Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission.

BACKGROUND: The spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies have identified important 'disease resistance single nucleotide polymorphisms (SNPs)', but how these affect the underlying traits is an unresolved question. Recent advances in computational statistics make it now possible to estimate the effects of SNPs on host traits from epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known about how to effectively design disease transmission experiments or field studies to maximise the precision with which these effects can be estimated. RESULTS: In this paper, we develop and validate analytical expressions for the precision of the estimates of SNP effects on the three above host traits for a disease transmission experiment with one or more non-interacting contact groups. Maximising these expressions leads to three distinct 'experimental' designs, each specifying a different set of ideal SNP genotype compositions across groups: (a) appropriate for a single contact-group, (b) a multi-group design termed "pure", and (c) a multi-group design termed "mixed", where 'pure' and 'mixed' refer to groupings that consist of individuals with uniformly the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than estimates for infectivity. Whereas the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferred because it uses information from naturally-occurring rather than artificial infections. The same design principles apply to estimates of the epidemiological impact of other categorical fixed effects, such as breed, line, family, sex, or vaccination status. Estimation of SNP effect precisions from a given experimental setup is implemented in an online software tool SIRE-PC. CONCLUSIONS: Methodology was developed to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables that underlie host susceptibility, infectivity and recoverability. Designs that maximize the precision of estimates were derived.

Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm.

Well parameterized epidemiological models including accurate representation of contacts are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here, we fit age-stratified models, including re-estimation of relative contact rates between age classes, to public data describing the 2020-2021 COVID-19 outbreak in England. This data includes age-stratified population size, cases, deaths, hospital admissions and results from the Coronavirus Infection Survey (almost 9000 observations in all). Fitting stochastic compartmental models to such detailed data is extremely challenging, especially considering the large number of model parameters being estimated (over 150). An efficient new inference algorithm ABC-MBP combining existing approximate Bayesian computation (ABC) methodology with model-based proposals (MBPs) is applied. Modified contact rates are inferred alongside time-varying reproduction numbers that quantify changes in overall transmission due to pandemic response, and age-stratified proportions of asymptomatic cases, hospitalization rates and deaths. These inferences are robust to a range of assumptions including the values of parameters that cannot be estimated from available data. ABC-MBP is shown to enable reliable joint analysis of complex epidemiological data yielding consistent parametrization of dynamic transmission models that can inform data-driven public health policy and interventions. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

FAIR data pipeline: provenance-driven data management for traceable scientific workflows.

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of 'following the science' are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline. Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. We believe that such tools should be promoted for use across all areas of policy-facing research. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Exact Bayesian inference of epidemiological parameters from mortality data: application to African swine fever virus.

Pathogens such as African swine fever virus (ASFV) are an increasing threat to global livestock production with implications for economic well-being and food security. Quantification of epidemiological parameters, such as transmission rates and latent and infectious periods, is critical to inform efficient disease control. Parameter estimation for livestock disease systems is often reliant upon transmission experiments, which provide valuable insights in the epidemiology of disease but which may also be unrepresentative of at-risk populations and incur economic and animal welfare costs. Routinely collected mortality data are a potential source of readily available and representative information regarding disease transmission early in outbreaks. We develop methodology to conduct exact Bayesian parameter inference from mortality data using reversible jump Markov chain Monte Carlo incorporating multiple routes of transmission (e.g. within-farm secondary and background transmission from external sources). We use this methodology to infer epidemiological parameters for ASFV using data from outbreaks on nine farms in the Russian Federation. This approach improves inference on transmission rates in comparison with previous methods based on approximate Bayesian computation, allows better estimation of time of introduction and could readily be applied to other outbreaks or pathogens.

Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data.

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking. In this paper we introduce a novel software tool called SIRE (standing for "Susceptibility, Infectivity and Recoverability Estimation"), which allows for the first time simultaneous estimation of the genetic effect of a single nucleotide polymorphism (SNP), as well as non-genetic influences on these three unobservable host traits. SIRE implements a flexible Bayesian algorithm which accommodates a wide range of disease surveillance data comprising any combination of recorded individual infection and/or recovery times, or disease diagnostic test results. Different genetic and non-genetic regulations and data scenarios (representing realistic recording schemes) were simulated to validate SIRE and to assess their impact on the precision, accuracy and bias of parameter estimates. This analysis revealed that with few exceptions, SIRE provides unbiased, accurate parameter estimates associated with all three host traits. For most scenarios, SNP effects associated with recoverability can be estimated with highest precision, followed by susceptibility. For infectivity, many epidemics with few individuals give substantially more statistical power to identify SNP effects than the reverse. Importantly, precise estimates of SNP and other effects could be obtained even in the case of incomplete, censored and relatively infrequent measurements of individuals' infection or survival status, albeit requiring more individuals to yield equivalent precision. SIRE represents a new tool for analysing a wide range of experimental and field disease data with the aim of discovering and validating SNPs and other factors controlling infectious disease transmission.

