Biology subjects

Vergne, T.

Publications and source records attributed to Vergne, T..

3 recordsLinked to original sources

bioRxiv2021

Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France

Phylodynamic methods have successfully been used to describe viral spread history but their applications for assessing specific control measures are rare. In 2016-17, France experienced a devastating epidemic of a highly pathogenic avian influenza virus (H5N8 clade 2.3.4.4b). Using 196 viral genomes, we conducted a phylodynamic analysis combined with generalised linear model and showed that the large-scale preventive culling of ducks significantly reduced the viral spread between departements (French administrative division). We also found that the virus likely spread more frequently between departements that shared borders, but the spread was not linked to duck transport between departements. Duck transport within departements increased the within-departement transmission intensity, although the association was weak. Together, these results indicated that the virus spread in short-distances, either between adjacent departements or within departements. Results also suggested that the restrictions on duck transport within departements might not have stopped the viral spread completely. Overall, by testing specific hypothesis related to different control measures, we demonstrated that phylodynamics methods are capable of investigating the impacts of control measures on viral spread.

evolutionary biology↗

bioRxiv2021

Modelling the deathbed of ASF-infected wild boars in South Korea using 2019-2020 national surveillance data

In September 2019, African swine fever (ASF) was reported in South Korea for the first time. Since then, more than 651 ASF cases in wild boars and 14 farm outbreaks have been notified in the country. The purpose of this study was to characterize the spatial distribution of ASF-positive wild boar carcasses to identify the risk factors associated with the presence of ASF and number of ASF-positive wild boar carcasses in the affected areas. To achieve this objective, we divided the study into two periods (October 2, 2019, to January 19, 2020, and January 19 to April 28, 2020) and aggregated the number of reported ASF-positive carcasses into a regular grid of hexagons. To account for imperfect detection, we adjusted spatial zero-inflated Poisson regression models to the number of ASF-positive wild boar carcasses per hexagons. During the first study period, only proximity to North Korea was identified as a risk factor for the presence of African swine fever virus (ASFV). In addition, there were more reports in the affected hexagons with a high habitat suitability for wild boar, low heat load index (HLI), and high human density. During the second study period, proximity to an ASF-positive carcass reported during the first period was the only significant risk factor for the presence of ASF-positive carcasses. Additionally, high HLI and low elevation were associated with an increased number of ASF-positive carcasses reported in the affected hexagons. Although the proportion of ASF-affected hexagons increased from 0.06 (95% credible interval [CrI]: 0.05-0.07) to 0.09 (95% CrI: 0.08-0.10), the probability of reporting ASF-affected hexagons increased substantially from 0.49 (95% CrI: 0.41-0.57) to 0.73 (95% CrI: 0.66-0.81) between the two study periods. These results can be used to further advance risk-based surveillance.

ecology↗

bioRxiv2020

Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data of the index case to investigate within-flock transmission dynamics. A stochastic epidemic model was adjusted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. Results suggested that the virus was introduced 4 days (95% credible interval: 3 - 5) prior to the day suspicion was reported and that the transmission rate was 3.7 day-1 (95%CI: 2.6 - 5.3). On average, ducks started being infectious 3.1 hours (95%CI: 0.4 - 8.0) after infection and remained infectious for 4.4 days (95%CI: 3.1 - 5.6). Model outputs also suggested that the number of infectious ducks was already 3239 (95%CI: 26 - 3706) the day before suspicion, emphasising the substantial latent threat this virus could pose to other poultry farms and to neighbouring wildlife. These estimations can be applied to upcoming outbreaks and made available to veterinary services within few hours. This study illustrates how mechanistic models can provide rapid relevant insights to contribute to the management of infectious disease outbreaks of farmed animals.

ecology↗