Fig 1.
Three working hypotheses represent the range of expert opinion about the dynamics of emerging viruses within bats. (A) Following an initial acute infection, the virus clears completely and bats remain refractory to infection (susceptible-infectious-recovered [SIR]). (B) The virus clears completely, but the bats’ immune response wanes over time, allowing individuals to be reinfected (susceptible-infectious-recovered-susceptible [SIRS]). (C) Following the acute phase of infection, a chronic infection remains, or the infection is latent and then reactivated (susceptible-infectious-latent-infectious [SILI]).
Fig 2.
Drivers of disease dynamics within hosts, and within populations, given persistent infections with latency and reactivation (SILI dynamics) or immunizing infections with or without waning immunity (SIR or SIRS dynamics).
A common factor among scenarios is seasonal forcing, which occurs through birth pulses, seasonal transmission, or periods of environmental or physiological stress. These factors affect SILI dynamics through reactivation and SIR or SIRS dynamics through transmission.
Table 1.
Criteria to differentiate Susceptible-Infectious-Recovered (SIR) dynamics, Susceptible-Infectious-Recovered-Susceptible (SIRS) dynamics, and Susceptible-Infectious-Latent- Infectious (SILI) dynamics in bats; strategies to predict the likelihood of spillover or to minimize the likelihood of spillover for viruses with each type of dynamics; and research that would improve our understanding of bat virus dynamics given each scenario†.
Table 2.
Summary of results from experimental inoculation of bats with emerging bat viruses (see S1 Table for more details and references).
Fig 3.
Different within- and between-host mechanisms are hypothesized to produce different evolutionary patterns of viral diversity at the level of populations and individuals.
Different shapes represent different viral strains within a population and different colors within a shape reflect variation within strains that have a recent common ancestor. (A) In the case of SIR/SIRS dynamics, acute infections are reintroduced and then cleared at the population level between each pulse. At each point in time, the pathogen within individuals in the population either has the same genotype (e.g., blue circles at pulse 1, red squares at pulse 2) or has closely related genotypes with a common ancestor (matching shape but different color). (B) In the case of SILI dynamics, individuals remain infected over time. Genetic diversity is determined in part by within-host viral evolution. Therefore, genotypes are likely to differ among individuals (many unique shape and color combinations, with some consistency over time). (C, D) Illustrative phylogenies of the virus populations across pulses. (C) In a scenario of viral extinction and reintroduction, all strains at a given pulse are closely related and have a recent common ancestor. (D) Divergent strains (different symbols) may be detectable within pulses, and distinctive strains are maintained across pulses. The hexagon and pentagon represent unsampled viral diversity present in the population.