Isolation of antibodies from bovine plasmablasts

Upon isolating two FMDV serotype O-specific antibodies (B77 and F145) from a natural bovine host[20], we aimed to isolate a cross-serotype NAb that can neutralize both serotype O and A. FMDV (O/Tibet/99) (hereafter named FMDV-OTi) and FMDV (A/WH/CHA/09) (hereafter named FMDV-AWH) were applied as baits to isolate specific memory B cells from natural bovine host blood, which displayed strong cross-reactivity with both serotype O and A. As revealed in fluorescence-activated cell sorting (FACS), CD21⁺IgM^- O_-FMDV⁺ A_-FMDV⁺ B cells are extremely rare, displaying 21 per million PBMCs. Via FACS, a total of 96 single CD21⁺IgM^- O_-FMDV⁺ A_-FMDV⁺ B cells were sorted for the amplification of the IgG BCR variable gene and the development of a FMDV serotype O and A cross-neutralizing scFv antibody (Fig 1A). Finally, 60 paired IgG clones from these cross-reactivity B cells were successfully amplified. Of these, 14 scFv antibodies displayed cross-reactivity with both FMDV serotype O and A. But, only R50 scFv antibody showed cross-neutralizing activity with both FMDV serotype O and A.

Fig 1

Isolation of NAbs.

(A) Confirmation of the phenotype and proportion of FMDV serotype O and serotype A cross-reactive plasmablasts in the peripheral blood by flow cytometry. Bovine PBMCs were analyzed by four-color flow cytometry. Gate 1 (P1) was selected to exclude cell debris, with lower values of SSC-A and FSC-A, and was further analyzed to gate singlets (P2) based on the diagonal streak of the FSC-A vs. FSC-H plot. The CD21⁺IgM^- B cells (P3) were gated to check the distributions of O_-FMDV^- A_-FMDV⁺ (P4), O_-FMDV⁺ A_-FMDV^- (P6) and O_-FMDV⁺ A_-FMDV⁺ (P5) population, in the presence (Bovine 2334 sample-P3) or absence (Bovine 2334 FMO-P3) of bait antigens. (B)The binding activity of R50 scFv with FMDV serotype O and A strains. The O/Mya/98, O/HN/CHA/93, O/XJ/CHA/2017, A/GDMM/CHA/2013 and A/WH/CHA/09 strains were separately used to infect BHK-21 cells. The binding activity of R50-ScFv (concentration, 0–50 μg/ml) with the infected BHK-21 cells was measured by flow cytometry. Data are presented as the mean ± standard error of the mean and represent two independent experiments. (C) Evaluation of bovine-derived FMDV-neutralizing scFv antibodies for neutralization and potency. Values are neutralization titer (NT) in μg/ml. An NT value of 100 μg/ml was used as a cutoff for neutralization, and >100 μg/ml was defined as showing no virus-neutralizing activity. NT values of 0–10 μg/ml are red, 10–25 μg/ml are orange, 25–50 μg/ml are blue, and ˃100 μg/ml are white.

To further investigate the neutralization breadth and potency of R50 scFv antibody, we propagated, purified three representative strains of FMDV serotype O (O/Mya/98; O/HN/CHA/93; O/Tibet/99) obtained from three currently epidemic topotypes (SEA, Cathay, and ME-SA, respectively) and two representative strains of FMDV serotype A (A/WH/CHA/09; A/GDMM/CHA/2013) from the Asia topotypes SEA-97/G1 and G2 in China[21], and separately examined their binding and neutralization abilities by flow cytometry and microneutralization assay. The flow cytometry showed that R50 scFv binds to the three topotypes of FMDV serotype O and the two distinctive strains of FMDV serotype A (Fig 1B). In line with the binding results, microneutralization assay also revealed that R50 scFv cross-neutralizes these strains of FMDV serotype O and A (Fig 1C). In contrast, B77 and F145 scFv only neutralize the three representative strains of FMDV serotype O(Fig 1C), as previously reported [20].

Overall architectures of the FMDV-NAb complexes

To clarify the mechanism of cross-serotype neutralization, we determined the structures of B77 and F145 scFv in complex with FMDV-OTi, as well as R50 scFv in complex with FMDV-OTi and FMDV-AWH (S1 Fig). The cryo-EM micrographs indicated the presence of scFv on the FMDV capsids at distinct locations (Fig 2). The final resolution of the cryo-EM reconstruction was estimated by the FSC 0.143 cutoff to be 3.90 Å for the FMDV-OTi-B77 complex, 3.68 Å for the FMDV-OTi-F145 complex, 3.94 Å for the FMDV-OTi-R50 complex and 3.49 Å for the FMDV-AWH-R50 complex (S1 Fig).

