Contrasting ecological and evolutionary signatures of whooping cough epidemiological dynamics

Pertussis ◽  
2018 ◽  
pp. 211-224
Author(s):  
Benjamin M. Althouse ◽  
Samuel V. Scarpino
Keyword(s):  
Mucosal Immunity ◽  
Protective Immunity ◽  
Whooping Cough ◽  
Natural Infection ◽  
Epidemiological Data ◽  
Relative Importance ◽  
Global Pattern ◽  
High Resolution Data ◽  
Reporting Rates ◽  
Over Time

The enigmatic global pattern of whooping cough incidence presents a unique set of challenges for controlling the disease and uncovering the mechanisms underlying its epidemiological dynamics. In countries experiencing an increase in cases, five hypotheses have been proposed to explain the resurgence: (1) there has been an increase in Bordetella pertussis reporting rates, (2) waning of protective immunity from vaccination or natural infection over time, (3) evolution of B. pertussis to escape protective immunity, (4) vaccines that fail to induce sterilizing (mucosal) immunity to B. pertussis, and (5) asymptomatic transmission from individuals vaccinated with the currently used acellular B. pertussis vaccines. Each of these five hypotheses can leave contrasting signatures in both epidemiological and genomic data; however, these hypotheses must also be evaluated against data from locations that are either not experiencing a resurgence or are witnessing a declining incidence. This chapter discusses how to—and whether it is possible to—disentangle the various mechanisms proposed for whooping cough’s resurgence. It identifies a pathological lack of data sufficient for testing hypotheses and demonstrates how detailed, high-resolution data (in geography, time, and age) are required to distinguish even the most basic models. The chapter further discusses how approaches linking genomic and epidemiological data, (i.e. phylodynamic models) may prove beneficial. The results suggest that while evidence exists for each of the five proposed hypotheses, it is unlikely that any single mechanism can account for the global pattern of whooping cough incidence and that determining the relative importance of each mechanism remains uniquely challenging.

scholarly journals Evolution of immune responses to SARS-CoV-2 in mild-moderate COVID-19

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adam K. Wheatley ◽  
Jennifer A. Juno ◽  
Jing J. Wang ◽  
Kevin J. Selva ◽  
Arnold Reynaldi ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Vaccine Development ◽  
Natural Infection ◽  
Population Level ◽  
Cell Dynamics ◽  
Follicular Helper ◽  
Cell Immunity ◽  
Specific Igg ◽  
Over Time

AbstractThe durability of infection-induced SARS-CoV-2 immunity has major implications for reinfection and vaccine development. Here, we show a comprehensive profile of antibody, B cell and T cell dynamics over time in a cohort of patients who have recovered from mild-moderate COVID-19. Binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection. A similar decline in Spike-specific CD4+ and circulating T follicular helper frequencies occurs. By contrast, S-specific IgG+ memory B cells consistently accumulate over time, eventually comprising a substantial fraction of circulating the memory B cell pool. Modelling of the concomitant immune kinetics predicts maintenance of serological neutralising activity above a titre of 1:40 in 50% of convalescent participants to 74 days, although there is probably additive protection from B cell and T cell immunity. This study indicates that SARS-CoV-2 immunity after infection might be transiently protective at a population level. Therefore, SARS-CoV-2 vaccines might require greater immunogenicity and durability than natural infection to drive long-term protection.

scholarly journals SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marta Giovanetti ◽  
Eleonora Cella ◽  
Francesca Benedetti ◽  
Brittany Rife Magalis ◽  
Vagner Fonseca ◽  
...  
Keyword(s):  
Public Health ◽  
Epidemiological Data ◽  
Health Interventions ◽  
Transmission Dynamics ◽  
Public Health Interventions ◽  
Viral Spread ◽  
Three Phase ◽  
Phylodynamic Analysis ◽  
Epidemic Wave ◽  
Over Time

AbstractWe investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as “hidden reservoirs” during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

Mucosal vaccines to prevent porcine reproductive and respiratory syndrome: a new perspective

2012 ◽  
Vol 13 (1) ◽  
pp. 21-37 ◽  
Author(s):  
Gourapura J. Renukaradhya ◽  
Varun Dwivedi ◽  
Cordelia Manickam ◽  
Basavaraj Binjawadagi ◽  
David Benfield
Keyword(s):  
Mucosal Immunity ◽  
Protective Immunity ◽  
Mucosal Immune Response ◽  
Respiratory Pathogens ◽  
Swine Industry ◽  
Prrs Virus ◽  
Mucosal Vaccines ◽  
Direct Delivery ◽  
New Perspective ◽  
Swine Herds

