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. Author manuscript; available in PMC: 2016 Jan 1.

Published in final edited form as: Virology. 2014 Nov 17;474:154–162. doi: 10.1016/j.virol.2014.10.024

Fig. 3 — Gene-specific maximum likelihood phylogenetic trees of the nonstructural and structural proteins of all currently classified 31 alphavirus species (48 total sequences in the analysis). In some cases, certain proteins (i.e., E3 and 6K) have been combined with their C-terminal adjacent larger protein (i.e., E2 and E1, respectively) due to the small size of the former. All bootstrap values >70% are shown and shaded appropriately. All trees were rooted using the most divergent pair of sequences in the data set (the fish alphaviruses, SPDV and its variant SDV) and which are therefore assumed to represent an outgroup. The sequences of the WEEV antigenic complex recombinants and EEEV/MADV are boxed. Sequences used in the analysis were: Aura virus (AURAV) BeAr 10315 (AF126284); Barmah Forest virus (BFV) BH2193 (BFU73745); Bebaru virus (BEBV) MM2345 (NC_016962); Buggy Creek virus (BCRV; FMV subtype) 81V1822 (HM147986); Cabassou virus (CABV) CaAr508 (AF075259); Chikungunya virus (CHIKV) ITA07-RA1 (EU244823), CHIKV IND-00-MH4 (EF027139), and CHIKV 37997 (AY726732); Eastern equine encephalitis virus (EEEV) FL93-939 (EF151502) and EEEV 82V2137 (U01034); Eilat virus (EILV) EO329 (NC_018615); Everglades virus (EVEV) Fe3-7c (AF075251); Fort Morgan virus (FMV) CM4-146 (NC_013528); Getah virus (GETV) LEIV 16275 Mag (EF631998) and GETV HB0234 (EU015062); Highlands J virus (HJV) 585-01 (NC_012561), HJV 744-01 (GU167952), and HJV B-230 (GQ227789); Madariaga virus (MADV) PE-3.0815 (DQ241303) and MADV BeAr 436087 (EF151503); Mayaro virus (MAYV) MAYLC (DQ001069); Middelburg virus (MIDV) 857 (EF536323); Mosso das Pedras virus (MDPV) 78V-3531(AF075257); Mucambo virus (MUCV) BeAn 8 (AF075253); Ndumu virus (NDUV) SAAr2204 (NC_016959); O’nyong-nyong virus (ONNV) SG650 (AF079456) and ONNV Igbo Ora strain IBH10964 (AF079457); Pixuna virus (PIXV) BeAr35645 (AF075256); Rio Negro virus (RNV) AG80-663 (AF075258); Ross River virus (RRV) 2975 (GQ433360); Sagiyama virus (SAGV; RRV subtype) (AB032553); Salmon pancreas disease virus (SPDV) F93125 (AJ316244); Semliki forest virus (SFV) L10 (AY112987) and SFV Me Tri (EU350586); Sindbis virus (SINV) SW6562 (AF429428), SINV Ockelbo strain Edsbyn 82-5 (M69205), and SIN-like virus S.A.AR86 (U38305); Sleeping disease virus (SDV; SPDV subtype) S49P (AJ316246); Southern elephant seal virus (SESV) McQI (NC_016960); Tonate virus (TONV) CaAn 410d (AF075254); Trocara virus (TROV) BeAr422431 (HM147991); Una virus (UNAV) BeAr 13136 (HM147992); Venezuelan equine encephalitis virus (VEEV) MX01-22 (AY823299); Western equine encephalitis virus (WEEV) McMillan (GQ287640), WEEV 71-V1658 (GQ287645), and WEEV AG80-646 (GQ287646). The FMV sequence is highlighted in bold italic.

Fig. 3 — Gene-specific maximum likelihood phylogenetic trees of the nonstructural and structural proteins of all currently classified 31 alphavirus species (48 total sequences in the analysis). In some cases, certain proteins (i.e., E3 and 6K) have been combined with their C-terminal adjacent larger protein (i.e., E2 and E1, respectively) due to the small size of the former. All bootstrap values >70% are shown and shaded appropriately. All trees were rooted using the most divergent pair of sequences in the data set (the fish alphaviruses, SPDV and its variant SDV) and which are therefore assumed to represent an outgroup. The sequences of the WEEV antigenic complex recombinants and EEEV/MADV are boxed. Sequences used in the analysis were: Aura virus (AURAV) BeAr 10315 (AF126284); Barmah Forest virus (BFV) BH2193 (BFU73745); Bebaru virus (BEBV) MM2345 (NC_016962); Buggy Creek virus (BCRV; FMV subtype) 81V1822 (HM147986); Cabassou virus (CABV) CaAr508 (AF075259); Chikungunya virus (CHIKV) ITA07-RA1 (EU244823), CHIKV IND-00-MH4 (EF027139), and CHIKV 37997 (AY726732); Eastern equine encephalitis virus (EEEV) FL93-939 (EF151502) and EEEV 82V2137 (U01034); Eilat virus (EILV) EO329 (NC_018615); Everglades virus (EVEV) Fe3-7c (AF075251); Fort Morgan virus (FMV) CM4-146 (NC_013528); Getah virus (GETV) LEIV 16275 Mag (EF631998) and GETV HB0234 (EU015062); Highlands J virus (HJV) 585-01 (NC_012561), HJV 744-01 (GU167952), and HJV B-230 (GQ227789); Madariaga virus (MADV) PE-3.0815 (DQ241303) and MADV BeAr 436087 (EF151503); Mayaro virus (MAYV) MAYLC (DQ001069); Middelburg virus (MIDV) 857 (EF536323); Mosso das Pedras virus (MDPV) 78V-3531(AF075257); Mucambo virus (MUCV) BeAn 8 (AF075253); Ndumu virus (NDUV) SAAr2204 (NC_016959); O’nyong-nyong virus (ONNV) SG650 (AF079456) and ONNV Igbo Ora strain IBH10964 (AF079457); Pixuna virus (PIXV) BeAr35645 (AF075256); Rio Negro virus (RNV) AG80-663 (AF075258); Ross River virus (RRV) 2975 (GQ433360); Sagiyama virus (SAGV; RRV subtype) (AB032553); Salmon pancreas disease virus (SPDV) F93125 (AJ316244); Semliki forest virus (SFV) L10 (AY112987) and SFV Me Tri (EU350586); Sindbis virus (SINV) SW6562 (AF429428), SINV Ockelbo strain Edsbyn 82-5 (M69205), and SIN-like virus S.A.AR86 (U38305); Sleeping disease virus (SDV; SPDV subtype) S49P (AJ316246); Southern elephant seal virus (SESV) McQI (NC_016960); Tonate virus (TONV) CaAn 410d (AF075254); Trocara virus (TROV) BeAr422431 (HM147991); Una virus (UNAV) BeAr 13136 (HM147992); Venezuelan equine encephalitis virus (VEEV) MX01-22 (AY823299); Western equine encephalitis virus (WEEV) McMillan (GQ287640), WEEV 71-V1658 (GQ287645), and WEEV AG80-646 (GQ287646). The FMV sequence is highlighted in bold italic.