Isolation and Phylogenetic Grouping of Equine Encephalosis Virus in Israel

During 2008–2009 in Israel, equine encephalosis virus (EEV) caused febrile outbreaks in horses. Phylogenetic analysis of segment 10 of the virus strains showed that they form a new cluster; analysis of segment 2 showed ≈92% sequence identity to EEV-3, the reference isolate. Thus, the source of this emerging EEV remains uncertain

Detection of Epizootic Hemorrhagic Disease Virus Serotype 1, Israel

During September 2016–February 2017, we detected epizootic hemorrhagic disease virus (EHDV) in ruminants in Israel. BLAST and phylogenetic analyses of segment 2 in 6 EHDVs isolated from field samples indicated a close relationship to the EHDV serotype 1 strain in Nigeria. Affected cattle had mostly mild or asymptomatic disease

Persistence of Lineage IV Peste-des-petits ruminants virus within Israel since 1993: An evolutionary perspective.

Peste-des-petits ruminants (PPR) is one of the most important infectious diseases of domesticated small ruminants. From the initial identification in 1942 in West Africa, PPR virus (PPRV) has spread throughout much of the developing world. PPRV is now considered endemic throughout Africa, with the notable exception of South Africa, the Middle-East and Israel, as well as South-, East-, and Central Asia. Despite this widespread dispersal, the evolution and transmission of PPRV in endemic populations is not well understood. This understanding will be critical in the planning of rational measures to eradicate PPRV by the planned time as defined by the FAO and OIE. To further advance the understanding of the evolution of PPRV the full genome sequence of 18 viruses isolated from Israel from consecutive years between 1997-2014 were generated. This data set is unique and crucial for the understanding of the evolution of PPRV, as it represents the first set of full-length sequence data available from consecutive years from a single geographic location. Analysis of these full genome sequences shows 96.2-99.9% nucleotide conservation across the Israel isolates and further demonstrates the strong purifying selection pressures on PPRV within Israel and globally. Four amino acid substitutions indicative of putative positive selection were additionally identified within the Israel isolates. The mean substitution rate per site per year was estimated to be 9.22 x 10-4 (95% HPD 6.206 x 10-4-1.26 x 10-3). Using Bayesian and phylogenetic analyses we further demonstrate that the PPRV isolates from Israel belongs to linage IV and form a single strong regional cluster within all other lineage IV viruses circulating worldwide implying a single incursion into Israel

Nucleotide and amino acid percentage differences between PPRV Lineages.

<p>Nucleotide and amino acid percentage differences between PPRV Lineages.</p

Maximum clade credibility (MCC) tree from Bayesian analysis of full-length PPRV genomes.

<p>The posterior probabilities are indicated by the size of the node, and TMRCA and 95% HPD of the branches are depicted. Accession number, country of origin, and sampling year of each isolate is shown. All sequences generated in this study are highlighted in red.</p

Sample details.

<p>Sample details.</p

Location of PPR outbreaks in Israel (1993–2014).

<p>Sampling locations are plotted in red, GPS co-ordinates derived from Google maps API [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177028#pone.0177028.ref049" target="_blank">49</a>]. Comparisons of the full length genome, and coding regions from the 18 Israel samples sequenced in this study. Indicated that the Israel isolates were more closely related than other groups (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177028#pone.0177028.t002" target="_blank">Table 2</a>). Overall the Israel sequences were found to be 96.2 to 99.9% identical at the nucleotide level. As has been previously reported the P gene was the most variable [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177028#pone.0177028.ref050" target="_blank">50</a>] and the matrix (M) gene the most conserved (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177028#pone.0177028.t002" target="_blank">Table 2</a>).</p

Mean ratio of nonsynonymous (dN) to synonymous (dS) substitutions for each site in the coding regions of PPRV.

<p>Proportions of dN and dS were calculated using the single-likely ancestor counting method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177028#pone.0177028.ref045" target="_blank">45</a>]. Dashed lines indicate gene boundaries.</p

Significant amino acid changes identified in PPRV lineage groups.

<p>Significant amino acid changes identified in PPRV lineage groups.</p