Fig 2

Cryo-EM structures.

(A-D) The central cross-sections through the cryo-EM maps of FMDV-OTi-B77 complex (A), FMDV-OTi-F145 complex (B), FMDV-OTi-R50 complex (C) and FMDV-AWH-R50 complex (D) are shown with the icosahedral two-, three- and five-fold axes. Each image in the 480-pixel boxes corresponds to 446 Å in each dimension. Scale bars, 100 Å. (E-H) Rendered images of the FMDV-OTi-B77 complex (E), FMDV-OTi-F145 complex (F), FMDV-OTi-R50 complex (G) and FMDV-AWH-R50 complex (H). Depth cueing with color is used to indicate radius (< 120 Å, blue; 130–150 Å, from cyan to yellow; > 160 Å, red). The icosahedral five- and three-fold axes are represented by pentagons and triangles, respectively. (I-L) Footprints of B77, F145 and R50 on the FMDV surface. The figure shows a 2D projection of the FMDV surface produced using RIVEM. 5-, 3-, and 2-fold icosahedral symmetry axes are marked as pentagons, triangles, and ovals, respectively, on one icosahedral asymmetrical unit. The spherical polar angles (θ, ϕ) define the location on the icosahedral surface. The depictions are radially depth cued from blue (radius = 130 Å) to red (radius = 155 Å). The residues in the scFv footprints are shown in purple.

Three B77 or F145 scFv molecules bind to the FMDV-OTi capsid around an icosahedral threefold axis (Fig 2A, 2B, 2E and 2F). By contrast, R50 scFv binds to a depression between the 2- and 5-fold axes of FMDV-OTi and FMDV-AWH (Fig 2C, 2D, 2G and 2H). In all cases, the cryo-EM densities were of sufficient quality to allow the atomic modeling of FMDV capsid proteins and the NAb scFv variable loops that are responsible for virus recognition. However, the densities of the bound NAbs away from the contact surface were not sufficiently clear to trace all main chains (S2 Fig). The footprints of B77, F145 and R50 on the capsid surface were also mapped (Fig 2I–2L).

The lengths of bovine HCDR3 feature a trimodal distribution: group 1 comprises very short HCDR3s (≤10 amino acids); group 2 comprises intermediate lengths (11 to 47 amino acids); and group 3 comprises ultralong HCDR3s (≥48 amino acids)[22,23]. The structures show that B77 contains an intermediate length HCDR3 loop with 18 amino acids, but F145 and R50 contain ultralong HCDR3 loops (50 and 61 amino acids, respectively) (S3 Table). The ultralong HCDR3s form an elongated “stalk” and a globular “knob” at the distal ends of the stalks, and the stalk region is essentially a display scaffold to deliver the knob domain, which functions as an effector domain that mediates the molecular recognition of antigen. The globular knob of F145 interacts with VP2, but the globular knob of R50 binds to a shallow depression on the capsid, contacting the two major capsid proteins VP1 and VP3 from two adjacent protomers (S3 Fig).

Interaction of B77 and F145 with FMDV-OTi

The complex structures show that B77 and F145 make similar contacts with the BC-loop and HI-loop of FMDV-OTi VP2. Residues in the VP2 BC-loop (_OTi-VP2T71 and _OTi-VP2S72) and in the VP2 HI-loop (_OTi-VP2N190 and _OTi-VP2Q196) interact with residues _B77-VHM56, _B77-VHT101, _B77-VHS105, _B77-VHL108 and _B77-VHW114 in the B77 heavy chain (S4 Table). The _OTi-VP2T71 and _OTi-VP2S72 side chains form hydrogen bond contacts with side chain atoms of _B77-VHT101 and _B77-VHW114 (Fig 3A and S4 Table). The side chains of _OTi-VP2T190 and _OTi-VP2Q196 form hydrogen bond contacts with the side chain atoms of _B77-VHM56 and _B77-VHS105 (Fig 3A and S4 Table). In addition, _OTi-VP2H65 and _OTi-VP2D68 in βB and the BC-loop interact with residues _B77-VHW93 and _B77-VHS95 in the light chain of B77 (S4 Table). The side chain of _OTi-VP2H65 forms hydrogen bonds or van der Waals contacts with the side chain atoms of _B77-VLS95 (Fig 3A and S4 Table). To further confirm the epitope, neutralization escape mutants were screened under B77 immune pressure. The B77-resistant mutants were isolated and characterized. An Asn→Ser mutation occurred at position 190 of VP2; this position is located in the virus-antibody binding interface and is strictly conserved among serotype O (S4 Table and Fig 3C).

