Whole Genome Characterization of Orthopoxvirus (OPV) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses

Abstract

Orthopoxviruses (OPVs) are diffused over the complete Eurasian continent, but previously described strains are mostly from northern Europe, and few infections have been reported from Italy. Here we present the extended genomic characterization of OPV Abatino, a novel OPV isolated in Italy from an infected Tonkean macaque, with zoonotic potential. Phylogenetic analysis based on 102 conserved OPV genes (core gene set) showed that OPV Abatino is most closely related to the Ectromelia virus species (ECTV), although placed on a separate branch of the phylogenetic tree, bringing substantial support to the hypothesis that this strain may be part of a novel OPV clade. Extending the analysis to the entire set of genes (coding sequences, CDS) further substantiated this hypothesis. In fact the genome of OPV Abatino included more CDS than ECTV; most of the extra genes (mainly located in the terminal genome regions), showed the highest similarity with cowpox virus (CPXV); however vaccinia virus (VACV) and monkeypox virus (MPXV) were the closest OPV for certain CDS. These findings suggest that OPV Abatino could be the result of complex evolutionary events, diverging from any other previously described OPV, and may indicate that previously reported cases in Italy could represent the tip of the iceberg yet to be explored.

Keywords: OPV Abatino; core gene set; cowpox virus; ectromelia virus; orthopoxvirus; phylogenetic tree.

Figure 1

Location and phylogenetic analysis of the core genome of Orthopoxvirus (OPV) Abatino: (a) Localization of individual 102 coding sequences (CDS), highly conserved across all analyzed OPV, within the OPV Abatino genome. CDS are annotated following vaccinia virus-Copenhagen (VACV-Cop) nomenclature; (b) phylogenetic analysis of the core genome of OPV Abatino, built with the 102 concatenated CDS in the context of representative OPV genomes. CPXV clades, defined according to [2,5,17,18,19], are identified with color codes; three cowpox virus (CPXV) strains with discordant or no specified classification are also reported in black characters. The OPV Abatino strain is highlighted in red. A New World OPV, i.e. Raccoonpox Virus (RACV), was used as an outgroup. The CDS used in this analysis are detailed in Supplementary Table S1.

Figure 2

CDS similarity and gene synteny of OPV Abatino along their nt position, compared with the two most phylogenetically related OPV strains (Ectromelia virus-Moscow (ECTV-Mos) and CPXV-Ger2010-MKY). The CDS blocks are color coded: blue blocks represent the CDS with higher similarity to ECTV; red blocks represent CDS with higher similarity to CPXV; orange blocks represent CDS with comparable similarity to both reference genomes. (a) Similarity plot of the all CDS of OPV Abatino. (b) Similarity plot of left terminal region. (c) Similarity plot of right terminal region of the OPV Abatino genome. Bars below the plots show as empty boxes the regions of either ECTV-Mos or CPXV-Ger2010-MKY genome lacking homologous CDS in OPV Abatino.