Strain Diversity and Spatial Distribution Are Linked to Epidemic Dynamics in Host Populations*

The inherently variable nature of epidemics renders predictions of when and where infection is expected to occur challenging. Differences in pathogen strain composition, diversity, fitness, and spatial distribution are generally ignored in epidemiological modeling and are rarely studied in natural populations, yet they may be important drivers of epidemic trajectories. To examine how these factors are linked to epidemics in natural host populations, we collected epidemiological and genetic data from 15 populations of the powdery mildew fungus, Podosphaera plantaginis, on Plantago lanceolata in the angstrom land Islands, Finland. In each population, we tracked spatiotemporal disease progression throughout one epidemic season and coupled our survey of infection with intensive field sampling of the pathogen. We found that strain composition varied greatly among populations in the landscape. Within populations, strain composition was driven by the sequence of strain activity: early-active strains reached higher abundances, leading to consistent strain compositions over time. Co-occurring strains also varied in their contribution to the growth of the local epidemic, and these fitness inequalities were linked to epidemic dynamics: a higher proportion of hosts became infected in populations containing strains that were more similar in fitness. Epidemic trajectories in the populations were also linked to strain diversity and spatial dynamics: higher infection rates occurred in populations containing higher strain diversity, while spatially clustered epidemics experienced lower infection rates. Together, our results suggest that spatial and/or temporal variation in the strain composition, diversity, and fitness of pathogen populations are important factors generating variation in epidemiological trajectories among infected host populations.Peer reviewe

Corrigendum to "Use of the nonavalent HPV vaccine in individuals previously fully or partially vaccinated with bivalent or quadrivalent HPV vaccines" [Vaccine 34 (2016) 757–761]

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Estimation of the individual residual risk of cervical cancer after vaccination with the nonavalent HPV vaccine

Background: The nonavalent HPV (9vHPV) vaccine is indicated for active immunisation of individuals from the age of 9 years against cervical, vulvar, vaginal and anal premalignant lesions and cancers causally related to vaccine HPV high risk types 16, 18, 31, 33, 45, 52 and 58, and to the HPV low risk types 6 and 11, causing genital warts. Objective: To estimate the lifetime risk (up to the age of 75 years) for developing cervical cancer after vaccinating a HPV naive girl (e.g. 9 to 12 years old) with the 9vHPV vaccine in the hypothetical absence of cervical cancer screening. Methods: We built Monte Carlo simulation models using historical pre-screening age-specific cancer incidence data and current mortality data from Denmark, Finland, Norway, Sweden and the UK. Estimates of genotype contribution fractions and vaccine efficacy were used to estimate the residual lifetime risk after vaccination assuming lifelong protection. Results: We estimated that, in the hypothetical absence of cervical screening and assuming lifelong protection, 9vHPV vaccination reduced the lifetime cervical cancer and mortality risks 7-fold with a residual lifetime cancer risks ranging from 1/572 (UK) to 1/238 (Denmark) and mortality risks ranging from 1/1488 (UK) to 1/851 (Denmark). After decades of repetitive cervical screenings, the lifetime cervical cancer and mortality risks was reduced between 2- and 4-fold depending on the country. Conclusion: Our simulations demonstrate how evidence can be generated to support decision-making by individual healthcare seekers regarding cervical cancer prevention

Rearranging agricultural landscapes towards habitat quality optimisation: In silico application to pest regulation