Fig 3

B77 and F145 bind to FMDV-OTi.

(A) Close-up view of FMDV-OTi-B77 interaction interface. VH and VL of B77 are purple and orange. Contacting residues are displayed as sticks with the same color scheme as in the main chain. Dashed lines indicate contacts with potential hydrogen bonds and salt bridges. Amino acid side chains are colored blue (nitrogen) and red (oxygen). (B) Close-up views of FMDV-OTi-F145 interaction interface. VH of F145 is cyan. (C) Sequence alignment of FMDV serotype O and serotype A. Residues with red or yellow backgrounds are identical or conserved, respectively. Residues at the FMDV-OTi-B77 and FMDV-OTi-F145 interfaces are indicated with red and black triangles, respectively. The same contacting residues are highlighted in blue boxes. Alignment was performed by CLUSTALW, and the figure was generated by ESPript. (D) Virus titers (pfu/ml) of the wild-type (O/Tibet/99) and its mutants (_VP2S72D, _VP2N190S and _VP2T191S) were determined by plaque forming assay. (E) Plaque phenotypes formed in BHK-21 cells and the sizes were correlated to the CPE patterns. (F) Neutralizing efficacy of F145 against the wild-type (O/Tibet/99) and mutants (_VP2S72D, _VP2N190S and _VP2T191S) were evaluated using a micro-neutralization assay. The neutralization titer (NT) represented the lowest antibody concentration required to fully prevent CPE. *** indicates significant difference to wild-type at P<0.001. ** indicates significant difference to wild-type at P<0.01.

F145 interacts with the VP2 BC-loop (_OTi-VP2T71 and _OTi-VP2S72) and the HI-loop (_OTi-VP2V189, _OTi-VP2N190, _OTi-VP2T191) (S5 Table). The side chains of _OTi-VP2S72 and _OTi-VP2T191 form hydrogen bond contacts with the side chain atoms of _F145-VHS119 and _F145-VHT128(Fig 3B and S5 Table). The amide nitrogen of _OTi-VP2N190 provides additional stabilization via hydrogen bonds with the hydroxyl group of _F145-VHD129 (Fig 3B and S5 Table). To further confirm the epitope, neutralization escape mutants were generated under F145 immune pressure. The F145-resistant mutants were isolated and characterized. A Ser→Ala mutation was found at position 72 in VP2, which is also located in the virus-antibody binding interface.

FMDV employs heparin sulfate (HS) and integrin (generally avβ6) as receptors[24,25]. In the cellular entry of FMDV-O, HS acts as a primary receptor that allows for rapid cell binding, thereby providing more time for virus binding to integrins[26]. FMDV binding to the integrin receptor is facilitated by a conserved arginine-glycine-aspartic (RGD) motif in the exposed GH-loop of VP1[25]. Structure comparisons of FMDV-integrin and FMDV-NAbs show obvious clashes between NAbs (B77 and F145) and the integrin receptor, suggesting that FMDV neutralization by B77 and F145 is facilitated by blocking virus-receptor interaction via steric hindrance (S7 Fig). Meanwhile, in vivo the antibodies are IgG molecules or some other multi-site entity, a situation that could result in aggregation of virus particles if one virus particle becomes crosslinked with another. Aggregation of virus particles can cause a reduction in the number of infectious virions available to interact with receptor and may result in the neutralization.

Determinant for the serotype O-specificity of F145 and B77

F145 and B77 neutralized FMDV-OTi but did not have a neutralizing effect against FMDV-AWH (Fig 1C). The structural alignment of FMDV-OTi and FMDV-AWH capsid proteins showed no substantial conformational changes in the VP2 BC-loop and HI-loop, which are the epitopes of B77 and F145 (S4 Fig). The sequence alignment of FMDV-OTi and FMDV-AWH exhibited distinct amino acid differences on the epitopes of B77 and F145, indicating that the variation of critical amino acid residues may be the determinant for serotype-specific recognition (Fig 3C).

For B77, we identified that the neutralization escape mutation _OTi-VP2N190→_AWH-VP2S190 enables the escape of antibody-mediated neutralization (virus neutralization [VN] titer >400 μg/ml) (Fig 3C and S8 Table). For F145, we mutated FMDV-OTi amino acid by FMDV-AWH’s sequence at the corresponding positions (S72D, N190S and T191S), rescued virions by reverse genetics approach and evaluated the neutralization capacity using virus neutralization test (VNT). All mutated viruses could be rescued with an acceptable attenuated proliferation and cytopathic effect (CPE) (Fig 3D and 3E). The VNT results showed that FMDV-OTi with the _OTi-VP2N190S mutation exhibited a 2.9-fold reduction in VN titer, and the _OTi-VP2S72D mutation resulted in a significant reduction (~30-fold) in VN titer (Fig 3F). These results suggest that VP2 S72 and N190 play the most essential roles in the serotype O-specific neutralization activity of F145 and B77.

