Unravelling direct and indirect contact patterns between duck farms in France and their association with the 2016-2017 epidemic of Highly Pathogenic Avian Influenza (H5N8)

Live animal movements generate direct contacts (via the exchange of live animals) and indirect contacts (via the transit of transport vehicles) between farms, which can contribute to the spread of pathogens. However, most analyses focus solely on direct contacts and can therefore underestimate the contribution of live animal movements in the spread of infectious diseases. Here, we used French live duck movement data (2016-2018) from one of the largest transport companies to compare direct and indirect contact patterns between duck farms and evaluate how these patterns were associated with the French 2016-2017 epidemic of highly pathogenic avian influenza H5N8. A total number of 614 farms were included in the study, and two directed networks were generated: the animal introduction network (exchange of live ducks) and the transit network (transit of transport vehicles). Following descriptive analyses, these two networks were scrutinized in relation to farm infection status during the epidemic. Results showed that farms were substantially more connected in the transit network than in the animal introduction network and that the transit of transport vehicles generated more opportunities for transmission than the exchange of live animals. We also showed that animal introduction and transit networks' statistics decreased substantially during the epidemic (January-March 2017) compared to non-epidemic periods (January-March 2016 and January-March 2018). We estimated a probability of 33.3 % that a farm exposed to the infection through either of the two live duck movement networks (i.e. that was in direct or indirect contact with a farm that was reported as infected in the following seven days) becomes infected within seven days after the contact. However, we also demonstrated that the level of exposure of farms by these two contact patterns was low, leading only to a handful of transmission events through these routes. As a consequence, we showed that live animal movement patterns are efficient transmission routes for HPAI but have been efficiently reduced to limit the spread during the French 2020-2021 epidemic. These results underpin the relevance of studying indirect contacts resulting from the movement of animals to understand their transmission potential and the importance of accounting for both routes when designing disease control strategies.

Exploring the Wind-Borne Spread of Highly Pathogenic Avian Influenza H5N8 During the 2016-2017 Epizootic in France

In winter 2016-2017, highly pathogenic avian influenza (HPAI) H5N8 virus spread in France, causing an unprecedented epizootic. During the epidemic, southwest France, where most outbreaks were reported, experienced severe weather, with three consecutive storms (Leiv, Kurt, and Marcel) from 3 to 5 February 2017. Although little information is available, one hypothesis is that the spread of HPAI-H5N8 from an infected poultry holding could have been passively facilitated by prevailing wind during the risk period. The aim of this study was therefore to assess the contribution of the wind-borne route to the spatial distribution of HPAI H5N8 outbreaks during the risk period at the beginning of February 2017. The PERLE model, an atmospheric dispersion model (ADM) developed by Météo-France, the French meteorological agency, was used to generate the predicted area at risk of infection from a suspected point source. Model outputs show that the spatial pattern of dust-particle deposition was directed east-southeast in accordance with wind direction. This contrasted with the spatial distribution of HPAI H5N8 outbreaks, which spread westward. These observations suggest that the wind-borne route alone was insufficient to explain the spatial distribution of outbreaks over large distances in southwest France at the beginning of February 2017. Finally, this study illustrates the relevance of close collaboration between governmental authorities, veterinary research institutes, and meteorological agencies involving interdisciplinary research for successful outbreak investigations.

Inferring within-herd transmission parameters for African swine fever virus using mortality data from outbreaks in the Russian Federation

Mortality data are routinely collected for many livestock and poultry species, and they are often used for epidemiological purposes, including estimating transmission parameters. In this study, we infer transmission rates for African swine fever virus (ASFV), an important transboundary disease of swine, using mortality data collected from nine pig herds in the Russian Federation with confirmed outbreaks of ASFV. Parameters in a stochastic model for the transmission of ASFV within a herd were estimated using approximate Bayesian computation. Estimates for the basic reproduction number varied amongst herds, ranging from 4.4 to 17.3. This was primarily a consequence of differences in transmission rate (range: 0.7-2.2), but also differences in the mean infectious period (range: 4.5-8.3 days). We also found differences amongst herds in the mean latent period (range: 5.8-9.7 days). Furthermore, our results suggest that ASFV could be circulating in a herd for several weeks before a substantial increase in mortality is observed in a herd, limiting the usefulness of mortality data as a means of early detection of an outbreak. However, our results also show that mortality data are a potential source of data from which to infer transmission parameters, at least for diseases which cause high mortality.

