Molecular phylogeny of modern coxsackievirus A16
First Online: 19 February 2007 Received: 14 November 2006 Accepted: 21 December 2006 DOI:
Cite this article as: Perera, D., Yusof, M., Podin, Y. et al. Arch Virol (2007) 152: 1201. doi:10.1007/s00705-006-0934-5 Summary.
A phylogenetic analysis of VP1 and VP4 nucleotide sequences of 52 recent CVA16 strains demonstrated two distinct CVA16 genogroups, A and B, with the prototype strain being the only member of genogroup A. CVA16 G-10, the prototype strain, showed a nucleotide difference of 27.7–30.2% and 19.9–25.2% in VP1 and VP4, respectively, in relation to other CVA16 strains, which formed two separate lineages in genogroup B with nucleotide variation of less than 13.4% and less than 16.3% in VP1 and VP4, respectively. Lineage 1 strains circulating before 2000 were later displaced by lineage 2 strains.
References Bendig, JWA, O’Brien, PS, Muir, P 2001 Serotype-specific detection of coxsackievirus A16 in clinical specimens by reverse transcription-nested PCR J Clin Microbiol 39 3690 3692 PubMed CrossRef Brown, BA, Oberste, MS, Alexander, JP, Kennett, ML, Pallansch, MA 1999 Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998 J Virol 73 9969 9975 PubMed Cardosa, MJ, Perera, D, Brown, BA, Cheon, D, Chan, HM, Chan, KP, Cho, H, McMinn, P 2003 Molecular epidemiology of human enterovirus 71 strains and recent outbreaks in the Asia-Pacific region: comparative analysis of the VP1 and VP4 genes Emerg Infect Dis 9 461 468 PubMed Chan, LG, Parashar, UD, Lye, MS, Ong, FG, Zaki, SR, Alexander, JP, Ho, KK, Han, LL, Pallansch, MA, Suleiman, AB, Jegathesan, M, Anderson, LJ 2000 Deaths of children during an outbreak of hand, foot, and mouth disease in Sarawak, Malaysia: clinical and pathological characteristics of the disease. For the Outbreak Study Group Clin Infect Dis 31 678 683 PubMed CrossRef Chang, LY, Lin, TY, Huang, YC, Tsao, KC, Shih, SR, Kuo, ML, Ning, HC, Chung, PW, Kang, CM 1999 Comparison of enterovirus 71 and coxsackie-virus A16 clinical illnesses during the Taiwan enterovirus epidemic, 1998 Pediatr Infect Dis J 18 1092 1096 PubMed CrossRef Felsenstein, J 1989 PHYLIP – phylogeny inference package (version 3.2) Cladistics 5 164 166 Ishiko, H, Shimada, Y, Yonaha, M, Hashimoto, O, Hayashi, A, Sakae, K, Takeda, N 2002 Molecular diagnosis of human enteroviruses by phylogeny-based classification by use of the VP4 sequence J Infect Dis 185 744 754 PubMed CrossRef Li, L, He, Y, Yang, H, Zhu, J, Xu, X, Dong, J, Zhu, Y, Jin, Q 2005 Genetic characteristics of human enterovirus 71 and coxsackievirus A16 circulating from 1999 to 2004 in Shenzhen, People’s Republic of China J Clin Microbiol 43 3835 3839 PubMed CrossRef Lin, TY, Twu, SJ, Ho, MS, Chang, LY, Lee, CY 2003 Enterovirus 71 outbreaks, Taiwan: occurrence and recognition Emerg Infect Dis 9 291 293 PubMed Lin, K-H Hwang, K-P Ke, G-M 13 other authors 2006 Evolution of EV71 genogroup in Taiwan from 1998 to 2005: an emerging of subgenogroup C4 of EV71 J Med Virol 78 254 262 PubMed CrossRef McMinn, P, Lindsay, K, Perera, D, Chan, HM, Chan, KP, Cardosa, MJ 2001 Phylogenetic analysis of enterovirus 71 strains isolated during linked epidemics in Malaysia, Singapore, and Western Australia J Virol 75 7732 7738 PubMed CrossRef Oberste, MS, Maher, K, Kilpatrick, DR, Pallansch, MA 1999 Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification J Virol 73 1941 1948 PubMed Oberste, MS, William, AN, Maher, K, Pallansch, MA 2003 Improved molecular identification of enteroviruses by RT-PCR and amplicon sequencing J Clin Virol 26 375 377 PubMed CrossRef Page, RD 1996 TreeView: an application to display phylogenetic trees on personal computers Comput Appl Biosci 12 357 358 PubMed Pallansch, MA, Roos, RP 2001 Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses Fields, BN Howley, PM Griffin, DE Lamb, RA Martin, MA Roizman, B Straus, SE Knipe, DM eds. Fields virology Lippincott Williams & Wilkins Publishers Philadelphia, Pennsylvania 723 775 Perera, D, Podin, Y, Akin, W, Tan, C-S, Cardosa, MJ 2004 Incorrect identification of recent Asian strains of coxsackievirus A16 as human enterovirus 71: improved primers for the specific detection of human enterovirus 71 by RT PCR BMC Infect Dis 4 4 11 CrossRef Podin, Y, Gias, ELM, Ong, F, Leong, Y-W, Yee, S-F, Yusof, MA, Perera, D, Teo, B, Wee, T-Y, Yao, S-C, Yao, S-K, Kiyu, A, Arif, MT, Cardosa, MJ 2006 Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years BMC Public Health 6 180 PubMed CrossRef Shimizu, H, Utama, A, Onnimala, N, Li, C, Li-Bi, Z, Yu-Jie, M, Pongsuwanna, Y, Miyamura, T 2004 Molecular epidemiology of enterovirus 71 infection in the Western Pacific Region Pediatr Int 46 231 235 PubMed CrossRef Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882 CrossRef Yamashita, T, Ito, M, Taniguchi, A, Sakae, K 2005 Prevalence of coxsackievirus A5, A6, and A10 in patients with herpangina in Aichi Prefecture, 2005 Jpn J Infect Dis 58 390 391 PubMed Yan, J-J, Su, I-J, Chen, P-F, Liu, C-C, Yu, C-K, Wang, J-R 2001 Complete genome analysis of enterovirus 71 isolated from an outbreak in Taiwan and rapid identification of enteroviruses 71 and coxsackievirus A16 by RT-PCR J Med Virol 65 331 339 PubMed CrossRef