Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens

Background  

In the recent past, the introduction of Classical Swine Fever Virus (CSFV) followed by between-herd spread has given rise to a number of large epidemics in The Netherlands and Belgium. Both these countries are pork-exporting countries. Particularly important in these epidemics has been the occurrence of substantial "neighborhood transmission" from herd to herd in the presence of base-line control measures prescribed by EU legislation. Here we propose a calculation procedure to map out "high-risk areas" for local between-herd spread of CSFV as a tool to support decision making on prevention and control of CSFV outbreaks. In this procedure the identification of such areas is based on an estimated inter-herd distance dependent probability of neighborhood transmission or "local transmission". Using this distance-dependent probability, we derive a threshold value for the local density of herds. In areas with local herd density above threshold, local transmission alone can already lead to epidemic spread, whereas in below-threshold areas this is not the case. The first type of area is termed 'high-risk' for spread of CSFV, while the latter type is termed 'low-risk'.     

Spread of porcine circovirus associated disease (PCVAD) in Ontario (Canada) swine herds: Part II. Matched case-control study

Background

The emergence of porcine circovirus associated disease (PCVAD) was associated with high mortality in swine populations worldwide. Studies performed in different regions identified spatial, temporal, and spatio-temporal trends as factors contributing to patterns of the disease spread. Patterns consistent with spatial trend and spatio-temporal clustering were already identified in this dataset. On the basis of these results, we have further investigated the nature of local spread in this report. The primary objective of this study was to evaluate risk factors for incidence cases of reported PCVAD.

Results

A time-matched case-control study was used as a study design approach, and conditional logistic regression as the analytical method. The main exposure of interest was local spread, which was defined as an unidentified mechanism of PCVAD spread between premises located within 3 kilometers of the Euclidean distance. Various modifications of variables indicative of local spread were also evaluated. The dataset contained 278 swine herds from Ontario originally sampled either from diagnostic laboratory submissions or directly from the target population. A PCVAD case was defined on the basis of the producer's recall. Existence of apparent local spread over the entire study period was confirmed (OR = 2.26, 95% CI: 1.06, 4.83), and was further identified to be time-varying in nature - herds experiencing outbreaks in the later part of the epidemic were more likely than control herds to be exposed to neighboring herds experiencing recent PCVAD outbreaks. More importantly, the pattern of local spread was driven by concurrent occurrence of PCVAD on premises under the same ownership (OR_{EXACTwithin ownership} = 25.6, 95% CI: 3.4, +inf; OR_{EXACToutside ownership} = 1.3, 95% CI: 0.45, 3.3). Other significant factors included PRRSv status of a herd (OR_EXACT = 1.9, 95% CI: 1.0, 3.9), after adjusting for geographical location by including the binary effect of the easting coordinate (Easting > 600 km = 1; OR_EXACT = 1.8, 95% CI: 0.5, 5.6).

Conclusions

These results preclude any conclusion regarding the existence of a mechanism of local spread through airborne transmission or indirectly through contaminated fomites or vectors, as simultaneous emergence of PCVAD could also be a result of concurrent change in contributing factors due to other mechanisms within ownerships.

     

Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees

Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high-quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum-length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled "Routemap" ( http://routemap.osu.edu ). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data.
© The Willi Hennig Society 2009.     

Spread of alien (non-indigenous) fish species <Emphasis Type="Italic">Neogobius melanostomus</Emphasis> in the Gulf of Gdansk (south Baltic)

The round goby (Neogobius melanostomus) was first noticed in the Gulf of Gdansk in 1990. This Ponto-Caspian fish was most likely introduced to the Baltic environment from ships ballast water. During the first years of invasion, slow population growth was observed in the initially colonized regions. From 1994, round goby gradually spread in all shallow water zones of the Gulf of Gdansk. The area occupied by the population and the number of fish grew rapidly. By the end of the nineties, round goby became a dominant fish in shallow waters of the western part of the Gulf of Gdansk, where the fish used all solid substrates on the bottom, including concrete piers, big stones or even dumped waste for spawning and refuge. The presence of round goby in the Vistula Lagoon and shallow waters near Rugia (Western Baltic) was noticed for the first time in 1999. The present state, size and condition of the round goby population in the Gulf of Gdansk led us to predict a continual spread of this species into new regions of the Baltic. In addition, the population of round goby is so large that the species has started playing a part in commercial fishing in the Gulf of Gdansk.     