FMDV-OTi-R50 and FMDV-AWH-R50 interfaces

R50 binds FMDV-OTi VP1 and VP3 by its heavy chain (Fig 4A). The antibody-interacting residues on the FMDV-OTi capsid are located in the VP1 BC-loop (residues _OTi-VP1V50 and _OTi-VP1D52), VP1 EF-loop (residues _OTi-VP1P94 and _OTi-VP1E95), VP1 GH-loop (residues _OTi-VP1R157, _OTi-VP1L159 and _OTi-VP1P160) and VP3 GH-loop (residues _OTi-VP3D173 and _OTi-VP3T177) (S6 Table). The interacting residues in R50 are located in HCDR3, including residues _R50-VHR119, _R50-VHW120, _R50-VHY130, _R50-VHN132, _R50-VHY138, _R50-VHG139, _R50-VHR140, _R50-VHC141 and _R50-VHT142 (S6 Table). The side chain of _R50-VHR140 extends into a deep cavity and forms interactions with _OTi-VP1D52 in the VP1 BC-loop and _OTi-VP1L159 in the VP1 GH-loop (Fig 4A and S6 Table). Residues _OTi-VP1V50, _OTi-VP1R157 and _OTi-VP1P161 also stabilize the virus-antibody interaction by interacting with _R50-VHW120 and _R50-VHT142(Fig 4A and S6 Table). In addition, the small protruding structure formed by _OTi-VP1P94 and _OTi-VP1E95 of the VP1 EF-loop makes contact with _R50-VHR119, _R50-VHC131 and _R50-VHN132(Fig 4A and S6 Table). One salt bridge between _OTi-VP1E95 and _R50-VHR119 was inferred because the centroids of the oppositely charged functional groups of the residues were within a 4 Å cutoff and because the Glu carbonyl oxygen atom was within 4 Å from the nitrogen atom of the Arg side chain (Fig 4A and S6 Table). Moreover, the side chains of _OTi-VP3D173 and _OTi-VP3T177 form hydrogen bonds with the side chains of _R50-VHY130 and _R50-VHY138, respectively (Fig 4A and S6 Table).

Fig 4

Structure of FMDV-OTi-R50 complex.

(A) Surface representation of FMDV-OTi-R50 showing the interaction interface between R50 (ribbon diagram) and the capsid. The interface is framed and shown as a close-up view in the right panel. The residues in R50 responsible for interacting with the capsid are shown as yellow sticks. The interface amino acid residues in VP3 (B) and VP1 (C) are colored magenta and labeled; the interface residues in R50 are colored yellow and labeled (D).

The interaction of R50 with FMDV-AWH is homologous to that observed in the FMDV-OTi-R50 complex; R50 makes contact with FMDV-AWH VP1 and VP3 (Fig 5A). In FMDV-AWH VP1, residues that participate in antibody binding are located in the BC-loop (residues _AWH-VP1V50 and _AWH-VP1D52), EF-loop (residues _AWH-VP1P94 and _AWH-VP1E95), and GH-loop (_AWH-VP1Q156, _AWH-VP1L157 and _AWH-VP1P158) (S7 Table). The antibody-interacting residues of FMDV-AWH VP3 are located in the GH-loop (residues _AWH-VP3D174 and _AWH-VP3V175) (S7 Table). The side chain of _R50-VHR140 extends into the deep cavities and contacts _AWH-VP1D52 in the BC-loop and _AWH-VP1L157 in the GH-loop (Fig 5A and S7 Table). Residues _AWH-VP1V50, _AWH-VP1Q156, _AWH-VP1P158 and _R50-VHW120 also help stabilize the virus-antibody interaction in this region (Fig 5A and S7 Table). Additionally, the small protruding structure formed by _AWH-VP1P94 and _AWH-VP1E95 of the EF-loop contacts the residues _R50-VHR119, _R50-VHC131 and _R50-VHN132(Fig 5A and S7 Table). The side chain of _AWH-VP1E95 can form salt bridges with the side chain of _R50-VHR119. Moreover, the side chains of _AWH-VP3D174 and _AWH-VP3V175 form hydrogen bonds with the side chains of _R50-VHY130 and _R50-VHY138, respectively (Fig 5A and S7 Table).

Fig 5

Structure of FMDV-AWH-R50 complex.

