key: cord-0931221-u4hinj0r
authors: Davis, C.; Logan, N.; Tyson, G.; Orton, R.; Harvey, W.; Haughney, J.; Perkins, J.; The COVID-19 Genomics UK Consortium,; Peacock, T.; Barclay, W. S.; Cherepanov, P.; Palmarini, M.; Murcia, P. R.; Patel, A. H.; Robertson, D. L.; Thomson, E. C.; Willett, B. J.
title: Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
date: 2021-06-28
journal: nan
DOI: 10.1101/2021.06.23.21259327
sha: e74eb4e61b1f3b14153b477ca6275091a9cebb4b
doc_id: 931221
cord_uid: u4hinj0r

Vaccines are proving to be highly effective in controlling hospitalisation and deaths associated with SARS-CoV-2 infection but the emergence of viral variants with novel antigenic profiles threatens to diminish their efficacy. Assessment of the ability of sera from vaccine recipients to neutralise SARS-CoV-2 variants will inform the success of strategies for minimising COVID19 cases and the design of effective antigenic formulations. Here, we examine the sensitivity of variants of concern (VOCs) representative of the B.1.617.1 and B.1.617.2 (first associated with infections in India) and B.1.351 (first associated with infection in South Africa) lineages of SARS-CoV-2 to neutralisation by sera from individuals vaccinated with the BNT162b2 (Pfizer/BioNTech) and ChAdOx1 (Oxford/AstraZeneca) vaccines. Across all vaccinated individuals, the spike glycoproteins from B.1.617.1 and B.1.617.2 conferred reductions in neutralisation of 4.31 and 5.11-fold respectively. The reduction seen with the B.1.617.2 lineage approached that conferred by the glycoprotein from B.1.351 (South African) variant (6.29-fold reduction) that is known to be associated with reduced vaccine efficacy. Neutralising antibody titres elicited by vaccination with two doses of BNT162b2 were significantly higher than those elicited by vaccination with two doses of ChAdOx1. Fold decreases in the magnitude of neutralisation titre following two doses of BNT162b2, conferred reductions in titre of 7.77, 11.30 and 9.56-fold respectively to B.1.617.1, B.1.617.2 and B.1.351 pseudoviruses, the reduction in neutralisation of the delta variant B.1.617.2 surpassing that of B.1.1351. Fold changes in those vaccinated with two doses of ChAdOx1 were 0.69, 4.01 and 1.48 respectively. The accumulation of mutations in these VOCs, and others, demonstrate the quantifiable risk of antigenic drift and subsequent reduction in vaccine efficacy. Accordingly, booster vaccines based on updated variants are likely to be required over time to prevent productive infection. This study also suggests that two dose regimes of vaccine are required for maximal BNT162b2 and ChAdOx1-induced immunity.

Recent data from Public Health England suggest that following exposure to this lineage, effectiveness of the BNT162b2 vaccine is reduced to 33.5% after one dose, and 87.9% following two doses 3 . Further, the two-dose effectiveness of the ChAdOX1 vaccine is reduced to 59.8% following exposure to B.1.617. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint reduce binding by several monoclonal antibodies 4, 5, 6, 7, 8 and convalescent plasma 6 . Globally, L452R has emerged independently in several lineages since November/December 2020 suggesting a role in immune-evasion and/or virus adaptation 9 . L452R is one of the defining mutations of the lineage B.1.427/B.1.429, a variant of interest (VOI) first identified in California and associated with reduced neutralisation titres with plasma from vaccinated or convalescent individuals 7 . Investigation of the effect of RBD mutations on binding of convalescent plasma by deep mutational scanning suggests the impact of E484Q is similar to that of E484K 10 , which has been shown widely to diminish antibody binding, including those elicited by vaccination 8, 11 .

In this study, we investigated the neutralising capacity of sera from participants in the COVID-19

DeplOyed VaccinE (DOVE) Cohort Study who had been vaccinated with the BNT162b2 mRNA vaccine (Pfizer-BioNTech ) or the ChAdOx1 adenovirus-vectored vaccine (Oxford-AstraZeneca) as part of the national deployed vaccine strategy. 

Sera were collected from 156 healthy individuals who had received one dose (n = 37) or two doses (n = 50) of BNT162b2 (Pfizer-BioNTech), or one dose (n= 50) or two doses (n = 18) of ChAdOx1 (Oxford/AstraZeneca) vaccines. Samples were screened initially by ELISA for reactivity with recombinant S1, RBD and N from the Wuhan-Hu-1 SARS-CoV-2 sequence. Of those individuals vaccinated with BNT162b2, only one individual given a single dose (1/37) failed to mount a detectable antibody response against S1, all other samples were positive for reactivity against both S1 and RBD (Fig. 3A) . In contrast, four individuals given a single dose (4/50) of ChAdOx1 failed to react with S1, although two of these samples bound the RBD antigen (Fig.3B ).