A Review of Coralilla (<Emphasis Type="Italic">Antigonon leptopus</Emphasis>): An Invasive and Popular Urban Bush Medicine in Jamaica

Antigonon leptopus is a smothering, habitat-transforming vine with showy pink flowers. Originating in Mexico, it is now widespread or invasive on tropical islands around the world, including the West Indies, as a consequence of active human dispersal and disturbance. Using mixed methods research, we assessed the species’ (1) historical geographic spread throughout the Americas, (2) local ethnobotanical importance in Jamaica, and (3) biomedical potential as an herbal medicine. Methods included georeferencing of time-stamped herbarium collections from pre-1900 to 2016, literature review, and ethnobotanical research in rural and urban Jamaica (n?=?58 participants). Results demonstrated that A. leptopus has spread aggressively in the West Indies since the 1950s. It has become a problematic invasive species in urban Jamaica, which has likely facilitated its local popularity as an herbal medicine. In urban Jamaica, ethnobotanical interviews ranked the species as the fourth most frequently reported medicinal plant. In contrast, A. leptopus was present but did not dominate the vegetation in rural Jamaica, and was never mentioned during interviews. The biomedical literature offers limited support for its biological activity, while showing no acute toxic effects. The ethnobotany of A. leptopus showcases the dynamic interplay between people, plants, and the environment.     

Determination of relatedness and geographical movements ofPistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis

The pistachio tree (Pistacia vera) has long been cultivated in south-central Asia and throughout the Mediterranean region of southern Europe, north Africa and the Middle East. We examined genetic diversity and patterns of relatedness amongfifteen P. vera cultivars, representing germplasm originating from throughout this range, by using Random Amplified Polymorphic DNA (RAPD) markers. The resulting data were used to construct a similarity matrix and to perform a UPGMA cluster analysis. These analyses revealed two major clusters of P. vera germplasm: a Mediterranean cluster, which includes cultivars originatingfrom the Mediterranean region of Europe, north Africa and the Middle East; and an Iranian-Caspian cluster, comprising germplasm originating from locations east of the Zagros mountains plus ’Peters’, a cultivar selected as a seedling of unknown origin in the U.S.A. The data presented here, in combination with historical and geographical records, support the hypothesis that pistachio cultivation originated in or near the present natural range of the species and was spread by cultivation to the Mediterranean region of the Middle East. This more limited pool was the germplasm source for subsequent spread of pistachio by cultivation throughout the Mediterranean region.     

Seasonal phase shift and the duration of activity time in the Burbot,Lota lota (L.) (Pisces,Gadidae)

Summary The locomotor activity of the Burbot (Lota lota L.) performs a phase-shift of 180 ° towards the Zeitgeber (natural light-dark-cycle) twice a year at high northern latitudes (Messaure, Swedish-Lapland, 66 ° 42 N, 20 ° 25 E). The duration of activity in 24 hours never exceeds 11 hours. Maximum values are achieved just before the phase-shift in September/October and in February respectively. It is suggested that this fish species, frequently spread in North-European waters, has a maximum limit in its daily activity time (10 to 11 hours) controlled by phase-shift when the length of day (during day-activity) or night (during night-activity) becomes too long. In the course of the year the Burbot places the position of its activity on the shorter part of the light-dark-cycle.Supported by Swedish Natural Science Research Council and Max-Planck-Gesellschaft zur Förderung der Wissenschaften.     

