Study: SARS-CoV-2 immune evasion by variant B.1.427/B.1.429

SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. 

 Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and is associated with acute respiratory distress syndrome (ARDS), but also with extra-pulmonary complications such as vascular thrombosis, coagulopathy, and a hyperinflammatory syndrome contributing to disease severity and mortality. SARS-CoV-2 infects target cells via the spike glycoprotein (S) that is organized as a homotrimer wherein each monomer is comprised of an S₁ and an S₂ subunit(1, 2). The S₁ subunit comprises the receptor-binding domain (RBD) and the N-terminal domain (NTD) as well as two other domains designated C and D(3, 4). The RBD interacts with the angiotensin-converting enzyme 2 (ACE2) entry receptor on host cells through a subset of RBD amino acids designated the receptor binding motif (RBM)(1, 2, 5–7). The NTD was suggested to bind DC-SIGN, L-SIGN, and AXL which may act as auxiliary receptors(8, 9). Both the RBD and the NTD are targeted by neutralizing antibodies (Abs) in infected or vaccinated individuals and a subset of RBD-specific mAbs is currently being evaluated in clinical trials or are authorized for use in COVID-19 patients (10–22). The S₂ subunit is the fusion machinery that merges viral and host membranes to initiate infection and is the target of Abs cross-reacting with multiple coronavirus subgenera due to its higher sequence conservation compared to the S₁ subunit(23–25).

The ongoing global spread of SARS-CoV-2 led to the emergence of a large number of viral lineages worldwide, including several variants of concern (VOC). Specifically, the B.1.1.7, B.1.351, and P.1 lineages that originated in the UK, South Africa, and Brazil, respectively, are characterized by the accumulation of a large number of mutations in the spike as well as in other genes(26–28). Some of these mutations lead to significant reductions in the neutralization potency of NTD- and RBD-specific mAbs, convalescent sera and Pfizer/BioNTech BNT162b2- or Moderna mRNA-1273-elicited sera(19, 29, 30). The B.1.1.7 variant is on track to become dominant worldwide due to its higher transmissibility(28), underscoring the importance of studying and understanding the consequences of SARS-CoV-2 antigenic drift.

The SARS-CoV-2 B.1.427/B.1.429 variant originated in California in May 2020 and has been detected in more than 29 countries to date(31, 32). It is characterized by the S13I, W152C mutations in the NTD and by the L452R mutation in the RBD. The fast rise in the number of cases associated with the B.1.427/B.1.429 lineages led to their classification as a VOC by the US Center for Disease Control (https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html).

Results

The prevalence of B.1.427/B.1.429 lineages is increasing exponentially

The novel SARS-CoV-2 VOC B.1.427/B.1.429 was reported for the first time at the beginning of 2021 in California(31, 33, 34). The two lineages B.1.427 and B.1.429 (belonging to clade 20C according to Nextstrain designation) share the same S mutations (S13I, W152C and L452R), but harbor different mutations in other SARS-CoV-2 genes. Molecular clock analysis suggest that the progenitor of both lineages emerged in May 2020, diverging to give rise to the B.1.427 and B.1.429 independent lineages in June-July 2020(31). As of March 26, 2021, 4,292 and 10,934 sequenced genomes are reported in GISAID for the B.1.427 and B.1.429 lineages, respectively. These VOCs were detected in California and in other US states, and more recently in 29 additional countries worldwide (Fig. 1 A to G). The number of B.1.427/B.1.429 genome sequences deposited increased rapidly since December 2020 (Fig. 1 B to E), with a prevalence exceeding 50% in California since February 2021. Collectively, this analysis illustrates the increased prevalence of the B.1.427/B.1.429 VOC, and their progressive geographical spread from California to other US states and countries, which is consistent with the recent finding of their increased transmissibility relative to currently circulating strains(31).

B.1.427/ B.1.429 S reduces sensitivity to vaccinees’ plasma

To assess the impact of the three mutations present in the B.1.427/B.1.429 S glycoprotein on neutralization, we first compared side-by-side the neutralization potency of mRNA vaccine-elicited Abs against wildtype (D614G) S and B.1.427/B.1.429 S pseudoviruses. We used plasma from eleven individuals who received two doses of Moderna mRNA-1273 vaccine and from fourteen individuals who received two doses of Pfizer/BioNtech BNT162b2 vaccine collected between 7 and 27 days after booster immunization. All vaccinees had substantial plasma neutralizing activity against wildtype SARS-CoV-2 S pseudotyped viruses. Using a lentiviral (HIV) pseudotyping system, geometric mean titers (GMTs) showed that the average neutralization potency of the Moderna mRNA1273-elicited plasma was reduced 2.8-fold for B.1.427/B.1.429 S (GMT: 204) compared to wildtype (D614G) S (GMT: 573) whereas it was reduced 4-fold with Pfizer/BioNtech BNT162b2-elicited plasma (wildtype GMT: 128 versus B.1.427/B.1.429 GMT: 535) (Fig. 2A-B). Using a vesicular stomatitis virus (VSV) pseudotyping system, we observed a 3-fold average reduction of Pfizer/BioNtech BNT162b2-elicited plasma neutralizing activity against B.1.427/B.1.429 S (GMT: 95) compared to wildtype (D614G) S (GMT: 257) pseudoviruses. In a parallel analysis, we analyzed 18 individuals, 5 of which were previously infected with SARS-CoV-2, who received two doses of Pfizer/BioNtech BNT162b2 vaccine and whose samples were collected between 14 and 28 days after booster immunization. We compared side-by-side the neutralization potency of Pfizer/BioNtech BNT162b2 vaccine-elicited Abs against wildtype (D614) S, B.1.427/B.1.429 S, as well as B.1.1.7 S, B.1.351 S and P.1 S VSV pseudotyped viruses using Vero E6 expressing TMPRSS2 as target cells. GMTs plasma neutralization potency was reduced 2.8-fold for B.1.427/B.1.429 S (GMT: 248) compared to wildtype (D614) S (GMT: 681), which is a comparable decrease to that observed with B.1.351 (GMT: 211, 3.2-fold reduction) and greater to that observed with B.1.1.7 and P.1 (GMT: 545 and 389, 1.2-fold and 1.7-fold reduction, respectively) pseudotyped viruses. These data indicate that the B.1.427/B.1.429 S mutations lead to a modest but significant reduction of neutralization potency from vaccine-elicited plasma due to the substitution of one RBD and two NTD residues.