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Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogenic human coronavirus that belongs to the sarbecovirus lineage of the genus Betacoronavirus. The ancestor strain has evolved into a number of variants of concern, with the Omicron variant of concern now having many distinct sublineages. The ongoing COVID-19 pandemic caused by SARS-CoV-2 has caused serious damage to public health and the global economy, and one strategy to combat COVID-19 has been the development of broadly neutralizing antibodies for prophylactic and therapeutic use. Many are in preclinical and clinical development, and a few have been approved for emergency use. Here we summarize neutralizing antibodies that target four key regions within the SARS-CoV-2 spike (S) protein, namely the N-terminal domain and the receptor-binding domain in the S1 subunit, and the stem helix region and the fusion peptide region in the S2 subunit. Understanding the characteristics of these broadly neutralizing antibodies will accelerate the development of new antibody therapeutics and provide guidance for the rational design of next-generation vaccines. The ancestral strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a number of variants of concern. In this Review, Wang and colleagues discuss progress in the development and characterization of broadly neutralizing antibodies to SARS-CoV-2, which may lead to new antibody therapeutics and inform the design of next-generation vaccines.
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Following the emergence of severe acute respiratory
syndrome coronavirus (SARS-CoV) in 2003 and Middle
East respiratory syndrome coronavirus (MERS-CoV) in
2012, a novel pathogenic human coronavirus (HCoV)
emerged in 2019 that soon spread around the world,
resulting in the COVID-19 pandemic1,2. This novel virus
was named ‘severe acute respiratory syndrome coro-
navirus 2’ (SARS-CoV-2) owing to its close sequence
homology (~79.6%) with SARS-CoV36. Compared
with SARS-CoV and MERS-CoV, SARS-CoV-2 has
a much lower case–fatality ratio. However, the high
proportions of asymptomatic or mildly symptomatic
infections caused by the original strain of SARS-CoV-2
and its ensuing variants have led to higher and more
rapid transmissibility of this virus, which has resulted in
serious complications for all populations of the world711.
Coronaviruses belong to the subfamily Coronavirinae
from the family Coronaviridae, and they are genotypi-
cally and serologically diversified into four major genera:
alphacoronaviruses (alpha-CoVs), betacoronaviruses
(beta-CoVs), gammacoronaviruses (gamma-CoVs)
and deltacoronaviruses (delta-CoVs)5,7. HCoVs are those
coronaviruses that can infect humans. Taxonomically,
historically occurring HCoV-229E and HCoV-NL63
are classified as alpha-CoVs, whereas HCoV-HKU1,
HCoV-OC43, SARS-CoV, SARS-CoV-2 and MERS-CoV
are beta-CoVs. Alpha-CoVs and beta-CoVs mainly
infect mammals, whereas gamma-CoVs and delta-CoVs
primarily infect birds. Both SARS-CoV-2 and
SARS-CoV belong to Sarbecovirus, which is a subgenus
of Betacoronavirus. By contrast, MERS-CoV belongs to
Merbecovirus, another subgenus of Betacoronavirus. Two
other HCoVs of note, HCoV-HKU1 and HCoV-OC43,
which can cause common cold-like illnesses, belong to
the subgenus Embecovirus of Betacoronavirus7,1214.
HCoVs contain phosphorylated nucleocapsid (N)
protein with a single-stranded genomic RNA as a core.
The viral core is encapsulated by phospholipid bilayers
to form spherical or pleomorphic particles 80–120 nm
in size, and is characterized by the presence of the outer
surface spike (S) protein7,8. The S protein is composed
of two subunits, S1 and S2. S1 contains an important
receptor-binding domain (RBD), which is responsible
for the recognition of host cell surface receptors that
enable virus entry. Both SARS-CoV and SARS-CoV-2
engage angiotensin-converting enzyme 2 (ACE2),
which is widely expressed by a variety of human cells,
as the primary entry receptor1517. Dipeptidyl pepti-
dase 4 (DPP4; also known as CD26) is the correspond-
ing entry receptor for MERS-CoV17,18. The S2 subunit
is mainly responsible for subsequent viral fusion with
and entry into the host cell. The junction of S1 and S2
Broadly neutralizing antibodies
to SARS-CoV-2 and other human
coronaviruses
YanjiaChen1,5, XiaoyuZhao1,5, HaoZhou
2,3,5, HuanzhangZhu1, ShiboJiang
4 ✉
and PengfeiWang
1 ✉
Abstract | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently
emerged pathogenic human coronavirus that belongs to the sarbecovirus lineage of the
genus Betacoronavirus. The ancestor strain has evolved into a number of variants of concern,
with the Omicron variant of concern now having many distinct sublineages. The ongoing
COVID-19 pandemic caused by SARS-CoV-2 has caused serious damage to public health and
the global economy, and one strategy to combat COVID-19 has been the development of broadly
neutralizing antibodies for prophylactic and therapeutic use. Many are in preclinical and clinical
development, and a few have been approved for emergency use. Here we summarize neutralizing
antibodies that target four key regions within the SARS-CoV-2 spike (S) protein, namely the
N-terminal domain and the receptor-binding domain in the S1 subunit, and the stem helix region
and the fusion peptide region in the S2 subunit. Understanding the characteristics of these
broadly neutralizing antibodies will accelerate the development of new antibody therapeutics
and provide guidance for the rational design of next-generation vaccines.
1State Key Laboratory of
Genetic Engineering, Shanghai
Institute of Infectious Disease
and Biosecurity, School of Life
Sciences, Fudan University,
Shanghai, China.
2Department of Microbiology,
Grossman School of Medicine,
New York University,
New York, NY, USA.
3College of Medical
Technology, Chengdu
University of Traditional
Chinese Medicine, Chengdu,
China.
4Key Laboratory of Medical
Molecular Virology (MOE/
NHC/CAMS), Shanghai
Institute of Infectious Disease
and Biosecurity, School of
Basic Medical Sciences, Fudan
University, Shanghai, China.
5These authors contributed
equally: Yanjia Chen,
Xiaoyu Zhao, Hao Zhou.
e-mail:
shibojiang@fudan.edu.cn;
pengfei_wang@fudan.edu.cn
https://doi.org/10.1038/
s41577-022-00784-3
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contains a specific furin cleavage site, which is cleaved by
host cell furin to facilitate virus entry into cells19. ACE2
engagement by the virus exposes the S2 cleavage site,
and S2 is further cleaved into two parts at this site by
transmembrane serine protease 2 (TMPRSS2) at the cell
membrane surface, facilitating the process of membrane
fusion between the host cell and the virus20. ACE2-bound
virus can also be internalized via endocytosis, and in this
case, cleavage of the S2 site is mediated by cathepsins,
especially cathepsin L in endosomes21 (FIG.1a).
Antibodies that recognize pathogens can be cat-
egorized as neutralizing antibodies (nAbs) or non-
neutralizing antibodies (non-nAbs). The difference
between the two generally depends on whether the
antibody binding to a specific pathogen can block cell
invasion or inhibit membrane fusion after recogni-
tion (in the case of nAbs), or not block cell invasion or
inhibit membrane fusion after recognition (in the case of
non-nAbs)22. In general, nAbs are effective in neutraliz-
ing pathogens, reducing pathogen titres and protecting
tissues or cells from infection. The neutralization activ-
ity of non-nAbs is usually undetectable2325, but they can
exert their protective effects through Fc-mediated effec-
tor functions, such as antibody-dependent cell-mediated
cytotoxicity, antibody-dependent cellular phagocytosis
and complement-dependent cytotoxicity25,26. In this
Review, we focus solely on the broadly neutralizing anti-
bodies (bnAbs) that target the neutralizing epitopes in
the N-terminal domain (NTD) and the RBD of the S1
subunit, and those that target the stem helix (SH) and
fusion peptide (FP) regions in the S2 subunit (FIG.1b,c).