New insights about vaccine effectiveness: Impact of attenuated PRRS-strain vaccination on heterologous strain transmission.

Vaccination is the main tool for controlling infectious diseases in livestock. Yet current vaccines only provide partial protection raising concerns about vaccine effectiveness in the field. Two successive transmission trials were performed involving 52 pigs to evaluate the effectiveness of a Porcine Reproductive and Respiratory Syndrome (PRRS) vaccinal strain candidate against horizontal transmission of a virulent heterologous strain. PRRS virus, above the specified limit of detection, was observed in serum and nasal secretions for all but one pig (the exception only tested positive for serum), indicating that vaccination did not protect pigs from becoming infected and shedding the heterologous strain. However, vaccination delayed the onset of viraemia, reduced the duration of shedding and significantly decreased viral load throughout infection. Serum antibody profiles indicated that 4 out of 13 (31%) vaccinates in one trial had no serological response (NSR). A Bayesian epidemiological model was fitted to the data to assess the impact of vaccination and presence of NSRs on PRRS virus transmission dynamics. Despite little evidence for reduction in the transmission rate, vaccinated animals were on average slower to become infectious, experienced a shorter infectious period and recovered faster. The overall PRRSV transmission potential, represented by the reproductive ratio R0 was lower for the vaccinated animals, although there was substantial overlap in the credibility intervals for both groups. Model selection suggests that transmission parameters of vaccinated pigs with NSR were more similar to those of unvaccinated animals. The presence of NSRs in a population, however, seemed to only marginally affect the transmission dynamics. The results suggest that even when vaccination can't prevent infection, it can still have beneficial impacts on the transmission dynamics and contribute to reducing a herd's R0. However, biosecurity and other measures need to be considered to decrease contact rates and lower R0 below 1.

Raoiella of the world (Trombidiformes: Tetranychoidea: Tenuipalpidae).

We describe 16 new species and redescribe six established species in the genus Raoiella-R. argenta sp. nov. Beard, R. australica Womersley, R. bauchani sp. nov. Beard Ochoa, R. calgoa sp. nov. Beard Ochoa, R. crebra sp. nov. Beard Ochoa, R. davisi sp. nov. Beard, R. didcota sp. nov. Beard, R. eugeniae (Mohanasundaram), R. goyderi sp. nov. Ochoa Beard, R. hallingi sp. nov. Beard, R. illyarrie sp. nov. Beard Ochoa, R. indica Hirst, R. karri sp. nov. Ochoa Beard, R. macfarlanei Pritchard Baker, R. marri sp. nov. Beard Ochoa, R. pandanae Mohanasundaram, R. pooleyi sp. nov. Beard Ochoa, R. shimpana Meyer, R. tallerack sp. nov. Beard Ochoa, R. taronga sp. nov. Beard Ochoa, R. todtiana sp. nov. Beard Ochoa, R. wandoo sp. nov. Beard Ochoa. We discuss molecular evidence of species separation, shared character states among groups of species, and patterns in the additions of leg setae throughout ontogeny that occur in the genus. We provide a key to the known species of Raoiella.

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell-fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91 human cell types of myeloid origin by use of CAGE profiling. The CAGE sequencing of these samples has allowed us to investigate diverse aspects of transcription control during myelopoiesis, such as identification of novel transcription factors, miRNAs, and noncoding RNAs specific to the myeloid lineage. We further reconstructed a transcription regulatory network by clustering coexpressed transcripts and associating them with enriched cis-regulatory motifs. With the use of the bidirectional expression as a proxy for enhancers, we predicted over 2000 novel enhancers, including an enhancer 38 kb downstream of IRF8 and an intronic enhancer in the KIT gene locus. Finally, we highlighted relevance of these data to dissect transcription dynamics during progressive maturation of granulocyte precursors. A multifaceted analysis of the myeloid transcriptome is made available (www.myeloidome.roslin.ed.ac.uk). This high-quality dataset provides a powerful resource to study transcriptional regulation during myelopoiesis and to infer the likely functions of unannotated genes in human innate immunity.

The role of the integument with respect to different modes of locomotion in the Nematalycidae (Endeostigmata).

