Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.

BACKGROUND: SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS: Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS: Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION: Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING: Full list of funders is provided at the end of the manuscript.

Determining the Transformation Kinetics of Water Oxidation Intermediates on Hematite Photoanode.

The oxygen evolution reaction (OER) from water is a sequential oxidation reaction process, involved in transformation of multiple reaction intermediates. For photo(electro)catalytic OER, revealing the intermediates transformation kinetics is quite challenging due to its coupling with photogenerated charge dynamics. Herein, we specifically study the transformation kinetics of the OER intermediates in rationally thin hematite photoanodes through increasing the ratio between surface intermediates and photogenerated charges in bulk. We directly identify the formation and consumption kinetics of one-hole OER intermediate (FeIV═O) in photoelectrochemical water oxidation using operando transient absorption (TA) spectroscopy. The microsecond formation kinetics of the FeIV═O species are sensitively changed by the excitation mode of Fe2O3. The subsecond consumption kinetics are closely dependent on surface FeIV═O species density, demonstrating that the cooperation of FeIV═O intermediates is the key to accelerating water oxidation kinetics on the Fe2O3 surface. This work provides insight into understanding and controlling water oxidation reaction kinetics on Fe2O3 surface.

Dynamic charge collecting mechanisms of cobalt phosphate on hematite photoanodes studied by photoinduced absorption spectroscopy.

Reaction sites, surface states, and surface loaded electrocatalysts are photoinduced charge storage sites and critical to photoelectrochemical (PEC) performance, however the charge transfer mechanisms involved in the three remain poorly understood. Herein, we studied the charge transfer processes in hematite (Fe2O3) without/with loaded cobalt phosphate (CoPi) by operando photoinduced absorption (PIA) spectroscopy. The loaded CoPi receives trapped holes in surface states at low potential and directly captures holes in the valence band at high potential. Through the dynamic hole storage mechanisms, loaded CoPi on Fe2O3 facilitates spatial charge separation and serves as a charge transfer mediator, instead of serving as a catalyst to change the water oxidation mechanism (constant third-order reaction). The spatial separation of photoinduced charges between Fe2O3 and CoPi results in more long-lived holes on the Fe2O3 surface to improve PEC water oxidation kinetically. The dynamic charge collecting mechanism sheds light on the understanding and designing of electrocatalyst loaded photoanodes.

Unraveling Sequential Oxidation Kinetics and Determining Roles of Multi-Cobalt Active Sites on Co3O4 Catalyst for Water Oxidation.

The multi-redox mechanism involving multi-sites has great implications to dictate the catalytic water oxidation. Understanding the sequential dynamics of multi-steps in oxygen evolution reaction (OER) cycles on working catalysts is a highly important but challenging issue. Here, using quasi-operando transient absorption (TA) spectroscopy and a typical photosensitization strategy, we succeeded in resolving the sequential oxidation kinetics involving multi-active sites for water oxidation in OER catalytic cycle, with Co3O4 nanoparticles as model catalysts. When OER initiates from fast oxidation of surface Co2+ ions, both surface Co2+ and Co3+ ions are active sites of the multi-cobalt centers for water oxidation. In the sequential kinetics (Co2+ → Co3+ → Co4+), the key characteristic is fast oxidation and slow consumption for all the cobalt species. Due to this characteristic, the Co4+ intermediate distribution plays a determining role in OER activity and results in the slow overall OER kinetics. These insights shed light on the kinetic understanding of water oxidation on heterogeneous catalysts with multi-sites.

Strain-Dependent Porcine Circovirus Type 2 (PCV2) Entry and Replication in T-Lymphoblasts.