The NTD
The S1 subunit of the SARS-CoV-2 S protein has two
important domains that are targets of monoclonal
antibodies (mAbs), namely the NTD and RBD. 4A8 is
one of the earliest identified nAbs targeting the NTD,
with its heavy chain complementarity-determining
regions (HCDRs) — HCDR1, HCDR2 and HCDR3 —
interacting with NTD residues27. Chi etal. defined five
structural loops (N1–N5) in the NTD, with N3 and N5
mediating interaction with 4A8 (REF.27). Similarly, other
NTD-targeting mAbs, such as COV2-2676, COV2-2489,
4-8 and 5-24, can also recognize the epitope comprising
the N1, N3 and N5 loops28,29. This strongly positively
charged epitope in the NTD was therefore dubbed ‘the
NTD supersite30,31. However, many naturally circulat-
ing SARS-CoV-2 variants carry mutations within the
NTD supersite, which could dampen the neutralization
activities of these NTD supersite-recognizing mAbs.
For example, a deletion of NTD amino acid residues
242–244 made 4A8, 4-8 and 5-24 almost completely lose
their ability to neutralize the SARS-CoV-2 Beta variant
of concern (VOC)32. Similarly, deletion of Y144 in the
NTD abolished the neutralization activities of the S2M28
(FIG.2a), S2X28 and S2X333 nAbs33. Of note, mAbs tar-
geting the non-supersite on the NTD have broad neutral-
izing potential. For example, mAb 5-7 (FIG.2a), isolated
a
b
NH2
S1/S2
NTD
COOH
RBD SD1 SD2 HR1 CH SH TM CTHR2CD
FP
S2
S1 NTD nAbs
4A8
COV2-2676
5-7
S2M28
C1717
C1520
S1 RBD nAbs
CB6
LY-CoV555
S309
CR3022
LY-CoV1404
2-36
Class 2
LY-CoV555
2-15
C121
A19-46.1
P2B-2F6
Class 3
S309
LY-CoV1404
COV2-2130
REGN10987
002-S21F2
n3113v
Class 4
CR3022
S2X259
ADG20
DH1047
2-36
n3130v
S2 SH nAbs
S2P6
CC40.8
WS6
S2 FP nAbs
76E1
COV44-62
COV44-79
VN01H1
VP12E7
C77G12
Class 1
CB6
REGN10933
S2E12
S2K146
B38
Fig. 1 | Neutralizing antibodies directed against the SARS-CoV-2 spike
protein. a | Schematic representation of the main domains of the severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein.
Arrows denote S1/S2 and S2 protease cleavage sites. b | Different groups
of neutralizing antibodies (nAbs) that target the S protein. Representative
nAbs targeting the S1 N-terminal domain (NTD), S1 receptor-binding
domain (RBD), and S2 stem helix (SH) and S2 fusion peptide (FP) regions
are shown with the S protein depicted in the RBD ‘up’ conformation.
c | RBD-directed nAbs can be divided into four main classes depending on
the epitopes they target in the RBD of the S protein. For each class, one
representative nAb bound to the RBD monomer is shown: class 1, CB6;
class 2, LY-CoV555; class 3, S309; class 4, CR3022. CD, connector domain;
CH, central helix; CT, cytoplasmic tail; HR, heptad repeat; SD, subdomain;
TM, transmembrane domain.
Furin
A protease belonging to the
proprotein convertase family
that processes latent precursor
proteins into biologically active
products.
Transmembrane serine
protease 2
(TMPRSS2). A plasma
membrane-anchored serine
protease that proteolytically
cleaves and activates the spike
(S) glycoproteins of human
coronaviruses and some other
viruses.
Cathepsins
A family of proteases that are
responsible for recycling
cellular proteins inside the
lysosomes, comprising serine,
aspartate and cysteine
peptidases, and that exhibit
endopeptidase or
exopeptidase activities.
Stem helix
(SH). A helix structure in the
S2 stem region that forms part
of the spike fusion machinery
and is conserved among
multiple betacoronaviruses.
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from a patient recovering from COVID-19 (REFS.29,34),
retained its neutralizing potency partially against the
SARS-CoV-2 Alpha and Beta VOC, as well as against
the Omicron BA.1, BA.1.1 and BA.3 sublineages32,35,36.
Although some residues in the NTD supersite are
highly mutatable under selection pressure, one feasi-
ble strategy for developing NTD-targeting bnAbs is to
identify 5-7-like mAbs, which bind the non-supersite
on the NTD. More importantly, as the bulk of NTD-
targeting antibodies did not compete with antibod-
ies targeting other regions of the S protein, such as
the RBD27,28,30, combining NTD-targeting antibod-
ies with antibodies binding non-NTD regions may
be an ideal way to combat COVID-19 (see TABLE1,
Supplementary Table S1 and FIG.2a for a summary of
more NTD-targeting nAbs3740).
The RBD
Most of the anti-SARS-CoV-2 antibodies discovered
to date target the RBD, and can be further divided into
different classes on the basis of their targeted epitopes.
Although several different classification systems have
been proposed, the most commonly referenced is that
proposed by Barnes etal.41, who grouped RBD-targeting
antibodies into four classes on the basis of their mode of
binding to the S protein (FIG.1c).
Class 1 RBD-targeting antibodies. The antibody-binding
epitope targeted by class 1 RBD-targeting antibodies
overlaps with the receptor-binding motif (RBM) in the
RBD, and antibodies in this class are mostly encoded by
VH3-53 and VH3-66 germ lines and recognize only the
‘up’ RBD conformation41. The substantial neutralization
Fusion peptide
(FP). A conserved hydrophobic
domain of a fusion protein that
inserts itself into membranes
during membrane fusion, which
is required for the fusogenic
activity of glycoproteins from
divergent virus families.
S1 NTD nAb
(supersite)
S1 NTD nAb
(non-supersite)
S1 RBD nAb
(class 1)
S1 RBD nAb
(class 3)
S1 RBD nAb
(class 4)
S1 RBD nAb
(class 2)
S2 SH nAb
S2 SH S2 FP
NTD RBD RBD
RBD RBD
S2M28 CB6 LY-CoV555
S309 CR3022
S2P6
NTD
5-7
S2 FP nAb
76E1
ge f h
a c db
Fig. 2 | Structures of neutralizing antibodies bound to the SARS-CoV-2 spike protein. Three-dimensional modelling
is used here to depict the complexes of representative neutralizing antibodies (nAbs) interacting with their targets in the
S1 and S2 subunits of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein. a | S1 N-terminal
domain (NTD) nAbs, supersite (S2M28, Protein Data Bank (PDB) ID 7LY3). b | S1 NTD nAbs, non-supersite (5-7 , PDB ID
7RW2). c | S1 receptor-binding domain (RBD) nAbs, class 1 (CB6, PDB ID 7C01). d | S1 RBD nAbs, class 2 (LY-CoV555, PDB
ID 7KMG). e | S1 RBD nAbs, class 3 (S309, PDB ID 7TLY). f | S1 RBD nAbs, class 4 (CR3022, PDB ID 7JN5). g | S2 stem helix
(SH) nAb (S2P6, PDB ID 7RNJ). h | S2 fusion peptide (FP) nAb (76E1, PDB ID 7X9E).
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mechanism of class 1 antibodies is achieved by their pre-
venting ACE2 from binding to the S protein. During the
early phase of the SARS-CoV-2 outbreak, many class 1
RBD-targeting antibodies were identified, such as CB6
and CT-P59 (REFS.42,43), and some were discovered by our
own group, including 1-20, 4-20 and 910-30 (REFS.29,44).
