Darren M. Green

Demographic structure and pathogen dynamics on the network of livestock movements in Great Britain

Using a novel interpretation of dynamic networks, we analyse the network of livestock movements in Great Britain in order to determine the risk of a large epidemic of foot-and-mouth disease (FMD). This network is exceptionally well characterized, as there are legal requirements that the date, source, destination and number of animals be recorded and held on central databases. We identify a percolation threshold in the structure of the livestock network, indicating that, while there is little possibility of a national epidemic of FMD in winter when the catastrophic 2001 epidemic began, there remains a risk in late summer or early autumn. These predictions are corroborated by a non-parametric simulation in which the movements of livestock in 2003 and 2004 are replayed as they occurred. Despite the risk, we show that the network displays small-world properties which can be exploited to target surveillance and control and drastically reduce this risk.

The network of sheep movements within Great Britain: network properties and their implications for infectious disease spread

During the 2001 foot and mouth disease epidemic in the UK, initial dissemination of the disease to widespread geographical regions was attributed to livestock movement, especially of sheep. In response, recording schemes to provide accurate data describing the movement of large livestock in Great Britain (GB) were introduced. Using these data, we reconstruct directed contact networks within the sheep industry and identify key epidemiological properties of these networks. There is clear seasonality in sheep movements, with a peak of intense activity in August and September and an associated high risk of a large epidemic. The high correlation between the in and out degree of nodes favours disease transmission. However, the contact networks were largely dissasortative: highly connected nodes mostly connect to nodes with few contacts, effectively slowing the spread of disease. This is a result of bipartite-like network properties, with most links occurring between highly active markets and less active farms. When comparing sheep movement networks (SMNs) to randomly generated networks with the same number of nodes and node degrees, despite structural differences (such as disassortativity and higher frequency of even path lengths in the SMNs), the characteristic path lengths within the SMNs are close to values computed from the corresponding random networks, showing that SMNs have ‘small-world’-like properties. Using the network properties, we show that targeted biosecurity or surveillance at highly connected nodes would be highly effective in preventing a large and widespread epidemic.

Disease dynamics over very different time-scales: foot-and-mouth disease and scrapie on the network of livestock movements in the UK

We analyse the relationship between the network of livestock movements in the UK and the dynamics of two diseases: foot-and-mouth disease (FMD), which has an incubation period of days, and scrapie, which incubates over years. For FMD, the time-scale of expected epidemics is similar to the time-scale of the evolution of the network. We argue that, under appropriate conditions, a static network analysis can be an appropriate tool for gaining insights into disease dynamics even when the relevant time-scales are similar, as with FMD. We show that a subclass of ‘linkage moves’ maintains the network structure, and so removing these links has a dramatic effect on the number of potentially infected farms, an effect corroborated by simulations. In contrast, because scrapie has a low probability of transmission per contact and a long incubation period, a static network representation is probably appropriate; however, the signature of the network in the pattern of transmission is likely to be faint. Scrapie-notifying farms were more likely to be associated with each other via trading at markets than were control farms; however, network community structure proves to be less representative of prevalence patterns than geographical region. These contradictory indicators emphasize that appropriate observation time frames and good discrimination among types of potentially infectious contacts are vital in order for network analysis to be a valuable epidemiological tool.

Modelling the initial spread of foot-and-mouth disease through animal movements

Livestock movements in Great Britain (GB) are well recorded and are a unique record of the network of connections among livestock-holding locations. These connections can be critical for disease spread, as in the 2001 epidemic of foot-and-mouth disease (FMD) in the UK. Here, the movement data are used to construct an individual-farm-based model of the initial spread of FMD in GB and determine the susceptibility of the GB livestock industry to future outbreaks under the current legislative requirements. Transmission through movements is modelled, with additional local spread unrelated to the known movements. Simulations show that movements can result in a large nationwide epidemic, but only if cattle are heavily involved, or the epidemic occurs in late summer or early autumn. Inclusion of random local spread can considerably increase epidemic size, but has only a small impact on the spatial extent of the disease. There is a geographical bias in the epidemic size reached, with larger epidemics originating in Scotland and the north of England than elsewhere.