Porcine circovirus type 2 (PCV2) is the etiological agent of PCV2-associated diseases (PCVAD). PCV2 targets lymphoblasts, and pigs suffering from PCVAD display lymphocyte depletion in lymphoid tissues. PCV2 infection of lymphoblasts has not been studied. Here, the replication cycle of PCV2 (abortion strain 1121 and PMWS strain Stoon1010) in T-lymphoblasts was examined. The expression of Rep and Cap were found for both viral strains, while progeny virus was detected for Stoon1010 but not for 1121. PCV2 attached to 11-26% (1121-Stoon1010) of the T-lymphoblasts while 2.6-12.7% of cells showed virus internalization. Chondroitin sulfate (CS) was present on 25% of T-lymphoblasts, and colocalized with PCV2 on 31-32% of the PCV2+ cells. Enzymatic removal of CS reduced PCV2 infection. PCV2 infection was decreased by chlorpromazine, cytochalasin D and Clostridium difficile toxin B for both viral strains and by amiloride for 1121 but not for Stoon1010. Inhibiting either endosome acidification or serine proteases strongly reduced PCV2 infection. Three-dimensional analysis of Cap structure demonstrated a better Cap-nucleic acid affinity for Stoon1010 than for 1121. Taken together, PCV2 binds to T-lymphoblasts partially via CS, enters via clathrin-mediated endocytosis, and disassembles under functions of a pH-drop and serine proteases. Strain Stoon1010 displayed an enhanced viral binding, a specific receptor-mediated endocytosis, an increased Cap-nucleic acid affinity, and a more productive infection in T-lymphoblasts than 1121 did, indicating an evolution from 1121 to Stoon1010.

Changes on the viral capsid surface during the evolution of porcine circovirus type 2 (PCV2) from 2009 till 2018 may lead to a better receptor binding.

Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated diseases (PCVAD). Three major PCV2 genotypes (PCV2a, PCV2b, and PCV2d) have been identified globally. Despite their worldwide distribution, the prevalence and genetic evolution of PCV2 in Belgium has not previously been determined. In this study, 319 samples from animals suffering from diseases likely to be associated with PCV2 were collected from 2009 to 2018 and analysed by virus titration. The overall prevalence of PCV2 in PCVAD-suspected cases was 15.7 per cent (50/319). The phylogenetic analysis demonstrated that at least three genotypes (PCV2a, PCV2b, and PCV2d) circulated in Belgium from 2009 till 2018, and that PCV2 evolved from PCV2a to PCV2b and from PCV2d-1 to PCV2d-2. Sequence comparison among the forty-three PCV2 isolates showed that they had 89.7-100 per cent nucleotide-sequence and 88.5-100 per cent amino-acid-sequence identities. Three amino acid sites were under positive selection. Three-dimensional analysis of genotype-specific amino acids revealed that most of the mutations were on the outside of the cap protein with a few conserved mutations present on the inner side. Mutations toward more basic amino acids were found on the upper and tail parts of two connecting capsid proteins which form one big contact region, most probably involved in receptor binding. The lower part was relatively conserved. This polarity change together with the formation of an extruding part drive the virus to a more efficient GAG receptor binding. Taken together, these results showed a genotype shift from PCV2a to PCV2b and later on from PCV2d-1 to PCV2d-2, and a PCV2 evolution toward a better receptor binding capacity.

Gammaherpesvirus BoHV-4 infects bovine respiratory epithelial cells mainly at the basolateral side.

Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus that is widespread in cattle. However, only a few studies about the pathogenesis of BoHV-4 primary infection have been reported. In the present study, ex vivo models with bovine nasal and tracheal mucosa explants were used to study the cellular BoHV-4-host interactions. Infection was observed in nasal but not in tracheal epithelial cells. To find a possible correlation between the integrity and restricted infection of the respiratory epithelium, both nasal mucosal and tracheal explants were treated with EGTA, a drug that disrupts the intercellular junctions, before inoculation. The infection was analyzed based on the number of plaques, plaque latitude and number of infected single cells, as determined by immunofluorescence. BoHV-4 infection in nasal mucosal explants was enhanced upon opening the tight junctions with EGTA. Infection in tracheal explants was only found after treatment with EGTA. In addition, primary bovine respiratory epithelial cells (BREC) were isolated, grown at the air-liquid interface and infected either at the apical or basolateral side by BoHV-4. The results showed that BoHV-4 preferentially bound to and entered BREC at the basolateral surfaces of both nasal and tracheal epithelial cells. The percentage of BoHV-4 infection was significantly increased both from nasal and tracheal epithelial cells after treatment with EGTA, which indicates that the BoHV-4 receptor is mainly located at the basolateral surface of these cells. Thus, our findings demonstrate that integrity of the respiratory epithelium is crucial in the host's innate defense against primary BoHV-4 infections.

Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses.

BACKGROUND: Porcine Circovirus Type 2 (PCV2) is a pathogen that has the ability to cause often devastating disease manifestations in pig populations with major economic implications. How PCV2 establishes subclinical persistence and why certain individuals progress to lethal lymphoid depletion remain to be elucidated. RESULTS: Here we present PorSignDB, a gene signature database describing in vivo porcine tissue physiology that we generated from a large compendium of in vivo transcriptional profiles and that we subsequently leveraged for deciphering the distinct physiological states underlying PCV2-affected lymph nodes. This systems genomics approach indicated that subclinical PCV2 infections suppress a myeloid leukocyte mediated immune response. However, in contrast an inflammatory myeloid cell activation is promoted in PCV2 patients with clinical manifestations. Functional genomics further uncovered STAT3 as a druggable PCV2 host factor candidate. Moreover, IL-2 supplementation of primary lymphocytes enabled ex vivo study of PCV2 replication in its target cell, the lymphoblast. CONCLUSION: Our systematic dissection of the mechanistic basis of PCV2 reveals that subclinical and clinical PCV2 display two diametrically opposed immunotranscriptomic recalibrations that represent distinct physiological states in vivo, which suggests a paradigm shift in this field. Finally, our PorSignDB signature database is publicly available as a community resource ( http://www.vetvirology.ugent.be/PorSignDB/ , included in Gene Sets from Community Contributors http://software.broadinstitute.org/gsea/msigdb/contributed_genesets.jsp ) and provides systems biologists with a valuable tool for catalyzing studies of human and veterinary disease. Finally, a primary porcine lymphoblast cell culture system paves the way for unraveling the impact of host genetics on PCV2 replication.

Breed Differences in PCV2 Uptake and Disintegration in Porcine Monocytes.

Porcine circovirus type 2 (PCV2) is associated with various diseases which are designated as PCV2-associated diseases (PCVADs). Their severity varies among breeds. In the diseased pigs, virus is present in monocytes, without replication or full degradation. PCV2 entry and viral outcome in primary porcine monocytes and the role of monocytes in PCV2 genetic susceptibility have not been studied. Here, virus uptake and trafficking were analyzed and compared among purebreds Piétrain, Landrace and Large White and hybrid Piétrain × Topigs20. Viral capsids were rapidly internalized into monocytes, followed by a slow disintegration to a residual level. PCV2 uptake was decreased by chlorpromazine, cytochalasin D and dynasore. The internalized capsids followed the endosomal trafficking pathway, ending up in lysosomes. PCV2 genome was nicked by lysosomal DNase II in vitro, but persisted in monocytes in vivo. Monocytes from purebred Piétrain and the hybrid showed a higher level of PCV2 uptake and disintegration, compared to those from Landrace and Large White. In conclusion, PCV2 entry occurs via clathrin-mediated endocytosis. After entry, viral capsids are partially disintegrated, while viral genomes largely escape from the pathway to avoid degradation. The degree of PCV2 uptake and disintegration differ among pig breeds.

Preferential use of Siglec-1 or Siglec-10 by type 1 and type 2 PRRSV strains to infect PK15S1-CD163 and PK15S10-CD163 cells.

