Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains

Qian Feng; Huan Yu; Yingying Liu; Chengqiang He; Jingsong Hu; Huachun Sang; Neizheng Ding; Mingxiao Ding; Yin Wan Wendy Fung; Lok Ting Lau; Albert Cheung Hoi Yu; Jianguo Chen

doi:10.1016/j.bbrc.2004.08.086

Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains

Qian Feng, Huan Yu, Yingying Liu, Chengqiang He, Jingsong Hu, Huachun Sang, Neizheng Ding, Mingxiao Ding, Yin Wan Wendy Fung, Lok Ting Lau, Albert Cheung Hoi Yu, Jianguo Chen^*

^*Corresponding author for this work

Office of the President and Vice-Chancellor

Research output: Contribution to journal › Journal article › peer-review

25 Citations (Scopus)

Abstract

The genome of a novel foot-and-mouth disease virus, HKN/2002, was 8104 nucleotides (nt) in length (excluding the poly(C) tract and poly(A) tail) and was composed of a 1042-nt 5′-untranslated region (UTR), a 6966-nt open reading frame, and a 93-nt 3′-UTR. Genome sequences of HKN/2002 and other known FMDV strains were compared. The VP1, VP2, and VP3-based neighbor-joining (NJ) trees were divided into distinct clusters according to different serotypes, while other region-based NJ trees exhibited some degree of intercross among serotypes. Mutations in HKN/2002 were revealed, including frequent deletions and insertions in the Ga-H loop of VP1, and deletion involving 10 amino acid residues in the 3A protein. An evolutionary relationship of HKN/2002 with an Asian FMDV lineage isolated from a Hong Kong swine host in 1970 was postulated. A 43-nt deletion identified in the 5′-UTR of HKN/2002 possibly contributed to the loss of one pseudo-knot domain.

Original language	English
Pages (from-to)	254-263
Number of pages	10
Journal	Biochemical and Biophysical Research Communications
Volume	323
Issue number	1
DOIs	https://doi.org/10.1016/j.bbrc.2004.08.086
Publication status	Published - 8 Oct 2004

Scopus Subject Areas

Biophysics
Biochemistry
Molecular Biology
Cell Biology

User-Defined Keywords

Alignment
Phylogenesis
Picornavirus
Sequence
Serotype

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.bbrc.2004.08.086

Cite this

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title = "Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains",

abstract = "The genome of a novel foot-and-mouth disease virus, HKN/2002, was 8104 nucleotides (nt) in length (excluding the poly(C) tract and poly(A) tail) and was composed of a 1042-nt 5′-untranslated region (UTR), a 6966-nt open reading frame, and a 93-nt 3′-UTR. Genome sequences of HKN/2002 and other known FMDV strains were compared. The VP1, VP2, and VP3-based neighbor-joining (NJ) trees were divided into distinct clusters according to different serotypes, while other region-based NJ trees exhibited some degree of intercross among serotypes. Mutations in HKN/2002 were revealed, including frequent deletions and insertions in the Ga-H loop of VP1, and deletion involving 10 amino acid residues in the 3A protein. An evolutionary relationship of HKN/2002 with an Asian FMDV lineage isolated from a Hong Kong swine host in 1970 was postulated. A 43-nt deletion identified in the 5′-UTR of HKN/2002 possibly contributed to the loss of one pseudo-knot domain.",

keywords = "Alignment, Phylogenesis, Picornavirus, Sequence, Serotype",

author = "Qian Feng and Huan Yu and Yingying Liu and Chengqiang He and Jingsong Hu and Huachun Sang and Neizheng Ding and Mingxiao Ding and Fung, {Yin Wan Wendy} and Lau, {Lok Ting} and Yu, {Albert Cheung Hoi} and Jianguo Chen",

note = "This work was supported by a Grant (G1999011904) from the Special Funds for Major State Basic Research of China (to J.C.), and partially supported by a small research grant from the Hong Kong DNA Chips Limited. Publisher Copyright: {\textcopyright} 2004 Elsevier Inc",

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AU - Feng, Qian

AU - Yu, Huan

AU - Liu, Yingying

AU - He, Chengqiang

AU - Hu, Jingsong

AU - Sang, Huachun

AU - Ding, Neizheng

AU - Ding, Mingxiao

AU - Fung, Yin Wan Wendy

AU - Lau, Lok Ting

AU - Yu, Albert Cheung Hoi

AU - Chen, Jianguo

N1 - This work was supported by a Grant (G1999011904) from the Special Funds for Major State Basic Research of China (to J.C.), and partially supported by a small research grant from the Hong Kong DNA Chips Limited. Publisher Copyright: © 2004 Elsevier Inc

PY - 2004/10/8

Y1 - 2004/10/8

N2 - The genome of a novel foot-and-mouth disease virus, HKN/2002, was 8104 nucleotides (nt) in length (excluding the poly(C) tract and poly(A) tail) and was composed of a 1042-nt 5′-untranslated region (UTR), a 6966-nt open reading frame, and a 93-nt 3′-UTR. Genome sequences of HKN/2002 and other known FMDV strains were compared. The VP1, VP2, and VP3-based neighbor-joining (NJ) trees were divided into distinct clusters according to different serotypes, while other region-based NJ trees exhibited some degree of intercross among serotypes. Mutations in HKN/2002 were revealed, including frequent deletions and insertions in the Ga-H loop of VP1, and deletion involving 10 amino acid residues in the 3A protein. An evolutionary relationship of HKN/2002 with an Asian FMDV lineage isolated from a Hong Kong swine host in 1970 was postulated. A 43-nt deletion identified in the 5′-UTR of HKN/2002 possibly contributed to the loss of one pseudo-knot domain.

AB - The genome of a novel foot-and-mouth disease virus, HKN/2002, was 8104 nucleotides (nt) in length (excluding the poly(C) tract and poly(A) tail) and was composed of a 1042-nt 5′-untranslated region (UTR), a 6966-nt open reading frame, and a 93-nt 3′-UTR. Genome sequences of HKN/2002 and other known FMDV strains were compared. The VP1, VP2, and VP3-based neighbor-joining (NJ) trees were divided into distinct clusters according to different serotypes, while other region-based NJ trees exhibited some degree of intercross among serotypes. Mutations in HKN/2002 were revealed, including frequent deletions and insertions in the Ga-H loop of VP1, and deletion involving 10 amino acid residues in the 3A protein. An evolutionary relationship of HKN/2002 with an Asian FMDV lineage isolated from a Hong Kong swine host in 1970 was postulated. A 43-nt deletion identified in the 5′-UTR of HKN/2002 possibly contributed to the loss of one pseudo-knot domain.

KW - Alignment

KW - Phylogenesis

KW - Picornavirus

KW - Sequence

KW - Serotype

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Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains

Abstract

Scopus Subject Areas

User-Defined Keywords

UN SDGs

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