Mathematical modelling of SARS-CoV-2 infection of human and animal host cells reveals differences in the infection rates and delays in viral particle production by infected cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV -2), a causative agent of COVID-19 disease, poses a significant threat to public health. Since its outbreak in December 2019, Wuhan, China, extensive collection of diverse data from cell culture and animal infections as well as population level data from an ongoing pandemic, has been vital in assessing strategies to battle its spread. Mathematical modelling plays a key role in quantifying determinants that drive virus infection dynamics, especially those relevant for epidemiological investigations and predictions as well as for proposing efficient mitigation strategies. We utilized a simple mathematical model to describe and explain experimental results on viral replication cycle kinetics during SARS-CoV-2 infection of animal and human derived cell lines, green monkey kidney cells, Vero-E6, and human lung epithelium cells, A549-ACE2, respectively. We conducted cell infections using two distinct initial viral concentrations and quantified viral loads over time. We then fitted the model to our experimental data and quantified the viral parameters. We showed that such cellular tropism generates significant differences in the infection rates and incubation times of SARS-CoV-2, that is, the times to the first release of newly synthesised viral progeny by SARS-CoV-2-infected cells. Specifically, the rate at which A549-ACE2 cells were infected by SARS-CoV-2 was 15 times lower than that in the case of Vero-E6 cell infection and the duration of latent phase of A549-ACE2 cells was 1.6 times longer than that of Vero-E6 cells. On the other hand, we found no statistically significant differences in other viral parameters, such as viral production rate or infected cell death rate. Since in vitro infection assays represent the first stage in the development of antiviral treatments against SARS-CoV-2, discrepancies in the viral parameter values across different cell hosts have to be identified and quantified to better target vaccine and antiviral research.

Defective viral genomes from chikungunya virus are broad-spectrum antivirals and prevent virus dissemination in mosquitoes

Defective viral genomes (DVGs) are truncated and/or rearranged viral genomes produced during virus replication. Described in many RNA virus families, some of them have interfering activity on their parental virus and/or strong immunostimulatory potential, and are being considered in antiviral approaches. Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes spp. that infected millions of humans in the last 15 years. Here, we describe the DVGs arising during CHIKV infection in vitro in mammalian and mosquito cells, and in vivo in experimentally infected Aedes aegypti mosquitoes. We combined experimental and computational approaches to select DVG candidates most likely to have inhibitory activity and showed that, indeed, they strongly interfere with CHIKV replication both in mammalian and mosquito cells. We further demonstrated that some DVGs present broad-spectrum activity, inhibiting several CHIKV strains and other alphaviruses. Finally, we showed that pre-treating Aedes aegypti with DVGs prevented viral dissemination in vivo.

Evolution of mate-finding Allee effect in prey

The search for mates is often accompanied with conspicuous behaviour or morphology that can be exploited by predators. Here we explore the evolutionary consequences of a trade-off that arises naturally between mate acquisition and risk of predation and study evolution of the rate at which male prey search for mates in a population subject to a mate-finding Allee effect and exposed to either generalist or specialist predators. Since we show that the mate search rate determines the strength of the mate-finding Allee effect, we can alternatively view this as evolution of the mate-finding Allee effect in prey. We contrast two different life histories and find that, predominantly, male prey either evolve towards the maximal mate search rate yielding the weakest possible mate-finding Allee effect (thus showing no adaptive response in mating behaviour to predation risk) or evolutionary bi-stability occurs. In the latter case, males evolve a relatively low mate search rate (hence a relatively strong mate-finding Allee effect, interpreted as an adaptive response of male prey to predation) when initially slow or the maximal mate search rate when initially fast. Disruptive selection does not occur in populations exposed to generalist predators but is possible when predators are specialists. The dimorphic phase, in which fast and conspicuous male prey coexist with slow and cryptic ones, is however but a transient in evolutionary dynamics as one branch goes extinct while the other evolves towards the maximal mate search rate.

Density-dependent selection on mate search and evolution of Allee effects

Sexually reproducing organisms require males and females to find each other. Increased difficulty of females finding mates as male density declines is the most frequently reported mechanism of Allee effects in animals. Evolving more effective mate search may alleviate Allee effects, but may depend on density regimes a population experiences. In particular, high-density populations may evolve mechanisms that induce Allee effects which become detrimental when populations are reduced and maintained at a low density. We develop an individual-based, eco-genetic model to study how mating systems and fitness trade-offs interact with changes in population density to drive evolution of the rate at which males or females search for mates. Finite mate search rate triggers Allee effects in our model and we explore how these Allee effects respond to such evolution. We allow a population to adapt to several population density regimes and examine whether high-density populations are likely to reverse adaptations attained at low densities. We find density-dependent selection in most of scenarios, leading to search rates that result in lower Allee thresholds in populations kept at lower densities. This mainly occurs when fecundity costs are imposed on mate search, and provides an explanation for why Allee effects are often observed in anthropogenically rare species. Optimizing selection, where the attained trait value minimizes the Allee threshold independent of population density, depended on the trade-off between search and survival, combined with monogamy when females were searching. Other scenarios led to runaway selection on the mate search rate, including evolutionary suicide. Trade-offs involved in mate search may thus be crucial to determining how density influences the evolution of Allee effects. Previous studies did not examine evolution of a trait related to the strength of Allee effects under density variation. We emphasize the crucial role that mating systems, fitness trade-offs and the evolving sex have in determining the density threshold for population persistence, in particular since evolution need not always take the Allee threshold to its minimum value.

Evolution of early male-killing in horizontally transmitted parasites

Early male-killing (MK) bacteria are vertically transmitted reproductive parasites which kill male offspring that inherit them. Whereas their incidence is well documented, characteristics allowing originally non-MK bacteria to gradually evolve MK ability remain unclear. We show that horizontal transmission is a mechanism enabling vertically transmitted bacteria to evolve fully efficient MK under a wide range of host and parasite characteristics, especially when the efficacy of vertical transmission is high. We also show that an almost 100% vertically transmitted and 100% effective male-killer may evolve from a purely horizontally transmitted non-MK ancestor, and that a 100% efficient male-killer can form a stable coexistence only with a non-MK bacterial strain. Our findings are in line with the empirical evidence on current MK bacteria, explain their high efficacy in killing infected male embryos and their variability within and across insect taxa, and suggest that they may have evolved independently in phylogenetically distinct species.