SARS-CoV-2 antibodies and COVID-19 severity

Background: The involvement of SARS-CoV-2 antibodies in mediating immunopathogenetic events in COVID-19 patients has been suggested. By using several experimental approaches, we investigated the potential association between SARS-CoV-2 IgGs recognizing the spike (S) protein receptor-binding domain (RBD), neutralizing antibodies (NtAb) targeting S, and COVID-19 severity. Patients and Methods: This unicenter, retrospective, observational study included 51 hospitalized patients (24 at the intensive care unit; ICU). A total of 93 sera from these patients collected at different time points from the onset of symptoms were analyzed. SARS-CoV-2 RBD IgGs were quantitated by ELISA and NtAb50 titers were measured in a GFP reporter-based pseudotyped virus platform. Demographic and clinical data, complete blood counts, as well as serum levels of ferritin, Dimer-D, C reactive protein (CRP), lactose dehydrogenase (LDH), and interleukin-6 (IL-6) were retrieved from clinical charts. Results: The overall correlation between levels of both antibody measurements was good (Rho=0.79; P=00.1). The percentage of patients who exhibited high NtAb50 titers (≥160) was similar (P=0.20) in ICU (79%) and non-ICU (60%) patients. Four ICU patients died; two of these achieved NtAb50 titers ≥1/160 while the other two exhibited a 1/80 titer. Very weak (Rho=>0.0-0.2-<0.4) correlations were observed between anti-RBD IgGs, NtAb50, and serum levels pro-inflammatory biomarkers. Conclusions: The data presented herein do not support an association between SARS-CoV-2 RBD IgG or NtAb50 levels and COVID-19 severityThis work was supported by a grant from the Generalitat Valenciana (Covid_19-SCI) to RG, and a grant by Valencian Government grant DIFEDER/2018/056 to JRD.N

Un ataque combinado químico, virológico, biofísico y estructural hace posible la obtención de nuevos inhibidores de entrada celular de SARS-CoV-2 y la caracterización de su mecanismo de inhibición

Resumen del trabajo presentado al 45º Congreso de la Sociedad Española de Bioquímica y Biología Molecular (SEBBM), celebrado en Zaragoza del 5 al 8 de septiembre de 2023.IBV-COVID19 Pipeline: C.Espinosa, N.Gougeard, M.P.Hernández-Sierra, A.Rubio-del-Campo, R.Ruiz-Partida, L.Villamayor.El virus SARS-CoV-2 causa el COVID-19 al infectar las células a través de la interacción de la proteína de su espícula (S) con el receptor celular enzima convertidora de angiotensina 2 (ACE2). Para buscar inhibidores de este paso clave en la infección viral, examinamos una biblioteca interna (IQM-CSIC, Madrid) de compuestos multivalentes derivados de triptófano, primero usando pseudopartículas de Virus de Estomatits Vesicular que expresaban S (I2SysBio, UV y CSIC, Valencia), identificando un compuesto como potente inhibidor de entrada no citotóxico. La optimización química (IQM-CSIC) generó otros dos potentes inhibidores de entrada no citotóxicos que, como 2, también inhibieron la entrada celular de SARS-CoV-2 genuino (I2SysBio). Los estudios con proteínas recombinantes puras (IBV-CSIC, Valencia) usando termofluor y termoforesis de microescala revelaron la unión de estos compuestos a S, y a su dominio de unión al receptor producido separadamente, probando interferencia con la interacción con ACE2. La criomicroscopía electrónica de S (IBV-CSIC), libre o unido al compuesto activo, arrojó luz sobre los mecanismos de inhibición por estos compuestos de la entrada viral a la célula. Esta actividad triinstitucional combinada ha identificado y caracterizado una nueva clase de inhibidores de entrada de SARS-CoV-2 de claro potencial preventivo o terapéutico de COVID-19.ECNextGeneration EUfund 2020/2094 de CSIC/PTI Salud Global; Crue/CSIC/Santander Fondo Supera Covid-19;CSIC-COV19-082; CIBERER-ISCIIICOV20/00437; Covid19-SCI/GValenciana (RG);PID2020- 120322RB-C21 (VR) y PID2020-116880GB-I00 (JLLl) Agenc. Estat Investig.Peer reviewe

