Of course, as shown by in vitro experiments of deep mutational scanning (Starr et al., 2020), some mutations have strong effects and many decrease the affinity of the receptor-binding domain (BBD) of the virus spike protein to the human ACE2 receptor so much that they are likely detrimental. 2 FROM NEUTRAL MUTANTS TO ‘VARIANTS’įor nearly a year, there was little clear evidence of phenotypic variations that could be linked to virus genetics. Finally, we present some hypotheses for future evolutionary dynamics. We then explain why some predict the virus population will evolve towards avirulence, before explaining why current trends do not follow this expectation. We first present the evidence for the evolution of SARS-CoV-2 virulence. Dots show the median values and shaded areas the 95% confidence intervals In panel b, counterfactual mean IFRs were obtained by weighting the age-stratified IFR data from O’Driscoll et al. ( 2020) by the relative frequencies of age classes from annual age pyramid data compiled by United Nations ( 2019). Individual SARS-CoV-2 infection fatality ratio (IFR) as a function of age (a) and population average IFRs in 8 countries according to their demography since 1950 (b). Furthermore, host immunity introduces another dimension of variation that needs to be accounted for when estimating the IFR. This implies that the age pyramid of a country shapes the IFR, even if the latter is assumed not to depend on nondemographic conditions, for example health care (Figure 1b). At the individual level, it is the metric that has the most direct meaning to a wide audience however, care must be taken at the population level because IFR strongly varies with age (O’Driscoll et al., 2020 Verity et al., 2020) (Figure 1a). In the following, unless stated otherwise and to simplify the reasoning, we will consider the infection fatality ratio (IFR), which is the proportion of infected hosts that die from the infection, to be a proxy of virulence. Overall, the choice of the most appropriate trait to measure to study virulence evolution should maximize measurement practicality and public health importance, but also, most importantly, trait values should affect infection fitness (Alizon & Michalakis, 2015). Contrarily to the other definitions, it has an evolutionary dimension because it involves the notion of fitness, which is notoriously difficult to measure. Finally, virulence is defined as the decrease in host fitness due to the infection (Read, 1994). Pathogenicity can be defined at the cellular level and characterizes some of the harmful interactions between the virus and host cells (Isenberg, 1988). However, it is important to stress that this trait varies depending on access to healthcare infrastructure or treatment availability. For SARS-CoV-2, lethality was rapidly shown to be 10 times that of seasonal influenza and also to strongly depend on age (Verity et al., 2020). Lethality, or fatality ratio, is the probability for an infected host to die in a given context. The others are defined at the level of an individual. Among the four, mortality is the only aspect that refers to the population (Bonita et al., 2006). When it comes to the negative effects of infectious diseases on their hosts, a set of related but distinct notions can be found in the literature: mortality, lethality, pathogenicity and virulence.
Here, we focus on the phenotypic evolution of infection life-history traits and, in particular, on virulence. 2020) and on its genetic evolution since then (van Dorp, Acman, et al., 2020 Worobey et al., 2020). Many reviews have been written on the evolutionary origin of the virus (Andersen et al., 2020 Boni et al. Its most likely origin is believed to be from viruses currently circulating in bat populations (World Health Organization, 2021c). The causative agent was rapidly identified as a novel coronavirus and named SARS-CoV-2 (Gorbalenya et al., 2020). In April 2021, the pandemic was still out of control in many countries all over the world. The year 2019 witnessed the emergence of one of the largest and fastest spreading pandemics ever, which had caused more than 80 million infections and claimed more than 1.8 million human lives throughout the world by the end of 2020 (World Health Organization, 2021b).
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