International audienceModern agriculture suffers from its dependence on chemical inputs and subsequent impacts on health and environment. Alternatively, protecting crops against pests can be achieved through the reinforcement of regulation ecological services. Our work propounds a data-driven methodological framework to derive relevant agricultural landscape rearrangements enhancing populations of beneficial organisms regulating pests.Building on spatialised entomological and geographic data, we developed a parsimonious reaction–diffusion model describing the population dynamics of beneficial organisms. Parameter estimation was carried out in a Bayesian framework accounting for uncertainty in the measurement.Thousands of agricultural landscapes were generated under agronomic specifications dealt with as constraint satisfaction problems. Population dynamics was simulated on each landscape with the fitted reaction-diffusion model mentioned above, and two metrics of abundances allowed the assessment of the regulation performance of the landscape spatial arrangements. One metric is a mean field performance criterion assessing the regulation performance from the landscape composition only, the other is a spatial performance metric assessing the performance resulting from the whole landscape spatial configuration. The former is computed with a non-spatialised form of the population dynamics model, the latter results from the reaction-diffusion model of the population dynamics. Comparing these metrics enabled to quantify the impact of spatial arrangements, hence allowing arrangements proposals. This framework was applied to the case study of a ground beetle species involved in the biological regulation of weeds. The arrangement proposals abides by the productive agronomic constraint that is the landscape composition, while they allow for significant habitat quality enhancement (or deterioration) for the beneficial organism (or a pest). Minor adaptations of our integrated data-driven approach would suit numerous situations ranging from the provision of enhanced ecosystem services to land management for conservation

Immunogenicity and safety of intramuscular versus subcutaneous administration of a combined measles, mumps, rubella, and varicella vaccine to children 12 to 18 months of age

This randomized trial conducted in France compared intramuscular (IM) and subcutaneous (SC) administration of two doses of a measles, mumps, rubella, and varicella (MMRV) combination vaccine (ProQuad®) administered one month apart to 405 children 12–18 months of age (NCT00402831). The 2-dose regimen of MMRV administered IM was shown to be as immunogenic as the 2-dose regimen administered SC for all antigens 6 weeks post-vaccination for the subjects who were initially seronegative for measles, mumps, rubella, or varicella (lower bounds of the two-sided 95% CIs for the difference in response rates for all antigens greater than −10% [range −2.1 for varicella to −3.0 for mumps]). The antibody response rates for all vaccine antigens 6 weeks after the second dose of MMRV were > 99% in both the IM and SC groups. Fewer subjects in the IM group experienced injection-site AEs compared with the SC group (17.8% and 28.6% post-dose 1, and 20.4% and 29.5% post-dose 2, respectively). From Day 0 to Day 4 post-dose 2, fewer subjects reported erythema and swelling in the IM group than in the SC group (15.4% and 27.0%, and 6.0% and 12.5%, respectively). In both groups, most injection-site AEs started during the first four days after vaccination; their intensity was mainly mild or ≤2.5 cm. The rates of fever were comparable between the two groups after each dose of MMRV. In conclusion, two doses of the MMRV vaccine were highly immunogenic and well tolerated when administered either SC or IM. ClinicalTrials.gov Identifier: NCT0040283

Strain Diversity and Spatial Distribution Are Linked to Epidemic Dynamics in Host Populations

The inherently variable nature of epidemics renders predictions of when and where infection is expected to occur challenging. Differences in pathogen strain composition, diversity, fitness, and spatial distribution are generally ignored in epidemiological modeling and are rarely studied in natural populations, yet they may be important drivers of epidemic trajectories. To examine how these factors are linked to epidemics in natural host populations, we collected epidemiological and genetic data from 15 populations of the powdery mildew fungus, Podosphaera plantaginis, on Plantago lanceolata in the Åland Islands, Finland. In each population, we tracked spatiotemporal disease progression throughout one epidemic season and coupled our survey of infection with intensive field sampling of the pathogen. We found that strain composition varied greatly among populations in the landscape. Within populations, strain composition was driven by the sequence of strain activity: early-active strains reached higher abundances, leading to consistent strain compositions over time. Co-occurring strains also varied in their contribution to the growth of the local epidemic, and these fitness inequalities were linked to epidemic dynamics: a higher proportion of hosts became infected in populations containing strains that were more similar in fitness. Epidemic trajectories in the populations were also linked to strain diversity and spatial dynamics: higher infection rates occurred in populations containing higher strain diversity, while spatially clustered epidemics experienced lower infection rates. Together, our results suggest that spatial and/or temporal variation in the strain composition, diversity, and fitness of pathogen populations are important factors generating variation in epidemiological trajectories among infected host populations