Identical rearrangement of NSP3 genes found in three independently isolated virus clones derived from mixed infection and multiple passages of Rotaviruses

Three rotavirus variants with a rearranged RNA segment derived from the NSP3 gene were isolated in three independent experiments of coinfection and multiple passages of simian rotavirus strain SA11 and single-VP7-gene- or NSP1-gene-substitution reassortants having genetic background of SA11. Sequenc...

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Bibliographic Details
Published in:Archives of virology 2008-03, Vol.153 (3), p.555-559
Main Authors: Alam, M. M, Kobayashi, N, Ishino, M, Nagashima, S, Paul, S. K, Chawla-Sarkar, M, Krishnan, T, Naik, T. N
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Biomedical and Life Sciences
Biomedicine
Brief Report
Cell Line
Cercopithecus aethiops
Cloning
Gene Rearrangement
Genes
Genes, Viral
Genomes
Infections
Infectious Diseases
Medical Microbiology
Molecular Sequence Data
Proteins
RNA polymerase
RNA, Viral - genetics
Rotavirus
Rotavirus - genetics
Rotavirus - isolation & purification
Sequence Analysis, RNA
Serial Passage
Viral Nonstructural Proteins - genetics
Virology
Viruses
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Summary:Three rotavirus variants with a rearranged RNA segment derived from the NSP3 gene were isolated in three independent experiments of coinfection and multiple passages of simian rotavirus strain SA11 and single-VP7-gene- or NSP1-gene-substitution reassortants having genetic background of SA11. Sequence analysis indicated that the three rearranged NSP3 genes had almost identical sequences and genomic structures organized by partial duplication of the open reading frame in a head-to-tail orientation following the termination codon. The junction site of the original NSP3 gene (first copy) and the duplicated portion (second copy) was identical among the three rearranged genes, while a direct repeat, i.e., a homologous sequence between the first copy and second template for duplication, typically located at the junction site, was not detected. However, short similar sequences were present at the end of the first copy and beginning of the second copy. These findings suggest that rearrangement of the NSP3 gene may occur at a certain preferential site which is related to sequence similarity between 3'-untranslated region and a region near the 5'-end of ORF.
ISSN:0304-8608
1432-8798
DOI:10.1007/s00705-007-0004-7