Analysis of the genome sequence of an alpaca coronavirus

Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA. <>
Virology (Impact Factor: 3.32). 08/2007; 365(1):198-203. DOI: 10.1016/j.virol.2007.03.035
Source: PubMed


Coronaviral infection of New World camelids was first identified in 1998 in llamas and alpacas with severe diarrhea. In order to understand this infection, one of the coronavirus isolates was sequenced and analyzed. It has a genome of 31,076 nt including the poly A tail at the 3' end. This virus designated as ACoV-00-1381 (ACoV) encodes all 10 open reading frames (ORFs) characteristic of Group 2 bovine coronavirus (BCoV). Phylogenetic analysis showed that the ACoV genome is clustered closely (>99.5% identity) with two BCoV strains, ENT and LUN, and was also closely related to other BCoV strains (Mebus, Quebec, DB2), a human corona virus (strain 043) (>96%), and porcine hemagglutinating encephalomyelitis virus (>93% identity). A total of 145 point mutations and one nucleotide deletion were found relative to the BCoV ENT. Most of the ORFs were highly conserved; however, the predicted spike protein (S) has 9 and 12 amino acid differences from BCoV LUN and ENT, respectively, and shows a higher relative number of changes than the other proteins. Phylogenetic analysis suggests that ACoV shares the same ancestor as BCoV ENT and LUN.

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    • "Unique aa substitutions were detected in all proteins of the bubaline virus but they were mainly within the S protein (Table 4). As observed in BCoV (Chouljenko et al., 1998), GiCoV (Hasoksuz et al., 2007) and ACoV (Jin et al., 2007), these changes occurred mostly in the S1 subunit which has been proven to be involved in receptor binding and host specificity in the well-characterized MHV (de Haan et al., 2006). Certain residues in the S protein had been associated to enteric or respiratory tropism of BCoV, including residues 531, 769 and 1026 (Chouljenko et al., 1998). "
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