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30 results for “Viral transmission”
Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency
<p>The danger posed by infectious agents necessitates the development of new tools to both predict and manage emerging diseases. One promising approach is the development of recombinant viral vaccines that are themselves infectious. Transmissible vaccines have been shown to greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. While this approach can be immensely useful in combating emerging diseases, the ability to self-replicate exposes vaccines to evolutionary change. As a recombinant transmissible vaccine mutates, selection is expected to favor variants with reduced efficacy against the pathogen and increased transmission rates. This creates a trade-off in vaccine design priorities between efficacy, reduction in transmission, and evolutionary stability. Here we ask how such trade-offs influence the overall performance of transmissible vaccines. We find that evolutionary instability can dramatically reduce performance, even for vaccine candidates with ideal efficacy and transmission dynamics. One method to increase functional stability is through the inclusion of multiple redundant antigens. We show that the inclusion of a second antigen can increase functional stability in the face of evolutionary pressures. However, the benefit of genetic redundancy plus any gain in efficacy must outweigh the reduction in transmission for dual-gene designs to be effective. Our results suggest that the successful application of recombinant transmissible vaccines will require consideration of evolutionary dynamics and epistatic effects, as well as basic measurements of epidemiological features.</p>
Data and Analyses for Host plant-mediation of viral transmission and its consequences for a native butterfly
<p>This contains R code for all analyses and creation of figures included in the publication entitled "Host plant-mediation of viral transmission and its Q1 consequences for a native butterfly". This article has now been accepted for publication under DOI: 10.1002/ecy.4282. The files containing the data analysis script have been updated to reflect the final analyses included in this paper. </p>
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Data from: Viral transmission and infection prevalence in a cannibalistic host–pathogen system
<div> <div> <div> <div> <p>Cannibalism, while prevalent in the natural world, is often viewed as detrimental to a cannibal's health, especially when they consume pathogen-infected conspecifics. The argument stems from the idea that cannibalizing infected individuals increases the chance of coming into contact with a pathogen and subsequently becoming infected. Using an insect pest, the fall armyworm (<em>Spodoptera frugiperda</em>), that readily cannibalizes at the larval stage and its lethal pathogen, we experimentally examined how cannibalism affects viral transmission at both an individual and population level. Prior to death, the pathogen in the system stops the larval host from growing, resulting in infected individuals being smaller than healthy individuals. This leads to size-structured cannibalism of infected individuals with the larger healthy larvae consuming the smaller infected larvae, which is commonly observed. At the individual level, we show that the probability of cannibalism is relatively high for both infected and uninfected individuals especially when the cannibal is larger than the victim. However, the probability of the cannibal becoming infected given that a pathogen-infected individual has been cannibalized is relatively low. On a population level, when cannibalism is allowed to occur transmission rates decline. Additionally, by cannibalizing infected larvae, cannibals lower the infection risk for non-cannibals. Thus, cannibalism can decrease infection prevalence and, therefore, may not be as deleterious as once thought. Under certain circumstances, cannibalizing infected individuals, from the uninfected host's perspective, may even be advantageous, as one obtains a meal and decreases competition for resources with little chance of becoming infected.</p> </div> </div> </div> </div>
Correlation of viral loads in disease transmission could affect early estimates of the reproduction number
<p>This dataset accompanies the an article titled, 'Correlation of viral loads in disease transmission could affect early estimates of the reproduction number', by T. Harris et al. which can be found at https://arxiv.org/abs/2211.08673.</p> <p>Abstract:</p> <p>Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate how correlations between the viral load of cases in transmission chains can affect estimates of these fundamental transmission properties. Our computational model simulates a disease transmission mechanism in which the viral load of the infector at the time of transmission influences the infectiousness of the infectee. These correlations in transmission pairs produce a population-level convergence process during which the distributions of initial viral loads in each subsequent generation converge to a steady state. We find that outbreaks arising from index cases with low initial viral loads give rise to early estimates of transmission properties that could be misleading. These findings demonstrate the potential for transmission mechanisms to affect estimates of the transmission properties of newly emerged viruses in ways that could be operationally significant to a public health response.</p> <p> </p> <p>Contents of this dataset include: </p> <ul> <li>Model code - including experiments (python3)</li> <li>Estimation code (R)</li> <li>Code used for figure production (python3 & R)</li> <li>Raw data produced from Experiments 1-3 and presented in the text (.csv & .Rdata)</li> </ul> <p>See 'README.md' in main upload folder for more information</p>