All samples from individuals immunised with two doses of either BNT162b2 or ChAdOx1 reacted strongly against both S1 and RBD. Antibody reactivity (A405nm) was significantly higher following the second dose of either BNT162b2 (S1 and RBD, p<0.0001) or ChAdOx1 (S1 p=0.0006; RBD p=0.0014) compared with a single dose of the respective vaccines. Moreover, reactivity against S1 was significantly greater in the groups immunised with either one (p=0.0152) or two (p=0.0145) doses of BNT162b2 in comparison with the groups immunised with one or two doses of ChAdOx1 respectively. Similarly, reactivity against RBD was higher in samples from the groups immunised with either one (p=0.0029) or two (p=0.0018) doses of BNT162b2 in comparison with one or two doses of ChAdOx1 respectively. Eight individuals were identified with reactivity . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint against SARS-CoV-2 N suggesting prior, undocumented exposure to SARS-CoV-2 or a related coronavirus. Exclusion of samples from these individuals did not affect the analyses (Table S1 ). Table S1 ). The mean antibody titre induced by vaccination with two doses of ChAdOx1 (mean titre = 1325.6, n=18) was significantly lower than that induced by two doses of BNT162b2 (mean titre = 11473). After a single dose of ChAdOx1, 17 of 50 of vaccinated individuals (34%) had antibody titres ≤50. In comparison, only 5 of 37 individuals (13.5%) vaccinated with a single dose of BNT162b2 had antibody titres ≤50. These data are consistent with ChAdOx1 inducing a weaker antibody response than BNT162b2 following primary immunisation. However, when the age distribution of the study cohorts was compared, it was notable that the age of participants vaccinated with the ChAdOx1 vaccine were on average 15 years older than those vaccinated with BNT162b2 (43 versus 58 respectively; Table S2 ), consistent with the shifting policy on age-group targeting mid-study. The mean titre of antibodies detected in individuals with BNT162b2 against all the VOCs analysed was higher than those present in sera from individuals vaccinated with ChAdOx1 ( Fig.3G -J). Vaccination with two doses of BNT162b2 induced significantly higher . CC-BY-ND 4.0 International license It is made available under a 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 June 28, 2021.

neutralising antibody titres against the Wuhan-Hu-1 virus than either one dose of BNT162b2, or two doses of ChAdOx1.

The against all the VOCs analysed was higher than those present in sera from individuals vaccinated with ChAdOx1. Vaccination with two doses of BNT162b2 induced significantly higher neutralising antibody titres against the Wuhan-Hu-1 virus than either one dose of BNT162b2, or two doses of ChAdOx1. Further, the mean antibody titre induced by vaccination with two doses of ChAdOx1 was significantly lower than that induced by two doses of BNT162b2. Due to vaccines being used in batches targeted at decreasing age groups in the UK, comparisons between neutralisation responses in recipients of the ChAdOx1 versus the BNT162b2, vaccines may be affected by the age differences between these groups (participants vaccinated with the ChAdOx1 were on average 15 years older than those vaccinated with BNT162b2 in our study) and will need further investigation as samples from broader populations of age-matched individuals become available.

. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

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We thank all the researchers who have shared genome data openly via the GISAID Initiative. . CC-BY-ND 4.0 International license It is made available under a 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 June 28, 2021. Preparation of SARS-CoV-2 antigens for ELISA. S1 and RBD antigens were prepared as described previously 16 . Briefly, the SARS-CoV-2 RBD and S1 constructs, spanning SARS-CoV-2 S (UniProt ID P59594) residues 319-541 (RVQPT…KCVNF) and 1-530 (MFVFL…GPKKS), respectively, were produced with C-terminal twin Strep tags in the mammalian expression vector pQ-3C-2xStrep38. 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 June 28, 2021. ;

Peterborough, UK). Plates were then washed 3x in PBS/Tween prior to incubation with 50µL of each serum sample diluted 1:100 in blocking buffer. Each plate included two pooled negative controls and two pooled positive controls. Sera were incubated for 1 hour at room temperature.

Plates were then washed 3x with PBS/Tween, before incubation for 1 hour with horseradish peroxidase (HRP)-conjugated rabbit anti-human IgG (Bethyl labs., Cambridge Bioscience, Cambridge, UK) diluted 1:2500 in blocking buffer. Plates were washed a further 3x in PBS/Tween before addition of the 3,3ʹ,5,5ʹ-tetramethylbenzidine (TMB) liquid substrate (Sigma Aldrich, Merck, Dorset, UK). Colour development was allowed to proceed for 10 minutes before the addition of 1M H2SO4 stop solution, at which point the absorbance was determined at 450nm on a Multiskan FC plate reader. Full validation of the S1 and RBD ELISA has been described previously 17 . . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; each of the three monomers and are labelled on the monomer with an upright RBD, shown in black. Scissors mark the approximate location of an exposed loop (residues 677-688), containing the furin cleavage site, and including residue 681, which is absent from the structure. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint

A B . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint Table S2 . Age distribution of DOVE study population. Median and mean were calculated using Graphpad Prism, descriptive statistics. Age distributions between groups were compared using One-way ANOVA and Tukey's multiple comparisons test, ** p<0.0001.

. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted June 28, 2021. ; https://doi.org/10.1101/2021.06.23.21259327 doi: medRxiv preprint

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 Table S1 . Fold reduction in neutralisation by viral variant.Table S1 -Fold reduction in neutralisation by viral variant. Mean neutralisation of viral variants by DOVE study sera were grouped by vaccine (BNT162b2 or ChAdOx1) and dose (one or two). Fold reduction was calculated by comparing group means. Fold reduction was also calculated from the data after exclusion of the 8/162 samples that possessed N-reactive antibodies by ELISA (Fold (-N +ves)). Significant difference between groups was calculated using One-way ANOVA and Tukey's multiple comparisons test (p values).