A comparative analysis of virus-cell interactions for two early Brazilian SARS-CoV-2 variants

The ultrastructural details of SARS-CoV-2 morphogenesis and cell-to-cell spread, particularly during the later stages of infection, are still incompletely understood. In this study, we employed a multi-modal microscopy approach to characterise the late-stage infectious cell cycle of two early SARS-CoV-2 variants, A.2 and B.1.1.33, in a Vero E6 cell model. Using a combination of transmission and scanning electron microscopy, immunofluorescence, and RT-qPCR, we analysed viral-host cell interactions at key time points post-infection. Our analysis showed distinct subcellular localisations for the S and N proteins at 24 hpi, the high density of virions adhering to the host cell surface and the morphological indication that these adhered virions can directly mediate cell-cell fusion, leading to syncytium formation via a fusion-from-without (FFWO) mechanism between Vero E6 cells. Quantitative analysis of viral RNA revealed that the A.2 variant exhibited more robust replication kinetics than B.1.1.33. Furthermore, we provide direct ultrastructural indications for alternative viral propagation strategies beyond canonical exocytosis. These mechanisms, which may contribute to immune evasion, also offer new insights into viral pathogenesis relevant to the consequences of COVID-19.