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Identification of cryptic putative IRESs within the ORF encoding the nonstructural proteins of the human rhinovirus 16 genome

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Abstract

Internal ribosome entry site (IRES)-dependent translation is a mechanism distinct from 5′ cap-dependent translation. IRES elements are located mainly in the 5′ untranslated regions (UTRs) of viral and eukaryotic mRNAs. However, IRESs are also found in the coding regions of some viral and eukaryotic genomes to initiate the translation of some functional truncated isoforms. Here, five putative IRES elements of human rhinovirus 16 (HRV16) were identified in the coding region of the nonstructural proteins P2 and P3 through fusion with green fluorescent protein (GFP) expression vectors and bicistronic vectors with a hairpin structure. These five putative IRESs were located at nucleotide positions 4286-4585, 5002-5126, 6245-6394, 6619-6718, and 6629-6778 in the HRV16 genome. The functionality of the five IRESs was confirmed by their ability to initiate GFP expression in vitro. This suggests that an alternative mechanism might be used to increase the efficiency of replication of HRV16.

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Funding

This work was supported by China Mega-Project for Infectious Disease [2018ZX10102001, 2018ZX10711001, 2018ZX10734401 and 2018ZX10734404], SKLID Development Grant (2011SKLID104) and Project of National Pathogen Resource Center (NPRC-32).

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Authors and Affiliations

  1. State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China

    Bingtian Shi, Qinqin Song, Juan Song, Dong Xia, Zhiqiang Xia, Mi Liu, Wenjun Wang, Ruifang Wang, Haijun Du & Jun Han

  2. Center for Biosafety Mega-Science, Chinese Academy of Sciences, 44 Xiao HongShan, Wuhan, 430071, Hubei, China

    Bingtian Shi, Qinqin Song, Juan Song, Dong Xia, Zhiqiang Xia, Mi Liu, Wenjun Wang, Ruifang Wang, Haijun Du & Jun Han

  3. Department of Pathology, School of Basic Medical Sciences, Shenzhen University, 1066 Xueyuan Avenue, Fuguang Community, Taoyuan Street, Nanshan District, A7-437, Lihu Campus, Shenzhen, China

    Xiaonuan Luo

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  1. Bingtian Shi
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  2. Qinqin Song
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  3. Xiaonuan Luo
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  4. Juan Song
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  11. Jun Han
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Contributions

Jun Han designed and conceived the experiments and analyzed the data; Bingtian Shi performed the experiments, analyzed data, and wrote the original draft; Qinqin Song, Xiaonuan Luo, Juan Song, Dong Xia, Zhiqiang Xia, Mi Liu, Wenjun Wang, Ruifang Wang, and Haijun Du supervised data; Jun Han revised the manuscript.

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Correspondence to Jun Han.

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Shi, B., Song, Q., Luo, X. et al. Identification of cryptic putative IRESs within the ORF encoding the nonstructural proteins of the human rhinovirus 16 genome. Arch Virol 166, 3373–3386 (2021). https://doi.org/10.1007/s00705-021-05209-5

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