Estimates for local and movement-based transmission of bovine tuberculosis in British cattle

Both badgers and livestock movements have been implicated in contributing to the ongoing epidemic of bovine tuberculosis (BTB) in British cattle. However, the relative contributions of these and other causes are not well quantified. We used cattle movement data to construct an individual (premises)-based model of BTB spread within Great Britain, accounting for spread due to recorded cattle movements and other causes. Outbreak data for 2004 were best explained by a model attributing 16% of herd infections directly to cattle movements, and a further 9% unexplained, potentially including spread from unrecorded movements. The best-fit model assumed low levels of cattle-to-cattle transmission. The remaining 75% of infection was attributed to local effects within specific high-risk areas. Annual and biennial testing is mandatory for herds deemed at high risk of infection, as is pre-movement testing from such herds. The herds identified as high risk in 2004 by our model are in broad agreement with those officially designated as such at that time. However, border areas at the edges of high-risk regions are different, suggesting possible areas that should be targeted to prevent further geographical spread of disease. With these areas expanding rapidly over the last decade, their close surveillance is important to both identify infected herds quickly, and limit their further growth.

Infectious disease control using contact tracing in random and scale-free networks

Contact tracing aims to identify and isolate individuals that have been in contact with infectious individuals. The efficacy of contact tracing and the hierarchy of traced nodes—nodes with higher degree traced first—is investigated and compared on random and scale-free (SF) networks with the same number of nodes N and average connection K. For values of the transmission rate larger than a threshold, the final epidemic size on SF networks is smaller than that on corresponding random networks. While in random networks new infectious and traced nodes from all classes have similar average degrees, in SF networks the average degree of nodes that are in more advanced stages of the disease is higher at any given time. On SF networks tracing removes possible sources of infection with high average degree. However a higher tracing effort is required to control the epidemic than on corresponding random networks due to the high initial velocity of spread towards the highly connected nodes. An increased latency period fails to significantly improve contact tracing efficacy. Contact tracing has a limited effect if the removal rate of susceptible nodes is relatively high, due to the fast local depletion of susceptible nodes.

Disease contact tracing in random and clustered networks

The efficacy of contact tracing, be it between individuals (e.g. sexually transmitted diseases or severe acute respiratory syndrome) or between groups of individuals (e.g. foot-and-mouth disease; FMD), is difficult to evaluate without precise knowledge of the underlying contact structure; i.e. who is connected to whom? Motivated by the 2001 FMD epidemic in the UK, we determine, using stochastic simulations and deterministic ‘moment closure’ models of disease transmission on networks of premises (nodes), network and disease properties that are important for contact tracing efficiency. For random networks with a high average number of connections per node, little clustering of connections and short latency periods, contact tracing is typically ineffective. In this case, isolation of infected nodes is the dominant factor in determining disease epidemic size and duration. If the latency period is longer and the average number of connections per node small, or if the network is spatially clustered, then the contact tracing performs better and an overall reduction in the proportion of nodes that are removed during an epidemic is observed.

Technical review of the energy and protein requirements of growing pigs: food intake

A review of work reported in the literature was used to present quantitative descriptions of protein use in the growing pig. These are detailed in the text, which also points to preferred values, and to anomalies and lacunae. The review was prepared with the objective of allowing from its content the inclusive and quantitative modelling of amino acid requirement. Requirement was approached as the sum of the component factors: maintenance and protein retention. Ileal true digestible protein and amino acid requirements are presented in a form consistent with that forwarded for energy. Thus both energy and protein elements can be conceptualized within a single coherent framework. Priority uses for absorbed amino acids were assumed to be (a) to support endogenous protein losses resultant from the passage of food and incomplete re-absorption prior to the terminal ileum, (b) to replace lost hair and skin, and (c) to cover the basic maintenance losses which will occur as a result of minimal protein turn-over even when protein retention is zero. The bulk of the protein requirement was directly linked to the daily rate of protein retention, for which the linear-plateau response was accepted. For determination of the maximum rate of protein retention the Gompertz function was proposed, although the use of a single value throughout the growth period was not dismissed. The balance of amino acids for protein retention is specified as different from that for maintenance. Central to the approach was the proposal that the inefficiency of use of ileal digested ideal protein, even when not supplied in excess, was an expression of protein losses occurring as a result of protein turn-over. The requirement for the satisfaction of the losses from protein turn-over occurring as a consequence of protein retention, and therefore additional to the requirements for maintenance, was identified. Quantification was attempted with sufficient success to warrant its inclusion into requirement estimation. It was concluded that this element addressed previously inadequately explained protein utilization inefficiencies. Algorithms are presented based upon protein turn-over which appear to be consistent with empirical findings.