Many of these antibodies lost their neutralizing activities
as a result of the E484K mutation seen in the Beta VOC,
Gamma VOC and other SARS-CoV-2 variants32,45,46.
While the neutralization potency of 1-20 is not appar-
ently affected by the E484K mutation, another common
mutation, N501Y, decreases the neutralizing potency of
1-20 almost 10-fold. It is possible that the synergy of var-
ious mutants in the Beta VOC resulted in the 600-fold
reduction in the neutralizing potency of 1-20 against
Beta compared with wild type SARS-CoV-2 (REF.32).
CB6 (FIG.2b) engages in polar and hydrophobic inter-
actions with wild type SARS-CoV-2 S protein primarily
through HCDR1, HCDR2 and HCDR3 (REF.42), but its
binding epitope is heavily mutated in the S protein of
VOC such as Beta and Omicron. In particular, the criti-
cal mutation K417N eliminates the neutralizing potency
of CB6 and limits its neutralizing breadth32. As a result,
the presence of common mutations in the RBD, such as
K417N, E484K and N501Y, to which most class 1 mAbs
bind, causes most of these antibodies that show great
neutralizing potency against wild type SARS-CoV-2 to
lose their neutralizing abilities for variants such as Beta,
Gamma and Omicron.
Nevertheless, S2E12 is one of the few class 1 mAbs
that retains broad-spectrum neutralizing activity47.
Although its binding region is similar to that of the other
class 1 mAbs mentioned earlier, S2E12 can still neutral-
ize all current VOC, showing exceptional neutralization
breadth47,48. The cryogenic electron microscopy struc-
ture revealed that S2E12 binds the receptor-binding
ridge, contacting 18 residues in the RBD. The S protein
F486 residue fills in a buried cavity lined by aromatic
residues formed by its interface of heavy and light chains,
while residue N487 initiates a polar interaction with
S2E12 (REF.47). Although common mutation sites, such
as E484 and S477, do exist in S2E12-binding variants,
they are not functional residues that interact with S2E12.
Moreover, they are located at the edge of the S2E12–RBD
interface, conferring considerable neutralizing activ-
ity of S2E12 against variants containing these highly
frequent mutation sites47. Another ACE2-mimic
antibody, S2K146, also demonstrates sizable neutral-
izing breadth against SARS-CoV-2 variants and other
sarbecoviruses49,50. As such, comparison of S2E12 and
S2K146 with other class 1 antibodies also highlights
the importance of microstructure for an antibody’s
neutralizing performance.
Class 2 RBD-targeting antibodies. Antibodies in class 2
are similar to those in class 1 on the basis of their bind-
ing to the RBM where the RBD interacts with ACE2.
Consistency also derives from the neutralizing mecha-
nism of these antibodies, which prevents the reciprocal
binding of the RBD to ACE2. Notably, mAbs in class 2
can bind both ‘up’ and ‘down’ conformations of the
S ptotein41. For example, LY-CoV555 (FIG.2b), which was
isolated from a patient recovering from COVID-19, both
bound and neutralized SARS-CoV-2 and displayed pro-
tective efficacy against SARS-CoV-2 in clinical trials51.
Although the antibody neutralized SARS-CoV-2 pseu-
dovirus very effectively (with a half-maximal inhibitory
concentration (IC50) of 0.004 g ml−1 (REF.48)), LY-CoV555
lost most of its neutralization activity against the sub-
sequently discovered VOC, which can be attributed
to critical single viral mutations such E484K and
Q493R32,36. As a result, the broadly neutralizing capacity
of LY-CoV555 was constrained as these mutations were
found to be prevalent in many SARS-CoV-2 variants.
Table 1 | Neutralizing antibodies targeting the N-terminal domain of the spike protein
Antibodies Binding epitope
in NTD
Mechanism of neutralization Viruses neutralized Refs.
4A8 Supersite Restrains the conformational
changes of the S protein
SARS-CoV-2 27
COV2-2676,
COV2-2489,
5-24, BLN12
Supersite Unknown SARS-CoV-2 28,29,34,37,38
4-8, BLN14 Supersite Unknown SARS-CoV-2; Alpha VOC 29,34,37,38
5-7 Non-supersite Restrains the conformational
changes of the S protein
SARS-CoV-2; Alpha and Beta
VOC; BA.1, BA.3
29,34
S2M28, S2X28,
S2X333
Supersite Prevents interaction with an
auxiliary receptor, proteolytic
activation or membrane fusion
SARS-CoV-2 33
C1717 Non-supersite Prevents access to the S2
cleavage site or destabilizes S1
SARS-CoV-2; Alpha, Beta and
Gamma VOC; BA.1
40
C1520, C1791 Non-supersite Unknown SARS-CoV-2; Alpha, Beta,
Gamma and Delta VOC; BA.1
40
ADI-56479 Supersite Inhibits the attachment of ACE2 SARS-CoV-2 39
The table provides an overview of neutralizing antibodies targeting the N-terminal domain (NTD) of the S1 subunit of the spike (S)
protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. SARS-CoV-2 indicates the
wild type strain. See Supplementary Table S1 for a more detailed description of each antibody. ACE2, angiotensin-converting
enzyme 2; VOC, variant of concern.
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Similarly, 2-15 (REF.29), another mAb isolated from a
patient with COVID-19, is also evaded as a result of the
E484K and Q493R mutations, which cause an antigenic
structure change32,36. Although the RBD region targeted
by class 1 and class 2 antibodies covers the RBM, the
amino acid identity of SARS-CoV and SARS-CoV-2 is
only 59% shared in the RBM and 94% shared for the
rest of the RBD excluding the RBM52. Hence, most anti-
bodies in class 1 and class 2 targeting this region do not
have a superior broad spectrum for the inhibition of
SARS-CoV and other SARS-like coronaviruses.
Class 3 RBD-targeting antibodies. Class 3 antibodies
bind the outside the ACE2-binding region, and they
can also bind to RBDs regardless of their ‘up’ and ‘down’
conformations41. Most class 3 antibodies, including
REGN10987, COV2-2130, 2-7,1-57, A19-61.1, P2G3,
S309 and LY-CoV1404, have demonstrated potent neu-
tralizing activities against SARS-CoV-2 variants29,48,5360.
S309 and LY-CoV1404 are two representative antibodies
with great neutralization breadth (REFS.56,57). S309 (FIG.2b)
was isolated from a patient recovering from SARS and
can efficiently bind to the SARS-CoV-2 S protein with-
out blocking the binding between ACE2 and the RBD56.
Structurally, S309 HCDR3 was shown by cryogenic elec-
tron microscopy to interact mainly with eight residues
(337–344) of the RBD helix, as well as with six residues
of the RBD β-sheet (356–361). In addition, the S309 light
chain complementarity-determining region 1 (LCDR1)
and LCDR2 directly interact with the epitope of the
S protein that spans residues 440–444 (REF.56). The epitopes
recognized by S309 are the most highly conserved resi-
dues in the SARS-CoV and SARS-CoV-2 RBDs, con-
ferring broad cross-reactivity on the S309 antibody56.
Moreover, S309 can broadly neutralize sarbecoviruses,
including all currently identified SARS-CoV-2 VOC, as
the epitope sequences recognized by S309 are highly con-
served among sarbecoviruses48,56. Interestingly, although
the single mutation S371L in SARS-CoV-2 causes the
loss of S309’s neutralizing potency, the detrimental
effect of S371L on S309 was counteracted by the com-
bined effect of amino acids near the point of mutation
in Omicron such that S309 can still effectively neutralize
Omicron (BA.1), with IC50 = 0.28 g ml−1 (REFS.48,56).
