Snapshot of the Phylogenetic Relationships among Avian Poxviruses Circulating in Portugal between 2017 and 2023

Abstract

Avipoxvirus (APV), a linear dsDNA virus belonging to the subfamily Chordopoxvirinae of the family Poxviridae, infects more than 278 species of domestic and wild birds. It is responsible for causing avian pox disease, characterized by its cutaneous and diphtheric forms. With a high transmission capacity, it can cause high economic losses and damage to the ecosystem. Several diagnostic methods are available, and bird vaccination can be an effective preventive measure. Ten APV-positive samples were analyzed to update the molecular characterization and phylogenetic analysis of viruses isolated in Portugal between 2017 and 2023. A P4b gene fragment was amplified using a PCR, and the nucleotide sequence of the amplicons was determined using Sanger sequencing. The sequences obtained were aligned using ClustalW, and a maximum likelihood phylogenetic tree was constructed. With this study, it was possible to verify that the analyzed sequences are distributed in subclades A1, A2, B1, and B3. Since some of them are quite similar to others from different countries and obtained in different years, it is possible to conclude that there have been several viral introductions in Portugal. Finally, it was possible to successfully update the data on Avipoxviruses in Portugal.

Keywords: Avipoxvirus; molecular characterization; phylogenetic analysis; portugal; viral introduction.

Figure 1

Alignment of the sequences obtained in this study. (A) Nucleotide sequences alignment; (B) deduced amino acid sequences alignment. Unique mutations observed in sequence 16735-20, when compared with all the sequences present in the phylogenetic tree, are heightened by a red square in both alignments.

Figure 2

The evolutionary history was inferred using the maximum likelihood method and the Tamura 3-parameter model [29]. The tree with the highest log likelihood (−3244.07) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura 3 parameter model and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (five categories (+G, parameter = 0.8553)). The rate variation model allowed some sites to be evolutionarily invariable ([+I], 23.87% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 63 nucleotide sequences. There was a total of 463 positions in the final dataset. Evolutionary analyses were conducted in MEGA11 [30]. Star pentagrams indicate the strains of this study. A, B, C, D and E characters indicate groups of strains belonging to clades A, B, C, D and E, respectively.