(A) Surface representation of FMDV-AWH-R50 showing the interaction interface between R50 (ribbon diagram) and the capsid. The interface is framed and shown as a close-up view in the right panel. The residues in R50 responsible for interacting with the capsid are indicated by light blue sticks. The interface amino acid residues in VP3 (B) and VP1 (C) are colored pink and labeled; the interface residues in R50 are colored light blue and labeled (D). (E) Sequence alignment of FMDV type O and A. Residues with red or yellow backgrounds are identical or conserved, respectively. Residues in the FMDV-OTi-R50 and FMDV-AWH-R50 interaction interfaces are indicated with black and red triangles, respectively. The same interface residues are highlighted in blue boxes. (F) Neutralizing efficacy of R50 against the wild-type (O/Tibet/99) and mutants was evaluated using a micro-neutralization assay. The neutralization titer (NT) represented the lowest antibody concentration required to fully prevent CPE. *** indicates significant difference to wild-type at P<0.001. ** indicates significant difference to wild-type at P<0.01. (G) Neutralizing efficacy of R50 against the wild-type (A/WH/CHA/09) and mutants were evaluated using a micro-neutralization assay.

The sequence alignment of FMDV serotype O and A shows that the common residues that contact R50 are strictly conserved in all five representative strains of FMDV serotypes O and A; these residues are _VP1V50, _VP1D52, _VP1P94, _VP1E95, _VP1L159 (corresponding to _VP1L157 of FMDV-AWH), _VP1P160 (corresponding to _VP1P158 of FMDV-AWH) and _VP3D173 (corresponding to _VP3D174 of FMDV-AWH) (Fig 5E). To validate the virus-antibody interactions, we substituted alanine for FMDV-OTi capsid residues whose side chains are involved in antibody binding. The mutated viruses were rescued and assessed for neutralization breadth and potency. Mutations at six individual sites (_OTi-VP1V50A, _OTi-VP1D52A, _OTi-VP1P94A, _OTi-VP1E95A, _OTi-VP1P160A and _OTi-VP3D173A) attenuated virus proliferation and produced less CPE. However, _OTi-VP1L159A increased virus proliferation and grew with greater CPE (S5 Fig). All these mutations reduced the antibody-mediated neutralization of R50. Particularly, the mutation _OTi-VP1E95A completely escaped antibody-mediated neutralization (VN titer > 250 μg/ml) (Fig 5F). Meanwhile, we also performed mutagenesis experiments on the FMDV-AWH capsid. The mutations at five individual sites (_AWH-VP1D52A, _AWH-VP1P94A, _AWH-VP1E95A, _AWH-VP1P158A and _AWH-VP3D174) attenuated virus proliferation and produced less CPE. However, _AWH-VP1L157A increased virus proliferation and grew with greater CPE (S6 Fig). All these mutations reduced the antibody-mediated neutralization of R50. In particular, the mutations _AWH-VP1D52A and _AWH-VP1E95A enabled complete escape of antibody-mediated neutralization (VN titer > 250 μg/ml) (Fig 5G). These results demonstrate the presence of conserved epitopes for the cross-serotype neutralization of FMDV by R50.

Notably, the R50 footprint on the FMDV capsid does not overlap with identified receptor binding sites (S7 and S8 Figs), indicating that R50 may not directly compete with the binding of receptor. Previous studies have reported that A9-Fab destabilized EV71 virions and as much as 70% of EV71 F-particles had been destroyed when incubated with A9-Fab at 37°C [27]. When we incubated FMDV-OTi or FMDV-AWH with R50 at a molar ratio of 1:240 for 30 s or 60 s at 4°C, the negative stain electron micrographs showed that R50 destabilized the virus particle and induced dissociation of virus particles into capsid pentamers, and very few particles remained intact after 60 s (S9 Fig). Meanwhile, the cryo-electron microscopy (cryo-EM) micrographs also showed significantly lower particle density when incubated for 30s (S1 Fig). In contrast to this remarkable effect, B77 did not induce significant decrease of particle density even after one hour incubation at 4°C (S9 Fig). These results indicated a possible neutralization mechanism of R50 by promoting the dissociation of FMDV virions before infection.

Ethics statement

All animal experiments in the study were approved by the Review Board of Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (permit no. LVRIAEC 2018–006) and were conducted in accordance with the Ethics Procedures and Guidelines for Animal Use of the People’s Republic of China.