Aptamer-capped nanoporous anodic alumina for SARS-CoV-2 spike protein detection

The COVID-19 pandemic, which began in 2019, has highlighted the importance of testing and tracking infected individuals as a means of mitigating the spread of the virus. In this context, the development of sensitive and rapid methods for the detection of SARS-CoV-2, the virus responsible for COVID-19, is crucial. Herein, a biosensor based on oligonucleotide-gated nanomaterials for the specific detection of SARS-CoV-2 spike protein is presented. The sensing system consists of a nanoporous anodic alumina disk loaded with the fluorescent indicator rhodamine B and capped with a DNA aptamer that selectively binds the SARS-CoV-2 spike protein. The system is initially evaluated using pseudotype virus systems based on vesicular stomatitis virus carrying different SARS-CoV-2 S-proteins on their surface. When the pseudotype virus is present, the cap of the solid is selectively removed, triggering the release of the dye from the pore voids to the medium. The nanodevice demonstrated its ability to detect pseudotype virus concentrations as low as 7.5·103 PFU mL. In addition, the nanodevice is tested on nasopharyngeal samples from individuals suspected of having COVID-19.This study was supported by the Spanish Government (projects PID2021-126304OB-C41, and PID2021-122875OB-100 (MCUI/AEI/FEDER, UE)), the Generalitat Valenciana (project no.2 RD 180/2020, CIPROM/2021/007), Supera COVID-19 Fund (DIACOVID project), the Universitat Politècnica de València−Instituto de Investigación Sanitaria La Fe (IIS-LaFe) (SARS-COV-2-SEEKER and VISION-COV projects), and by the European Commission –NextGenerationEU, through CSIC's Global Health Platform (PTI Salud Global) to Ron Geller. The project leading to this application has received funding from the European Union's Horizon EUROPE research and innovation programme under grant agreement No 101093042. Isabel Caballos thanks the Instituto de Salud Carlos III for her predoctoral fellowship (IFI21/00008). Alba López-Palacios thanks the Ministerio de Universidades for her predoctoral grant (FPU20/05297). Ron Geller holds a Ramon y Cajal fellowship from the Spanish Ministerio de Economía y Competitividad (RYC-2015-17517).Peer reviewe

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness

Preservation of anti-SARS-CoV-2 neutralising antibodies in convalescent plasma after pathogen reduction with methylene blue and visible light

Background - COVID-19 convalescent plasma (CCP) is an experimental treatment against SARS-CoV-2. Although there has so far been no evidence of transmission through transfusion, pathogen reduction technologies (PRT) have been applied to CCP to mitigate risk of infectious disease. This study aims to assess the impact of methylene blue (MB) plus visible light PRT on the virus-neutralising activity of the specific antibodies against SARS-CoV-2. Material and methods - Thirty-five plasma doses collected by plasmapheresis from COVID-19 convalescent donors were subjected to MB plus visible light PRT. Anti-SARS-CoV-2 RBD S1 epitope IgGs antibodies were quantified by ELISA. Titres of SARS-CoV-2 neutralising antibodies (NtAbs) were measured before and after the PRT process. A Spearman's correlation was run to determine the relationship between antibody neutralisation ability and SARS-CoV-2 IgG ELISA ratio. Pre- and post-inactivation neutralising antibody titres were evaluated using a Wilcoxon test. Results - The plasma pathogen reduction procedure did not diminish NtAbS titres and so did not cause a change in the viral neutralisation capacity of CCP. There was a strong correlation between pre-and post-PRT NtAbs and anti-SARS-CoV-2 IgGs titres. Discussion - Our results showed PRT with MB did not impair the CCP passive immunity preserving its potential therapeutic potency. Therefore, PRT of CCP should be recommended to mitigate the risk for transmission of transfusionassociated infectious disease. There is a good correlation between SARS-CoV-2 IgG titres determined by ELISA and the neutralising capacity. This allows blood centres to select CCP donors based on IgG ELISA titres avoiding the much more labour-intensive laboratory processes for determining neutralising antibodies.Peer reviewe

New findings with the IBV decoy for cell entry inhibition of SARS-CoV-2, and unique structural data for soluble dimeric ACE2 bound to the viral S trimer

