Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
Volume 30, Number 8—August 2024
Research
Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus Below the Subgroup Level
Table 1
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.
1These authors were co–principal investigators.
2These authors contributed equally to this article.
3Current affiliation: Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada.
4Current affiliation: Sciensano, Infectious Diseases in Humans, Unit (Re)-Emerging Viruses, Brussels, Belgium.