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

Adoptive transfer of ex vivo expanded SARS‐CoV‐2‐specific cytotoxic lymphocytes: A viable strategy for COVID‐19 immunosuppressed patients?

Cellular and humoral response to acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infections is on focus of research. We evaluate herein the feasibility of expanding virus‐specific T cells (VST) against SARS‐CoV‐2 ex vivo through a standard protocol proven effective for other viruses. The experiment was performed in three different donors' scenarios: (a) SARS‐CoV‐2 asymptomatic infection/negative serology, (b) SARS‐CoV‐2 symptomatic infection/positive serology, and (c) no history of SARS‐CoV‐2 infection/negative serology. We were able to obtain an expanded VST product from donors 1 and 2 (1.6x and 1.8x increase of baseline VST count, respectively) consisting in CD3 + cells (80.3% and 62.7%, respectively) with CD4 + dominance (60% in both donors). Higher numbers of VST were obtained from the donor 2 as compared to donor 1. T‐cell clonality test showed oligoclonal reproducible peaks on a polyclonal background for both donors. In contrast, VST could be neither expanded nor primed in a donor without evidence of prior infection. This proof‐of‐concept study supports the feasibility of expanding ex vivo SARS‐CoV‐2‐specific VST from blood of convalescent donors. The results raise the question of whether the selection of seropositive donors may be a strategy to obtain cell lines enriched in their SARS‐CoV‐2‐specificity for future adoptive transfer to immunosuppressed patients.The neutralization antibody assay was supported by Valencian government grant Covid_19-SCI as well as the Spanish National Research Council grants CSIC-COV19-082 and CSIC-COV-19-104 to RG.Peer reviewe