The evolution of dispersal

A non-local model for dispersal with continuous time and space is carefully justified and discussed. The necessary mathematical background is developed and we point out some interesting and challenging problems. While the basic model is not new, a spread parameter (effectively the width of the dispersal kernel) has been introduced along with a conventional rate paramter, and we compare their competitive advantages and disadvantages in a spatially heterogeneous environment. We show that, as in the case of reaction-diffusion models, for fixed spread slower rates of diffusion are always optimal. However, fixing the dispersal rate and varying the spread while assuming a constant cost of dispersal leads to more complicated results. For example, in a fairly general setting given two phenotypes with different, but small spread, the smaller spread is selected while in the case of large spread the larger spread is selected. S. Martinez was partially supported by Fondecyt 1020126 and Fondecyt Lineas Complementarias 8000010. K. Mischaikow was supported in part by NSF Grant DMS 0107396. Key words or phases:Non-local dispersal – Integral kernel – Evolution of dispersal     

Local variations in spatial synchrony of influenza epidemics

Background

Understanding the mechanism of influenza spread across multiple geographic scales is not complete. While the mechanism of dissemination across regions and states of the United States has been described, understanding the determinants of dissemination between counties has not been elucidated. The paucity of high resolution spatial-temporal influenza incidence data to evaluate disease structure is often not available.

Methodology and Findings

We report on the underlying relationship between the spread of influenza and human movement between counties of one state. Significant synchrony in the timing of epidemics exists across the entire state and decay with distance (regional correlation = 62%). Synchrony as a function of population size display evidence of hierarchical spread with more synchronized epidemics occurring among the most populated counties. A gravity model describing movement between two populations is a stronger predictor of influenza spread than adult movement to and from workplaces suggesting that non-routine and leisure travel drive local epidemics.

Conclusions

These findings highlight the complex nature of influenza spread across multiple geographic scales.     

Local spread of classical swine fever upon virus introduction into The Netherlands: Mapping of areas at high risk

Background

In the recent past, the introduction of Classical Swine Fever Virus (CSFV) followed by between-herd spread has given rise to a number of large epidemics in The Netherlands and Belgium. Both these countries are pork-exporting countries. Particularly important in these epidemics has been the occurrence of substantial "neighborhood transmission" from herd to herd in the presence of base-line control measures prescribed by EU legislation. Here we propose a calculation procedure to map out "high-risk areas" for local between-herd spread of CSFV as a tool to support decision making on prevention and control of CSFV outbreaks. In this procedure the identification of such areas is based on an estimated inter-herd distance dependent probability of neighborhood transmission or "local transmission". Using this distance-dependent probability, we derive a threshold value for the local density of herds. In areas with local herd density above threshold, local transmission alone can already lead to epidemic spread, whereas in below-threshold areas this is not the case. The first type of area is termed 'high-risk' for spread of CSFV, while the latter type is termed 'low-risk'.

Results

As we show for the case of The Netherlands, once the distance-dependent probability of local transmission has been estimated from CSFV outbreak data, it is possible to produce a map of the country in which areas of high-risk herds and of low-risk herds are identified. We made these maps even more informative by estimating border zones between the two types of areas. In these border zones the risk of local transmission of infection to a nearby high-risk area exceeds a certain level.

Conclusion

The risk maps provide an easily understandable visualization of the spatial heterogeneities in transmission risk. They serve as a tool for area-specific designs of control strategies, and possibly also for spatial planning of areas where livestock farming is allowed. Similar risk maps can in principle be constructed for other highly-transmissible livestock infections that spread via neighborhood transmission.

     

Potential Geographic Distribution of the Novel Avian-Origin Influenza A (H7N9) Virus

Background

In late March 2013, a new avian-origin influenza virus emerged in eastern China. This H7N9 subtype virus has since infected 240 people and killed 60, and has awakened global concern as a potential pandemic threat. Ecological niche modeling has seen increasing applications as a useful tool in mapping geographic potential and risk of disease transmission.

Methodology/Principals

We developed two datasets based on seasonal variation in Normalized Difference Vegetation Index (NDVI) from the MODIS sensor to characterize environmental dimensions of H7N9 virus. One-third of well-documented cases was used to test robustness of models calibrated based on the remaining two-thirds, and model significance was tested using partial ROC approaches. A final niche model was calibrated using all records available.

