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  1. ; ( , PLOS ONE)
    Yang, Junyuan (Ed.)
    The ongoing COVID-19 pandemic has killed at least 1.1 million people in the United States and over 6.7 million globally. Accurately estimating the age-specific infection fatality rate (IFR) of SARS-CoV-2 for different populations is crucial for assessing and understanding the impact of COVID-19 and for appropriately allocating vaccines and treatments to at-risk groups. We estimated age-specific IFRs of wild-type SARS-CoV-2 using published seroprevalence, case, and death data from New York City (NYC) from March to May 2020, using a Bayesian framework that accounted for delays between key epidemiological events. IFRs increased 3-4-fold with every 20 years of age, from 0.06% in individuals between 18–45 years old to 4.7% in individuals over 75. We then compared IFRs in NYC to several city- and country-wide estimates including England, Switzerland (Geneva), Sweden (Stockholm), Belgium, Mexico, and Brazil, as well as a global estimate. IFRs in NYC were higher for individuals younger than 65 years old than most other populations, but similar for older individuals. IFRs for age groups less than 65 decreased with income and increased with income inequality measured using the Gini index. These results demonstrate that the age-specific fatality of COVID-19 differs among developed countries and raises questions about factors underlying these differences, including underlying health conditions and healthcare access. 
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    Free, publicly-accessible full text available May 17, 2024
  2. ; ( , PLOS ONE)
    Ansari, Ali R. (Ed.)
    Null models provide a critical baseline for the evaluation of predictive disease models. Many studies consider only the grand mean null model (i.e. R 2 ) when evaluating the predictive ability of a model, which is insufficient to convey the predictive power of a model. We evaluated ten null models for human cases of West Nile virus (WNV), a zoonotic mosquito-borne disease introduced to the United States in 1999. The Negative Binomial, Historical (i.e. using previous cases to predict future cases) and Always Absent null models were the strongest overall, and the majority of null models significantly outperformed the grand mean. The length of the training timeseries increased the performance of most null models in US counties where WNV cases were frequent, but improvements were similar for most null models, so relative scores remained unchanged. We argue that a combination of null models is needed to evaluate the forecasting performance of predictive models for infectious diseases and the grand mean is the lowest bar. 
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    Free, publicly-accessible full text available May 5, 2024
  3. ; ; ; ; ; ; ; ( , Ecology Letters)
    Free, publicly-accessible full text available May 1, 2024
  4. ; ; ; ; ; ; ; ; ; ; et al ( , Biology Letters)
    Understanding host persistence with emerging pathogens is essential for conserving populations. Hosts may initially survive pathogen invasions through pre-adaptive mechanisms. However, whether pre-adaptive traits are directionally selected to increase in frequency depends on the heritability and environmental dependence of the trait and the costs of trait maintenance. Body condition is likely an important pre-adaptive mechanism aiding in host survival, although can be seasonally variable in wildlife hosts. We used data collected over 7 years on bat body mass, infection and survival to determine the role of host body condition during the invasion and establishment of the emerging disease, white-nose syndrome. We found that when the pathogen first invaded, bats with higher body mass were more likely to survive, but this effect dissipated following the initial epizootic. We also found that heavier bats lost more weight overwinter, but fat loss depended on infection severity. Lastly, we found mixed support that bat mass increased in the population after pathogen arrival; high annual plasticity in individual bat masses may have reduced the potential for directional selection. Overall, our results suggest that some factors that contribute to host survival during pathogen invasion may diminish over time and are potentially replaced by other host adaptations. 
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  5. ; ; ; ; ; ; ; ; ; ; et al ( , Proceedings of the Royal Society B: Biological Sciences)
    Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behaviour. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects. 
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  6. ; ; ; ; ; ; ( , Malaria Journal)
    Abstract Background

    Plasmodiumparasites that cause bird malaria occur in all continents except Antarctica and are primarily transmitted by mosquitoes in the genusCulex.Culex quinquefasciatus, the mosquito vector of avian malaria in Hawaiʻi, became established in the islands in the 1820s. While the deadly effects of malaria on endemic bird species have been documented for many decades, vector-parasite interactions in avian malaria systems are relatively understudied.

     Methods

    To evaluate the gene expression response of mosquitoes exposed to aPlasmodiuminfection intensity known to occur naturally in Hawaiʻi, offspring of wild-collected HawaiianCx. quinquefasciatuswere fed on a domestic canary infected with a fresh isolate ofPlasmodium relictumGRW4 from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. Transcriptomes of five infected and three uninfected individual mosquitoes were sequenced at each of three stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands.

     Results

    Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor, and further studies should assess its role as aPlasmodiumagonist inC. quinquefasciatus. Overall, the differential gene expression response of HawaiianCulexexposed to aPlasmodiuminfection intensity known to occur naturally in Hawaiʻi was low, but more pronounced during ookinete invasion.