Previous research on the locomotion of the Nematalycidae has only been undertaken on Gordialycus, which is by far the most elongated genus of the family. Gordialycus is dependent on an unusual form of peristalsis to move around. It was not known whether the genera of Nematalycidae with shorter bodies also used this mode of locomotion. Our videographic recordings of Osperalycus did not reveal peristalsis. Instead, this mite appears to move around the mineral regolith via the expansion and constriction of the metapodosomal and genital region, allowing greater versatility in the way that the annular regions contract and extend. This type of locomotion would enable relatively short bodied nematalycids to anchor themselves into secure positions before extending their anterior regions through tight spaces. Low-temperature scanning electron micrographs show that the short bodied genera have integumental features that appear to be associated with this mode of locomotion. Peristalsis is almost certainly a more derived form of locomotion that is an adaptation to the unusually long body form of Gordialycus.

TRES predicts transcription control in embryonic stem cells.

SUMMARY: Unraveling transcriptional circuits controlling embryonic stem cell maintenance and fate has great potential for improving our understanding of normal development as well as disease. To facilitate this, we have developed a novel web tool called 'TRES' that predicts the likely upstream regulators for a given gene list. This is achieved by integrating transcription factor (TF) binding events from 187 ChIP-sequencing and ChIP-on-chip datasets in murine and human embryonic stem (ES) cells with over 1000 mammalian TF sequence motifs. Using 114 TF perturbation gene sets, as well as 115 co-expression clusters in ES cells, we validate the utility of this approach. AVAILABILITY AND IMPLEMENTATION: TRES is freely available at http://www.tres.roslin.ed.ac.uk. CONTACT: Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Investigating cataract referral practices used by Australian optometrists.

BACKGROUND: The patient pathway to cataract surgery in Australia generally begins with optometric services; however, little is known about the cataract surgery referral criteria used by optometrists in Australia. METHODS: Members of Optometrists Association Australia were invited to complete an online survey in April 2013. The survey elicited information on practice demographics, professional characteristics of optometrists and cataract surgery referral considerations. RESULTS: We received responses from 533 of 4272 (13 per cent) practising optometrists. Over three-quarters (407 of 528, 77 per cent) indicated a visual acuity (VA) cataract referral benchmark of 6/9 to 6/12. Almost all respondents (499 out of 532, 94 per cent) stated they included glare sensitivity as part of their referral criteria, whereas a considerably lower proportion (40 of 528, eight per cent) used contrast sensitivity testing. Patient-centred factors such as hobbies (94 per cent) and driving (73 per cent) featured in the decision to refer patients sooner, while a patient not wanting surgery (79 per cent) was the most frequent reason cited for delaying referral. Respondents practising in more advantaged socioeconomic areas were 2.4 times more likely to refer privately (95% CI 1.6-3.6) and less likely to consider surgical costs as an important consideration (p < 0.001). Almost all respondents (97 per cent) who referred publicly discussed public hospital waiting times with their patients (median minimum wait estimate of 12 to 18 months), compared to the smaller proportion (64 per cent) of respondents discussing private waiting times (median minimum wait estimate of one to two months). CONCLUSION: While modest reductions in VA were sufficient to prompt referral for cataract surgery by Australian optometrists, patient-reported visual disability guided the optometrist's overall referral decision. Socioeconomic status of practice location influenced the choice to refer publicly versus privately and surgical costs were also considered.

Use of low-temperature scanning electron microscopy to compare and characterize three classes of snow cover.

This study, which uses low-temperature scanning electron microscopy (LTSEM), systematically sampled and characterized snow crystals that were collected from three unique classes of snow cover: prairie, taiga, and alpine. These classes, which were defined in previous field studies, result from exposure to unique climatic variables relating to wind, precipitation, and air temperature. Snow samples were taken at 10 cm depth intervals from the walls of freshly excavated snow pits. The depth of the snow pits for the prairie, taiga, and alpine covers were 28, 81, and 110 cm, respectively. Visual examination revealed that the prairie snow cover consisted of two distinct layers whereas the taiga and alpine covers had four distinct layers. Visual measurements were able to establish the range of crystal sizes that occurred in each layer, the temperature within the pit, and the snow density. The LTSEM observations revealed the detailed structures of the types of crystals that occurred in the snow covers, and documented the metamorphosis that transpired in the descending layers. Briefly, the top layers from two of the snow covers consisted of freshly fallen snow crystals that could be readily distinguished as plates and columns (prairie) or graupel (taiga). Alternatively, the top layer in the alpine cover consisted of older dendritic crystal fragments that had undergone early metamorphosis, that is, they had lost their sharp edges and had begun to show signs of joining or bonding with neighboring crystals. A unique layer, known as sun crust, was found in the prairie snow cover; however, successive samplings from all three snow covers showed similar stages of metamorphism that led to the formation of depth hoar crystals. These changes included the gradual development of large, three-dimensional crystals having clearly defined flat faces, sharp edges, internal depressions, and facets. The study, which indicates that LTSEM can be used to enhance visual data by systematically characterizing snow crystals that are collected at remote locations, is important for understanding the physics of snowpacks and the metamorphosis that leads to potential avalanche situations. In addition, the metamorphosis of snow crystals must be considered when microwave radiometry is used to estimate the snow water equivalent in the winter snowpack, because large snow crystals more effectively scatter passive microwave radiation than small crystals.

