Figure 2. Phylogenetic position of BerSQPV (bold) from a red squirrel in Berlin, Germany, within the Chordopoxvirinae. We used MAFFT (12) to perform multiple alignments of all complete genome sequences within a species of the Chordopoxvirinae subfamily available in GenBank. The minimum pairwise identity found within any of these intraspecies alignments was 79.1%; the maximum pairwise identity of BerSQPV with any chordopoxvirus genome available was 47%. Because of this extreme difference in minimum pairwise identities, we selected individual prototype genomes for each species and the viruses with highest identity to BerSQPV for phylogenetic analysis (as indicated in figure). We performed a multiple alignment of these representative sequences with the BerSQPV genome and removed low-quality regions from the alignment using Gblocks version 0.91(13), yielding a stripped alignment of 52,563 gap-free positions. The maximum-likelihood tree was then calculated using PhyML(14) (general time reversible plus gamma, 4 substitution rate categories, no invariable sites, BEST topology search, χ2-based parametric branch supports). Scale bar indicates nucleotide substitutions per site. BPSV, bovine papular stomatitis virus BV-AR02 (NC_005337); CMLV, camelpox virus CMS (AY009089); CNPV, canarypox virus Wheatley C93 (NC_005309); CPXV, cowpox virus Brighton Red (AF482758); CRV, Nile crocodilepox virus (NC_008030); DPV, deerpox virus W-848–83 (NC_006966); ECTV, ectromelia virus Moscow (AF012825); FWPV, fowlpox virus NVSL (NC_002188); GTPV, goatpox virus Pellor (NC_004003); LSDV, lumpy skin disease virus NI-2490 (NC_003027); MOCV, Molluscum contagiosum virus subtype 1 (NC_001731); MPXV, monkeypox virus Zaire-96-I-16 (AF380138); MYXV, myxoma virus Lausanne (NC_001132); ORFV, Orf virus OV-SA00 (NC_005336); PCPV, pseudocowpox virus VR634 (NC_013804); PEPV, penguinpox virus (KJ859677); PGPV, pigeonpox virus FeP2 (NC_024447); RCNV, raccoonpox virus Herman (NC_027213); RDPV, red deer pox virus (KM502564); RFV, rabbit fibroma virus Kasza (AF170722); SKPV, skunkpox virus (KU749310); SPPV, sheeppox virus 17077–99 (NC_004002); UK SQPV, squirrel poxvirus Red squirrel UK (HE601899); SWPV, swinepox virus 17077–99 (NC_003389); TATV, taterapox virus Dahomey 1968 (NC_008291); TKPV, turkeypox virus HU1124/2011 (KP728110); TPV, tanapox virus (EF420156); FukVACV, vaccinia virus Copenhagen (M35027); VARV, variola major virus Bangladesh-1975 (L22579); VPXV, volepox virus (KU749311); YLDV, Yaba-like disease virus (NC_002642); YMTV, Yaba monkey tumor virus (NC_005179); Yoka, Yokapox virus (NC_015960)].