Cellular entry mediators define whether the cell is permissive to PRRSV infection. Porcine sialoadhesin (pSn, Siglec-1) and CD163 are main entry mediators facilitating infection of porcine macrophages by PRRSV. Recently, Siglec-10 was demonstrated to be an alternative receptor for PRRSV. To examine if virulence and pathogenicity of PRRSV strains could be correlated with the use of different Siglecs, a PK15 cell line recombinantly expressing Siglec-1 and CD163 (PK15S1-CD163) and a PK15 cell line recombinantly expressing Siglec-10 and CD163 (PK15S10-CD163) were used to compare the virus replication of 7 genotype 1 subtype 1 strains (G1s1), 2 genotype 1 subtype 3 (G1s3) strains and 5 genotype 2 (G2) strains. Some strains (08VA (G1s1), 13V117 (G1s1), 17V035 (G1s1), VR2332 (G2)) were poor virus producers (<104 TCID50/mL), while other strains (07V063 (G1s1), 13V091 (G1s1), Su1-Bel (G1s3), MN-184 (G2), Korea17 (G2) and SDSU-73 (G2)) easily grew up to ≥106 TCID50/mL. PK15S10-CD163 cells exhibited a higher efficiency in virus production per infected cell than the PK15S1-CD163 cells. The G1s1 strains LV and 07V063 infected more cells in the PK15S1-CD163, whereas the 94V360 and 08VA strains preferred PK15S10-CD163. The highly virulent G1s3 strains Lena and Su1-Bel showed a strong preference for PK15S1-CD163. The G2 strains MN-184, SDSU-73, Korea17 had a much higher infection rate in PK15S10-CD163, while the reference strain VR2332 and the NADC30 strain had a slight preference for PK15S1-CD163. Differences in receptor use may influence the outcome of a PRRSV infection in pigs and explain in part the virulence/pathogenicity of PRRSV strains.

Primary replication and invasion of the bovine gammaherpesvirus BoHV-4 in the genital mucosae.

Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus that is widespread in cattle. Ex vivo models with bovine genital tract mucosa explants were set up to study molecular/cellular BoHV-4-host interactions. Bovine posterior vagina, cervix and uterus body were collected from cows at two stages of the reproductive cycle for making mucosa explants. The BoHV-4 replication kinetics and characteristics within the three different mucosae of animals in the follicular and luteal phase were assessed by virus titration. The number of plaques, plaque latitude and number of infected cells were determined by immunofluorescence. BoHV-4 replicated in a productive way in all genital mucosal tissues. It infected single individual cells in both epithelium and lamina propria of the genital mucosae at 24 hours post-inoculation (hpi). Later, small BoHV-4 epithelial plaques were formed that did not spread through the basement membrane. 50% of the number of BoHV-4 infected cells were identified as cytokeratin+ and CD172a+ cells in the three parts of the genital tract at 24 hpi. Upon a direct injection of genital explants with BoHV-4, fibrocytes became infected, indicating that the unidentified 50% of the infected cells are most probably fibrocytes. In this study, in vivo-related in vitro genital tract models were successfully established and the early stage of the pathogenesis of a genital infection was clarified: BoHV-4 starts with a productive infection of epithelial cells in the reproductive tract, forming small foci followed by a non-productive infection of surveilling monocytic cells which help BoHV-4 to invade into deeper tissues.

PK-15 cells transfected with porcine CD163 by PiggyBac transposon system are susceptible to porcine reproductive and respiratory syndrome virus.

The PiggyBac (PB) transposon system is a non-viral DNA-transfer system in which a transposase directs integration of a PB transposon into a TTAA site in the genome. Transgenic expression of porcine CD163 is necessary and sufficient to confer non-permissive cells susceptible to infection with porcine reproductive and respiratory syndrome virus (PRRSV). Such permissive cells can be used as a tool for PRRSV cellular receptor and other studies. One of the problems in studying PRRSV is the lack of porcine cell lines. In this study, efficient transfection and expression of porcine CD163 in PK-15 cells by PB transposition was demonstrated. The stable PK-15CD163 cell line was used in PRRSV infection assays. The data indicated that the average PB transgene copy number per genome was approximately 10. In line with previous literature the integration of PB into the genome had a bias toward the TTAA chromosomal site. The PK-15CD163 cell line was susceptible to infection by different PRRSV strains and the virus grew to similar titers compared to the Marc-145 cell line. This simplification of PK-15CD163 cell line production will provide a valuable tool to facilitate PRRSV cellular receptor studies and to accelerate existing vectors for PK-15 cell-based gene transfer and expression.