Analysis of the genome sequence of an alpaca coronavirus

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

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


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.

Original languageEnglish
Pages (from-to)198-203
Number of pages6
Issue number1
StatePublished - 15 Aug 2007
Externally publishedYes

Bibliographical note

Funding Information:
This study was supported by a grant (F0434A) from the Alpaca Research Foundation.


  • Alpaca
  • Alpaca coronavirus
  • Bovine coronavirus
  • Coronavirus


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