Survival of African Swine Fever Virus in Excretions from Pigs Experimentally Infected with the Georgia 2007/1 Isolate

African swine fever virus (ASFV) causes a lethal haemorrhagic disease of swine which can be transmitted through direct contact with infected animals and their excretions or indirect contact with contaminated fomites. The shedding of ASFV by infected pigs and the stability of ASFV in the environment will determine the extent of environmental contamination. The recent outbreaks of ASF in Europe make it essential to develop disease transmission models in order to design effective control strategies to prevent further spread of ASF. In this study, we assessed the shedding and stability of ASFV in faeces, urine and oral fluid from pigs infected with the Georgia 2007/1 ASFV isolate. The half-life of infectious ASFV in faeces was found to range from 0.65 days when stored at 4°C to 0.29 days when stored at 37°C, while in urine it was found to range from 2.19 days (4°C) to 0.41 days (37°C). Based on these half-lives and the estimated dose required for infection, faeces and urine would be estimated to remain infectious for 8.48 and 15.33 days at 4°C and 3.71 and 2.88 days at 37°C, respectively. The half-life of ASFV DNA was 8 to 9 days in faeces and 2 to 3 days in oral fluid at all temperatures. In urine, the half-life of ASFV DNA was found to be 32.54 days at 4°C decreasing to 19.48 days at 37°C. These results indicate that ASFV in excretions may be an important route of ASFV transmission.

Effectiveness and practicality of control strategies for African swine fever: what do we really know?

African swine fever (ASF) is a major pig health problem, and the causative virus is moving closer to Western European regions where pig density is high. Stopping or slowing down the spread of ASF requires mitigation strategies that are both effective and practical. Based on the elicitation of ASF expert opinion, this study identified surveillance and intervention strategies for ASF that are perceived as the most effective by providing the best combination between effectiveness and practicality. Among the 20 surveillance strategies that were identified, passive surveillance of wild boar and syndromic surveillance of pig mortality were considered to be the most effective surveillance strategies for controlling ASF virus spread. Among the 22 intervention strategies that were identified, culling of all infected herds and movement bans for neighbouring herds were regarded as the most effective intervention strategies. Active surveillance and carcase removal in wild boar populations were rated as the most effective surveillance and intervention strategies, but were also considered to be the least practical, suggesting that more research is needed to develop more effective methods for controlling ASF in wild boar populations.

Exploring pig trade patterns to inform the design of risk-based disease surveillance and control strategies

An understanding of the patterns of animal contact networks provides essential information for the design of risk-based animal disease surveillance and control strategies. This study characterises pig movements throughout England and Wales between 2009 and 2013 with a view to characterising spatial and temporal patterns, network topology and trade communities. Data were extracted from the Animal and Plant Health Agency (APHA)'s RADAR (Rapid Analysis and Detection of Animal-related Risks) database, and analysed using descriptive and network approaches. A total of 61,937,855 pigs were moved through 872,493 movements of batches in England and Wales during the 5-year study period. Results show that the network exhibited scale-free and small-world topologies, indicating the potential for diseases to quickly spread within the pig industry. The findings also provide suggestions for how risk-based surveillance strategies could be optimised in the country by taking account of highly connected holdings, geographical regions and time periods with the greatest number of movements and pigs moved, as these are likely to be at higher risk for disease introduction. This study is also the first attempt to identify trade communities in the country, information which could be used to facilitate the pig trade and maintain disease-free status across the country in the event of an outbreak.