Virus production and purification

FMDV (O/Tibet/99) or FMDV (A/WH/CHA/09) was grown in baby hamster kidney BHK-21 cells. Inactivated O/Tibet/99 and A/WH/CHA/09 whole virus antigens were kindly provided by an FMD inactivated vaccine manufacturer. For further purification, virus antigens in the supernatant were precipitated by incubating at 4°C overnight in 8% (w/v) PEG 6,000. The precipitated virus antigens were harvested by centrifugation at 3,500 g for 1 h at 4°C, followed by resuspension in pH 7.4 PBS (phosphate-buffered saline) (137 mM NaCl, 2.7 mM KCl, 50 mM Na₂HPO₄ and 10 mM KH₂PO₄). The viruses were purified through a sucrose cushion that transferred the samples to an ultracentrifuge tube. A 10 ml aliquot of 30% (w/v) sucrose was gently added to the bottom of the suspension, and the sample was centrifuged at 35,000 g for 1.5 h. The sucrose was removed from the pellet, and 500 μl of PBS was added to cover the pellet. The supernatant was purified over a 20–60% sucrose gradient and fractionated by centrifugation at 35,000 g for 4 h at 4°C. The fractions were analyzed by negative stain electron microscopy, and the virus fraction was transferred to a 100 kDa MWCO centrifugal filter for buffer exchange with PBS to remove the sucrose.

Bovine infection

One 1-year-old healthy Qinchuan bovine (Bos Taurus), a Chinese breed of beef bovine, was raised in an animal biosafety level 3 laboratory for the sorting of antigen-specific antibody-secreting B cells after FMDV infection. The bovine, designated as #2334, was first challenged subcutaneously at two sites on the tongue with 10,000 BID₅₀ (50% bovine infective dose) of bovine-adapted O/Mya/98 and then received a boost vaccination with O/HN/CHA/93 and O/Tibet/99 respectively on days 35 and 132, as described in our previous report[20]. After day 225, the animal was further challenged subcutaneously at two sites on the tongue with 10,000 BID₅₀ (50% bovine infective dose) of FMDV (A/WH/CHA/09). Serum samples were collected at days 114 after this infection, and heparinized peripheral blood was taken from the jugular veins of the bovine for PBMC isolation.

Identification of FMDV serotype O and A cross-neutralizing Plasmablasts in infected Bovine

PBMCs were isolated from the heparinized blood samples of the bovine with HISTOPAQUE 1.083 (Sigma-Aldrich, USA) according to the manufacturer’s instructions. The PBMCs were then used to identify FMDV serotype O and serotype A cross-reactive plasmablasts. Purified FMDV (O/Tibet/99) inactivated 146S antigen was labeled with Lightning-Link Rapid FluoProbes 647H (Innova Biosciences, San Diego, USA) according to the manufacturer’s instructions. Purified FMDV (A/WH/CHA/09) inactivated 146S antigen was labeled with Pacific Blue (Thermo Scientific, USA) according to the manufacturer’s instructions. Freshly isolated PBMCs were stained with O-FMDV 146S-FluoProbes 647H, A-FMDV 146S-Pacific Blue, mouse anti-bovine CD21-RPE (Bio-Rad, USA) and mouse anti-bovine IgM-FITC (Bio-Rad, USA) for 30 min at 4°C in PBS containing 2 mM EDTA and 0.5% BSA. The parallel staining of PBMCs that lacked O-FMDV 146S-FluoProbes 647H and A-FMDV 146S-Pacific Blue was used as fluorescence minus one (FMO) control. The stained samples were immediately analyzed by flow cytometry, and one million PBMCs were acquired for counting the proportion of FMDV serotype O and A cross-reactive plasmablasts.

Single-Cell sorting of FMDV serotype O and serotype A cross-neutralizing plasmablasts from bovine PBMCs using flow cytometry

The bovine PBMCs stained as above were sorted by flow cytometry (BD FACS Aria II, USA) using a 100 μm nozzle. Single-cell mode was set to sort the FMDV CD21⁺IgM^- O_-FMDV⁺ A_-FMDV⁺ cells using flow rate of 10,000 events/s. The subsequent single-cell lysis and cDNA synthesis procedures were performed in accordance with our previous report[20]. The obtained cDNA templates were stored at −20°C for subsequent PCR amplification.

Cloning of scFv gene and construction of pcDNA3.4-scFv expression vector

Amplification of the antibody variable region genes (VH and VL) was performed by nested PCR using primers for bovine IgG gamma and lambda chains (Ig γ and Ig λ; S1 Table)[20]. Because the λ chain accounts for 95% of the bovine light chains, only the λ light chain was amplified by PCR. The final PCR products of paired VH and VL were Sanger sequenced. Single-chain fragment variable (scFv) was designed by splicing the VH and VL genes using a flexible linker (GGGGSGGGGSGGGGS). The N- and C-termini of the scFv included a signal peptide (MNPLWTLLFVLSAPRGVLS) of bovine Ig γ and a His tag, respectively. The scFv genes were synthesized by GenScript Inc. (www.genscript.com) with codon optimization and were expressed in CHO cells, followed by cloning into the pcDNA3.4 vector. The cloned scFv-expressing plasmids were amplified in E. coli and extracted and purified using an Endo Free Maxi plasmid kit (TIANGEN, China).