Resumen del trabajo presentado a las III Jornadas Científicas PTI+ Salud Global, celebradas en el Centro de Ciencias Humanas y Sociales (CCHS), CSIC (Madrid) del 20 al 22 de noviembre de 2023.[Background] The SARS-CoV-2 spike protein (S) mediates the interaction of the virus with cellular membrane receptor (angiotensin-converting enzyme 2, ACE2). In previous PTI meetings, we reported heterologous production in vitro of the ACE2 extracellular domains modified by site-directed mutagenesis to increase its affinity for the S protein, to enable it to be used as viral entry inhibitor (decoy) by competing with the membrane-bound cellular receptor. We now test the value of these decoys for: 1) binding to S variants that emerged during the evolution of the pandemic in viral lineages of concern; and 2) inhibiting experimental cellular infection by pseudotyped virus expressing these S variants. Cellular syncytia formation has been described in several organs as a manifestation of severe COVID-19, and likely has pathogenic impact. To test further our decoys’ effectiveness, we studied their impact on cellular syncytia formation within an experimental in vitro cell culture model. Searching for effective decoys, we produced monomeric and dimeric ACE2 proteins, depending on the respective absence/presence of the extracellular collectrin domain. Interestingly, there are no reported structures of dimeric soluble ACE2 bound to the S protein. After extensive knowledge-guided trial-and-error, we succeeded in visualizing by cryo-electron microscopy (cryoEM) this interaction (~7-Å-resolution), and in understanding the challenges inherent in determining such a complex structural organization.[Methods] 1) Recombinant production and purification of the monomeric or dimeric ACE2, their decoys the receptor binding domain (RBD) and the S protein variants of interest. We used baculovirus/insect cells to produce ACE2s and RBDs, and human Expi293F cells for the S proteins. 2) Biolayer interferometry for assessing protein-protein interactions; 3) Use of a model system for monitoring viral cellular infection and its inhibition by decoys. We used a pseudotyped engineered vesicular stomatitis virus expressing and exposing at its surface the desired S protein variant, to infect appropriate SARS-CoV-2-susceptible mammalian cells; 4) Single-particle cryoEM; 5) Syncytia formation testing using an engineered cultured cell system in which heterologous surface expression of the S protein in one cell type induces syncytium formation in other cells expressing membrane-bound ACE2.[Results] Our decoys proved highly effective in preventing cellular infection by pseudotyped virus expressing the S proteins of different SARS-CoV-2 variants of concern. Biophysical results have validated the maintained interaction between the decoy and the various S protein variants. When introduced into the cellular model system for syncytia formation, the decoys proved capable of decreasing such formation. Puzzlingly, the monomeric decoy was more effective than the dimeric one. The cryoEM images unveiled an ACE2 dimer configuration, where the subunits, resembling the previously reported monomer, were oriented at an angle of >60º, in which the vortex was the interlinked collectrin domains. Both catalytic domains engage with a single RBD of one subunit from different S trimers. The formation of a network at high stoichiometries of both components poses a challenge for structure determination by cryoEM.[Conclusions] Unlike therapeutic antibodies, which proved ineffective on variants not initially used for their production, our decoys should be effective in preventing infection by all widely widespread SARS-CoV-2 variants.Peer reviewe

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has now reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.This research work was supported by the European Commission–NextGenerationEU through the CSIC Global Health Platform. Additionally, authors would like to acknowledge economic support from the Spanish Ministry of Science and Innovation through Grants: PID2019-104757RB-I00 funded by MCIN/AEI/ 10.13039/501100011033, RTI2018-094399-A-I00, and “ERDF A way of making Europe”, by the “European Union”, Grant SEV 2017-0712 funded by MCIN/AEI /10.13039/501100011033, the “Comunidad Autónoma de Madrid" through Grant: S2017/BMD3817, and the European Union (EU) and Horizon 2020 through grants: Marie-Curie Fellowship EnLaCES (MSCA IF 2020, Proposal: 101024130) (to JK), HighResCells (ERC - 2018 - SyG, Proposal: 810057), and iNEXT-Discovery (Proposal: 871037). AM, VR, JB and JLL are funded by CIBERER-ISCIII (proposal: COV20/00437), Fondo Supera COVID-19 (proposal: CSICCOVID19-082), Banco Santander (Proposal: BlockAce), and CSIC PTI Salud Global (Proposal: 202080E110). VR is funded by the Spanish Ministry of Science and Innovation through Grant PID2020-120322RB-C21. IC is funded by project PID2019-104477RB-100, Fondo COVID COV20/00140 and ERC CoG 101001038. MC is funded by the RyC program from the Spanish Ministry of Science and Innovation, the Generalitat Valenciana (SEJI/2019/011).N

The role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

Resumen del trabajo presentado a las II Jornadas Científicas PTI + Salud Global, celebradas los días 5 y 6 de octubre de 2022 en el Auditorio Santiago Grisolía de Valencia (España).Peer reviewe

Evolutionary genomics of SARS-CoV-2: keys for viral success

Resumen del trabajo presentado al 44º Congreso de la Sociedad Española de Bioquímica y Biología Molecular, celebrado en Málaga del 6 al 9 de septiembre de 2022.Peer reviewe

Genomic surveillance and impact of SARS-CoV-2 mutations

Resumen del póster presentado a las II Jornadas Científicas PTI + Salud Global, celebradas los días 5 y 6 de octubre de 2022 en el Auditorio Santiago Grisolía de Valencia (España).Peer reviewe