Genome Sequences of Akhmeta Virus, an Early Divergent Old World Orthopoxvirus

Abstract

Annotated whole genome sequences of three isolates of the Akhmeta virus (AKMV), a novel species of orthopoxvirus (OPXV), isolated from the Akhmeta and Vani regions of the country Georgia, are presented and discussed. The AKMV genome is similar in genomic content and structure to that of the cowpox virus (CPXV), but a lower sequence identity was found between AKMV and Old World OPXVs than between other known species of Old World OPXVs. Phylogenetic analysis showed that AKMV diverged prior to other Old World OPXV. AKMV isolates formed a monophyletic clade in the OPXV phylogeny, yet the sequence variability between AKMV isolates was higher than between the monkeypox virus strains in the Congo basin and West Africa. An AKMV isolate from Vani contained approximately six kb sequence in the left terminal region that shared a higher similarity with CPXV than with other AKMV isolates, whereas the rest of the genome was most similar to AKMV, suggesting recombination between AKMV and CPXV in a region containing several host range and virulence genes.

Keywords: Akhmeta virus; cowpox virus; orthopoxvirus; recombination.

Figure 1

The ITR alignment of selected orthopoxvirus (OPXV) sequences. Alignment position is indicated at the top. Sequence conservation is shown with an identity graph (100% green, at least 30% and under 100% greeny-brown, under 30% red). Yellow boxes indicate non-repetitive (NR) unique sequences NR1, NR2, and NR3 from left to right, respectively. Faint purple boxes indicate tandem repeat (TR) TR1 and TR2. Blue boxes show the location of annotated genes with arrows pointing in the direction of transcription within the NR3. Black bars represent partially aligned genome sequences, horizontal lines represent alignment gaps; * missing the NR2. Detailed information about each ITR region is listed in Supplementary Table S4.

Figure 2

Phylogenetic analysis of OPXV species using the 100-kb central region of genome. Twenty-two selected OPXVs were aligned using MAFFT and gap columns were removed. A phylogenetic tree was constructed using BEAST (v2.4.7). Posterior probability is 1 at each node of the reconstructed tree, indicatingthe phylogeny is well supported. The tree was drawn in the scale of substitutions per site. The identity matrix table of these OPXV sequences is presented in Supplementary Table S5.

Figure 3

A recombination event in the AKMV_VANI10 sequence was investigated using Simplot. The identity of AKMV_VANI10 to each of the selected sequences was plotted on the Y-axis, and the X-axis indicates the position of alignment. Each colored line represents one virus. Orange, AKMV_AKHM13-88; pink, CPXV_AUS99; yellow, CPXV_GRI-90; blue, CPXV_HumLit08/1; cyan, CPXV_HumGra07/1; and green, CPXV_BR. Arrows indicate positions of coding regions.