Publication: RNA transcription analysis and completion of the genome sequence of yellow head nidovirus
Issued Date
2008-09-01
Resource Type
ISSN
01681702
Other identifier(s)
2-s2.0-46249107600
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Mahidol University
Rights Holder(s)
SCOPUS
Bibliographic Citation
Virus Research. Vol.136, No.1-2 (2008), 157-165
Suggested Citation
Nusra Sittidilokratna, Sirintip Dangtip, Jeff A. Cowley, Peter J. Walker RNA transcription analysis and completion of the genome sequence of yellow head nidovirus. Virus Research. Vol.136, No.1-2 (2008), 157-165. doi:10.1016/j.virusres.2008.05.008 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/18871
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Title
RNA transcription analysis and completion of the genome sequence of yellow head nidovirus
Abstract
Yellow head virus (YHV) is a pathogen of the black tiger shrimp (Penaeus monodon) and, with gill-associated virus (GAV), is one of two known invertebrate nidoviruses. We describe sequences of the large replicase gene (ORF1a) and 5′- and 3′-terminal UTRs, completing the 26,662 nt sequence of the YHV genome. ORF1a (12,219 nt) encodes a ∼462,662 Da polypeptide containing a putative 3C-like protease and a putative papain-like protease with the canonical C/H catalytic dyad and α + β fold. The read-through pp1ab polyprotein contains putative uridylate-specific endoribonuclease and ribose-2′-O-methyl transferase domains, and an exonuclease domain incorporating unusual dual Zn2+-binding fingers. Upstream of ORF1a, the 71 nt 5′-UTR shares 82.4% identity with the 68 nt 5′-UTR of GAV. The 677 nt 3′-terminal region contains a single 60 nt ORF, commencing 298 nt downstream of ORF3, that is identical to N-terminal coding region of the 249 nt GAV ORF4. Northern blots using RNA from YHV-infected shrimp and probes directed at ORF1a, ORF1b, ORF2 and ORF3 identified a nested set of 3′-coterminal RNAs comprising the full-length genomic RNA and two sub-genomic (sg) mRNAs. Intergenic sequences upstream of ORF2 and ORF3 share high identity with GAV, particularly in the conserved domains predicted to mediate sgmRNA transcription. Crown Copyright © 2008.