Conclusions/Significance

Central-eastern China appears to represent an area of high risk for H7N9 spread, but suitable areas were distributed more spottily in the north and only along the coast in the south; highly suitable areas also were identified in western Taiwan. Areas identified as presenting high risk for H7N9 spread tend to present consistent NDVI values through the year, whereas unsuitable areas show greater seasonal variation.     

Enhancement of the Influenza A Hemagglutinin (HA)-Mediated Cell-Cell Fusion and Virus Entry by the Viral Neuraminidase (NA)

Background

The major role of the neuraminidase (NA) protein of influenza A virus is related to its sialidase activity, which disrupts the interaction between the envelope hemagglutin (HA) protein and the sialic acid receptors expressed at the surface of infected cells. This enzymatic activity is known to promote the release and spread of progeny viral particles following their production by infected cells, but a potential role of NA in earlier steps of the viral life cycle has never been clearly demonstrated. In this study we have examined the impact of NA expression on influenza HA-mediated viral membrane fusion and virion infectivity.

Methodology/Principal Findings

The role of NA in the early stages of influenza virus replication was examined using a cell-cell fusion assay that mimics HA-mediated membrane fusion, and a virion infectivity assay using HIV-based pseudoparticles expressing influenza HA and/or NA proteins. In the cell-cell fusion assay, which bypasses the endocytocytosis step that is characteristic of influenza virus entry, we found that in proper HA maturation conditions, NA clearly enhanced fusion in a dose-dependent manner. Similarly, expression of NA at the surface of pseudoparticles significantly enhanced virion infectivity. Further experiments using exogeneous soluble NA revealed that the most likely mechanism for enhancement of fusion and infectivity by NA was related to desialylation of virion-expressed HA.

Conclusion/Significance

The NA protein of influenza A virus is not only required for virion release and spread but also plays a critical role in virion infectivity and HA-mediated membrane fusion.     

Red brome (<Emphasis Type="Italic">Bromus rubens</Emphasis> subsp. <Emphasis Type="Italic">madritensis</Emphasis>) in North America: possible modes for early introductions,subsequent spread

Although invasions by exotic plants have increased dramatically as human travel and commerce have increased, few have been comprehensively described. Understanding the patterns of invasive species spread over space and time will help guide management activities and policy. Tracing the earliest appearances of an exotic plant reveals likely sites of introduction, paving the way for genetic studies to quantify founder events and identify potential source populations. Red brome (Bromus madritensis subsp. rubens) is a Mediterranean winter annual grass that has invaded even relatively undisturbed areas of western North America, where it threatens native plant communities. This study used herbarium records and contemporary published accounts to trace the early introductions and subsequent spread of red brome in western North America. The results challenge the most frequently cited sources describing the early history of this grass and suggest three possible modes for early introductions: the California Gold Rush and Central Valley wheat, southern California shipping, and northern California sheep. Subsequent periods of most rapid spread into new areas, from 1930 to 1942, and of greatest spread into new regions, during the past 50 years, coincide with warm Pacific Decadal Oscillation regimes, which are linked to increased winter precipitation in the southwestern USA and northern Mexico. Global environmental change, including increased atmospheric CO₂ levels and N deposition, may be contributing to the success of red brome, relative to native species.     

Sanitary control of the territory: data bases on the spread of some quarantine infections

The data bases (DB) on the spread of plague, yellow fever and contagious virus hemorrhagic fevers (CVHF) in foreign countries have been created. These DB contain information on the main international air and sea ports and their relationships with natural focal territories. The data base "Sanitary control. Yellow fever" contains information on different species serving as vectors for yellow fever virus. Information on the circulation of the causative agents of Ebola fever, Lassa fever and Marburg disease in African countries has been introduced into DB, the differentiation of countries by the degree of the potential danger of the CVHF spread has been made.     

