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

Abstract

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.

Molecular identification of local field isolated fowl pox virus strain from Giza governorate of Egypt

“…3) agree with that reported by into SPF chickens revealed that about 100% showed other authors where application of the PCR for the takes at fourth day post inoculation in wing web sites of diagnosis of FPV infection gave a positive 578bp inoculation, while 75% of the inoculated pigeons fragment [34] and with others who also used PCR for showed thickening of the thighs (sites of inoculation in identification and characterization of FPV strain pigeons). In addition, neither negative control chickens [11,35]. Data obtained by others [30] also adds more nor pigeons showed lesions or symptoms related to support to our results.…”

First phylogenetic analysis of Avipoxvirus (APV) in Brazil

“…The closest turkeys avipoxvirus 4b virion core protein sequences found in GenBank ® , in the subclade A1, were from Italy (GQ180212) and Germany (AY530304), which were identical to our samples on the level of nucleotide and amino acid sequence. The turkey APV DNA sequenced here appears to be closely related to a falcon APV (AM050376) isolate from United Arab Emirates (Jarmin et al 2006), a turkey (AM050387) isolate from United Kingdon (Jarmin et al 2006) and an ostrich (AY530305) without any isolation location defined (Lüschow et al 2004), and all of them belonging to A2 clade. The closest turkey APV sequence found in A2 clade was from Italy (GQ180212), and varied 9% on the amino acid level.…”

“…Hence, the amplification of a 578-base pair (bp) region of P4b, a highly conserved gene of APV, is commonly used to diagnose APV infections, which is highly conserved amongst all poxviruses (Binns et al 1989). The P4b gene has already been reported in other phylogenetic studies of APV to distinguish between clades A, B, C, A1-4 and B1-2 (Lüschow et al 2004, Weli et al 2004, Jarmin et al 2006). In addition, conventional and real time PCR techniques provide results more rapidly than virus isolation.…”

“…The APV specific PCR was performed using a primer pair described by Huw Lee & Hwa Lee (1997) based on P4b sequence of FPV virus strain HP444. FPV specific PCR was performed using a primer pair described by Jarmin et al (2006), with a forward primer with slight modifications described by Manarolla et al (2010). APV and FPV amplifications were performed as described by Manarolla et al (2010), except that the final extension of APV specific PCR was 10 min at 72°C.…”

“…Nonetheless, turkeys isolates may fail to grow in these cell lines, even after repeated passages (Tripathy & Reed 2013). According to Jarmin et al (2006), APV replicates within the cytoplasm of the cells that they infect, causing type A cytoplasmic inclusions (Tripathy & Reed 2013).…”