High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1

Abstract

SARS-CoV-2 variants with undetermined properties have emerged intermittently throughout the COVID-19 pandemic. Some variants possess unique phenotypes and mutations which allow further characterization of viral evolution and spike functions. Around 1100 cases of the B.1.640.1 variant were reported in Africa and Europe between 2021 and 2022, before the expansion of Omicron. Here, we analyzed the biological properties of a B.1.640.1 isolate and its spike. Compared to the ancestral spike, B.1.640.1 carried 14 amino acid substitutions and deletions. B.1.640.1 escaped binding by some anti-NTD and -RBD monoclonal antibodies, and neutralization by sera from convalescent and vaccinated individuals. In cell lines, infection generated large syncytia and a high cytopathic effect. In primary airway cells, B.1.640.1 replicated less than Omicron BA.1 and triggered more syncytia and cell death than other variants. The B.1.640.1 spike was highly fusogenic when expressed alone. This was mediated by two poorly characterized and infrequent mutations located in the spike S2 domain, T859N and D936H. Altogether, our results highlight the cytopathy of a hyper-fusogenic SARS-CoV-2 variant, supplanted upon the emergence of Omicron BA.1.ImportanceOur results highlight the plasticity of SARS-CoV-2 spike to generate highly fusogenic and cytopathic strains with the causative mutations being uncharacterized in previous variants. We describe mechanisms regulating the formation of syncytia and the subsequent consequences in cell lines and a primary culture model, which are poorly understood.

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion

“…S7 ). As previously reported by us and others, the ancestral D614G and Delta strains were more fusogenic than the early Omicron BA.1 and BA.4/5 variants 35 , 39 , 43 , 44 . BQ.1.1 and XBB.1.5/XBB.1.9.1 spikes partially regained fusogenicity, whereas XBB.1.16.1 and the more recent EG.5.1.1 and BA.2.86.1 spikes displayed a lower fusogenic potential than BA.4/5 spike (Fig.…”

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion

“…The cells were infected with each variant at a similar low viral inoculum (100 µl of viral stocks containing 2x10 3 infectious units/ml). As previously reported (Mlcochova et al ., 2021; Willett et al, 2022) (Suzuki et al ., 2022) (Bolland et al ., 2023), BA.1 replicated faster than Delta and D614G, as quantified by viral RNA release monitored every day up to 4 days pi (Fig. 4a, b).…”

“…SARS-CoV-2 spikes (from D614G, Delta, BA.1, BA.4/5, BQ1.1, XBB.1.5/9, XBB.1.16, EG.5.1, BA.2.86 isolated) were human codon-optimized and produced in silico (GeneArt, Thermo Fisher Scientific) as described (Bolland et al ., 2023; Buchrieser et al ., 2020). Spike sequences were cloned into a phCMV backbone (GenBank: AJ318514) using Gateway cloning (Thermo Fisher Scientific) or restriction enzyme digestion followed by ligation with T4 DNA ligase (New England Biolabs).…”

“…Spike sequences were cloned into a phCMV backbone (GenBank: AJ318514) using Gateway cloning (Thermo Fisher Scientific) or restriction enzyme digestion followed by ligation with T4 DNA ligase (New England Biolabs). The pQCXIP-Empty plasmid was used as a negative control (Bolland et al ., 2023; Buchrieser et al ., 2020). All plasmids were sequenced by the Eurofins Genomics TubeSeq service.…”

“…To assess the fusion of the respective spike constructs, syncytia formation assays were performed as described (Bolland et al ., 2023; Buchrieser et al ., 2020). Briefly, 293T-GFP-11 cells were transfected in suspension at 37°C for 30 minutes.…”