Abstract
In winter 2016–7 the highly pathogenic avian influenza (HPAI) virus, H5N8 subtype, clade 2.3.4.4 group B, circulated extensively both in wild and domestic birds in Europe. Northern Italy was hit by three epidemic waves: the first in January–May 2017, the second in July–December 2017, and the latest in March 2018. To genetically characterize the viruses circulating in Italy we used the Illumina MiSeq platform to sequence the complete genome of representative viruses from each infected farm, for a total of 86 cases in poultry and 17 in wild birds. Maximum likelihood phylogenetic analyses performed using PhyML version 3.1 identified multiple viral introductions of distinct genotypes of HPAI H5N8 viruses in Italy at the beginning of the epidemic (January–February 2017). During the second epidemic wave a single genetic group originating from the virus A/wild duck/Poland/82A/2016 seemed to have been selected, further evolving into two different clusters, namely Italy-A and Italy-B. We identified four clusters of secondary outbreaks, the largest being the epidemic in the province of Brescia between October 2017 and March 2018, which had affected 26 farms. Evolutionary and phylogeographic analyses performed with the BEAST v1.8.4 package (applying a Bayesian Markov chain Monte Carlo approach, using a constant size coalescent tree prior and a SRD06 model of nucleotide substitution) indicated that different viral introductions had probably occurred through migratory birds from West Russia, Siberia, Central and East Europe. The discrete and continuous phylogeographic analyses showed that group Italy-A had probably emerged between February and April 2017 in the province of Mantua and had then spread eastwards, circulating in the Veneto region and eastern Lombardy; on the contrary, Italy-B had arisen between March and July 2017 in the central part of Lombardy and had spread westwards, circulating in the western part of Lombardy, Emilia Romagna, and Piedmont regions. This study was instrumental to reconstruct the virus dissemination routes and indicated that wild and domestic birds from Lombardy most likely represented the key source for the re-emergence and spread of the HPAI virus during the second and the third epidemic waves. This key spatial information will help to define appropriate disease control strategies.
High Genetic Diversity of Newcastle Disease Virus in Wild and Domestic Birds in Northeastern China from 2013 to 2015 Reveals Potential Epidemic Trends