Expression and purification of NAb scFv

Single-chain fragment variable (scFv) antibodies were expressed in ExpiCHO-S cells (Invitrogen, USA) following the manufacturer’s instructions. Briefly, the CHO cells were routinely cultured at 37°C with ≥80% relative humidity and 8% CO2 in 125 mL flasks that were fixed in an orbital shaker platform at a speed of 125 rpm with a 25 mm shaking diameter. After the cell density reached 6 × 10⁶ cells/ml, the cells were collected and resuspended in fresh media for transfection. The pcDNA3.4-scFv plasmid was transfected into ExpiCHO-S cells with an ExpiFectamine CHO transfection kit (Invitrogen, USA). An enhancer and feed component were added at 18 h post transfection according to a standard protocol. ScFv-containing supernatants were harvested 10 days after transfection. The expressed scFv was initially purified with a HisTrap excel column. The obtained eluate was concentrated using a 100 kDa ultrafiltration tube and then further purified by size exclusion chromatography using a Superdex-200 increase 10/300 column and an AKTA plus protein purification system (GE Life Sciences, USA). The purity and size of each single-chain fragment variable (scFv) antibody was assessed by SDS-PAGE. The concentrations of the final obtained scFvs were determined by measuring their corresponding absorption values at a wavelength of 280 nm.

Binding affinity measurement of R50 scFv

Baby hamster kidney-21 (BHK-21) cells in 24-well plate were respectively infected with different FMDV strains at a multiplicity of infection (MOI) of 0.01 and incubated for 4 h at 37°C. Subsequently, these infected cells were fixed and permeated for 20 min using a fixation and permeabilization solution (BD Biosciences, USA). After washing with PBS buffer, 1 × 10⁶ infected cells/sample was stained with diluted R50-ScFv and subsequently incubated with anti-HIS FITC antibody (Genescript, China) and 3B4B1-Alexa647 (Fluorescence-labeled antibody (clone:3B4B1) against the nonstructural protein 3B of FMDV) for 30 min at room temperature (20–25°C). After two washes, the stained cells were loaded for FC (BD LSRFortessa, USA), and 10000 Alexa647 positive cells were recorded. The percent of FITC positive cells in Alexa647 positive cells was used to assess the binding activity of R50 scFv.

Virus neutralizing test

The NAb scFvs were titrated for viral neutralizing activity against three representative strains from the three topotypes of FMDV serotype O and the Asia topotype of FMDV serotype A by using a microneutralization assay as previously described[21]. The five strains of FMDV were O/Mya/98 (SEA topotype), O/HN/CHA/93 (Cathay topotype), O/Tibet/99 (ME-SA topotype), A/GDMM/CHA/2013 (genotype 2 in SEA-97 lineage of Asia topotype), and A/WH/CHA/09 (genotype 1 in SEA-97 lineage of Asia topotype). Briefly, scFv antibody samples were 2-fold serially diluted in 96-well cell culture plates in a total volume of 50 μl, and 100 TCID50 of FMDV in 50 μl of culture media was added to each well. After incubation for 1 h at 37°C, ~5×10⁴ BHK-21 cells in 100 μl of media were added to each well as an indicator of residual infectivity. Normal cell wells, and 10, 100, and 1,000 TCID50 virus control wells were used in each plate. The plates were incubated at 37°C with 5% CO2 for 48 h and then fixed in acetone-methanol (volume ratio = 1:1) and stained with a 0.2% crystal violet solution. The endpoint titer was determined as the reciprocal of the lowest antibody dilution to fully prevent a cytopathic effect (CPE) by 100 TCID₅₀ FMDV in each well. The neutralizing activity was expressed as the virus neutralization (VN) titer, which was calculated as the initial antibody concentration divided by the endpoint titer.

Rescue and titration of mutated viruses

Full-length cDNAs were generated by the exchange-cassette strategy to replace the whole P1 coding region of an existing pOFS plasmid with the respective genes of O/Tibet/99 and A/WH/CHA/09. Site-directed mutagenesis was used to introduce nucleic acid mutations to produce full-length cDNAs with single amino acid substitutions[35]. All mutant constructs were confirmed by nucleotide sequencing. The mutant viruses were rescued as previously described[36]. Briefly, Not I-linearized mutant plasmids were transfected into BSR/T7 cells using Lipofectamine 2000 following the manufacturer’s instructions. The transfected cells were monitored daily for the appearance of CPE. At 72 h post transfection, culture supernatants were harvested and passaged on BHK-21 cells. The mutant virus titers were measured using the plaque forming unit (PFU) assay[37]. Confluent monolayers of BHK-21 cells were infected with 10-fold serially diluted FMDV samples in 6-well plates. The 0.6% Tragacanth gum was added after 1 h of incubation. Plaques were visualized at 48 h postinfection (p.i.) by fixing with acetone-methanol and staining with crystal violet. The amount of plaque was observed and statistically analyzed.