Collecting, shipping, storing, and imaging snow crystals and ice grains with low-temperature scanning electron microscopy.

Methods to collect, transport, and store samples of snow and ice have been developed that enable detailed observations of these samples with a technique known as low-temperature scanning electron microscopy (LTSEM). This technique increases the resolution and ease with which samples of snow and ice can be observed, studied, and photographed. Samples are easily collected in the field and have been shipped to the electron microscopy laboratory by common air carrier from distances as far as 5,000 miles. Delicate specimens of snow crystals and ice grains survive the shipment procedures and have been stored for as long as 3 years without undergoing any structural changes. The samples are not subjected to the melting or sublimation artifacts. LTSEM allows individual crystals to be observed for several hours with no detectable changes. Furthermore, the instrument permits recording of photographs containing the parallax information necessary for three-dimensional imaging of the true shapes of snowflakes, snow crystals, snow clusters, ice grains, and interspersed air spaces. This study presents detailed descriptions of the procedures that have been used successfully in the field and the laboratory to collect, ship, store, and image snow crystals and ice grains.

Rime and graupel: description and characterization as revealed by low-temperature scanning electron microscopy.

Snow crystals, which form by vapor deposition, occasionally come in contact with supercooled cloud droplets during their formation and descent. When this occurs, the droplets adhere and freeze to the snow crystals in a process known as accretion. During the early stages of accretion, discrete snow crystals exhibiting frozen cloud droplets are referred to as rime. If this process continues, the snow crystal may become completely engulfed in frozen cloud droplets. The resulting particle is known as graupel. Light microscopic investigations have studied rime and graupel for nearly 100 years. However, the limiting resolution and depth of field associated with the light microscope have prevented detailed descriptions of the microscopic cloud droplets and the three-dimensional topography of the rime and graupel particles. This study uses low-temperature scanning electron microscopy to characterize the frozen precipitates that are commonly known as rime and graupel. Rime, consisting of frozen cloud droplets, is observed on all types of snow crystals including needles, columns, plates, and dendrites. The droplets, which vary in size from 10 to 100 microm, frequently accumulate along one face of a single snow crystal, but are found more randomly distributed on aggregations consisting of two or more snow crystals (snowflakes). The early stages of riming are characterized by the presence of frozen cloud droplets that appear as a layer of flattened hemispheres on the surface of the snow crystal. As this process continues, the cloud droplets appear more sinuous and elongate as they contact and freeze to the rimed crystals. The advanced stages of this process result in graupel, a particle 1 to 3 mm across, composed of hundreds of frozen cloud droplets interspersed with considerable air spaces; the original snow crystal is no longer discernible. This study increases our knowledge about the process and characteristics of riming and suggests that the initial appearance of the flattened hemispheres may result from impact of the leading face of the snow crystal with cloud droplets. The elongated and sinuous configurations of frozen cloud droplets that are encountered on the more advanced stages suggest that aerodynamic forces propel cloud droplets to the trailing face of the descending crystal where they make contact and freeze.

Irregular snow crystals: structural features as revealed by low temperature scanning electron microscopy.

For nearly 50 years, investigators using light microscopy have vaguely alluded to a unique type of snow crystal that has become known as an irregular snow crystal. However, the limited resolution and depth-of-field of the light microscope has prevented investigators from characterizing these crystals. In this study, a field-emission scanning electron microscope, equipped with a cold stage, was used to document the structural features, physical associations, and atmospheric metamorphosis of irregular snow crystals. The crystals appear as irregular hexagons, measuring 60 to 90 mm across, when viewed from the a-axis. Their length (c-axis) rarely exceeds the diameter. The irregular crystals are occasionally found as secondary particles on other larger forms of snow crystals; however, they most frequently occur in aggregates consisting of more than 100 irregular crystals. In the aggregates, the irregular crystals have their axes oriented parallel to one another and, collectively, tend to form columnar structures. Occasionally, these columnar structures exhibit rounded faces along one side, suggesting atmospheric metamorphoses during formation and descent. In extreme cases of metamorphoses, the aggregates would be difficult to distinguish from graupel. Frost, consisting of irregular crystals, has also been encountered, suggesting that atmospheric conditions that favor their growth can also occur terrestrially.