The role of booster vaccination and ongoing viral evolution in seasonal circulation of SARS-CoV-2.

Periodic resurgences of COVID-19 in the coming years can be expected, while public health interventions may be able to reduce their intensity. We used a transmission model to assess how the use of booster doses and non-pharmaceutical interventions (NPIs) amid ongoing pathogen evolution might influence future transmission waves. We find that incidence is likely to increase as NPIs relax, with a second seasonally driven surge expected in autumn 2022. However, booster doses can greatly reduce the intensity of both waves and reduce cumulative deaths by 20% between 7 January 2022 and 7 January 2023. Reintroducing NPIs during the autumn as incidence begins to increase again could also be impactful. Combining boosters and NPIs results in a 30% decrease in cumulative deaths, with potential for greater impacts if variant-adapted boosters are used. Reintroducing these NPIs in autumn 2022 as transmission rates increase provides similar benefits to sustaining NPIs indefinitely (307 000 deaths with indefinite NPIs and boosters compared with 304 000 deaths with transient NPIs and boosters). If novel variants with increased transmissibility or immune escape emerge, deaths will be higher, but vaccination and NPIs are expected to remain effective tools to decrease both cumulative and peak health system burden, providing proportionally similar relative impacts.

The ecosystem services of animal microbiomes.

Microbiologists often evaluate microbial community dynamics by formulating functional hypotheses based on ecological processes. Indeed, many of the methods and terms currently used to describe animal microbiomes derive from ecology and evolutionary biology. As our understanding of the composition and functional dynamics of "the microbiome" grows, we increasingly refer to the host as an ecosystem within which microbial processes play out. Even so, an ecosystem service framework that extends to the context of the host has thus far been lacking. Here, we argue that ecosystem services are a useful framework with which to consider the value of microbes to their hosts. We discuss those "microbiome services" in the specific context of the mammalian gut, providing a context from which to develop new hypotheses and to evaluate microbial functions in future studies and novel systems.

The impact of climate on the disease dynamics of cholera.

The size of infectious disease outbreaks frequently depends on climate influences as well as on the level of immunity in the host population. This is particularly the case with vectorborne and waterborne diseases, for which pathogen transmissibility critically depends on ecological conditions. Here, a mathematical model that was applied to the bacterium Vibrio cholerae to understand its disease dynamics in Bangladesh is reviewed. When interfaced with empirical case data on cholera, the model shows that climate plays a pivotal role in modulating the size of outbreaks, with local, regional, and global indices of climate variability showing a link with pathogen transmissibility. Furthermore, the incidence of cholera may occasionally be surprisingly low at times when climate seems to favour cholera transmission.

Shifting patterns: malaria dynamics and rainfall variability in an African highland.

The long-term patterns of malaria in the East African highlands typically involve not only a general upward trend in cases but also a dramatic increase in the size of epidemic outbreaks. The role of climate variability in driving epidemic cycles at interannual time scales remains controversial, in part because it has been seen as conflicting with the alternative explanation of purely endogenous cycles exclusively generated by the nonlinear dynamics of the disease. We analyse a long temporal record of monthly cases from 1970 to 2003 in a highland of western Kenya with both a time-series epidemiological model (time-series susceptible-infected-recovered) and a statistical approach specifically developed for non-stationary patterns. Results show that multiyear cycles of malaria outbreaks appear in the 1980s, concomitant with the timing of a regime shift in the dynamics of cases; the cycles become more pronounced in the 1990s, when the coupling between disease and rainfall is also stronger as the variance of rainfall increased at the frequencies of coupling. Disease dynamics and climate forcing play complementary and interacting roles at different temporal scales. Thus, these mechanisms should not be viewed as alternative and their interaction needs to be integrated in the development of future predictive models.

Live attenuated HIV vaccines: predicting the tradeoff between efficacy and safety.

The utility of live attenuated vaccines for controlling HIV epidemics is being debated. Live attenuated HIV vaccines (LAHVs) could be extremely effective in protecting against infection with wild-type strains, but may not be completely safe as the attenuated strain could cause AIDS in some vaccinated individuals. We present a theoretical framework for evaluating the consequences of the tradeoff between vaccine efficacy (in terms of preventing new infections with wild-type strains) and safety (in terms of vaccine-induced AIDS deaths). We use our framework to predict, for Zimbabwe and Thailand, the epidemiological impact of 1,000 different (specified by efficacy and safety characteristics) LAHVs. We predict that paradoxically: (i) in Zimbabwe (where transmission is high) LAHVs would significantly decrease the AIDS death rate, but (ii) in Thailand (where transmission is low) exactly the same vaccines (in terms of efficacy and safety characteristics) would increase the AIDS death rate. Our results imply that a threshold transmission rate exists that determines whether any given LAHV has a beneficial or a detrimental impact. We also determine the vaccine perversity point, which is defined in terms of the fraction of vaccinated individuals who progress to AIDS as a result of the vaccine strain. Vaccination with any LAHV that causes more than 5% of vaccinated individuals to progress to AIDS in 25 years would, even 50 years later, lead to perversity (i.e., increase the annual AIDS death rate) in Thailand; these same vaccines would lead to decreases in the annual AIDS death rate in Zimbabwe.