Similarly, LY-CoV1404 can also bind to the viral
RBDs, irrespective of their ‘up’ and ‘down’ conforma-
tions. However, LY-CoV1404 differs from S309 in that
it binds a part of the RBD epitope that overlaps with
the ACE2-binding domain57. As the epitope bound by
LY-CoV1404 is structurally closer to that recognized
by class 3 antibodies, LY-CoV1404 also belongs to the
class 3 antibody group57. The neutralization mechanism
of LY-CoV1404 is achieved by its preventing ACE2 from
binding to the RBD57. Of note, the epitope bound by
LY-CoV1404 is also conserved in SARS-CoV-2 and its
variants. Although the epitope targeted by LY-CoV1404
was associated with two high-frequency mutations
at positions 439 and 501, these two mutations did not
affect the binding of LY-CoV1404 to and its neutral-
izing potency against SARS-CoV-2 and its variants
containing these mutations57. Compared with S309,
LY-CoV1404 was able to neutralize all SARS-CoV-2
VOC without much change in neutralization potency,
especially against the Omicron variants48. Among the
antibodies approved for clinical trials, LY-CoV1404 was
the only antibody that retained its neutralization potency
against Omicron sublineages35,36,48,57,61,62. Taken together,
these findings suggest LY-CoV1404 is a specific and
effective mAb for the treatment of COVID-19.
Recently, another class 3 mAb, named ‘SP1-77’, was
obtained from a humanized mouse model (the V1–2/
Vκ1–33-rearranging mouse model). SP1-77 showed
potent neutralization activity against all currently known
SARS-CoV-2 variants, including the recently emerging
Omicron variant BA.1 (IC50 = 6.5 ng ml−1), and its subline-
ages BA.2 (IC50 = 33 ng ml−1), BA.3 (IC50 = 7 ng ml−1), BA.4/
BA.5 (IC50 = 16 ng ml−1) and BA.2.12.1 (IC50 = 8 ng ml−1)63.
Interestingly, SP1-77 does not block the RBD–ACE2
binding interaction or viral endocytosis, but instead
mediates virus neutralization by preventing shedding of
S1, which blocks membrane fusion63. This study provides
insight into how a non-ACE2 blocking antibody can also
potently neutralize SARS-CoV-2 infection.
Class 4 RBD-targeting antibodies. The epitope recog-
nized by class 4 antibodies is highly conserved in the
RBD, and these antibodies bind to the RBD, but do
not directly block ACE2–RBD binding. This epitope
has also been described as a cryptic region, which is
consistent with the well-described cryptic epitope
recognized by the CR3022 antibody (FIG.2b), an anti-
body isolated from a patient who had recovered from
SARS-CoV infection41,64. The epitope targeted by class 4
antibodies is conserved by up to 86% in SARS-CoV and
SARS-CoV-2, and CR3022 is thus able to effectively
bind to both coronaviruses64. Owing to a glycosylation
site on N370 within the targeted epitope in SARS-CoV,
CR3022 binds to SARS-CoV with greater affinity than to
SARS-CoV-2. Of note, CR3022 can bind to SARS-CoV-2
only when at least two RBDs are in the ‘up’ conforma-
tion, which partly explains its lower binding affinity for
SARS-CoV-2 and poor neutralizing potency against this
virus (IC50 > 400 g ml−1)64.
The 2-36 antibody identified by our group competes
with CR3022 for binding to the SARS-CoV-2 RBD, and
is therefore classified as a class 4 antibody29,65. Similarly
to CR3022, 2-36 also recognizes and binds the RBD in
the ‘up’ conformation. Cryogenic electron microscopy
data revealed that HCDR3 of 2-36 forms the majority of
interactions by recognizing loops on the RBD spanning
residues 369–385, whereas HCDR1 and LCDR2 of the
antibody interact to a lesser extent with the RBD65.
The interaction between 2-36 and the SARS-CoV-2 RBD
is dependent mainly on hydrophobic effects, as HCDR3
of 2-36 contains a large number of hydrophobic amino
acids. Compared with CR3022, 2-36 can more effec-
tively neutralize SARS-CoV, SARS-CoV-2 and related
sarbecoviruses that use ACE2 as the entry receptor, with
IC50 < 0.1 g ml−1 in both authentic virus and pseudovirus
assays65. 2-36 retained its neutralization potency against
the SARS-CoV-2 Alpha, Beta, Gamma and Delta VOC65,
and retained partial activity against Omicron BA.1, with
IC50 ~ 1 g ml−1 (REFS.35,36). Taken together, these findings
indicate that 2-36, as a bnAb to SARS-CoV-2 and related
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sarbecoviruses, could be a specific drug candidate for
the treatment or prevention of COVID-19 after proper
engineering, and its binding epitope is a promising target
for the development of pan-sarbecovirus vaccines.
Another class 4 antibody, S2X259, can also broadly
neutralize SARS-CoV-2 and related sarbecoviruses66.
A very recent study demonstrated that S2X259 lost its
neutralizing activity against SARS-CoV-2 strains con-
taining the G504D mutant66. Fortunately, the G504D sub-
stitution is rarely observed in SARS-CoV-2 strains, with a
mutant rate below 0.002%66. This antibody can neutralize
not only many currently circulating SARS-CoV-2 var-
iants and SARS-CoV but also a panel of SARS-related
sarbecoviruses. Other known class 4 antibodies, such as
ADG20, DH1047, COVA1-16 and H014, also demon-
strate neutralizing breadth against SARS-CoV-2,
SARS-CoV and other relevant sarbecoviruses6771. This
suggests that the epitope recognized by class 4 antibodies
is an ideal target for the development of bnAbs.
In summary, RBD-targeting antibodies in class 1 and
class 2 will probably lose their neutralizing abilities with
the emergence of the next major SARS-CoV-2 variant
that carries new mutations in the RBM; thus, their neu-
tralizing breadth is limited. By contrast, antibodies in
class 3 and class 4 that bind highly conserved epitopes
hold promise as candidates for neutralizing SARS-CoV-2
variants and other SARS-like coronaviruses. This sug-
gests that selecting such conserved epitopes for vaccine
design may elicit potent broad-spectrum antibodies
that could help to overcome the current COVID-19
pandemic. In addition, it is clear that epitopes of
RBD-targeting antibodies in class 1 and class 2 over-
lap with the ACE2 footprint on the RBD, and these
antibodies achieve neutralizing activities by directly
blocking the interaction between the RBD and ACE2.
However, the major class 3 and class 4 antibodies do
not show such explicit neutralization mechanisms, and
their mechanisms of neutralization need to be further
explored. Studies of antibodies such as SP1-77 may pro-
vide insight into the neutralizing mechanisms of other,
similar RBD-binding (but non-RBM-targeting) antibod-
ies (See TABLE2, Supplementary Table S2 and FIG.2b for
a summary of more RBD-targeting nAbs5862,7281).
The S2 SH region
The SARS-CoV-2 S protein is composed of S1 and S2
subunits. Most SARS-CoV-2 nAbs target the neutraliz-
ing epitopes in the NTD and RBD in the S1 subunit.
However, such epitopes are likely to succumb to selec-
tive pressure, increasing the likelihood of immune
escape by virus mutants. By contrast, the neutralizing
epitopes in the S2 subunit are more conserved than
those in the S1 subunit82. Therefore, nAbs target-
ing the S2 epitopes would have a greater probability
of being broad-spectrum nAbs to SARS-CoV-2 and
other HCoVs. For example, S2P6 (FIG.2c), which was
isolated from a patient recovering from COVID-19,
could broadly neutralize all beta-CoVs by targeting the
S2 subunit83. Further study revealed that the epitope
bound by this antibody is located in the S2 SH region
that spans 14 residues (1146–1159), which is conserved
across beta-CoVs. Moreover, the S2 SH region interacts
with the S2P6 antibody’s HCDR1, HCDR2 and HCDR3,
as well as with its LCDR1 and LCDR3, mainly through
the formation of hydrophobic interactions and hydro-
gen bonds. Single-substitution analysis revealed that
mutations at positions 1148, 1151–1153 and 1155–1156
abolished S2P6 binding affinity, suggesting that these
are critical residues for S2P6 binding83. Unlike the
neutralization mechanism of antibodies targeting S1,
S2P6 can inhibit SARS-CoV-2 infection by prevent-
ing S protein-mediated fusion of viral and cellular
membrane83. The Fc effector functions of S2P6 also play
a critical role in fighting coronavirus infection invivo83.
