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Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong

Cyril CY Yip1, Susanna KP Lau1234*, Janice YC Lo5, Kwok-Hung Chan1, Patrick CY Woo1234 and Kwok-Yung Yuen1234*

Author Affiliations

1 Department of Microbiology, The University of Hong Kong, Hong Kong, China

2 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China

3 Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China

4 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China

5 Centre for Health Protection, Department of Health, Hong Kong, China

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Virology Journal 2013, 10:222  doi:10.1186/1743-422X-10-222

Published: 4 July 2013

Additional files

Additional file 1: Table S1:

Estimation of nonsynonymous and synonymous substitution rates in the seven genomes of EV71 subgenotype C4 (proposed genotype D).

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Additional file 2: Figure S1:

Comparative sequence analysis of the 2A-2B junction (A). Multiple alignment of the nucleotide sequences of EV71 “genotype D” strain V10-2234054, EV71 genotype B strain Nagoya and genotype C strain 4643-TW98. In EV71 genotype B and EV71 genotype C, only the nucleotides different from those in EV71 strain V10-2234054 are depicted. The nucleotides in EV71 genotype C that are the same as those in EV71 strain V10-2234054 but different from those in EV71 genotype B are highlighted in grey, and those in EV71 genotype B that are the same as those in V10-2234054 but different from those in EV71 genotype C are highlighted in black. Comparative sequence analysis of the 3C region (B). Multiple alignment of the nucleotide sequences of EV71 strain V10-2234054, EV71 genotype B strain Nagoya and CVA16 strain G-10. In EV71 genotype B and CVA16 strain G-10, only the nucleotides different from those in EV71 strain V10-2234054 are depicted. The nucleotides in EV71 genotype B that are the same as those in EV71 strain V10-2234054 but different from those in CVA16 strain G-10 are highlighted in grey, and those in CVA16 strain G-10 that are the same as those in V10-2234054 but different from those in EV71 genotype B are highlighted in black. The predicted breakpoint position by bootscan analysis is indicated by an arrow.

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Additional file 3: Table S2:

Primers used for PCR and sequencing of the partial VP2-VP3, 2C and 3D gene regions and the complete VP1 gene of the 22 EV71 strains.

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Additional file 4: Table S3:

Primers used for complete genome sequencing on eight EV71 strains.

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Additional file 5: Table S4:

List of EV71 strains used in the present study.

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