group and at least 10-fold higher in the previously vaccinated group (Fig. 1b) . A significant increase of anti-Omicron spike, but not anti-ancestral spike, antibodies were observed in the vaccinated group within 13 days following Omicron infection. Antibody levels did not increase in the naïve group within 13 days following infection. These findings are mirrored by anti-spike antibody levels from other variants ( Supplementary Fig. 1a ).

At this point in the pandemic, a critical question is whether prior BNT162b2 vaccination can prompt development of neutralizing antibodies in Omicron infected individuals. Here, we assessed neutralization capacity using the angiotensin-converting enzyme 2 (ACE2) binding inhibition assay, against the ancestral and Omicron spike proteins in our cohorts shortly after Omicron infection (Days 1-2) and after 13 days (Fig.   1c) . A significant increase in neutralizing activity was observed only in the vaccinated group. These findings parallel increases in anti-spike activity levels against other variants as well ( Supplementary Fig. 1b) .

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. To understand the impact of prior vaccination on the genomic immune response to Omicron infection, we investigated the immune transcriptome (Fig. 1a) . These data sets were compared to reference populations that were naïve (no previous SARS-CoV-2 infection and no vaccination) (Lee et. al, Cell Reports, in press) and to patients that had been infected with the Alpha variant 3 . Bulk RNA-seq on buffy coats isolated within the first two days after validated Omicron infection was performed with an average sequencing depth of 200 million reads per sample (Supplementary Table 2 (Fig. 2a) . The differences observed between the three cohorts were of a quantitative rather than a qualitative nature. We directly analyzed the expression of the genes that were preferentially activated in the unvaccinated Omicron patients as compared to the vaccinated ones (Fig. 2b , Supplementary Table 2) .

Expression of these genes not only increased in the unvaccinated Omicron cohort but were further elevated in the patients infected with the Alpha variant.

Many of the genes, including members of the interferon induced gene family and the neutrophil activation marker CD177, are associated with severe COVID-19 disease.

Since, in many cases, their expression in hospitalized Alpha patients is equivalent to Omicron patients that are either asymptomatic or mildly symptomatic, their activity might reflect the immune status of the patients, rather disease severity. We also identified genes that had not previously linked to COVID-19, such as USP18, an IFN-induced gene encoding a negative regulator of type I IFN signaling 4 , which highly activated in unvaccinated Omicron patients and Alpha patients.

for use under a CC0 license.

This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The antiviral response gene OAS1 is of particular interest as it harbors a mutation traced back to the Neanderthal genome that results in a splice variant associated with protection from severe COVID-19 5 . RNA-seq data revealed that the rs10774671 haplotype was found in 83% of our control population, 86% and 85% in the unvaccinated and vaccinated Omicron population, respectively and 96% of the Alpha population.

Widespread Omicron infection of unvaccinated and vaccinated people, which results in milder disease relative to previous variants, has been reported 6 . However, unlike the response to Delta breakthrough infection [7] [8] [9] , Omicron breakthrough infections result in lower levels of neutralizing antibodies 10 . The muted antibody response may be due to the high share of asymptomatic and mild infections as is also indicated by a less active immune transcriptome shown in our study. However, individuals with prior vaccination showed significant neutralization activity, even with a muted transcriptional response. Naïve individuals demonstrated significantly higher transcriptional response but a less robust humoral response. The response in both groups of individuals was quantitatively less when compared to the transcriptional response of hospitalized individuals with Alpha infection.

In summary, prior vaccination modifies the transcriptional response to Omicron infection but induces a more robust antibody response.

There are several limitations to the current study. The study was conducted on volunteers from a specific geographical area, Tyrol (Austria). Another limitation is the confinement of the study to a timeframe of two weeks following Omicron infection. Some of the data collected on breakthrough infections was reliant on retrospective chart review and not collected as part of a prospective study.

This study was approved (EK Nr: This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Austria, which is responsible for all human research studies conducted in the State of Tyrol (Austria). Participant information was coded and anonymized.

