Increased RNA virus population diversity improves adaptability

The replication machinery of most RNA viruses lacks proofreading mechanisms. As a result, RNA virus populations harbor a large amount of genetic diversity that confers them the ability to rapidly adapt to changes in their environment. In this work, we investigate whether further increasing the initial population diversity of a model RNA virus can improve adaptation to a single selection pressure, thermal inactivation. For this, we experimentally increased the diversity of coxsackievirus B3 (CVB3) populations across the capsid region. We then compared the ability of these high diversity CVB3 populations to achieve resistance to thermal inactivation relative to standard CVB3 populations in an experimental evolution setting. We find that viral populations with high diversity are better able to achieve resistance to thermal inactivation at both the temperature employed during experimental evolution as well as at a more extreme temperature. Moreover, we identify mutations in the CVB3 capsid that confer resistance to thermal inactivation, finding significant mutational epistasis. Our results indicate that even naturally diverse RNA virus populations can benefit from experimental augmentation of population diversity for optimal adaptation and support the use of such viral populations in directed evolution efforts that aim to select viruses with desired characteristics.This work was funded by a Grant from the Spanish Ministerio de Ciencia, Innovación y Universidades to RG (BFU2017-86094-R). RG holds the Ramón y Cajal fellowship from the Spanish Ministry of Economy and Competitiveness (RYC-2015-17517) and FM an FPI grant from the Spanish Ministerio de Ciencia, Innovación y Universidades (BES-2016-076677)

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

Neutralizing antibodies against Omicron BA.4/5 after COVID-19 vaccination in SARS-CoV-2 experienced versus naïve individuals in the general population

This work was supported in part by the European Commission NextGenerationEU fund, awarded to RG through CSIC's Global Health Platform (PTI Salud Global).Peer reviewe

Combinatorial analysis of deletion repair in SARS-CoV-2 variants of concern

Resumen del póster 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 spike protein of SARS-CoV-2 is a key determinant of viral fitness and immune evasion, and its N-terminal domain (NTD) is prone to mutations that may confer fitness advantages to the virus. Most variants of concern (VOCs), including Alpha, Delta, and Omicron, have harbored distinct NTD lineage-defining mutations. However, the relationship between genotype and the impact on viral transmission and viral phenotype is not yet fully understood.[Methods] We analyzed over 10 million SARS-CoV-2 genomes from GISAID to investigate the prevalence and estimate the transmission of different combinations of NTD mutations across the Alpha and the Omicron variants. Additionally, we characterized the viral phenotype of deletion repair events in a surrogate in vitro system, assessing their infectivity, fusogenicity, thermal stability, protein surface expression, and neutralization sensitivity.[Results] Some NTD mutations, such the repair of deleted amino acids at sites S:69/70 and S:144 in Alpha viruses, were associated with an increased transmission rate and higher frequency among older age groups. These deletion repairs were also detected in Omicron, but with different patterns and effects. For instance, the repair of deletion at site S:143/145 in Omicron enhanced viral fusogenicity and neutralization by sera from vaccinated individuals. However, the repair of the deletion at site S:69/70 reduced viral infectivity and did not affect these traits. The co-occurrence of both repairs resulted in reduced fusogenicity.[Conclusions] Our study reveals the complex interplay between NTD mutations, including those that lead to deletion repair, and viral success in SARS-CoV-2. This may have implications for viral transmission, immunity, and vaccine efficacy. Our findings improve our understanding of SARS- CoV-2 evolution, and provide insights for future research and public health interventions.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

Identification of the transcriptome and TCR repertoire against SARS-CoV-2 immunodominant peptides from long-term convalescent COVID-19 patients

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).N

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