Several studies reported that S2P6 can broadly neutral-
ize beta-CoVs, including SARS-CoV-2 and SARS-like
viruses, which belong to the subgenus Sarbecovirus,
MERS-CoV, which belongs to subgenus Merbecovirus,
and HCoV-HKU1 and HCoV-OC43, which belong
to the subgenus Embecovirus. S2P6 shows variable
IC50 of 1.4 g ml−1 for SARS-CoV-2, 2.4 g ml−1 for
SARS-CoV, 17.1 g ml−1 for MERS-CoV and 1.3 µg ml−1
for HCoV-OC43 (REF.83). Although S2P6 does not show
as great neutralizing potency as some RBD-targeting
antibodies, it still has the potential to become a very
effective antibody drug for the treatment of COVID-19
or diseases caused by other coronaviruses owing to its
broad-spectrum neutralizing properties.
Another antibody targeting the S2 SH region, CC40.8,
was isolated from a patient with COVID-19 (REF.84). It
binds to residues from 1140 to 1164, and was found to
broadly bind and neutralize beta-CoVs84. An invivo
study in hamsters confirmed that CC40.8 mediates effec-
tive protection against SARS-CoV-2 infection84. WS6, an
antibody isolated from an mRNA-immunized mouse,
also binds the SARS-CoV-2 S2 SH region that spans res-
idues 1143–1159 (REF.85). Mechanistically, WS6 can neu-
tralize SARS-CoV-2 by inhibiting the membrane fusion
process following virus contact with ACE2 (REF.85). As
expected, WS6 can also broadly neutralize beta-CoVs,
and pseudovirus neutralization experiments showed
its neutralizing potency against all SARS-CoV-2 VOC,
with IC50 ranging from 2.46 to 26.52 g ml−1 (REF.85). The
three bnAbs mentioned here all target the S2 SH epitope,
highlighting the importance of finding and developing
bnAbs that recognize these conserved epitopes.
The S2 FPs
Apart from the SH region mentioned earlier, S2 FPs are
also highly conserved among all coronavirus genera,
suggesting that broad-spectrum antibodies could be
found by targeting this epitope8688. Some recently iden-
tified antibodies to this epitope have excellent broadly
neutralizing activity against alpha-CoVs, beta-CoVs
and even some gamma-CoVs and delta-CoVs86,87. For
example, COV44-62 and COV44-79, which were both
isolated from patients recovering from COVID-19,
can bind the S2 FP region through recognition of the
‘RSFIEDLLF’ motif. Interestingly, these antibodies
do not compete with S2P6, the aforementioned S2
SH-targeting antibody, for binding to the SARS-CoV-2
S protein86, suggesting the possibility of combining
S2 SH and S2 FP recognition in a bispecific antibody.
Crystal structure analysis revealed that COV44-62
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Table 2 | Neutralizing antibodies targeting the receptor-binding domain of the spike protein
Antibodies Binding epitope
in RBD
Mechanism of neutralization Viruses neutralized Refs.
1-20, 4-20, 910-30,
CB1
Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2 29,42,44
CB6, CC12.3 Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha and Delta VOC 42,48,67,72
REGN10933 Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha and Delta VOC; BA.2.75 48,53,62
CT-P59 Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC
43,48
A23-58.1, S2E12 Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.2.75
4749,58,81
S2K146 Class 1 Blocks the interaction between the RBD
and ACE2
Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1, BA.2, BA.3,
BA.4/5, BA.2.75)
49,50,80,81
B38 Class 1 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Beta VOC 73
2-15, LY-CoV555,
C121, C144
Class 2 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha VOC 29,32,48,51,74
COV2-2196 Class 2 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.3, BA.2.75
48,54,61,62,80
A19-46.1 Class 2 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta and Gamma VOC 48,58
P2B-2F6 Class 2 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2 77
S309 Class 3 Leads to trimeric S protein crosslinking,
causes steric hindrance or aggregation of
virions
Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1, BA.2, BA.3,
BA.4/5, BA.2.75)
36,48,56,61,62
LY-CoV1404 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.3, BA.4/5, BA.2.75
36,48,57,61,62
COV2-2130 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.3, BA.4/5, BA.2.75
48,54,61,62,80
REGN10987 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.4/5
48,53,61,62
SP1-77 Class 3 Prevents the shedding of S1 and blocks
membrane fusion
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.3, BA.4/5
63
A19-61.1 Class 3 Causes steric hindrance between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1
48,58
1-57 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta and Gamma VOC 29,32,46,55
2-7 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta and Gamma VOC;
BA.1, BA.2, BA.4/5
29,32,46,55,61
002-S21F2 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2
76
P2G3 Class 3 Blocks the interaction between the RBD
and ACE2
SARS-CoV-2; Alpha, Beta, Gamma and Delta
VOC; BA.1, BA.2, BA.4/5
59,60
n3113v Class 3 Inhibits SARS-CoV-2 S protein-mediated
membrane fusion
SARS-CoV-2; Alpha, Beta, Gamma, Delta and
Omicron VOC
78,79
CR3022 Class 4 Unknown SARS-CoV 64
2-36 Class 4 Causes steric hindrance between the RBD
and ACE2
Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1)
29,36,65
S2X259 Class 4 Blocks the interaction between the RBD
and ACE2
Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1)
50,66
ADG20 Class 4 Competes with ACE2 for RBD binding Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1)
67,68
DH1047 Class 4 Unknown Sarbecoviruses (SARS-CoV; SARS-CoV-2; Alpha,
Beta, Gamma and Delta VOC; BA.1)
61,69
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interacts with S2, that spans residues 814–824, mainly
through hydrogen bonds, salt bridges and hydrophobic
interactions within HCDR1, HCDR2, HCDR3, LCDR1
and LCDR3. Similarly, COV44-79 utilizes HCDR1,
HCDR2, HCDR3 and LCDR3 to bind SARS-CoV-2
and interacts with S2 residues 812–823 (REF.86). Of note,
both antibodies broadly neutralize beta-CoVs, but show
some differences in activity against MERS-CoV. The
neutralizing activity of COV44-62 against MERS-CoV
could be detected, whereas that of COV44-79 could not.
These antibodies can also act against the more distantly
evolved alpha-CoVs, including HCoV-NL63 and HCoV-
229E, although they are less potent at neutralizing these
viruses, with IC50 ~ 10 g ml−1 (REF.86). Peptide alanine
scanning revealed that E819, D820, L822 and F823 in the
S2 FP region are crucial for COV44-62 binding, whereas
R815, E819, D820 and F823 are crucial for COV44-79
binding86. More importantly, the entire FP sequence is
highly conserved among the four coronavirus genera86,
giving antibodies targeting this region an extremely
broad ability to neutralize SARS-CoV-2 and numerous
other coronaviruses.
Another panel of nAbs targeting S2 FP — VN01H1,
VP12E7 and C77G12 — were recently identified87.
