Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera

Abstract

The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.

Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS-CoV-2 Infection in an Immunocompromised Patient

“…As of the causative forces behind SARS-CoV-2 evolution, little space has remained for speculations, as more and more studies point at the significance of endogenous immune response or exogenous antibodies administration (either monoclonal antibodies or convalescent plasma derivatives) in shaping genomic diversity and pushing viral evolution forward. These comprehend both in vitro studies, conducted by culturing virus to monoclonal antibody [ 7 ] or polyclonal sera [ 8 ] selective pressure or by monitoring virus evolution within immunocompromised patients with a diminished or abolished immune response, often compensated by immunological treatments (convalescent plasma or monoclonal antibodies). In this perspective, these studies have often highlighted how infection in immunosuppressed patients with haematological malignancies treated with B-cell-depleting therapies may lead to persistent and uncontrolled viral replication as the most recognized sequela of acute infection.…”

Omicron Sub-Lineage BA.5 and Recombinant XBB Evasion from Antibody Neutralisation in BNT162b2 Vaccine Recipients

“…Viral strains were isolated on cell culture from residual clinical specimens (nasopharyngeal swabs) provided to the Unit of Microbiology, Greater Romagna Area Hub Laboratory, Cesena, Italy, for routine diagnostic purposes and randomly selected for sequencing as part of a national project to monitor temporal trends of distribution and prevalence of SARS-CoV-2 viral variants in Italy, as previously described [ 8 ]. Each isolated strain was thereafter sequenced to reconfirm the lineage identification provided for the clinical specimen.…”

“…Sera samples were tested at a starting dilution of 1:10 and then further diluted 1:2 until 1:5120. Microneutralisation assay on cell culture was performed as previously described [ 8 ]. Each serum dilution was incubated on Vero E6 cell cultures with 100 TCID50/mL of the considered viral lineages.…”

“…The emergence of VOCs has been linked to increased seroprevalence, which has been hypothesised to be a key factor behind SARS-CoV-2 evolution, capable of exerting a selective pressure toward an augmented viral fitness over preceding variants in the context of an immune population. This hypothesis was later experimentally demonstrated in vitro [ 7 , 8 ].…”