Spatial waves of advance with bistable dynamics: cytoplasmic and genetic analogues of Allee effects

Unlike unconditionally advantageous "Fisherian" variants that tend to spread throughout a species range once introduced anywhere, "bistable" variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or "engineered underdominance" to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.     

2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates

Background

In April 2009, novel swine-origin influenza viruses (S-OIV) were identified in patients from Mexico and the United States. The viruses were genetically characterized as a novel influenza A (H1N1) strain originating in swine, and within a very short time the S-OIV strain spread across the globe via human-to-human contact.

Methodology

We conducted a comprehensive computational search of all available sequences of the surface proteins of H1N1 swine influenza isolates and found that a similar strain to S-OIV appeared in Thailand in 2000. The earlier isolates caused infections in pigs but only one sequenced human case, A/Thailand/271/2005 (H1N1).

Significance

Differences between the Thai cases and S-OIV may help shed light on the ability of the current outbreak strain to spread rapidly among humans.     

First records of the non-indigenous signal crayfish (<Emphasis Type="Italic">Pacifastacus leniusculus</Emphasis>) and its threat to noble crayfish (<Emphasis Type="Italic">Astacus astacus</Emphasis>) populations in Estonia

This study gives an overview of status and distribution of signal crayfish (Pacifastacus leniusculus), the first NICS in Estonia and its influence on native noble crayfish (Astacus astacus) populations. The first specimen of signal crayfish was caught during the monitoring of noble crayfish in North Estonia in 2008. The signal crayfish has since been found in three additional sites. Test fishing has indicated that the abundance of signal crayfish has been fluctuating between years and among localities. It has had strong negative impact on abundance of one noble crayfish population. The disconnected distribution of signal crayfish strongly suggests that these populations are the result of human-assisted introductions. Real-time PCR analyses proved that signal crayfish carry the causative agent of the crayfish plague, an oomycete Aphanomyces astaci, thus contributing to its spread. Mortalities in noble crayfish populations had been caused by A. astaci strains from A, B and E genotype group.     

Muller's ratchet and the accumulation of favourable mutations

Under the influence of recurrent deleterious mutation and selection, asexual and sexual populations reach a deterministic equilibrium with individuals carrying 0,1,2,. . . harmful mutations. When a favourable mutation (aA) occurs in an asexual population it will usually occur in an individual who has one or more (k) deleterious mutations. Muller's ratchet then applies as A will thereafter never occur in an individual with less than k mutations. If the selective advantage of A is less than the selective disadvantage of k harmful mutations then A will not spread. If it is greater it may spread carrying k deleterious mutations to fixation. Sexual populations are not affected in this way. A will spread through the population experiencing genomes with 0,1,2,. . . deleterious mutations in accordance with the deterministic equilibrium.     

The spread of the western flower thrips Frankliniella occidentalis (Pergande)

Abstract 1 Since the late 1970s, the western flower thrips has spread from its original distribution in western North America to become a major worldwide crop pest. 2 A wide range of data sources have been used to map the original distribution in the U.S.A. and Canada, and the progress of the spread in the U.S.A., Canada, Europe, northern Africa and Australia. 3 The possible reasons for the start of the spread are discussed. The most likely reason is that intensive insecticide use in horticulture in the 1970s and 1980s selected an insecticide resistant strain or strains. These then established in glasshouses across North America and spread from there to Europe, Asia, Africa and Australia. 4 The international spread of the western flower thrips occurred predominantly by the movement of horticultural material, such as cuttings, seedlings and potted plants. Within Europe, an outward spread from the original outbreak in the Netherlands is discernible. The speed of spread was 229 ± 20 km/year. 5 The spread has not been restricted to glasshouses. The western flower thrips has established outdoors in areas with milder winters; for example, across the southern U.S.A., southern Europe and Australia. It also overwinters in some regions with colder winters. 6 Polyphagous phytophagous thrips have many factors predisposing them to become worldwide crop pests, particularly in glasshouses. Some other species that might spread in a similar way to the western flower thrips are listed.