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. 2018 Dec 12;13(12):e0207480. doi: 10.1371/journal.pone.0207480

Table 2. Proteins affected by the 27 recombination events.

The predicted proteins are listed, as well as their putative functions. Predicted protein names are in bold if the complete ORF forms part of the recombination region. The number of amino acid differences between the predicted proteins of the minor and major parent are listed for the complete ORF. All the amino acid substitutions between the recombinant virus and the major parent groups are indicated along with their positions in the protein.

Recom- bination Event Number Protein(s) Amino acid differences (Minor and major parent) Amino acid differences (Recombinant to major parent)
1 LSD144 (LW144a and LW144b) (Kelch-like protein); LSD145 (Ankyrin repeat protein) LSD144: 36 aa; LSD145: 44 aa; LSD144: 218 I>D = N; 234 S>N; 338; Translation identical to minor parent, thus 252–267 is FIYISDPNWYSKKYDI; 337^338 del>E; 375 Y>E; 385 D>S; 423 S>T; 456 E>A; 529 S>A; 548 terminate similar to major parent; LSD145: 8 I>V; 22 I>L; 121 S>G; 139 I>V; 144 V>I; 181 T>I; 189 F>L = L; 196 G>N; 202 S>R; 205 N>D; 210 T>S; 216 C>S; 241 K>Q; 261 M>V; 269 L>I; 273 N>S; 292 S>N; 309 S>P; 336 V>I; 340 I>V; 341 E>D; 342 H>N; 349 D>E; 353 Y>H;
2 LSD134 (LW134a and LW134b); LSD135 (putative IFN-alpha/beta binding protein); LSD136 (hypothetical protein); LSD137 (hypothetical protein); LSD138 (IG domain OX-2-like protein) LSD134: 81 aa; LSD135: 7 aa; LSD136: 3 aa; LSD137: 4 aa; LSD138: 6 aa; LSD134: 2 G>K; Translation similar to minor parent, thus 720–783 is QSLRRYSSSDYETIGENIYESIREPEYALLSKPRVLNPRSHIPLPSVPKDDIPFTQQKRKVID; 886 S>N; 1056 K>R = R; 1900 S>A; 2007^2008 del>N; 2018 N>del; LSD135: 11 L>S; 65 T>K; 129 A>T; 156 R>Q; 213 I>L; 249 S>P; 346 R>Y; LSD136: 32 V>I; 76 S>L; 80 N>D = D; 141 V>I; LSD137: 58 H>P; 106 V>I; 143 T>A; 212 S>A; LSD138: 14 G>S; 24 S>T; 43 S>N; 93 V>I; 100 Q>K;
3 LSD008 (Putative soluble interferon gamma receptor) LSD009 (Putative alpha amanitin-sensitive protein) LSD008: 20 aa; LSD009: 13 aa; LSD008: 16 S>Y; 32 N>K; 34 G>E; 36 I>T; 39 D>V; 40 N>S; 41 S>D; 45 K>R; LSD009: 129 R>K; 135 T>A; 142 T>A; 147 Y>H; 151 D>E; 166 H>R; 179 I>V; 185 I>M; 187 C>Y; 188 M>I; 200 K>T; 201 G>C;
4 LSD131 (Superoxide dismutase-like protein); LSD132 (hypothetical protein); LSD133 (DNA ligase-like protein); LSD134 (LW134a) (Similar to variola virus B22R) LSD131: (53 aa truncation); LSD132: 5 aa; LSD133: 8 aa; LSD131: C-terminal identical to minor parent, thus 84–161 is FNNERHIGDLGNIYSNKYGISYIYILDGKISLVGDYSIIGRSLVISEKNDDLGKGYNFKSFIDGNSGNGVAYGIIGIA; LSD132: 19 V>L; 63^64 del> T; 69 L>V; 98 T>N; 145 G>D; LSD133: 165 V>I; 275 S>N; 312 L>S; 446 N>K; 514 S>A;
5 LSD084 (Putative early transcription factor small subunit); LSD085 (RNA polymerase subunit); LSD086 (mutT motif protein); LSD087 (mutT motif protein); LSD088 (putative transcription termination factor); LSD089 (mRNA capping enzyme small subunit) LSD084: 2 aa; LSD085: 1 aa; LSD086: 9 aa; LSD087: 2 aa and 53 aa C-terminal truncation; LSD088: 1 aa; LSD089: 2 aa; LSD084: 353 L>G; 581 D>N; LSD085: 136 M>T; LSD086: 191 L>F; Translation similar to minor parent, thus 207–213 NTLVNSK; LSD087: 12 D>G; 46 V>I; C-terminal similar to minor parent, thus 199–253 SNKEIKSLVFFDSLYNGIEGDIIRFVLDISRLKCFGNKGYELYNKNTFKSLKSFF; LSD088: 24 V>I; LSD089: Identical to major parent;
6 LSD154 (putative ER-localized apoptosis regulator); LSD155 (hypothetical protein); LSD156 (hypothetical protein) LSD155: No difference; LSD156: 2 aa LSD155: 36 I>N = N; 43 G>V = V; 80 S>T = T; 81 R>S = S; LSD156: 92 F>Y = Y; 136 F>I = I; 144 I>M;
7 LSD049 (putative RNA helicase); LSD050 (putative metalloprotease); LSD051 (putative transcriptional elongation factor); LSD052 (hypothetical protein); LSD053 (putative glutaredoxin); LSD054 (hypothetical protein); LSD055 (Similar to G5.5R, RPO7); LSD056 (hypothetical protein); LSD057 (putative virion core protein) LSD049: 5 aa; LSD050: 1 aa; LSD051: No differences; LSD052: 1 aa; LSD053: No differences; LSD054: 3 aa; LSD055: No differences; LSD056: 1 aa; LSD057: 2 aa LSD049: 145 A>T; 623 K>R; 673 V>I; LSD050: Identical to major parent; LSD051: Identical to both parents; LSD052: 33 K>N; LSD053: Identical to both parents; LSD054: 54 S>G; 184 M>I; LSD055: Identical to both parents; LSD056: 171 K>R = R; 174 N>D; LSD057: 257 V>A; 372 V>I;