Among them, VN01H1 and VP12E7 can neutralize
all alpha-CoV and beta-CoV pseudoviruses, including
HCoV-NL63, HCoV-229E, SARS-CoV, SARS-CoV-2
and MERS-CoV; C77G12 exhibited higher neutrali-
zation potency than VN01H1 and VP12E7, but only
against beta-CoVs87. Crystal structures showed that all
three antibodies concealed the R815 residue at the inter-
face when interacting with the S protein. Furthermore,
R815 is not only a conserved residue in the S protein but
is also the site of cleavage of S2 by TMPRSS2, suggesting
that these three antibodies neutralize SARS-CoV-2 by
preventing S2 cleavage, thereby inhibiting subsequent
membrane fusion87. Intriguingly, a potent synergistic
neutralization activity was found when C77G12 was
combined with S2E12, a nAb in RBD class 1, implying
that the FP is most likely a cryptic epitope that is nor-
mally inaccessible, but when the RBD interacts with
ACE2 or ACE2-mimic antibodies, the exposed epitope
is more accessibly bound by FP-targeting antibodies87.
More recently, 76E1 (FIG.2d) was identified as another
S2 FP-targeting nAb that shows extraordinary neutral-
izing breadth, including for alpha-CoVs, beta-CoVs
and a few gamma-CoVs and delta-CoVs88. It has been
proved that 76E1 can potently neutralize SARS-CoV-2
both invitro and invivo88. Like C77G12, a synergistic
effect of 76E1 can be observed when the S protein con-
tacts some RBD-targeting nAbs as well as ACE2 (REF.88).
Taken together, these findings show that S2-directed
antibodies target prominently conserved epitopes and
exhibit the broadest neutralizing spectrum to date.
Therefore, they can guide the design of bnAbs to highly
variable SARS-CoV-2 variants and even other HCoVs
(see TABLE3, Supplementary Table S3 and FIGS.2c,d for
a summary of the S2-targeting nAbs mentioned above).
Conclusion
The engineering of already discovered antibodies can
be used to improve their performance, including their
neutralizing potency and breadth. One approach is to
construct libraries containing a large number of different
V/V sequences by phage or yeast display methods to
yield antibodies with better performance8992. Another
approach is to try different formats of antibodies, such
as nanobodies. In contrast to human IgG, camelid anti-
bodies (also known as nanobodies or Vs), lack a light
chain and are composed of two identical heavy chains.
The nanobody is the smallest antigen-binding fragment
(~15 kDa) discovered to date9395. Owing to their smaller
size, nanobodies can bind more cryptic epitopes that
are not easily accessible. Together with their high tissue
penetration ability, they can also be formulated as an
inhalable atomized powder78,96.
Other effective approaches to improve antibody
function include engineering them into bispecific or
multispecific antibodies97100, which can bind to multiple
epitopes simultaneously and synergistically. Combining
two or more bnAbs targeting different epitopes as
therapeutics (for example, different RBD class anti-
bodies) or combining RBD-targeting antibodies with
NTD-targeting and/or S2-targeting antibodies might
be a feasible strategy against COVID-19. Some antibody
cocktails, such as S2E12 and C77G12, 76E1 and CB6,
and COV2-2196 and COV2-2130, have already been
explored54,87,88, but more combinations need to be tested
in clinical trials. Furthermore, some ACE2-targeting
antibodies have been reported to confer protection in
animal models against infection by SARS-CoV-2 and
other SARS-like coronaviruses by competing with
Antibodies Binding epitope
in RBD
Mechanism of neutralization Viruses neutralized Refs.
COVA1-16 Class 4 Causes steric hindrance between the RBD
and ACE2
Sarbecoviruses (SARS-CoV; SARS-CoV-2) 70
H014 Class 4 Prevents attachment of SARS-CoV-2
to ACE2
Sarbecoviruses (SARS-CoV; SARS-CoV-2; Beta
VOC)
71
EY6A Class 4 Interferes with ACE2 attachment SARS-CoV-2 75
n3130v Class 4 Induces S protein trimer to adopt unstable
‘up’ states
SARS-CoV-2; Alpha, Beta, Gamma, Delta and
Omicron VOC
78
The table provides an overview of neutralizing antibodies targeting the receptor-binding domain (RBD) of the spike (S) protein of severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. ‘SARS-CoV-2’ indicates the wild-type strain. See Supplementary Table S2 for a more detailed
description of each antibody. ACE2, angiotensin-converting enzyme 2; VOC, variant of concern.
Table 2 (cont.) | Neutralizing antibodies targeting the receptor-binding domain of the spike protein
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the S protein for receptor binding101,102, and these
antibodies could be used in combination with the
S protein-targeting antibodies. Therefore, we can take
advantage of the synergistic enhancement between anti-
bodies to make them exert better neutralization and
protective effects invivo.
The emergence of numerous SARS-CoV-2 variants
calls for the generation of bnAbs as a therapy for
COVID-19. In this Review, we have described some
representative nAbs that bind the NTD and RBD in the
S1 subunit and the SH and FP regions in the S2 subunit of
SARS-CoV-2 and have summarized more known nAbs in
TABLES13. Overall, antibodies in RBD class 1 and class 2,
as well as those targeting the NTD supersite, are more likely
to lose their neutralizing activities as the viral epitopes they
target are more prone to mutate. By contrast, antibodies
targeting the more conserved S2 epitopes are able to exert
an incredibly broad neutralization spectrum against
HCoVs, including alpha-CoVs and beta-CoVs. However,
despite their having a broader neutralization spectrum, it
is important to point out that the S2 antibodies are much
less potent than RBD-targeting antibodies. Therefore,
these findings put great emphasis on balancing the
breadth and potency of nAbs when one is selecting nAbs
as candidates for antibody therapy for COVID-19. On the
other hand, comprehending the characteristics of these
bnAbs could provide guidance for devising more effec-
tive vaccines. Consistent with others103105, we stress the
importance of focusing on conserved viral epitopes for
the development of broad-spectrum antibody therapies,
as well as for vaccine design. In general, the immunogens
with conserved epitopes — such as the FP and SH regions
in the S2 subunit83,8688 — are unable to elicit potent nAb
responses, possibly owing to their inappropriate confor-
mation and/or low immunogenicity. Therefore, vaccines
containing different conformations of these immu-
nogens should be tested in combination with a highly
potent adjuvant, such as the STING agonist-based adjuvant
CF501 (REF.106). Another feasible strategy for the design
of next-generation vaccines would be heterologous or
multivalent immunization with S proteins from different
HCoVs, which might induce the host immune system to
generate bnAbs to highly conserved viral epitopes present
in these coronaviruses.
Published online xx xx xxxx
Table 3 | Neutralizing antibodies targeting the S2 subunit of the spike protein
Antibodies Binding epitope
in S2 subunit
Mechanism of
neutralization
Viruses neutralized Refs.
S2P6 S2 stem helix Inhibits membrane fusion Beta-CoVs (sarbecoviruses,
merbecoviruses and embecoviruses)
83
CC40.8 S2 stem helix Inhibits membrane fusion Beta-CoVs (sarbecoviruses,
HCoV-HKU1)
84
WS6 S2 stem helix Inhibits membrane fusion Beta-CoVs (sarbecoviruses) 85
COV44-79 S2 fusion peptide Inhibits membrane fusion Alpha-CoVs and beta-CoVs (except
MERS-CoV)
86
COV44-62, VN01H1,
VP12E7 , 76E1
S2 fusion peptide Inhibits membrane fusion Alpha-CoVs and beta-CoVs 8688
C77G12 S2 fusion peptide Inhibits membrane fusion Beta-CoVs 87
The table provides an overview of neutralizing antibodies targeting the S2 subunit of the spike (S) protein of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. See Supplementary Table S3 for a more detailed
description of each antibody. alpha-CoV, alphacoronavirus; beta-CoV, betacoronavirus; HCoV, human coronavirus; MERS-CoV,
Middle East respiratory syndrome coronavirus.