Growth of carcass components and its relation with conformation in pigs of three types

The growth of carcass tissues and developmental changes in tissue distribution were studied in three pig types which were selected to have morphologies that could be described as attenuated, blocky and flabby. These were achieved by incorporating, respectively, Landrace, Pietrain and Meishan genes to give commercial types (designated L, P and M,) exhibiting some of the phenotypic qualities of these breeds. Twenty-five female pigs of each type with an average start weight of 27.2 kg were fed ad libitum and slaughtered over a (nominal) live weight range of 35-115 kg. Relations were quantified using the logarithmic transformation of data in the allometric model. Significant type differences in relative growth rates (the b coefficient or slope in the logarithmic plot) were not common, occurring in 14% of the relationships examined, whereas 61% of differences in the constant term (a or intercept in the logarithmic plot) were significant. Increase in carcass weight with age was not different between the types but in relation to slaughter live weight (dressing percentage) P had the highest value, M the lowest. Carcass dimensions showed that, relative to body length, P had the widest ham and shoulder over the whole size range whereas M had a deep (ventral-dorsal) shoulder and wide belly, attributes of shape that would be regarded as undesirable by the meat trade. Relative to carcass weight, L was only slightly longer (3 mm) in the body than M at the heavy end of the weight range but markedly longer (29 mm) than P. These differences in carcass conformation were also evident in the shape of pelvic limb muscles which, at a given length, were lightest and narrowest in M and, in some cases, heavier and wider in P than in L. Pelvic limb volume relative to limb length was greatest in P and least in M. Carcass composition (at a given prepared side weight) of P was characterized by low fat and high lean weights, and a high lean to bone ratio. Subcutaneous fat b was lowest in P, indicating that P was early maturing, but M carcasses had the most subcutaneous and intermuscular fat, also indicative of early maturing. There was, thus, no simple relation between maturity characteristics and carcass composition. M carcasses also had the greatest weight of skin. P had a light hindloin and heavy pelvic limb, M a heavy shoulder, hindloin and flank but a light pelvic limb; L had a light shoulder but a heavy foreloin. The distribution of individual tissues mirrored these differences in joint weights to a varying extent; in most cases the match (relatively heavy/light) was with a single tissue. These data, thus, indicated some pig type differences in tissue distribution and of particular significance was the relatively light lean mass in the pelvic limb of M. The results showed important differences in carcass quality between commercially available pig types differing in conformation.

A protocol for horizontal averaging of unit process data—including estimates for uncertainty

PurposeQuantitative uncertainties are a direct consequence of averaging, a common procedure when building life cycle inventories (LCIs). This averaging can be amongst locations, times, products, scales or production technologies. To date, however, quantified uncertainties at the unit process level have largely been generated using a Numerical Unit Spread Assessment Pedigree (NUSAP) approach and often disregard inherent uncertainties (inaccurate measurements) and spread (variability around means).MethodsA decision tree for primary and secondary data at the unit process level was initially created. Around this decision tree, a protocol was developed with the recognition that dispersions can be either results of inherent uncertainty, spread amongst data points or products of unrepresentative data. In order to estimate the characteristics of uncertainties for secondary data, a method for weighting means amongst studies is proposed. As for unrepresentativeness, the origin and adaptation of NUSAP to the field of life cycle assessment are discussed, and recommendations are given.Results and discussionBy using the proposed protocol, cross-referencing of outdated data is avoided, and user influence on results is reduced. In the meantime, more accurate estimates can be made for horizontally averaged data with accompanying spread and inherent uncertainties, as these deviations often contribute substantially towards the overall dispersion.ConclusionsIn this article, we highlight the importance of including inherent uncertainties and spread alongside the NUSAP pedigree. As uncertainty data often are missing in LCI literature, we here describe a method for evaluating these by taking several reported values into account. While this protocol presents a practical way towards estimating overall dispersion, better reporting in literature is promoted in order to determine real uncertainty parameters.