key: cord-0929877-fnk3bdf1
authors: Dejnirattisai, Wanwisa; Zhou, Daming; Supasa, Piyada; Liu, Chang; Mentzer, Alexander J.; Ginn, Helen M.; Zhao, Yuguang; Duyvesteyn, Helen M.E.; Tuekprakhon, Aekkachai; Nutalai, Rungtiwa; Wang, Beibei; Paesen, Guido C.; López-Camacho, César; Slon-Campos, Jose; Walter, Thomas S.; Skelly, Donal; Clemens, Sue Ann Costa; Naveca, Felipe Gomes; Nascimento, Valdinete; Nascimento, Fernanda; da Costa, Cristiano Fernandes; Resende, Paola C.; Pauvolid-Correa, Alex; Siqueira, Marilda M.; Dold, Christina; Levin, Robert; Dong, Tao; Pollard, Andrew J.; Knight, Julian C.; Crook, Derrick; Lambe, Teresa; Clutterbuck, Elizabeth; Bibi, Sagida; Flaxman, Amy; Bittaye, Mustapha; Belij-Rammerstorfer, Sandra; Gilbert, Sarah; Carroll, Miles W.; Klenerman, Paul; Barnes, Eleanor; Dunachie, Susanna J.; Paterson, Neil G.; Williams, Mark A.; Hall, David R.; Hulswit, Ruben J. G.; Bowden, Thomas A.; Fry, Elizabeth E.; Mongkolsapaya, Juthathip; Ren, Jingshan; Stuart, David I.; Screaton, Gavin R.
title: Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2
date: 2021-03-19
journal: bioRxiv
DOI: 10.1101/2021.03.12.435194
sha: 99083f4961a3114359cc70cdc87623d3c3eb2273
doc_id: 929877
cord_uid: fnk3bdf1

Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations: P.1 from Brazil, B.1.351 from South Africa and B.1.1.7 from the UK (12, 10 and 9 changes in the spike respectively). All have mutations in the ACE2 binding site with P.1 and B.1.351 having a virtually identical triplet: E484K, K417N/T and N501Y, which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine induced antibody responses than B.1.351 suggesting that changes outside the RBD impact neutralisation. Monoclonal antibody 222 neutralises all three variants despite interacting with two of the ACE2 binding site mutations, we explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.

For more than a year SARS-CoV-2 has caused enormous global dislocation, leading to more Of most concern are changes in the RBD. P.1 has three: K417T, E484K and N501Y, B.1.351 123 also has three: K417N, E484K and N501Y whereas, B.1.1.7 contains the single N501Y 124 mutation. All of these changes have the potential to modulate ACE2/RBD affinity potentially 125 leading to increased transmissibility, for which there is now good evidence in B.1.1.7. In 126 addition, these mutated residues also have the potential to modulate neutralization of SARS- December 2020 leading to further hospitalizations. This second wave corresponded with the 155 rapid emergence of P.1, not seen before December when it was found in 52% of cases, rising 156 to 85% by January 2021 (Figure S1 ). concern because of their potential to promote escape from the neutralizing antibody response 166 which predominately targets this region ( Figure 1D ) (Dejnirattisai et al., 2021) . We searched Of note, two of the NTD changes in P.1 introduce N-linked glycosylation sequons T20N (TRT 176 to NRT) and R190S (NLR to NLS, Figure 1E ). The NTD, in the absence of these changes, 177 reasonably well populated with glycosylation sites, indeed it has been suggested that a single The effects of RBD mutations on ACE2 affinity. 185 We have previously measured the affinity of RBD/ACE2 interaction for Wuhan, B. showing that binding to P.1 is essentially indistinguishable from B.1.351 (4.0 nM).

To better understand RBD-ACE2 interactions we determined the crystal structure of the RBD-193 ACE2 complex at 3.1 Å resolution (Methods , Table S1 ). As expected the mode of RBD-ACE2 created is open to solvent, so there is no obvious reason why the mutation would increase 205 affinity for ACE2, and this is consistent with directed evolution studies (Zahradník et al., 2021) 206 where this mutation was rarely selected in RBDs with increased affinity for ACE2. antibody to achieve complete neutralization could be due to partial glycosylation at residue 20, 278 which is some 16 Å from bound Fab 159, however the L18F mutation is even closer and likely 279 to diminish affinity ( Figure 4A ). Since it has been proposed that there is a single supersite for 280 potent NTD binding antibodies we would expect the binding of many of these to be affected 281 (Cerutti et al., 2021) . contribution to binding may be offset by the loss of entropy in the lysine sidechain. We note 326 that CDR-H3 of 222, at 13 residues is slightly longer than found in the majority of potent VH3-327 53 antibodies, however this seems unlikely to be responsible for the resilience of 222, rather it 328 13 seems that there is little binding energy in general from the CDR3-H3, since most of the binding 329 energy contribution of the heavy chain comes from CDR-H1 and CDR-H2 which do not 330 interact with RBD residue 417, meaning that many VH3-53 antibodies are likely to be resilient 331 to the common N/T mutations ( Figure 4B ). against all three variants, and common cross-protective responses, will be found.

The recent emergence of a number of variants of concern has led to efforts to design new 489 vaccines which will be able to protect against the viral variants. Exactly which variants or Table S2 624 Neutralization curves for monoclonal antibodies in different stages of development for Table S2 . The coordinates and structure factors of the crystallographic complexes are available from the 675 PDB with accession codes (see Table S1 ). Mabscape is available from 

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