Archives of Virology

, Volume 155, Issue 9, pp 1413–1424 | Cite as

Emergence of enterovirus 71 “double-recombinant” strains belonging to a novel genotype D originating from southern China: first evidence for combination of intratypic and intertypic recombination events in EV71

  • Cyril C. Y. Yip
  • Susanna K. P. Lau
  • Boping Zhou
  • Ming-Xia Zhang
  • Hoi-Wah Tsoi
  • Kwok-Hung Chan
  • Xin-Chun Chen
  • Patrick C. Y. Woo
  • Kwok-Yung Yuen
Original Article

Abstract

Hand–foot–mouth disease due to enterovirus 71 (EV71) and coxsackievirus A16 (CA16) has recently caused large outbreaks in mainland China in 2008. We performed complete genome sequencing on two EV71 (SZ/HK08-5 and SZ/HK08-6) and two CA16 (SZ/HK08-3 and SZ/HK08-7) strains from patients in Shenzhen, China. Phylogenetic, similarity plot and bootscan analyses revealed recombination between EV71 genotypes B and C at the 2A–2B junction, and between EV71 genotype B and CA16 strain G-10 in the 3C region for EV71 strains. A similar phenomenon was also found upon further gene sequencing with other EV71 strains. Recombination between CA16 strain G-10 and EV71 genotype A at the 2A–2B junction was also observed for CA16 strains. The present “double-recombinant” EV71 strains circulating in China and other EV71 subgenotype “C4” strains represent an additional genotype, D. CA16 strains should also be classified into two genotypes. This represents the first evidence for a combination of intratypic and intertypic recombination in EV71 strains.

Supplementary material

705_2010_722_MOESM1_ESM.doc (50 kb)
Fig. S1. (a) Comparative sequence analysis of the 2A-2B junction. Multiple alignment of the nucleotide sequences of EV71 strain SZ/HK08-5, EV71 genotype B strain MS/7423/87 and genotype C strain Tainan/4643/98. In EV71 genotype B and EV71 genotype C, only the nucleotides that are different from those in EV71 strain SZ/HK08-5 are depicted. The nucleotides in EV71 genotype C that are the same as those in EV71 strain SZ/HK08-5 but different from those in EV71 genotype B are highlighted in gray, and those in EV71 genotype B that are the same as those in SZ/HK08-5 but different from those in EV71 genotype C are highlighted in black. (b) Comparative sequence analysis of the 3A-3C region. Multiple alignment of the nucleotide sequences of EV71 strain SZ/HK08-5, EV71 genotype B MS/7423/87 and CA16 strain G-10. In EV71 genotype B and CA16 strain G-10, only the nucleotides that are different from those in EV71 strain SZ/HK08-5 are depicted. The nucleotides in EV71 genotype B that are the same as those in EV71 strain SZ/HK08-5 but different from those in CA16 strain G-10 are highlighted in gray, and those in CA16 strain G-10 that are the same as those in SZ/HK08-5 but different from those in EV71 genotype B are highlighted in black. The breakpoint position predicted by bootscan analysis is indicated by an arrow (DOC 50 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Cyril C. Y. Yip
    • 4
  • Susanna K. P. Lau
    • 1
    • 2
    • 3
    • 4
  • Boping Zhou
    • 5
  • Ming-Xia Zhang
    • 5
  • Hoi-Wah Tsoi
    • 4
  • Kwok-Hung Chan
    • 4
  • Xin-Chun Chen
    • 5
  • Patrick C. Y. Woo
    • 1
    • 2
    • 3
    • 4
  • Kwok-Yung Yuen
    • 1
    • 2
    • 3
    • 4
  1. 1.State Key Laboratory of Emerging Infectious DiseasesQueen Mary Hospital, The University of Hong KongHong KongChina
  2. 2.Research Centre of Infection and ImmunologyThe University of Hong KongHong KongChina
  3. 3.Carol Yu Centre for InfectionThe University of Hong KongHong KongChina
  4. 4.Department of MicrobiologyThe University of Hong KongHong KongChina
  5. 5.Shenzhen East Lake HospitalShenzhenPeople’s Republic of China

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