Treating Kidney Donors With Valganciclovir to Reduce Viral Transmission to Recipients
ClinicalTrials.gov study NCT01329185. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Viral transmission and infection prevalence in a cannibalistic host–pathogen system
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Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
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Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency
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Trans-generational viral transmission and immune priming are dose-dependent
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Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women
Background: Effective antiretroviral therapy during pregnancy minimizes the risk of vertical HIV transmission. Some women present late in their pregnancy for first antenatal visit; whether these women achieve viral suppression by delivery and how suppression varies with time on ART is unclear. Methods: We conducted a prospective cohort study of HIV-infected pregnant women initiating antiretroviral therapy for the first time from June 2015 to November 2016. Multivariable Poisson models with robust variance estimators were used to estimate risk ratios (RR) and 95% confidence intervals (CI) of the association between duration of ART and both viral load (VL) ≥1000 copies/ml and VL ≥40 copies/ml at delivery. Results: Of the 252 women who had viral load testing at delivery, 40 (16%) and 78 (31%) had VL ≥1000 copies/ml and VL ≥40 copies/ml, respectively. The proportion of women with poor adherence to ART was higher among women who were on ART for ≤12 weeks (9/50 = 18.0%) than among those who were on ART for 13-35 weeks (18/194 = 9.3%). Compared to women who were on ART for ≤12 weeks, women who were on ART for 13-20 weeks (RR = 0.52; 95% CI: 0.36-0.74) or 21-35 weeks (RR = 0.26; 95% CI: 0.14-0.48) had a lower risk of VL ≥40 copies/ml at delivery. Similar comparisons for VL ≥1000 copies/ml at delivery showed decrease in risk although not significant for those on ART 13-20 weeks. Conclusion: Longer duration of ART during pregnancy was associated with suppressed viral load at delivery. Early ANC attendance in pregnancy to facilitate prompt ART initiation for HIV-positive women is essential in the effort to eliminate HIV vertical transmission.
Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America
Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly-pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.
A Study to Assess the Reduction of Human Papillomavirus (HPV) Viral Infectivity and Transmission in HPV-Positive Women After Vaccination With 9vHPV (RIFT-HPV)
ClinicalTrials.gov study NCT05334706. IPD Sharing: NO. Countries: 1. Publications: 11.
Transmissibility and Viral Load of SARS-CoV-2 in Oral Secretions
ClinicalTrials.gov study NCT04348240. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Viral and Antiretroviral Dynamics in HIV-1 Mother-to-Child Transmission Fluids
ClinicalTrials.gov study NCT03284645. IPD Sharing: NO. Countries: 1. Publications: 1.
Prospective Analysis of Seasonal Influenza - Viral Transmission and Evolution in the City of Basel, Switzerland
ClinicalTrials.gov study NCT03010007. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America
Open the record for dataset details and reuse information.
Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women
Open the record for dataset details and reuse information.
Experimental cross species transmission of a major viral pathogen in bees is predominantly from honeybees to bumblebees
<p>Cross-species transmission of a pathogen from a reservoir to a recipient host species, spillover, can have major impacts on biodiversity, domestic species and human health. <i>Deformed wing virus</i> (DWV) is a panzootic RNA virus in honeybees that is causal in their elevated colony losses, and several correlative field studies have suggested spillover of DWV from managed honeybees to wild bee species such as bumblebees. Yet unequivocal demonstration of DWV spillover is lacking whilst spillback, the transmission of DWV from a recipient back to the reservoir host, is rarely considered. Here we show in fully crossed laboratory experiments that transmission of DWV (genotype A) from honeybees to bumblebees occurs readily, yet we neither detected viral transmission from bumblebees to honeybees nor onward transmission from experimentally infected to uninoculated bumblebees. Our results support the potential for viral spillover from honeybees to other bee species in the field when robbing resources from heterospecific nests or when visiting the same flowers. They also underscore the importance of studies on the virulence of DWV in wild bee species so as to evaluate viral impact on individual and population fitness as well as viral adaption to new host species.</p>
Viral and Immunologic Factors Contributing to the Lack of HIV Transmission Among Couples in Rakai, Uganda
ClinicalTrials.gov study NCT00342160. IPD Sharing: Not stated. Countries: 1. Publications: 3.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.