AbstractPorcine reproductive and respiratory syndrome (PRRS) is an economically important infectious disease of swine. Constant emergence of variant strains of PRRS virus (PPRSV) and virus-mediated immune evasion followed by viral persistence result in increased incidence and recurrence of PRRS in swine herds. Current live and killed PRRSV vaccines administered by a parenteral route are ineffective in inducing complete protection. Thus, new approaches in design and delivery of PRRSV vaccines are needed to reduce the disease burden of the swine industry. Induction of an effective mucosal immunity to several respiratory pathogens by direct delivery of a vaccine to mucosal sites has proven to be effective in a mouse model. However, there are challenges in eliciting mucosal immunity to PRRS due to our limited understanding of safe and potent mucosal adjuvants, which could potentiate the mucosal immune response to PRRSV. The purpose of this review is to discuss methods for induction of protective mucosal immune responses in the respiratory tract of pigs. The manuscript also discusses how PRRSV modulates innate, adaptive and immunoregulatory responses at both mucosal and systemic sites of infected and/or vaccinated pigs. This information may help in the design of innovative mucosal vaccines to elicit superior cross-protective immunity against divergent field strains of PRRSV.

scholarly journals Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter

2018 ◽  
Author(s):  
Umer Zeeshan Ijaz ◽  
Lojika Sivaloganathan ◽  
Aaron Mckenna ◽  
Anne Richmond ◽  
Carmel Kelly ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Driving Forces ◽  
Natural Infection ◽  
Environmental Drivers ◽  
Natural Setting ◽  
Window Of Opportunity ◽  
Microbiome Analysis ◽  
Conversion Rates ◽  
Chicken Cecum ◽  
Over Time

AbstractChickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. As such, there has been a motivation to decrease the number of Campylobacter within chickens and thus reduce the risk of infection to humans. The lack of day-to-day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day-to-day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; n=396) combining metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilisation of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter appears. Campylobacter was identified at day 16 which was one day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and can help elucidate the mechanism through which Campylobacter within chickens can be reduced.

scholarly journals A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daliang Ning ◽  
Mengting Yuan ◽  
Linwei Wu ◽  
Ya Zhang ◽  
Xue Guo ◽  
...  
Keyword(s):  
Animal Ecology ◽  
Microbial Community ◽  
Community Assembly ◽  
Null Model ◽  
High Accuracy ◽  
Relative Importance ◽  
Experimental Warming ◽  
Community Based ◽  
Microbial Community Assembly ◽  
Over Time

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), and specificity (0.95–0.98) on simulated communities, which are 10–160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and ‘drift’ (59%). Interestingly, warming decreases ‘drift’ over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.

scholarly journals A Computational Model of Tonal Tension Profile of Chord Progressions in the Tonal Interval Space

Entropy ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. 1291
Author(s):  
María Navarro-Cáceres ◽  
Marcelo Caetano ◽  
Gilberto Bernardes ◽  
Mercedes Sánchez-Barba ◽  
Javier Merchán Sánchez-Jara
Keyword(s):  
State Of The Art ◽  
Objective Measure ◽  
Global Changes ◽  
Voice Leading ◽  
Relative Importance ◽  
Tonal Music ◽  
Harmonic Motion ◽  
Proposed Model ◽  
Interval Space ◽  
Over Time

In tonal music, musical tension is strongly associated with musical expression, particularly with expectations and emotions. Most listeners are able to perceive musical tension subjectively, yet musical tension is difficult to be measured objectively, as it is connected with musical parameters such as rhythm, dynamics, melody, harmony, and timbre. Musical tension specifically associated with melodic and harmonic motion is called tonal tension. In this article, we are interested in perceived changes of tonal tension over time for chord progressions, dubbed tonal tension profiles. We propose an objective measure capable of capturing tension profile according to different tonal music parameters, namely, tonal distance, dissonance, voice leading, and hierarchical tension. We performed two experiments to validate the proposed model of tonal tension profile and compared against Lerdahl’s model and MorpheuS across 12 chord progressions. Our results show that the considered four tonal parameters contribute differently to the perception of tonal tension. In our model, their relative importance adopts the following weights, summing to unity: dissonance (0.402), hierarchical tension (0.246), tonal distance (0.202), and voice leading (0.193). The assumption that listeners perceive global changes in tonal tension as prototypical profiles is strongly suggested in our results, which outperform the state-of-the-art models.

scholarly journals A Live and Inactivated Chlamydia trachomatis Mouse Pneumonitis Strain Induces the Maturation of Dendritic Cells That Are Phenotypically and Immunologically Distinct

