Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016-2017 epidemic in Italy

Abstract

Between October 2016 and December 2017, several European Countries had been involved in a massive Highly Pathogenic Avian Influenza (HPAI) epidemic sustained by H5N8 subtype virus. Starting on December 2016, also Italy was affected by H5N8 HPAI virus, with cases occurring in two epidemic waves: the first between December 2016 and May 2017, and the second in July-December 2017. Eighty-three outbreaks were recorded in poultry, 67 of which (80.72%) occurring in the second wave. A total of 14 cases were reported in wild birds. Epidemiological information and genetic analyses were conjointly used to get insight on the spread dynamics. Analyses indicated multiple introductions from wild birds to the poultry sector in the first epidemic wave, and noteworthy lateral spread from October 2017 in a limited geographical area with high poultry densities. Turkeys, layers and backyards were the mainly affected types of poultry production. Two genetic sub-groups were detected in the second wave in non-overlapping geographical areas, leading to speculate on the involvement of different wild bird populations. The integration of epidemiological data and genetic analyses allowed to unravel the transmission dynamics of H5N8 virus in Italy, and could be exploited to timely support in implementing tailored control measures.

Figure 1

Distribution of H5Nx HPAI cases In Italy in 2016-2017; Cases are classified per epidemic wave (first wave: blue; second wave: magenta), and per type (Domestic poultry: circle; Wild birds: cross).

Figure 2

Weekly H5Nx cases in domestic poultry (red columns) and wild birds (blue columns) in Italy in 2016-2017; the dates refer to the onset of symptoms for poultry farms, and finding day for wild birds.

Figure 3

Distribution in space and time of cases classified into Italy-A and Italy-B subgroups; cases are classified as belonging to either the Italy-A or the Italy-B groups. ‘Current cases’ refers to cases occurred in the period of reference indicated for each panel, ‘Previous cases’ refers to cases occurred in preceding periods.

Figure 4

Median-joining phylogenetic network of the eight concatenated gene segments of the 2016-2017 Italian HPAI H5N8 viruses. Each unique sequence genotype is represented by a circle sized relatively to its frequency in the data set. Branches represent the shortest trees and are proportional to the number of nucleotide mutations (in blue) that separate each node. Median vectors are indicated as black circles.

Figure 5

Representation of the network of contacts during for the 2017 H5N8 HPAI epidemic in Italy; numbers reported in the graph refer to the outbreak ID.

Figure 6

Second epidemic wave - Epidemic curve indicating the occurrence of primary (red) and secondary (blue) cases. The x-axis report date of symptoms onset.