Figure 3. A) Partial amino acid alignment of A56R vaccinia virus Copenhagen (VACV-COP). Sequences were retrieved from GenBank and aligned using the BioEdit program (www.mbio.ncsu.edu/bioedit/bioedit.html). VACV-COP (M35027, 161908-161957) is used as the reference sequence; International Union of Pure and Applied Chemistry symbols, amino acids; dots, residues identical to the reference sequence; dashes, gaps created by the alignment; gold box surrounds the 18-nt deletion once proposed as a Brazilian (BRZ)-VACV molecular identifier. RPXV-UTR, rabbitpox virus-Utrecht; HSPV, horsepox virus; MVA, modified vaccinia Ankara; LIVP, Liverpool; BFL, buffalopox; BAV, BeAn 58058 virus; SAV, SpAn232 virus; VBH, Belo Horizonte virus; GP, Guarani virus; ARAV, Araçatuba virus; CTGV, Cantagalo virus; PSTV, Passatempo virus; IOC, Institute Oswaldo Cruz. B) Depiction of the rpo132-ATI-p4c-A27 region in Cowpox virus Brighton Red (CPXV-BR) and VACV strains. Positions of primers RNApol, ATI-low, ATI-up, and P4c1 are illustrated. These primers have been used for the molecular diagnosis of Brazilian (BRZ)-VACV (5,26). The 300-bp fragment amplified by primers RNApol and P4c1 from GP1V and VBH was sequenced by Trindade et al. (9,13). Sequence outside this region is unknown. ATI-f is used to designate coding regions that resemble fragments of the wild-type (CPXV-BR) ATI gene. The gap in VACV-COP lies within the A26L gene. *This gene is often referred to as ATI due to its original description. However, the coding region is actually a fusion of the C-terminus of ATI and the N-terminus of P4c where the sequence in between has been deleted. The gene is currently identified by the Poxviridae Bioinformatics Resource (http://athena.bioc.uvic.ca/database.php?db=poxviridae) as belonging to the P4c precursor family. †Western Reserve is presumed similar in structure to SpAn232 virus, GP2V, ARAV, and PSTV due to similar restriction fragment length polymorphism results (6,7,11,13).
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