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Avipoxvirus phylogenetics: identification of a PCR length polymorphism that discriminates between the two major clades

Susan Jarmin^1,

Stephen M. Laidlaw^1,

Michael A. Skinner^1,

¹ Institute for Animal Health, Compton, Newbury, Berkshire RG20 7NN, UK
² Veterinary Laboratory Agency, New Haw, Addlestone, Surrey KT15 3NB, UK

Correspondence
Michael A. Skinner
m.skinner{at}imperial.ac.uk

Avipoxvirus infections have been observed in an extensive range of wild, captive and domesticated avian hosts, yet little is known about the genome diversity and host-range specificity of the causative agent(s). Genome-sequence data are largely restricted to Fowlpox virus (FWPV) and Canarypox virus (CNPV), which have been sequenced completely, showing considerable divergence between them. It is therefore proving difficult, by empirical approaches, to identify pan-genus, avipoxvirus-specific oligonucleotide probes for PCR and sequencing to support phylogenetic studies. A previous preliminary study used the fpv167 locus, which encodes orthologues of vaccinia virus core protein P4b (A3). PCR per se did not discriminate between viruses, but restriction-enzyme or sequence analysis indicated that the avipoxviruses clustered either with FWPV or with CNPV. Here, further study of the P4b locus demonstrated a third cluster, from psittacine birds. A newly identified locus, flanking fpv140 (orthologue of vaccinia virus H3L), confirms the taxonomic structure. This locus is particularly useful in that viruses from the fowlpox-like and canarypox-like clusters can be discriminated by PCR on the basis of fragment size, whilst sequence comparison allows discrimination for the first time between Pigeonpox virus and Turkeypox virus. Except within the psittacines, virus and avian host taxonomies do not show tight correlation, with viruses from the same species located in very different clades. Nor are all the existing recognized avipoxvirus species, defined primarily by avian host species (such as CNPV and Sparrowpox virus), resolved within the present structure.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are shown in Table 1.

Present address: Department of Virology, Imperial College London, Faculty of Medicine, St Mary's Campus, Norfolk Place, London W2 1PG, UK.

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				S. A. Jarmin, R. Manvell, R. E. Gough, S. M. Laidlaw, and M. A. Skinner Retention of 1.2 kbp of 'novel' genomic sequence in two European field isolates and some vaccine strains of Fowlpox virus extends open reading frame fpv241 J. Gen. Virol., December 1, 2006; 87(12): 3545 - 3549. [Abstract] [Full Text] [PDF]