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. 2007 Aug 15;365(1):198-203.
doi: 10.1016/j.virol.2007.03.035. Epub 2007 Apr 24.

Analysis of the genome sequence of an alpaca coronavirus

L Jin  1 , C K Cebra, R J Baker, D E Mattson, S A Cohen, D E Alvarado, G F Rohrmann
Affiliations

Analysis of the genome sequence of an alpaca coronavirus

L Jin et al. Virology. .

Abstract

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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Figures

Fig. 1
Fig. 1
Map of the alpaca coronavirus genome (GenBank accession no. DQ915164) and ORFs of the viral coding sequence. NS1, non-structural protein gene 1; HE, hemagglutinin-esterase gene; S, spike gene; NS2, non-structural protein gene 2; E, envelope protein gene; M, membrane protein gene; N, nucleocapsid gene; I, internal ORF. The numbers above and below each ORF correspond to the nt coordinates of each gene.
Fig. 2
Fig. 2
A maximum-likelihood phylogenetic tree of selected coronavirus genomes. ACoV (GenBank accession no. DQ915164) was compared to other Group 2 Coronaviruses including porcine hemagglutinating encephalomyelitis virus (PHEV VW572, GenBank accession no. YP_459958); human coronavirus OC43 (HCoV-OC43, AY391777); bovine coronavirus Mebus strain (BCoV-Meb, U00735); bovine coronavirus Quebec strain (BCoV-Q, D00662); bovine coronavirus DB2 strain (BCoV-DB2, DQ811784); bovine coronavirus ENT strain (BCoV-ENT, Q91A22); bovine coronavirus LUN strain (BCoV-LUN, AF391542). The scale bar represents the genetic distance (nucleotide substitution per site).
Fig. 3
Fig. 3
A phylogenetic tree of selected Group 2 spike proteins and hemagglutinin-esterase amino acid sequences. (A) The S proteins from the selected strains were analyzed by the neighbor-joining method. (B) The hemagglutinin-esterase protein of the alpaca strain was compared to other selected Group 2 coronavirus hemagglutinin-esterase proteins. For information on the viruses analyzed, see legend to Fig. 2.
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