2005 ◽  
Vol 73 (3) ◽  
pp. 1568-1577 ◽  
Author(s):  
Jose Rey-Ladino ◽  
Kasra M. Koochesfahani ◽  
Michelle L. Zaharik ◽  
Caixia Shen ◽  
Robert C. Brunham
Keyword(s):  
T Cells ◽  
Dendritic Cells ◽  
Chlamydia Trachomatis ◽  
Mhc Class Ii ◽  
Protective Immunity ◽  
Ex Vivo ◽  
Natural Infection ◽  
Pulsed Dc ◽  
Low Levels ◽  
Dc Maturation

ABSTRACT The intracellular bacterial pathogen Chlamydia trachomatis is a major cause of sexually transmitted disease worldwide. While protective immunity does appear to develop following natural chlamydial infection in humans, early vaccine trials using heat-killed C. trachomatis resulted in limited and transient protection with possible enhanced disease during follow-up. Thus, immunity following natural infection with live chlamydia may differ from immune responses induced by immunization with inactivated chlamydia. To study this differing immunology, we used murine bone marrow-derived dendritic cells (DC) to examine DC maturation and immune effector function induced by live and UV-irradiated C. trachomatis elementary bodies (live EBs and UV-EB, respectively). DC exposed to live EBs acquired a mature DC morphology; expressed high levels of major histocompatibility complex (MHC) class II, CD80, CD86, CD40, and ICAM-1; produced elevated amounts of interleukin-12 and tumor necrosis factor alpha; and were efficiently recognized by Chlamydia-specific CD4+ T cells. In contrast, UV-EB-pulsed DC expressed low levels of CD40 and CD86 but displayed high levels of MHC class II, ICAM-1, and CD80; secreted low levels of proinflammatory cytokines; and exhibited reduced recognition by Chlamydia-specific CD4+ T cells. Adoptive transfer of live EB-pulsed DC was more effective than that of UV-EB-pulsed DC at protecting mice against challenge with live C. trachomatis. The expression of DC maturation markers and immune protection induced by UV-EB could be significantly enhanced by costimulation of DC ex vivo with UV-EB and oligodeoxynucleotides containing cytosine phosphate guanosine; however, the level of protection was significantly less than that achieved by using DC pulsed ex vivo with viable EBs. Thus, exposure of DC to live EBs results in a mature DC phenotype which is able to promote protective immunity, while exposure to UV-EB generates a semimature DC phenotype with less protective potential. This result may explain in part the differences in protective immunity induced by natural infection and immunization with whole inactivated organisms and is relevant to rational chlamydia vaccine design strategies.

scholarly journals The Dynamics of Bird Diversity in the New World

2020 ◽  
Vol 69 (6) ◽  
pp. 1180-1199 ◽  
Author(s):  
Antonin Machac
Keyword(s):  
Species Richness ◽  
New World ◽  
Dominant Role ◽  
Bird Diversity ◽  
Biodiversity Hotspots ◽  
Relative Importance ◽  
Diversification Rates ◽  
The Andes ◽  
The Rich ◽  
Over Time

Abstract Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.]

Detection of medium-sized ground-dwelling mammals using infrared digital cameras: an alternative way forward?

2010 ◽  
Vol 32 (2) ◽  
pp. 165 ◽  
Author(s):  
Andrew W. Claridge ◽  
David J. Paull ◽  
Simon C. Barry
Keyword(s):  
Detection Rate ◽  
Detection Efficiency ◽  
Digital Cameras ◽  
Target Species ◽  
Detection Rates ◽  
Reporting Rates ◽  
Swamp Wallaby ◽  
Over Time

Infrared digital cameras were used to examine temporal detection rates of medium-sized ground-dwelling mammals in a coastal woodland landscape. From three successive deployments at fixed stations, a range of mammals was detected, including three target species: the long-nosed bandicoot, the long-nosed potoroo and the southern brown bandicoot. Reporting rates of target species were largely consistent and in some cases high. The swamp wallaby was the most commonly detected species, ranging from 47–67% of cameras on any given deployment. Long-nosed bandicoots were detected at 37–53% of cameras, long-nosed potoroos 13–23% and southern brown bandicoots 10–17%. In total, bandicoots and potoroos were detected at 23 of 30 sites (77%) while forage-diggings of these mammals were universally present. There were differences in the detection rate of bandicoots and potoroos in relation to 24-hourly cycles: all three species were less likely to be detected between dawn and dusk than dusk and dawn. Otherwise, with few exceptions, the rate at which bandicoots and potoroos were detected over time within a deployment did not vary markedly. Infrared digital cameras offer great potential as sampling devices for bandicoots and potoroos because of their greater detection efficiency relative to other techniques.

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