STING agonist
A modulator of stimulator
of interferon genes (STING)
that can facilitate the
phosphorylation of the
transcription factor interferon
regulatory factor 3 (IRF3),
resulting in an increase in the
expression of type I interferon
genes, through the binding of
STING to cyclic GMP–AMP
(cGAMP).
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Acknowledgements
This work was sponsored by the National Natural Science
Foundation of China (32270142) and the Shanghai Rising-Star
Program (22QA1408800) to P.W. X.Z. acknowledges support
from the International Postdoctoral Exchange Fellowship
Program (Talent-Introduction Program, YJ20220071).
Author contributions
P.W. and S.J. conceived ideas. Y.C. X.Z. and P.W. wrote the
article. H. Zhou, H. Zhu and S.J. reviewed and edited the manu-
script. Y.C. created the tables and H. Zhou prepared the
figures with suggestions from P.W. and S.J. All authors
reviewed and approved the manuscript before submission.
Competing interests
P.W. has filed patent applications for antibodies 4-8,5-24,
5-7,1-20, 4-20, 910-30, 2-15, 2-7,1-57 and 2-36. The other
authors declare no competing interests.
Peer review information
Nature Reviews Immunology thanks S. Liu, Y. Wang and the
other, anonymous, reviewer(s) for their contribution to the peer
review of this work.
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.
Springer Nature or its licensor holds exclusive rights to this
article under a publishing agreement with the author(s) or
other rightsholder(s); author self-archiving of the accepted
manuscript version of this article is solely governed by the
terms of such publishing agreement and applicable law.
Supplementary information
The online version contains supplementary material available
at https://doi.org/10.1038/s41577-022-00784-3.
© Springer Nature Limited 2022
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Immunology
Reviews
... To evade the host immune system, enveloped viruses hijack the host cell's glycosylation machinery to cover S with a dense coat of host carbohydrates, known as a glycan shield (Casalino et al., 2020;Chawla et al., 2022;Grant et al., 2020;Turoňová et al., 2020;Watanabe et al., 2020b;Watanabe et al., 2019). In SARS-CoV-2 the glycan shield screens effectively over 60% of the S protein surface (Casalino et al., 2020), leaving the RBD, when open, and regions of the N-terminal domain (NTD) vulnerable to immune recognition (Bangaru et al., 2022;Carabelli et al., 2023;Chawla et al., 2022;Chen et al., 2023;Harvey et al., 2021;Piccoli et al., 2020). The RBD targeted by approximately 90% of serum neutralising antibodies (Piccoli et al., 2020) and thus a highly effective model not only to screen antibody specificity Lan et al., 2020;Lin et al., 2022) and interactions with host cell co-receptors (Clausen et al., 2020;Mycroft-West et al., 2020;Nguyen et al., 2022), but also as a protein scaffold for COVID-19 vaccines (Dickey et al., 2022;Kleanthous et al., 2021;Montgomerie et al., 2023;Ochoa-Azze et al., 2022;Tai et al., 2020;Valdes-Balbin et al., 2021;Yang et al., 2022). ...
... The structured region is supported by a largely hydrophobic beta sheet core, framed by two flanking, partially helical loops (aa 335-345 and aa 365-375), linked by a bridging N-glycan at N343, see Figure 1b. The aa 335-345 loop carries the N343 glycosylation site and it is part of an important antigenic region targeted by Class 2 and 3 antibodies (Bangaru et al., 2022;Barnes et al., 2020;Carabelli et al., 2023;Chen et al., 2023). In the bridging conformation, the N343 glycan pentasaccharide extends across the RBD beta sheet to reach the aa 365-375 loop forming highly populated hydrogen bonding and dispersion interactions with the backbone and with the sidechains of residues 365-375, see Figure 1b,c and Appendix 1-figure 2. The bridging N343 glycan shields the hydrophobic beta sheet core of the RBD from the surrounding water, preventing energetically unfavourable contacts. ...
... The RBM encompasses aa 439-506 and counts all the RBD residues in direct contact with ACE2 (Lan et al., 2020). The RBM is heavily targeted by both Class 1 and 2 antibodies (Bangaru et al., 2022;Barnes et al., 2020;Carabelli et al., 2023;Chen et al., 2023) and under high evolutionary pressure, with all VoCs carrying mutations in this region. As shown by earlier MD simulations studies (Casalino et al., 2020;Harbison et al., 2022;Sztain et al., 2021;Williams et al., 2022), the RBM in unbound S is largely unstructured and dynamic, an insight also supported by the low resolution cryo-EM maps of this region (Gobeil et al., 2022;Walls et al., 2020;Wrapp et al., 2020). ...
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Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N -glycosylation at N343 and how this glycan’s structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N -glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
... Bebtelovimab (LY-CoV1404), while highly efficient in neutralizing many SARS-CoV-2 variants, including early Omicron subvariants, escaped neutralization by subsequently emerging BQ.1.1 and XBB lineages 15, 17 . Another mAb isolated from a SARS-CoV convalescent individual, Sotrovimab (S309), maintained its neutralizing activity against most emerged SARS-CoV-2 variants due to recognition of a conserved epitope 4,8,18,19 . ...
... While the S2 subunit exhibits greater conservation compared to S1, antibodies targeting S2 typically exhibit suboptimal potency for achieving protection 4,[24][25][26] . Recently, we reported the isolation of potent and broadly neutralizing antibodies from a vaccinated donor who received a special five-dose COVID-19 vaccination schedule. ...
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Monoclonal antibody (mAb) therapeutics hold promise for both preventing and treating infectious diseases, especially among vulnerable populations. However, the emergence of various variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents challenges for current mAb treatments, emphasizing the need for more potent and broadly neutralizing antibodies. In this study, we employed an unbiased screening approach to discover broadly neutralizing antibodies and successfully isolated two mAbs from individuals with only exposure to ancestral SARS-CoV-2. One of these antibodies, CYFN1006-1, exhibited robust cross-neutralization against a spectrum of SARS-CoV-2 variants, including the latest JN.1 and KP.2 variants, with consistent IC50 values ranging from ~1 to 5 ng/mL. Notably, it also displayed broad neutralization activity against SARS-CoV and related sarbecoviruses, such as WIV1, SHC014, RaTG13, and GD-Pangolin. Structural analysis revealed that these mAbs target shared hotspot but mutation-resistant epitopes, with their Fabs locking the RBD in the "down" conformation through interactions with adjacent Fabs and RBDs, and cross-linking Spike trimers into di-trimers to block viral infection. In vivo studies conducted in a JN.1-infected hamster model validated the protective efficacy of CYFN1006-1, emphasizing its therapeutic potential. These findings suggest that, through meticulous approaches, rare antibodies with cross-neutralization activities against SARS-CoV-2 and related sarbecoviruses can be identified from individuals with exclusively ancestral virus exposure.
... We consider the contribution of fitness (infectivity) from RBD to the virus, denoted F , as proportional to the fraction of RBD that are folded and free from antibodies. We also consider the experimental observation that RBD on the spike protein could adopt two distinct conformations: "up" and "down", with only "up" RBD exposing the receptor-binding motif (14)(15)(16)(17). As a result, we adopt a multistate microscopic configuration model for the RBD that includes the following states: unfolded; folded in both up and down states and free; folded in up and down states, and bound to ACE2; and finally, folded, in up and down states, and bound to one of four distinct antibodies. ...
... Studies have established that RBD could adopt either up or down conformations on the spike protein (14)(15)(16)(17). Despite this, many investigations have measured binding affinities using isolated RBDs, neglecting the complex dynamics between the spike protein and RBD. ...