8 LSD035 (LW036) (hypothetical protein); LSD037 (hypothetical protein); LSD038 (hypothetical protein); LSD039 (DNA polymerase) LSD037: 4 aa; LSD038: No differences; LSD039: 8 aa LSD037: 251 V>F; 300 V>I; 437 I>V; 564 G>V; LSD038: Identical to both parents; LSD039: Identical to major parent;
9 LSD059 (putative myrostylated protein); LSD060 (putative myristylated IMV envelope protein); LSD061 (hypothetical protein); LSD062 (hypothetical protein); LSD063 (putative DNA-binding virion core protein) LSD059: 1 aa; LSD060: No differences; LSD061: 3 aa; LSD062: 2 aa; LSD063: No differences LSD059: Identical to major parent; LSD060: Identical to both parents; LSD061: 13 D>E; 82 L >S = A; LSD062: 185 R>K; 273 I>V; LSD063: Identical to both parents;
10 LSD102 (hypothetical protein); LSD103 (putative virion core protein); LSD104 (putative IMV membrane protein); LSD105 (putative IMV membrane protein); LSD106 (putative virulence factor); LSD102: 3 aa; LSD103: 2 aa; LSD104: No differences; LSD105: No differences; LSD106: No differences LSD102: Identical to major parent; LSD103: 50 T>N; 72 P>T; 89 S>G = G; LSD104: Identical to both parents; LSD105: Identical to both parents; LSD106: Identical to both parents;
11 LSD097 (hypothetical protein); LSD098 (putative early transcription factor large subunit); LSD097: 2 aa; LSD098: 6 aa; LSD097: 25 V>A; 65 L>V; LSD098: 652 T>I;
12 LSD139 (putative Ser/Thr protein kinase); LSD140 (putative RING finger host range protein); LSD141 (putative EEV host range protein); LSD139: 5 aa; LSD140: 10 aa; LSD141: 4 aa; LSD139: 263 G>V; 272 S>P; LSD140: 5 S>I; 132 T>M>K; 187 K>N; 228 N>D; LSD141: 38 E>K
13 LSD071 (RNA polymerase subunit); LSD072 (putative protein-tyrosine phosphatase); LSD073 (hypothetical protein) LSD071: 4 aa; LSD072: No differences; LSD073: 2 aa; LSD071: 879 N>S; LSD072: Identical to both parents; LSD073: 26 T>S
14 LSD147 (ankyrin repeat protein) LSD147: 1 aa; LSD147: Identical to major parent;
15 LSD081 (putative virion protein); LSD082 (uracil DNA glycosylase); LSD081: 2 aa; LSD082: 1 aa; LSD081: 227 S>N; LSD082: 54 R>Q
16 LSD110 (putative DNA helicase transcriptional elongation factor); LSD111 (hypothetical protein) LSD110: 7 aa; LSD111: No differences; LSD010: Identical to major parent; LSD111: Identical to both parents;
17 LSD108 (putative myristylated membrane protein) LSD108: 3 aa; LSD108: 171 S>A;
18 LSD023 (hypothetical protein) LSD023: No differences; LSD023: Identical to both parents;
19 LSD034 (putative PKR inhibitor); LSD036 (LW035a) (RNA polymerase subunit); LSD034: 1 aa; LSD036 (LW035a): 1 aa; LSD034: Identical to major parent; LSD035: P>S = S; LSD036: Identical to major parent;
20 LSD019 (kelch-like protein) LSD019: 4 aa and a 150 aa N-terminal truncation Identical frameshift to LW019a and LW019b. LSD019: 84 A>V; 89 K>R; 104 V>A;
21 LSD075 (RNA polymerase-associated protein) LSD075: 5 aa; LSD075: 692 S>N; 739 F>L;
22 LSD091 (putative late transcription factor); LSD092 (putative late transcription factor); LSD091: No differences; LSD092: No differences; LSD091: Identical to both parents; LSD092: Identical to both parents;
23 LSD027 (putative EEV maturation protein); LSD027: 6 aa LSD027: 327 D>N;
24 LSD042 (hypothetical protein) LSD042: 4 aa; LSD042: 190 A>T; 230 P>S;
25 LSD002 (hypothetical protein); LSD003 (putative ER-localized apoptosis regulator; LSD002: No differences; LSD003: 2 aa; LSD002: Identical to both parents; LSD003: Identical to major parent;
26 LSD020 (ribonuclease reductase small subunit); LSD021 (hypothetical protein) LSD020: 3 aa; LSD021: 3 aa; LSD020: Identical to major parent; LSD21: 78 T>K;
27 LSD079 (mRNA capping enzyme large subunit) LSD079: 4 aa; LSD079: Identical to major parent;