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Volume 30, Number 8—August 2024
Research

Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level

Stephanie Goya1Comments to Author , Christopher Ruis2, Richard A. Neher2, Adam Meijer, Ammar Aziz, Angie S. Hinrichs, Anne von Gottberg, Cornelius Roemer, Daniel G. Amoako3, Dolores Acuña, Jakob McBroome, James R. Otieno, Jinal N. Bhiman, Josie Everatt, Juan C. Muñoz-Escalante, Kaat Ramaekers4, Kate Duggan, Lance D. Presser, Laura Urbanska, Marietjie Venter, Nicole Wolter, Teresa C.T. Peret, Vahid Salimi, Varsha Potdar, Vítor Borges, and Mariana Viegas1
Author affiliations: University of Washington, Seattle, Washington, USA (S. Goya); University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska); National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser); World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz); University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome); National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter); University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter); University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako); Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas); National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas); Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno); Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante); Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers); University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan); University of Pretoria, Pretoria, South Africa (M. Venter); University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret); Tehran University of Medical Sciences, Tehran, Iran (V. Salimi); ICMR National Institute of Virology, Pune, India (V. Potdar); National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)

Main Article

Table 2

Amino acids defining lineages in human respiratory syncytial virus B*

Lineage NS1 NS2 N P M SH G F M2–1 M2–2 L
B.1 103(K)I; 133(T)P; 222(K)D 114(Y)H 148(E)D; 948(N)H; 1177(I)M; 1613(K)N; 2014(A)S
B.2 124(D)N 24(E)D 66(I)T 95(S)P†; 118(I)T; 137(I)T; 150(S)P; 206(I)T; 220(M)T; 221(P)T; 275(S)L†; 283(Y)S; 289(S)P; 298(I)T; 311(X)Q†; 314(X)Q 103(V)A†; 209(K)Q; 312(H)P 41(Y)H; 49(C)R†; 68(T)A 308(I)V; 1742(T)M; 2021(N)D
B.3 4(H)N; 77(Q)S; 101(S)P; 137(I)T; 140(S)P; 150(S)P; 152(S)P; 154(N)I; 206(I)T; 221(P)L; 283(Y)S; 298(I)T; 311(X)Q 103(V)A†; 209(K)Q; 312(H)P; 518(T)A†; 529(T)A 184(T)N; 308(I)V; 1043(I)V; 1547(K)R; 1700(N)D; 1764(K)R; 2021(N)D; 2042(T)I
B.4 45(A)T; 105(M)I† 89(I)T 57(L)Q 4(H)N; 32(R)K; 101(S)P; 109(S)P; 137(I)T; 140(S)P; 143(T)N; 150(S)P; 152(S)P; 205(T)P; 206(I)T; 217(P)L; 221(P)L; 235(L)P; 283(Y)S; 298(I)T; 311(X)Q 103(V)A; 209(K)Q; 312(H)P; 529(T)A 184(T)N; 308(I)V; 1043(I)V; 1250(G)S; 1700(N)D; 1726(S)R; 1764(K)R; 2021(N)D; 2042(T)I; 2065(K)N
B.D 138(N)H 372(A)T† 138(T)S†; 157delKK†; 221(L)P†; 227(T)I†; 239dupERDTSTSQSTVLDTTTSKHT; 285(H)Y†; 311(X)Q†; 314(X)Q† 45(F)L† 142(N)S† 177(H)Y; 1716(M)I†; 1787(A)E†
B.D.1 82(T)S 89(T)I 290(E)G†; 311(Q)X† 1593(N)S
B.D.1.1 63(I)V 75(T)S; 204(P)T; 217(L)P; 227(I)T 19(A)T 59(M)I; 1250(G)S
B.D.2 145(I)V 87(I)T; 178(Q)R†; 239(E)K 23(T)A 181(V)I 1250(G)S; 1588(I)L
B.D.3 4(T)K; 80(K)T† 87(I)T; 217(L)P; 268(I)T; 285(Y)H; 299(P)S; 311(Q)X 123(K)G; 124(N)S 188(T)P 3(K)N; 43(H)Y 1489(A)V; 1588(I)L
B.D.4 49(T)I 198(I)T 103(A)V; 172(L)Q 181(V)I
B.D.4.1 216(H)Y† 107(T)A; 136(R)T; 252(T)I†; 279(I)T 173(S)L 715(I)V†; 1712(T)A
B.D.4.1.1 64(N)D† 131(A)T†; 137(T)I†; 288(T)I† 191(K)R; 206(I)M; 209(Q)R 1479(V)A†; 1716(I)V†
B.D.E.1 100(S)G†; 214(P)S; 221(P)L; 252(I)T; 256(K)N†; 268(I)T; 275(S)P; 285(Y)H 190(S)N; 211(S)N; 389(S)P 27(M)T†; 35(D)N; 49(C)F 570(K)R†; 1759(R)K
B.D.E.2 303(I)V 176(N)S; 269(A)V; 274(T)A† 1707(H)N
B.D.E.3 1(M)V 104(Q)H; 128(H)Y; 135(G)S; 141(T)K; 299(P)S†; 311(X)Q† 19(A)V; 526(M)V 75(H)Y† 1965(V)A†
B.D.E.4 61(N)T 135(G)S†; 138(S)F†; 300(T)A; 303(E)G 164(V)M; 309(V)L; 824(I)M†; 1489(A)T/M; 1732(C)Y

*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/B/AUS/VIC-RCH056/2019 (lineage B.D.4.1.1, National Center for Biotechnology Information Virus (https://www.ncbi.nlm.nih.gov/labs/virus) accession no. OP975389.1, GISAID EpiRSV (https://www.gisaid.org) accession no. EPI_ISL_1653999), 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.

Main Article

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.

Page created: June 21, 2024
Page updated: July 20, 2024
Page reviewed: July 20, 2024
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