     Conclusions

    This is the first analysis of the transcriptional responses of vectors to malaria parasites in non-mammalian systems. Interestingly, few similarities were found between the response ofCulexinfected with a birdPlasmodiumand those reported inAnophelesinfected with humanPlasmodium. The relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism support conclusions of low fitness costs often documented in experimental challenges ofCulexwith avianPlasmodium.

     
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  7. ; ( , PLOS Computational Biology)
    Funk, Sebastian (Ed.)
    Simultaneously controlling COVID-19 epidemics and limiting economic and societal impacts presents a difficult challenge, especially with limited public health budgets. Testing, contact tracing, and isolating/quarantining is a key strategy that has been used to reduce transmission of SARS-CoV-2, the virus that causes COVID-19 and other pathogens. However, manual contact tracing is a time-consuming process and as case numbers increase a smaller fraction of cases’ contacts can be traced, leading to additional virus spread. Delays between symptom onset and being tested (and receiving results), and a low fraction of symptomatic cases being tested and traced can also reduce the impact of contact tracing on transmission. We examined the relationship between increasing cases and delays and the pathogen reproductive number R t , and the implications for infection dynamics using deterministic and stochastic compartmental models of SARS-CoV-2. We found that R t increased sigmoidally with the number of cases due to decreasing contact tracing efficacy. This relationship results in accelerating epidemics because R t initially increases, rather than declines, as infections increase. Shifting contact tracers from locations with high and low case burdens relative to capacity to locations with intermediate case burdens maximizes their impact in reducing R t (but minimizing total infections may be more complicated). Contact tracing efficacy decreased sharply with increasing delays between symptom onset and tracing and with lower fraction of symptomatic infections being tested. Finally, testing and tracing reductions in R t can sometimes greatly delay epidemics due to the highly heterogeneous transmission dynamics of SARS-CoV-2. These results demonstrate the importance of having an expandable or mobile team of contact tracers that can be used to control surges in cases. They also highlight the synergistic value of high capacity, easy access testing and rapid turn-around of testing results, and outreach efforts to encourage symptomatic cases to be tested immediately after symptom onset. 
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  8. ; ; ( , Nature Reviews Microbiology)
    null (Ed.)
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  9. ; ; ; ; ; ; ; ; ( , Nature Communications)
    null (Ed.)
    Abstract Habitat alteration can influence suitability, creating ecological traps where habitat preference and fitness are mismatched. Despite their importance, ecological traps are notoriously difficult to identify and their impact on host–pathogen dynamics remains largely unexplored. Here we assess individual bat survival and habitat preferences in the midwestern United States before, during, and after the invasion of the fungal pathogen that causes white-nose syndrome. Despite strong selection pressures, most hosts continued to select habitats where disease severity was highest and survival was lowest, causing continued population declines. However, some individuals used refugia where survival was higher. Over time, a higher proportion of the total population used refugia than before pathogen arrival. Our results demonstrate that host preferences for habitats with high disease-induced mortality can create ecological traps that threaten populations, even in the presence of accessible refugia. 
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  10. ; ; ; ; ; ; ; ; ; ; et al ( , Journal of Applied Ecology)
    Abstract

    Emerging infectious diseases have caused population declines and biodiversity loss. The ability of pathogens to survive in the environment, independent of their host, can exacerbate disease impacts and increase the likelihood of species extinction. Control of pathogens with environmental stages remains a significant challenge for conservation and effective management strategies are urgently needed.

    We examined the effectiveness of managing environmental exposure to reduce the impacts of an emerging infectious disease of bats, white‐nose syndrome (WNS). We used a chemical disinfectant, chlorine dioxide (ClO2), to experimentally reducePseudogymnoascus destructans, the fungal pathogen causing WNS, in the environment. We combined laboratory experiments with 3 years of field trials at four abandoned mines to determine whether ClO2could effectively removeP. destructansfrom the environment, reduce host infection and limit population impacts.

    ClO2was effective at killingP. destructansin vitro across multiple concentrations. In field settings, higher concentrations of ClO2treatment were needed to sufficiently reduce viableP. destructansconidia in the environment.

    The reduction in the environmental reservoir at treatment sites resulted in lower fungal loads on bats compared to untreated control populations. Survival following treatment was also higher in little brown bats (Myotis lucifugus), and trended higher for tricolored bats (Perimyotis subflavus).

    Synthesis and applications. Our results highlight that targeted management of sources for environmental transmission can be an effective control strategy for wildlife disease. We found that successfully reducing pathogen in the environment decreased disease severity and increased survival, but required higher treatment exposure than was effective in laboratory experiments, and the effects varied among species. More broadly, our findings have implications for other emerging wildlife diseases with free‐living pathogen stages by highlighting how the degree of environmental contamination can have cascading impacts on hosts, presenting an opportunity for intervention.

     
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