Table 1.
Summary of orf virus-affected farms and animals.
Fig 1.
Skin lesions at the mouth of a goat suspected contagious ecthyma caused by orf virus infection.
Scabby mouth lesions showing wheals, ecthyma, pustules, or scales at the lips of a goat.
Table 2.
Primers for screening PCR, B2L and A32L gene amplification.
Table 3.
Representative Parapoxvirus B2L and A32L gene nucleotide sequences retrieved from GenBank using for genetic characterization and phylogenetic tree construction.
Fig 2.
Confirmatory polymerase chain reaction (PCR) product of ORFV in all examined samples.
Orf virus (ORFV) (507 base pair) was detected with gel electrophoresis using ORFV specific primer set [11]. Pattani/2020 served as positive control. Negative control was included in the last lane.
Fig 3.
Phylogenetic analysis of orf virus isolates A) Phylogenetic tree of B2L gene.
The maximum-likelihood tree of B2L gene was constructed from B2L gene nucleotide sequences. B) Phylogenetic analysis of A32L gene. The maximum-likelihood tree of A32L gene was constructed from A32L gene nucleotide sequences. Seven ORFV Southern Thai isolates and isolates retrieved from the GenBank database were included. The tree was generated using the T92 + G + I model with 1000 bootstrap replicates. Bootstrap values are indicated at branch nodes. Blue dots represent the ORFV B2L genes identified in this study. Red dots represent the ORFV A32L genes identified in this study. Cluster of the viruses are indicated in the right.
Fig 4.
Bayesian maximum confidence (MCC) trees for the orf viruses from Southern Thailand.
Bayesian phylogenetic trees were constructed for the A) B2L gene and B) A32L gene using the BEAST v1.10.5.0 software, and were visualized with FigTree (v1.4.4). The scale by factor with offset by 2024 indicates node ages on the branch nodes. The time scale is displayed at the bottom of the trees. Southern Thai isolates of the B2L gene are marked with a blue circle, while Southern Thai isolates of the A32L gene are marked with a red circle.
Fig 5.
Scatter plots of ORF virus isolates based on discriminant analysis of principal components (DAPC) using A) B2L and B) A32L nucleotide sequences.
Individual viral isolates are represented as dots, and groups are indicated by inertia ellipses. The bar plot of discriminant analysis (DA) eigenvalues is shown in the inset panel. The first two discriminant functions correspond to the x- and y-axes, respectively. Genetic clusters are represented in different colors. A) B2L gene, Cluster 1 (light blue), Korea/2009 (GQ328006) and Brazil/1993 (JN088051); Cluster 2 (dark blue), China/2023 (PP733997) and Malaysia/2020 (OP279270); Cluster 3 (light green), Songkhla/2024 (PV173487, PV173488); Cluster 4 (dark green), Pattani/2024 (PV173489–PV173492), Malaysia/2018 (OK169620, MW537048), and Malaysia/2014 (KR024023, KR024024, KR024025); Cluster 5 (light pink), Pattani/2020 (PV173486) and Assam/2009 (JN846834); Cluster 6 (dark pink), Brazil/1992 (JN088052); and Cluster 7 (light orange), China/2024 (PP805860), China/2014 (KU199831), and China/2012 (KC568397). B) A32L gene, Cluster 1 (light blue), Ethiopia/2012 (KT438543, KT438544); Cluster 2 (dark blue), Ethiopia/2010 (KT438540) and Ethiopia/2008 (KT438539); Cluster 3 (light green), Pattani/2024 (PV173482–PV173485); Cluster 4 (dark green), China/2012 (KP010354, KP010356) and Assam/2010 (JN183069); Cluster 5 (light pink), New Zealand/1987 (DQ184476) and USA/1982 (AY386263); Cluster 6 (dark pink), Taiwan/2006 (EU327509); Cluster 7 (light orange), Ethiopia/2012 (KT438531–KT438533); and Cluster 8 (dark orange), Songkhla/2024 (PV173480, PV173481), Pattani/2020 (PV173479), Malaysia/2018 (MW537048), India/2018 (MH766377), India/2017 (MT332357), and USA/2000 (AY386264).
Fig 6.
Carboxyl-terminal heterogeneity in the A32L gene-encoded ATPase of ORFV.
Comparative analysis of amino acid sequences of ATPase protein of Southern Thai isolates and references isolates retrieved from Genbank were aligned using ClustalW method in Bioedit (V.7.2). The deletions of amino acid residues in Songkhla isolates from 2024 and Pattani isolate from 2020 was highlighted in blue box. The presence of unique serine (S) amino acid in Pattani isolates from 2024 were highlighted in pink box.