Table 1. Amino acids defining lineages in human respiratory syncytial virus A*.
| Lineage | NS1 | NS2 | N | P | M | SH | G | F | M2–1 | M2–2 | L |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A.1 | 105(I)L | 38(R)K | 216(Y)H | 73(V)A† | 91(C)S | 15(K)R; 38(I)V; 71(L)S; 74(A)T; 101(F)P; 104(L)P; 111(T)I; 121(R)G; 141(I)A; 157(N)S; 215(L)P; 222(P)S; 233(K)E; 250(N)S; 254(G)R; 258(H)L; 286(K)M; 304(Y)S; 310(L)P†; 317(S)P; 321(N)R | 8(T)A; 16(A)I; 122(T)A | 18(N)T; 44(Q)P; 51(P)L; 80(D)E | 81(I)L; 104(T)A; 162(L)S; 232(I)T; 240(N)S; 255(H)N; 445(V)I; 603(N)D; 754(R)G; 821(V)I; 1180(F)L; 1657(Y)H; 1718(T)A; 1731(D)E; 1756(T)A; 1773(T)M; 1778(K)R; 1969(T)M; 2019(V)A | ||
| A.2 | 4(N)T; 107(I)T/N; 121(R)S; 123(K)E; 225(V)A; 244(I)R; 251(N)S; 256(P)L†; 263(F)L; 286(K)E†; 314(S)P† | 20(F)L; 124(K)N | 120(L)P; 179(L)S | 1(M)T†; 25(R)S†; 54(T)P; 68(T)A | 174(D)G; 237(Q)H; 1551(K)R; 1721(I)V; 1723(S)C | ||||||
| A.2.1 | 7(D)G | 64(L)V | 73(V)A | 57(A)V; 108(T)I†; 161(N)D; 303(V)I; 321(N)D | 125(T)N; 518(A)V; 547(L)F | 182(S)N | 48(I)T | 148(D)N†; 1724(N)D | |||
| A.2.1.1 | 117(L)P†; 124(S)P; 146(P)L; 206(P)Q | 2(E)D; 13(T)A | 104(T)A†; 144(G)E; 257(E)D†; 1757(M)T; 1847(N)S | ||||||||
| A.3 | 84(R)K | 4(N)T; 15(K)R; 107(I)T; 111(T)P†; 289(F)L | 20(F)L† | 120(L)P; 179(L)S | 1(M)T; 54(T)P; 68(T)A; 69(I)T | 224(N)S; 237(Q)H/Y; 1551(K)R; 1721(I)V; 1764(K)R | |||||
| A.3.1 | 38(R)K | 106(E)G†; 111(P)S; 237(N)D; 286(K)E; 316(P)S | 105(N)S; 574(S)N | 125(I)V† | 25(S)N; 39(F)I; 50(S)P; 52(N)D | 6(N)S†; 177(H)Q†; 216(N)S; 388(V)I; 575(E)D; 754(R)K; 1180(F)L; 1471(H)N; 1700(N)S†; 1730(N)S; 1745(L)S; 2135(Y)H; 2163(H)N | |||||
| A.3.1.1 | 142(Q)L; 208(I)L; 297(N)Y | 276(N)S; 540(S)A | 103(I)T; 240(N)S; 1725(D)E/G; 2163(N)Y | ||||||||
| A.D | 232(E)G†; 253(T)K†; 260dup>QEETLHSTTSEGYLSPSQVYTTSG | 598(Y)H† | |||||||||
| A.D.1 | 43(M)I | 142(L)S; 320 (T)A† | 143(N)D; 179(T)S/L; 1653(I)V; 1661(K)N | ||||||||
| A.D.1.1 | 121(S)G; 273(Y)H | 2(T)I | 124(V)I; 234(I)V; 970(N)S; 1187(D)G; 1236(T)S | ||||||||
| A.D.1.2 | 104(I)F | 25(K)R† | 51(H)Q | 129(T)I†; 174(S)N | 1789(S)F | ||||||
| A.D.1.3 | 9(I)L | 3(T)I | 100(S)I†; 225(V)A; 263(E)Q; 265(L)P; 270(S)P†; 277(S)P; 280(Y)H; 291(S)P; 297(Y)H; 310(L)P; 316(S)P†; 321(K)X; 753(D)G† | 755(D)G†; 2111(N)H | |||||||
| A.D.2 | 134(K)I; 262(E)K | 46(N)S | 598(H)Y†; 1731(D)G | ||||||||
| A.D.2.1 | 69(T)A | 21(I)V | 67(H)N; 107(T)P; 120(P)T; 240(K)R; 280(Y)H; 287(E)D; 294(S)P; 303(V)I; 319(T)S | 144(G)E; 610(P)S; 1599(H)R | |||||||
| A.D.2.2 | 240(R)K; 243(I)S; 303(I)V | 1731(D)G; 1950(I)L | |||||||||
| A.D.2.2.1 | 224(E)G; 265(L)I; 274(L)P | 171(L)P; 256(K)R | |||||||||
| A.D.3 | 92(T)M† | 113(T)I; 131(V)D†; 178(N)G†; 258(H)Q†; 266(H)L† | 12(T)I | 79(T)A | 835(L)M | ||||||
| A.D.3.1 | 101(F)S; 151(R)H; 225(V)A; 230(P)T†; 250(S)F†; 263(E)K | 20(L)F; 276(S)N | 48(I)L | ||||||||
| A.D.4 | 63(I)V/A | 47(L)Q | 57(A)T†; 206(P)Q; 310(L)P† | 1726(K)R | |||||||
| A.D.4.1 | 122(E)D | 90(Y)H; 111(S)F†; 283(S)P; 312(Q)X; 319(T)A | 123(K)Q; 384(I)T | 9(F)Y; 173(I)V | 1(T)M | 1617(V)I | |||||
| A.D.5 | 206(P)Q; 303(V)A†; 320(T)A† | 122(T)A | 1723(S)G | ||||||||
| A.D.5.1 | 216(Y)H | 57(A)V; 118(T)I†; 209(K)R; 319(T)I | 23(A)S† | ||||||||
| A.D.5.2 | 69(T)I | 57(A)V; 209(K)R† | 103(A)T† | 26(C)Y† | |||||||
| A.D.5.3 | 3(T)A; 8(T)A | 189(I)T; 225(V)A; 243(I)T; 276(P)Q†; 280(Y)H; 284(G)D†; 314(L)P† | 15(L)F; 419(K)E | 52(K)R; 173(I)V† | 27(R)K; 64(D)E | 114(R)K; 179(T)A; 335(V)I; 1051(N)S |
*The lineage-defining amino acids within each viral protein are detailed. This description provides the location of the amino acid using the genome coordinates hRSV/A/England/397/2017 (lineage A.D.2.2.1, National Center for Biotechnology Information Virus accession no. PP109421.1, GISAID EpiRSV accession no. EPI_ISL_412866), followed by the amino acid found in the parental lineage in parentheses. Finally, the amino acid substitution that drives it to become a lineage is specified. X represents an amino acid deletion. NS, nonstructural protein; N, nucleocapsid; P, phosphoprotein; M, matrix protein; SH, small hydrophobic protein; G, attachment glycoprotein; F, fusion glycoprotein; M2, M2 protein; L, large polymerase protein †Amino acid changes detected in not all but >90% of the lineage sequences.