Distribution of ingoing and outgoing contact chains of pig holdings in France according to different farm categories (1 to 31 December 2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]).

<p>BS: boar station, SEL: nucleus, MU: multiplication, FA: farrowing, FF: farrowing-to-finishing, FI: finishing, FPW: farrowing-post-weaning, PW: post-weaning, PWF: post-weaning-finishing, SP: small producers.</p

Types of network models built to represent pig movements.

<p>Nodes L and U correspond to holdings where loading and unloading operations occurred, respectively. The number corresponds to the chronology of animal collection by a truck in one round. Fig 1.a describes the actual round of a given truck, whereas Fig 1.b and Fig 1.c describes how the links between holdings were modelled, depending on the transmission route of the pathogen considered. In the Animal Introduction Model—AIM (Fig 1.b), movements forming a round were replaced with direct movements between holdings, i.e. intermediate transit movements of a truck through a farm without unloading any animal were neglected. This network accounts for the transmission of a disease only through the introduction of animals into farms. In the Transit Model—TM (Fig 1.c), each holding was assumed to be linked to every other upstream and downstream farm in a given round through incoming and outgoing links, respectively. This type of network can be used to explore the spread of a pathogen both through the introduction of animals to farms and through the indirect route.</p

Mapping of the pig movement network in France (second half of 2014) applying the two different models (Animal Introduction Model [AIM] and Transit Model [TM]) to the whole network, the breeding farm subnetwork and the production farm subnetwork.

<p>The points are active holdings only (i.e. farms having had at least one movement over the semester). Their size is proportional to their degree. Direct movements to slaughterhouses are excluded. BS: boar station, SEL: nucleus, MU: multiplication, FA: farrowing, FF: farrowing-to-finishing, FI: finishing, FPW: farrowing-post-weaning, PW: post-weaning, PWF: post-weaning-finishing, SP: small producers.</p

Pig movements in France: Designing network models fitting the transmission route of pathogens

<div><p>Pathogen spread between farms results from interaction between the epidemiological characteristics of infectious agents, such as transmission route, and the contact structure between holdings. The objective of our study was to design network models of pig movements matching with epidemiological features of pathogens. Our first model represents the transmission of infectious diseases between farms only through the introduction of animals to holdings (Animal Introduction Model AIM), whereas the second one also accounts for pathogen spread through intermediate transit of trucks through farms even without any animal unloading (i.e. indirect transmission–Transit Model TM). To take the pyramidal organisation of pig production into consideration, these networks were studied at three different scales: the whole network and two subnetworks containing only breeding or production farms. The two models were applied to pig movement data recorded in France from June 2012 to December 2014. For each type of model, we calculated network descriptive statistics, looked for weakly/strongly connected components (WCCs/SCCs) and communities, and analysed temporal patterns. Whatever the model, the network exhibited scale-free and small-world topologies. Differences in centrality values between the two models showed that nucleus, multiplication and post-weaning farms played a key role in the spread of diseases transmitted exclusively by the introduction of infected animals, whereas farrowing and farrow-to-finish herds appeared more vulnerable to the introduction of infectious diseases through indirect contacts. The second network was less fragmented than the first one, a giant SCC being detected. The topology of network communities also varied with modelling assumptions: in the first approach, a huge geographically dispersed community was found, whereas the second model highlighted several small geographically clustered communities. These results underline the relevance of developing network models corresponding to pathogen features (e.g. their transmission route), and the need to target specific types of holdings/areas for surveillance depending on the epidemiological context.</p></div

Mapping of the eight largest communities in the pig movement network in France (second half of 2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork).

<p>Mapping of the eight largest communities in the pig movement network in France (second half of 2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork).</p

Node loyalty distributions in the pig movement network in France (second half of 2012 / first half of 2013) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]).

<p>Node loyalty distributions in the pig movement network in France (second half of 2012 / first half of 2013) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]).</p

Distribution of degree, betweenness and closeness centralities of pig holdings in France according to different farm categories (second half of 2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]).

<p>BS: boar station, SEL: nucleus, MU: multiplication, FA: farrowing, FF: farrowing-to-finishing, FI: finishing, FPW: farrowing-post-weaning, PW: post-weaning, PWF: post-weaning-finishing, SP: small producers.</p

Distribution of pig farm degrees (log scale) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork) (second half of 2014).

<p>Distribution of pig farm degrees (log scale) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork) (second half of 2014).</p

Connected components in the pig movement network in France (2012–2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork).

<p>Connected components in the pig movement network in France (2012–2014) using the two different network models (Animal Introduction Model [AIM] and Transit Model [TM]) and in three different considered populations (whole network, breeding farm subnetwork, production farm subnetwork).</p

Survival analysis of swIAV within-herd persistence according to the level of susceptibility to infection for MDA-positive piglets.

<p>100 simulations per scenario, χ² Log rank test = 8.48, <i>p</i>-value = .004.</p