title: Evolution of infectious bronchitis virus in Taiwan: positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity.
abstract: RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5' end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA-N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein.
authors.affiliation: Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
authors.forename: Shu-Ming
authors.initials: SM
authors.lastname: Kuo
authors.affiliation: Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
authors.forename: Hsiao-Wei
authors.initials: HW
authors.lastname: Kao
authors.affiliation: Institute of Genomics and Bioinformatics, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
authors.forename: Ming-Hon
authors.initials: MH
authors.lastname: Hou
authors.affiliation: School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan.
authors.forename: Ching-Ho
authors.initials: CH
authors.lastname: Wang
authors.affiliation: Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
authors.forename: Siou-Hong
authors.initials: SH
authors.lastname: Lin
authors.affiliation: Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Department of Physical Therapy, Graduate Institute of Rehabilitation Science, China Medical University, Taichung, Taiwan. Electronic address: suhonglin@nchu.edu.tw.
authors.forename: Hong-Lin
authors.initials: HL
authors.lastname: Su
mesh_terms: D000818:Animals; D002645:Chickens; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D019143:Evolution, Molecular; D001351:Infectious bronchitis virus / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D019251:Nucleocapsid / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019590:Nucleocapsid Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D013624:Taiwan / Q000453:epidemiology
chemical_list: D019590:Nucleocapsid Proteins; D012367:RNA, Viral; C039919:RNA, recombinant; D012313:RNA