Abstract
Enterovirus 80 (EV80) is a newly identified serotype of the species Human enterovirus B. An EV80 strain designated HZ01/SD/CHN/2004 was isolated from an acute flaccid paralysis case in Shandong, China, in 2004. Complete genome comparison revealed 79.5% similarity with the prototype strain and an insertion of 36 nucleotides in the 3′ end of the VP1 coding region. Intertypic recombination with other serotypes was observed. This is the first report of the complete genome of EV80 in China.
GENOME ANNOUNCEMENT
Enteroviruses (EV) form one genus of the family Picornaviridae in the new order Picornavirales of small, nonenveloped, and plus-sense RNA viruses (3). The genome is about 7,500 nucleotides (nt) in length, with a single open reading frame including a capsid protein region (P1) and nonstructural regions (P2 and P3) (7).
Human enteroviruses (HEV) consist of more than 110 serotypes, which are classified into four species: HEV-A to HEV-D (2, 7). Enterovirus 80 (EV80) is a newly identified member of HEV-B. Its prototype strain CA67-10387 was isolated in the United States in 1967. Subsequently, several other EV80 strains were isolated from acute flaccid paralysis (AFP) cases or healthy persons in Oman, Kenya, and India (1, 6). Until now, only one complete genome sequence of EV80 (the prototype strain) has been available. Here, we report the isolation and identification of an EV80 strain isolated from an AFP patient in Shandong Province, China, in 2004.
The strain HZ01/SD/CHN/2004 (abbreviated as 04HZ01) was isolated from the stool specimen of a 1-year-old boy using a human rhabdomyosarcoma cell line. The patient had not developed residual paralysis at a 60-day follow-up. The genome of strain 04HZ01 was sequenced with an ABI 3130 genetic analyzer (Applied Biosystems) using the Sanger method. The complete genome length was 7,464 nt, encoding a polypeptide of 2,206 amino acids. The coding sequence was flanked by a noncoding 5′ untranslated region (5′ UTR) of 742 nt and a noncoding 3′ UTR of 101 nt. In the VP1 nucleotide sequence, strain 04HZ01 showed 75.8% identity to the prototype strain CA67-10387. Because 75% of the VP1 sequence is the cutoff value for type identity (5), the great divergence reveals near-saturation in allowable substitutions within a type, suggesting that this “new” type of EV80 has been circulating for many years.
Strain 04HZ01 had 79.5% and 78.6% similarities to the prototype virus in the complete genome and polypeptide coding regions, respectively. Interestingly, compared with the prototype strain CA67-10387, an insertion of 36 nucleotides was observed between positions 3320 to 3321 (numbering according to prototype strain) in the VP1 coding region of strain 04HZ01, resulting in an insertion of 12 amino acids in the encoded protein. No evidence of recombination in this region of strain 04HZ01 was observed, suggesting that this insertion did not result from recombination with other HEV strains. The length of the 3′ end of the VP1 coding region varies among different types, whereas to the best of our knowledge, insertion of a fragment up to 36 nucleotides within a type has not been reported yet. More study is needed to elucidate the influence on its antigenicity.
The similarity plot and bootscanning analysis indicated that multiple recombination events occurred between EV80 and echovirus 19 (nt positions 3980 to 4160) and echovirus 27 (nt positions 4820 to 4960) prototype strains in the nonstructural coding region. These findings further demonstrate that intertypic recombination is common among different serotypes of enteroviruses (4, 8).
Nucleotide sequence accession number.
The complete genome sequence of the EV80 strain HZ01/SD/CHN/2004 was deposited in GenBank under the accession number JX644073.
ACKNOWLEDGMENTS
This study was supported by the Shandong Provincial Natural Science Foundation, China (ZR2012HM007), and two grants from the Health Department of Shandong Province (2011QZ013 and 2011HZ058).
REFERENCES
- 1. Khetsuriani N, et al. 2009. Limited duration of vaccine poliovirus and other enterovirus excretion among human immunodeficiency virus infected children in Kenya. BMC Infect. Dis. 9:136. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Knowles NJ, et al. 2011. Picornaviridae, p 855–880 In King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. (ed), Virus taxonomy: classification and nomenclature of viruses: ninth report of the International Committee on Taxonomy of Viruses. Elsevier, San Diego, CA [Google Scholar]
- 3. Le Gall O, et al. 2008. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture. Arch. Virol. 153:715–727 [DOI] [PubMed] [Google Scholar]
- 4. Lukashev AN, et al. 2003. Recombination in circulating enteroviruses. J. Virol. 77:10423–10431 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. 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 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Oberste MS, et al. 2007. Molecular identification of 13 new enterovirus types, EV79-88, EV97, and EV100-101, members of the species Human Enterovirus B. Virus Res. 128:34–42 [DOI] [PubMed] [Google Scholar]
- 7. Pallansch M, Roos R. 2007. Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses, p 839–893 In Knipe DM, et al. (ed), Fields virology, 5th ed Lippincott Williams & Wilkins, Philadelphia, PA [Google Scholar]
- 8. Santti J, Hyypiä T, Kinnunen L, Salminen M. 1999. Evidence of recombination among enteroviruses. J. Virol. 73:8741–8749 [DOI] [PMC free article] [PubMed] [Google Scholar]