key: cord-0830143-ud8q6jds
authors: Laurie, Matthew T; Liu, Jamin; Sunshine, Sara; Peng, James; Black, Douglas; Mitchell, Anthea M; Mann, Sabrina A; Pilarowski, Genay; Zorn, Kelsey C; Rubio, Luis; Bravo, Sara; Marquez, Carina; Sabatino Jr., Joseph J; Mittl, Kristen; Petersen, Maya; Havlir, Diane; DeRisi, Joseph
title: SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron
date: 2022-01-03
journal: J Infect Dis
DOI: 10.1093/infdis/jiab635
sha: 8c40c04d9618c458245014daf9b1076846fed1fc
doc_id: 830143
cord_uid: ud8q6jds

The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.

A c c e p t e d M a n u s c r i p t [4] . Because serum neutralization titer is an important correlate of real-world protective immunity, these findings suggest that antibody responses elicited by exposure to ancestral spike versions (Wuhan or D614G) will be less effective at preventing future infection by certain variants [5] . However, the diversity and prevalence of variants have fluctuated greatly throughout the pandemic, creating a complex population of individuals that may have inherently different capacity to neutralize certain variants depending on the specific genotype of their previous exposures, including vaccination [6] .

In this study, we address the question of variant-elicited immune specificity by determining the breadth of neutralizing activity elicited by exposure to specific SARS-CoV-2 variants, vaccines, or both. To accomplish this, we collected serum from subjects with prior infections by variants B.1 (D614G mutation only), B.1.429 (Epsilon), P.2 (Zeta), B.1.1.519, and B.1.617.2 (Delta), which were identified by viral sequencing. We also collected serum from mRNA vaccine recipients who were infected with the B.1 ancestral spike lineage prior to vaccination, infected with B.1.429 prior to vaccination, or had no prior infection. We Our results provide a quantitative comparison of the degree of neutralization specificity produced by different exposures. We also demonstrate the effect of serial exposure to different spike versions in broadening the cross-reactivity of neutralizing antibody responses.

Together, these findings describe correlates of protective immunity within the rapidly evolving landscape of SARS-CoV-2 variants and are highly relevant to the design of future vaccination strategies targeting spike antigens.

Samples for laboratory studies were obtained under informed consent from participants in an ongoing community program -Unidos en Salud‖, which provides SARS-CoV-2 testing, genomic surveillance, and vaccination services in San Francisco, California [7] . Subjects with and without symptoms of COVID-19 were screened with the BinaxNOW rapid antigen assay (supplied by California Department of Public Health). Positive rapid tests were followed by immediate disclosure and outreach to household members for testing, supportive community services, and academic partnership for research studies. All samples were sequenced using ARTIC Network V3 primers on an Illumina NovaSeq platform and consensus genomes generated from the resulting raw .fastq files using IDseq [8] . Table S1 .

SARS-CoV-2 pseudoviruses bearing spike proteins of variants of interest were generated using a recombinant vesicular stomatitis virus expressing GFP in place of the VSV glycoprotein (rVSV∆G-GFP) described previously [10] . (Table S3 ) [11] . All neutralization assays were repeated in a total of three independent experiments with each experiment containing two technical replicates for each condition. Cells were verified to be free of mycoplasma contamination with the MycoAlert Mycoplasma detection kit (Lonza).

Pseudovirus flow cytometry data was analyzed with FlowJo to determine the percentage of (Figure 1 ). Foldchanges in both NT 50 and NT 90 are reported since these values often differ in magnitude due to differences in neutralization curve slope between different variants and sera. In D614Gexposed and vaccine-exposed serum, we observed approximately 2 to 3-fold decreases in average neutralization titer against B.1.429 pseudovirus compared to D614G pseudovirus.

As expected, B.1.429-exposed serum neutralized B.1.429 pseudovirus more efficiently than 1 and B.1.351. Interestingly, although B.1.1.529 (Omicron) substantially escaped neutralization in all convalescent sera and serum from recipients of two vaccine doses, a much more modest 4 to 8-fold reduction in neutralization titer was observed in sera from individuals with previous infection plus vaccination or three vaccine doses.

In this study, we observe that vaccination and natural SARS-CoV-2 infection elicit neutralizing antibody responses that are most potent against variants that bear spike mutations present in the immunizing exposure. This trend is exemplified by variants with mutations at the spike E484 position, which were neutralized more effectively by E484Kexposed serum than other serum types. Importantly, we also show that B.1.617.2 (Delta) is 1 and B.1.351 by Delta-exposed serum further reinforces the notion that cross-neutralization is heavily impacted by antigenic distance between variants [12] .

Together, these results demonstrate that serum neutralization specificity is strongest against variants fully homologous to the exposure, but even single shared spike mutations, particularly those in highly antigenic regions such as the RBD, can enhance crossneutralization as supported in other studies [3, 6, 13] . 

The Delta SARS-CoV-2 variant has a higher viral load than the Beta and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients

Mapping mutations to the SARS-CoV-2

RBD that escape binding by different classes of antibodies

BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants

Immune correlates of protection by mRNA-1273 vaccine against SARS-CoV-2 in nonhuman primates

Reduced neutralization of SARS-CoV-2

1.617 by vaccine and convalescent serum

Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco

IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

Establishment of the WHO International Standard and Reference Panel for anti-SARS-CoV-2 antibody

The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants

Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants

Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice

Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine-boosted nonhuman primates

We would like to thank Dr. Chuka Didigu, Dorothy Park CRNA, Salu Ribeiro, and Bay Area Phlebotomy and Laboratory services for performing blood draws of study subjects. We thank Dr. Andreas Puschnik for providing the engineered cell line used in this study. We thank Susana Elledge and Dr. James Wells for providing reagents and advice on antibody assays.We thank Drs. Peter Kim, Don Ganem, Sandy Schmidt, and Cori Bargmann for technical assistance and discussion.

Dr. DeRisi is a member of the scientific advisory board of The Public Health Company, Inc., and is scientific advisor for Allen & Co. Dr. DeRisi also reports options granted for service on the Scientific Advisory Board of The Public Health Company. None of the other authors have any potential conflicts.

A c c e p t e d M a n u s c r i p t 13 A c c e p t e d M a n u s c r i p t