A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa

Althaus, C. L.; Baggio, S.; Reichmuth, M. L.; Hodcroft, E. B.; Riou, J.; Neher, R. A.; Jacquerioz, F.; Spechbach, H.; Salamun, J.; Vetter, P.; Williamson, C.; Hsiao, N.-y.; Preiser, W.; Davies, M.-A.; Lessells, R. J.; de Olivera, T.; Kaiser, L.; Eckerle, I.

Several SARS-CoV-2 variants of concern (VOC) are spreading rapidly in different regions of the world. The underlying mechanisms behind their transmission advantage remain unclear. We measured viral load in 950 individuals and found that infections with variant Alpha exhibit a higher viral load and longer viral shedding compared to non-VOC. We then used a transmission model to analyze the spread of variant Alpha in Geneva, Switzerland, and variant Beta in South Africa. We estimated that Alpha is either associated with a 37% (95% compatibility interval, CI: 25-63%) increase in transmissibility or a 51% (95% CI: 32-80%) increase of the infectious duration, or a combination of the two mechanisms. Assuming 50% immune evasion for Beta, we estimated a 23% (95% CI: 10-37%) increase in transmissibility or a 38% (95% CI: 15-78%) increase of the infectious duration for this variant. Beta is expected to outgrow Alpha in regions where the level of naturally acquired immunity from previously circulating variants exceeds 20% to 40%. Close monitoring of Alpha and Beta in regions with different levels of immunity will help to anticipate the global spread of these and future variants.