Segmentation of viral genomes into multiple RNAs creates the potential for replication of incomplete viral genomes (IVGs). Here we use a single-cell approach to quantify influenza A virus IVGs and examine their fitness implications. We find that each segment of influenza A/Panama/2007/99 (H3N2) virus has a 58% probability of being replicated in a cell infected with a single virion. Theoretical methods predict that IVGs carry high costs in a well-mixed system, as 3.6 virions are required for replication of a full genome. Spatial structure is predicted to mitigate these costs, however, and experimental manipulations of spatial structure indicate that local spread facilitates complementation. A virus entirely dependent on co-infection was used to assess relevance of IVGs in vivo. This virus grows robustly in guinea pigs, but is less infectious and does not transmit. Thus, co-infection allows IVGs to contribute to within-host spread, but complete genomes may be critical for transmission.

Determining the duration of protective immunity requires quantifying the magnitude and rate of loss of antibodies to different virus and vaccine antigens. A key complication is heterogeneity in both the magnitude and decay rate of responses of different individuals to a given vaccine, as well as of a given individual to different vaccines. We analyzed longitudinal data on antibody titers in 45 individuals to characterize the extent of this heterogeneity and used models to determine how it affected the longevity of protective immunity to measles, rubella, vaccinia, tetanus, and diphtheria. Our analysis showed that the magnitude of responses in different individuals varied between 12- and 200-fold (95% coverage) depending on the antigen. Heterogeneity in the magnitude and decay rate contribute comparably to variation in the longevity of protective immunity between different individuals. We found that some individuals have, on average, slightly longer-lasting memory than others—on average, they have higher antibody levels with slower decay rates. We identified different patterns for the loss of protective levels of antibodies to different vaccine and virus antigens. Specifically, we found that for the first 25 to 50 years, virtually all individuals have protective antibody titers against diphtheria and tetanus, respectively, but about 10% of the population subsequently lose protective immunity per decade. In contrast, at the outset, not all individuals had protective titers against measles, rubella, and vaccinia. However, these antibody titers wane much more slowly, with a loss of protective immunity in only 1% to 3% of the population per decade. Our results highlight the importance of long-term longitudinal studies for estimating the duration of protective immunity and suggest both how vaccines might be improved and how boosting schedules might be reevaluated.

Animal groups frequently move in a highly organized manner, as represented by flocks of birds and schools of fish. Despite being an everyday occurrence, we do not fully understand how this works. In particular, what social interactions between animals give rise to the flock structures we observe? This question is often investigated using self-propelled particle models where particles represent the individual animals. These models differ in the social interactions used, individual particle properties, and various technical assumptions. One particular technical assumption relates to whether all particles update their headings and positions at exactly the same time (synchronous update) or not (asynchronous update). Here, we investigate the causal effects of this assumption in an attraction-only model and find that it has a dramatic impact. Polarized groups do not form when synchronous update is used, but are produced with asynchronous update, and this phenomenon is robust with respect to variation in particle displacements and inclusion of noise. Given that many important models have been implemented with synchronous update only, we speculate that our understanding of the social interactions on which they are based may be incomplete. Perhaps previously unobserved phenomena will emerge if other potentially more realistic update schemes are used.

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Dominant species often have disproportionately high abundance in restored communities compared to native remnants, which potentially could reduce the conservation value of restorations. Research is needed to determine how the abundance of dominant species in restoration plantings affects community assembly, species diversity, and ecosystem function. Most studies of dominant