A total of 57 patients infected with Omicron, 34 with no history of prior vaccination and 23 patients who had received 2-3 doses of the BNT162b2 vaccine (Table S1) This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Whole blood was collected, and total RNA was extracted from the buffy coat and purified The raw data were subjected to QC analyses using the FastQC tool (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). mRNA-seq read quality control was done using Trimmomatic 11 (version 0.36) and STAR RNA-seq 12 (version STAR 2.5.4a) using 150 bp paired-end mode was used to align the reads (hg19).

HTSeq 13 (version 0.9.1) was to retrieve the raw counts and subsequently, Bioconductor package DESeq2 14 in R (https://www.R-project.org/) was used to normalize the counts for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 30, 2022. ; https://doi.org/10.1101/2022.03.24.22272837 doi: medRxiv preprint across samples and perform differential expression gene analysis. Additionally, the RUVSeq 15 package was applied to remove confounding factors. The data were prefiltered keeping only genes with at least ten reads in total. The visualization was done using dplyr (https://CRAN.R-project.org/package=dplyr) and ggplot2 16 . The genes with log2 fold change >1 or <-1 and adjusted p-value (pAdj) <0.05 corrected for multiple testing using the Benjamini-Hochberg method were considered significant and then conducted gene enrichment analysis (GSEA, https://www.gsea-msigdb.org/gsea/msigdb).

Differential expression gene (DEG) identification used Bioconductor package DESeq2 in R. P-values were calculated using a paired, two-side Wilcoxon test and adjusted p-value (pAdj) corrected using the Benjamini-Hochberg method. Genes with log2 fold change >1 or <-1, pAdj <0.05 and without 0 value from all sample were considered significant. For significance of each GSEA category, significantly regulated gene sets were evaluated with the Kolmogorov-Smirnov statistic. P-values of antibody between two groups were calculated using one-tailed Wilcoxon rank t-test on GraphPad Prism software (version 9.0.0). A value of *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 was considered statistically significant.

RNA-seq data from buffy coat of healthy control and COVID-19 Alpha patients were obtained GSE189039, GSE190747 and GSE190680. The RNA-seq data from this study will be uploaded in GEO before publishing the manuscript. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (Table S1 ). Blood was collected from study participants at two timepoints after testing PCR positive. b, Plasma IgG antibody binding the SARS-CoV-2 RBD (spike) from the ancestral and Omicron strains in the unvaccinated and vaccinated Omicron patients. c, Neutralizing antibody response to virus spike protein of the ancestral and Omicron variants. p-value between two groups is from one-tailed Wilcoxon rank ttest. *p < 0.05, **p < 0.01, ***p < 0, ****P < 0.0001. Line at median.

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 30, 2022. ; https://doi.org/10.1101/2022.03.24.22272837 doi: medRxiv preprint

Omicron, the great escape artist

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module

USP18 -a multifunctional component in the interferon response

Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

SARS-CoV-2 breakthrough infections elicit potent, broad, and durable neutralizing antibody responses

Characterization of immune responses in fully vaccinated individuals following breakthrough infection with the SARS-CoV-2 delta variant

Trimmomatic: a flexible trimmer for Illumina sequence data

STAR: ultrafast universal RNA-seq aligner

HTSeq--a Python framework to work with highthroughput sequencing data

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Normalization of RNA-seq data using factor analysis of control genes or samples

Ggplot2 : elegant graphics for data analysis

MiXCR: software for comprehensive adaptive immunity profiling

Antigen receptor repertoire profiling from RNA-seq data

The authors declare not competing interests.Transl Med, eabn6150 (2022).for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. of SARS-CoV-2 variants. p-value between two groups is from one-tailed Wilcoxon rank ttest. *p < 0.05, **p < 0.01, ***p < 0, ****P < 0.0001. Line at median.for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted March 30, 2022. ; https://doi.org/10.1101/2022.03.24.22272837 doi: medRxiv preprint