Evaluation of VP4-VP2 sequencing for molecular typing of human enteroviruses.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

Enterovirus*/genetics ; Enterovirus*/classification ; Enterovirus*/isolation & purification; Humans ; Capsid Proteins/genetics ; Molecular Typing/methods ; Enterovirus Infections/virology ; Enterovirus Infections/diagnosis ; Phylogeny ; Rhinovirus/genetics ; Rhinovirus/classification ; Rhinovirus/isolation & purification ; Amino Acid Sequence

Enteroviruses and rhinoviruses are highly diverse, with over 300 identified types. Reverse transcription-polymerase chain reaction (RT-PCR) assays targeting their VP1, VP4, and partial VP2 (VP4-pVP2) genomic regions are used for detection and identification. The VP4-pVP2 region is particularly sensitive to RT-PCR detection, making it efficient for clinical specimen analysis. However, a standard type identification method using this region is lacking. This study aimed to establish such a method by examining the divergence of VP4-pVP2 amino acid sequences between enterovirus and rhinovirus prototypes. Pairwise analysis of 249 types indicated a 95% threshold for enterovirus intra-species identification but not for rhinovirus prototypes. Protein BLAST search analyses of representative enterovirus prototypes, including EV-A71, EV-D68, CVA6, CVA10, CVA16, and polioviruses (PVs), validated the 95% threshold for typing, with a few exceptions such as PV1-PV2 and CVA6-CVA10, as well as some EV-C types. This study proposes a criterion for typing based on VP4-pVP2 amino acids, which can aid in rapid enterovirus diagnosis during routine clinical or environmental surveillance and emergency outbreaks. Our research confirms the reliability of the suggested VP4-pVP2-based threshold for typing and its potential application in laboratory settings.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Kitamura, Arita. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cell Host Microbe. 2020 May 13;27(5):736-751.e8. (PMID: 32330425)
J Clin Virol. 2011 Jun;51(2):121-5. (PMID: 21514213)
J Gen Virol. 2010 Oct;91(Pt 10):2409-19. (PMID: 20610666)
Lancet Infect Dis. 2010 Nov;10(11):778-90. (PMID: 20961813)
Appl Environ Microbiol. 2023 Apr 26;89(4):e0185322. (PMID: 36975804)
J Clin Microbiol. 2020 Aug 24;58(9):. (PMID: 32611795)
J Gen Virol. 2015 Jun;96(Pt 6):1374-1379. (PMID: 25667329)
Infect Immun. 1982 Aug;37(2):642-7. (PMID: 6288568)
Arch Virol. 2020 Mar;165(3):793-797. (PMID: 31980941)
J Clin Virol. 2018 Apr;101:11-17. (PMID: 29414181)
J Gen Virol. 2005 Feb;86(Pt 2):445-451. (PMID: 15659764)
J Virol. 1999 Mar;73(3):1941-8. (PMID: 9971773)
Appl Environ Microbiol. 2011 Jun;77(11):3786-92. (PMID: 21478313)
J Clin Microbiol. 2000 Mar;38(3):1170-4. (PMID: 10699015)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
MMWR Morb Mortal Wkly Rep. 2022 Aug 19;71(33):1065-1068. (PMID: 35980868)
Int J Infect Dis. 2020 Oct;99:156-162. (PMID: 32663604)
Euro Surveill. 2017 Nov;22(45):. (PMID: 29162204)
J Infect Dis. 2002 Mar 15;185(6):744-54. (PMID: 11920292)
J Med Virol. 2010 Apr;82(4):649-57. (PMID: 20166171)
J Med Virol. 2018 Jan;90(1):3-7. (PMID: 28857219)
Viruses. 2023 Oct 18;15(10):. (PMID: 37896890)
J Med Microbiol. 2016 Dec;65(12):1465-1471. (PMID: 27902407)
J Gen Virol. 2006 Jan;87(Pt 1):119-128. (PMID: 16361424)
J Virol. 2003 Aug;77(16):8973-84. (PMID: 12885914)
Mol Biol Evol. 1987 Jul;4(4):406-25. (PMID: 3447015)
PLoS One. 2017 Jan 12;12(1):e0169067. (PMID: 28081564)
Appl Environ Microbiol. 2019 Nov 27;85(24):. (PMID: 31585989)
J Gen Virol. 2009 Jul;90(Pt 7):1713-1723. (PMID: 19264596)
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027. (PMID: 33892491)
Appl Environ Microbiol. 2014 Aug;80(15):4683-91. (PMID: 24837389)
J Clin Microbiol. 2006 Aug;44(8):2698-704. (PMID: 16891480)
Appl Environ Microbiol. 2006 Sep;72(9):6381-7. (PMID: 16957267)
J Clin Microbiol. 1999 May;37(5):1288-93. (PMID: 10203472)
J Clin Microbiol. 2015 Jan;53(1):73-8. (PMID: 25339406)

0 (Capsid Proteins)

Date Created: 20241210 Date Completed: 20241210 Latest Revision: 20250104

20250104

PMC11630573

10.1371/journal.pone.0311806

39656727