Chasing Jenner's vaccine: revisiting cowpox virus classification

Abstract

Cowpox virus (CPXV) is described as the source of the first vaccine used to prevent the onset and spread of an infectious disease. It is one of the earliest described members of the genus Orthopoxvirus, which includes the viruses that cause smallpox and monkeypox in humans. Both the historic and current literature describe "cowpox" as a disease with a single etiologic agent. Genotypic data presented herein indicate that CPXV is not a single species, but a composite of several (up to 5) species that can infect cows, humans, and other animals. The practice of naming agents after the host in which the resultant disease manifests obfuscates the true taxonomic relationships of "cowpox" isolates. These data support the elevation of as many as four new species within the traditional "cowpox" group and suggest that both wild and modern vaccine strains of Vaccinia virus are most closely related to CPXV of continental Europe rather than the United Kingdom, the homeland of the vaccine.

Figure 1. CPXV Phylogeny.

The tree search was based on a complete coding region alignment (C23L-B29R) with gapped columns removed (145,177 bp). Posterior probabilities are shown to the right of each node in black. Uncorrected p distance measures were calculated from the matrix and are shown to the left of each node. Red indicates distances greater than or equal to the distance between TATV and the VARV clade (0.0154); blue indicates a distance less than this value. Additional distance measures between nodes and taxa are underlined and designated by dashed arrows. Asterisks indicate distance values at nodes where patristic distance values are above the VARV-TATV threshold and conflict with uncorrected p values. Cowpox-like (groups 1–4) and Vaccinia-like (group 5) clades are indicated to the right. Brackets encompass isolates or groups of isolates where distance measures separate them from their nearest neighbours at least as much as the distance between TATV and VARV. Each of these groups is labelled with a number (1–5).

Figure 2. Map of CPXV isolate origins.

The place of origin for each CPXV isolate is designated on the map. The inset shows CPXV isolates divided into five distinct clusters corresponding to those in Figure 1 and grouped by dashed lines.

Figure 3. Alignment of three CPXV genes.

Alignment images were created in Geneious Pro™ 5.3. Isolate names are provided to the right along with the branching relationships and numbered groups presented in Figure 1. Sequence areas depicted were extracted from the following coding regions: (A) CPXV_BR_021 (VACV_COP_C11R), secreted virulence factor, vaccinia growth factor (VGF; epidermal growth factor-like protein), promotes cell survival; (B) CPXV_BR_191 (VACV_COP_A53R), CrmC, viroceptor, soluble virus tumor necrosis factor receptor homolog, binds and antagonizes TNF-α; (C) CPXV_BR_212 (VACV_COP_B19R), viroceptor, soluble IFN α/β receptor homolog, binds and antagonizes IFN α/β. Numbers along the top of the alignment refer to the position of the region in the full genome alignment (supplementary material). Grey indicates conserved bases while colors (red, blue, yellow, green) indicate differences (A, C, G, T, respectively) with regard to the reference sequence (CPXV_GER1980_EP4) highlighted in yellow. Colored boxes identify shared nucleotide states that reflect monophyletic relationships seen in the tree. Notations below each alignment describe subsequent amino acid changes (standard IUPAC code).