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... Thousands of neutralizing antibodies targeting different epitopes of the spike protein have been identified and characterized [12][13][14][15][16][17][18][19] . The majority of these antibodies recognize the RBD of the spike protein, while a small subset targets the NTD, SD1, SD2, or S2 stem-helix 20 . S3H3 antibody 21 targeting SD1 as well as 12-16 and 12-19 antibodies 22 targeting the NTD-SD1 were able to neutralize XBB.1.5 and BQ.1.1. ...
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The Omicron subvariants BQ.1.1, XBB.1.5, and XBB.1.16 of SARS-CoV-2 are known for their adeptness at evading immune responses. Here, we isolate a neutralizing antibody, 7F3, with the capacity to neutralize all tested SARS-CoV-2 variants, including BQ.1.1, XBB.1.5, and XBB.1.16. 7F3 targets the receptor-binding motif (RBM) region and exhibits broad binding to a panel of 37 RBD mutant proteins. We develop the IgG-like bispecific antibody G7-Fc using 7F3 and the cross-neutralizing antibody GW01. G7-Fc demonstrates robust neutralizing activity against all 28 tested SARS-CoV-2 variants and sarbecoviruses, providing potent prophylaxis and therapeutic efficacy against XBB.1 infection in both K18-ACE and BALB/c female mice. Cryo-EM structure analysis of the G7-Fc in complex with the Omicron XBB spike (S) trimer reveals a trimer-dimer conformation, with G7-Fc synergistically targeting two distinct RBD epitopes and blocking ACE2 binding. Comparative analysis of 7F3 and LY-CoV1404 epitopes highlights a distinct and highly conserved epitope in the RBM region bound by 7F3, facilitating neutralization of the immune-evasive Omicron variant XBB.1.16. G7-Fc holds promise as a potential prophylactic countermeasure against SARS-CoV-2, particularly against circulating and emerging variants.
... Therapeutic antibodies against spike have been extensively used to treat COVID-19 patients at risk for progressing to severe disease [34]. The monoclonal antibody Bebtelovimab (LY-CoV-1404) was shown to reduce disease severity [35], and retained its efficacy against the BA.1 and BA.2 variants that appeared in late 2021 [36][37][38]. ...
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... For example, Ivermectin blocks the virus-membrane fusion by competitively inhibiting the interaction between the S protein and ACE2 (Yan et al., 2022). Neutralizing antibodies, such as monoclonal antibodies, single-domain antibodies, convalescent plasma and polyclonal antibody preparations, inhibit viral entry into host cells by binding to the S protein and activate host effector pathways to eliminate virus-infected cells (Chen et al., 2023d). The virus-cell fusion can be inhibited by peptides such as EK1, which mimic the SARS-CoV-2 spike HR2 and disrupt the interaction between HR1 and HR2. ...
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The rapid spread of SARS-CoV-2 variants poses a constant threat of escape from monoclonal antibody and vaccine countermeasures. Mutations in the ACE2 receptor binding site on the surface S protein have been shown to disrupt antibody binding and prevent viral neutralization. Here we used a directed evolution-based approach to engineer three neutralizing antibodies for enhanced binding to S protein. The engineered antibodies showed increased in vitro functional activity in terms of neutralization potency and/or breadth of neutralization against viral variants. Deep mutational scanning revealed that higher binding affinity reduces the total number of viral escape mutations. Studies in the Syrian hamster model showed two examples where the affinity-matured antibody provided superior protection compared to the parental antibody. These data suggest that monoclonal antibodies for anti-viral indications would benefit from affinity maturation to reduce viral escape pathways and appropriate affinity maturation in vaccine immunization could help resist viral variation.
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The SARS-CoV-2 Omicron variant has very high levels of transmission, is resistant to neutralization by authorized therapeutic human monoclonal antibodies (mAb) and is less sensitive to vaccine-mediated immunity. To provide additional therapies against Omicron, we isolated a mAb named P2G3 from a previously infected vaccinated donor and showed that it has picomolar-range neutralizing activity against Omicron BA.1, BA.1.1, BA.2 and all other variants tested. We solved the structure of P2G3 Fab in complex with the Omicron spike using cryo-electron microscopy at 3.04 Å resolution to identify the P2G3 epitope as a Class 3 mAb that is different from mAb-binding spike epitopes reported previously. Using a SARS-CoV-2 Omicron monkey challenge model, we show that P2G3 alone, or in combination with P5C3 (a broadly active Class 1 mAb previously identified), confers complete prophylactic or therapeutic protection. Although we could select for SARS-CoV-2 mutants escaping neutralization by P2G3 or by P5C3 in vitro, they had low infectivity and ‘escape’ mutations are extremely rare in public sequence databases. We conclude that this combination of mAbs has potential as an anti-Omicron drug. A potent mAb shows promise in monkeys either alone or in a combination therapy for either prophylaxis or treatment of infection with SARS-CoV-2 Omicron BA.1, BA.1.1 and BA.2.
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Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike elicits diverse antibodies, but it is unclear if any of the antibodies can neutralize broadly against other beta-coronaviruses. Here, we report antibody WS6 from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, Middle East respiratory syndrome (MERS)-CoV, and hCoV-OC43. The crystal structure at 2 Å resolution of WS6 revealed recognition to center on a conserved S2 helix, which was occluded in both pre- and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion and post-viral attachment. Comparison of WS6 with other recently identified antibodies that broadly neutralize beta-coronaviruses indicated a stem-helical supersite—centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156—to be a promising target for vaccine design.
Preprint
The rapid evolution of SARS-CoV-2 has led to a severe attrition of the pool of monoclonal antibodies still available for COVID-19 prophylaxis or treatment. Omicron subvariants notably escape most antibodies developed so far, with Bebtelovimab last amongst clinically approved therapeutic antibodies to display still good activity against all of them including the currently dominant BA.4/BA.5. We recently described P2G3, a broadly active SARS-CoV-2 monoclonal antibody, which targets a region of Spike partly overlapping with the site recognized by Bebtelovimab. Here, we reveal that P2G3 efficiently neutralizes SARS-CoV-2 omicron subvariants including BA.4/BA.5. We further demonstrate that P2G3 neutralizes Omicron BA.2 and BA.4 mutants escaping Bebtelovimab blockade, whereas the converse is not true. Funding EU COVICIS program; private foundation advised by CARIGEST SA.
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The Omicron subvariants BA.2.75 is rapidly raising in India. BA.2.75 also shows a local growth advantage compared to BA.2.38 and BA.4/BA.5. Its immune evasion capability and receptor binding affinity is unclear and requires investigation. Here, we show that BA.2.75 is more neutralization evasive than BA.2.12.1 against the plasma from post-vaccination BA.2 infection, but less compared to BA.4/BA.5. However, as shown in a small sample of plasma from post-vaccination Delta infection, BA.2.75 seems to be more immune evasive than BA.4/BA.5 in Delta-stimulated immune background, which may explain BA. 2.75's growth advantage over BA.4/BA.5 in India. The additional N460K, G446S, D339H and R493Q mutations carried by BA.2.75 allows it to escape BA.2-effective neutralizing antibodies of different RBD epitopes, and BA.2.75 has a distinct antibody escaping profile from BA.4/BA.5. Compared to BA.2, REGN10933 and COV2-2196 partially recovered neutralization against BA.2.75 due to R493Q reversion. However, the efficacy of their corresponding cocktail was not significantly changed, since REGN10987 and COV2-2130 showed reduced neutralizing activity due to G446S. BA.2.75 exhibits higher ACE2-binding affinity than BA.4/BA.5, which should be contributed by R493Q and N460K, according to deep mutational scanning (DMS) results. This affinity-strengthening feature is being further examined and verified, which will be updated soon.