Generation of neutralization escape mutants

Neutralization escape mutants were generated through consecutive passages of FMDV in BHK-21 cells under the selective pressure of neutralizing scFv antibodies, according to a previous report with minor modifications[31]. Briefly, tenfold serial dilutions of FMDV (O/Tibet/99) in 50 μl were incubated with 50 μl of varying concentrations of scFv sample (20 μg/ml to 50 μg/ml) in 96-well microplates. The mixtures were used to infect 100 μl of BHK-21 cells (10⁶ cells/ml), which were incubated at 37°C for 48 h to allow virus propagation to occur. The first passage virus was harvested from the wells seeded with the highest dilution of virus that produced an approximately 80–100% cytopathic effect (CPE). Subsequent rounds of pressure selection were performed in 24-well plates in which the passaged virus (200 μl) was incubated with an equal volume of twofold concentration of antibodies in each well containing 400 μl of BHK-21 cells. The harvested virus was subjected to several additional rounds of selection until it completely escaped from neutralization upon the addition of scFv at concentrations greater than 1 mg/ml. The P1 region of the obtained neutralization escape mutants was amplified by one-step RT-PCR as described previously[38] using the primers Pan204+: ACCTCCAACGGGTGGTACGC/NK61: GACATGTCCTCTTGCATCTG) and were subsequently verified by sequencing. Mutated amino acids were determined by aligning the entire mutant P1 region to its parent virus.

Cryo-EM sample preparation and data collection

FMDV and antibodies were incubated at a molar ratio of 1:240 in a volume of 50 μl for 30 min (B77), 10 min (F145) and 30 s (R50) at 4°C. A 3 μl aliquot of the mixture was applied to a glow-discharged carbon-coated gold grid (GIG, Au 1.2/1.3, 200 mesh; Jiangsu Lantuo Biotechnology Co. Ltd., China). The grid was blotted for 5 s in 100% relative humidity and plunge-frozen in liquid ethane using a Vitrobot mark IV (Thermo Fisher, USA). The cryo-EM data were collected at 200 kV with a FEI Arctica (Thermo Fisher, USA) and a direct electron detector (Falcon II, Thermo Fisher) at Tsinghua University. Micrograph images were collected as movies (19 frames, 1.2 s) and recorded at −2.4 to −1.4 μm underfocus at a calibrated magnification of ×110 kX, resulting in a pixel size of 0.932 Å per pixel. The data collection and refinement statistics are summarized in S2 Table.

Image processing and three-dimensional reconstruction

Similar image processing procedures were employed for all data sets. Individual frames from each micrograph movie were aligned and averaged using MotionCor2[39] to produce drift-corrected images. Particles were picked and selected in Relion-2.1[40], and contrast transfer function (CTF) parameters were estimated using CTFFIND4[41] and integrated in Relion-2.1. Subsequent steps in three-dimensional (3D) reconstruction used Relion-2.1 in accordance with recommended gold-standard refinement procedures[40]. The final selected particles were further processed in THUNDER[42], which is a particle filter-based cryo-EM image processing software. The local defocus of each particle was determined by refining the defocus parameter during expectation maximization in THUNDER. For all reconstructions, the final resolution was assessed using the standard FSC = 0.143 criterion.

Model building and refinement

The X-ray structure of native FMDV O1BFS (PDB:1BBT)[43] was manually placed into the cryo-EM map for FMDV particles and rigid-body fitted with UCSF Chimera[44]. The X-ray structure of native BOV-7 (PDB: 6E9U)[23] was manually placed into the cryo-EM map for scFv and rigid-body fitted with UCSF Chimera[44]. The fitting was further improved with real-space refinement using Phenix[45]. Manual model building was performed using Coot[46] in combination with real-space refinement with Phenix[45] to adjust the mismatches between the model and the target protein. The density maps were kept constant during the entire fitting process, and the atomic coordinates were subjected to refinement. The additional structures reported in this work were built and refined by using FMDV (O/Tibet/99) particles as a starting model and rigid-body fitted and refined. Validation was conducted using the MolProbity function integrated within Phenix. The refinement statistics are presented in S2 Table.