Determination of the whole-genome consensus sequence of the prototype DS-1 rotavirus using sequence-independent genome amplification and 454® pyrosequencing

The prototype DS-1 rotavirus strain, is characterised by a short electropherotype and G2P[4] serotype specificity. Following sequence-independent genome amplification and 454® pyrosequencing of genomic cDNA, differences between the newly determined consensus sequence and GenBank sequences were observed in 10 of the 11 genome segments. Only the consensus sequence of genome segment 1 was identical to sequences deposited in GenBank. A novel isoleucine at position 397 in a hydrophobic region of VP4 is described. An additional 7 N-terminal amino acids was found in NSP1. For genome segment 10 the first 34 and last 30 nucleotides of the 5′ and 3′-terminal ends, respectively, were identified. Genome segment 11 was found to be 821 bp long, which is 148 bp longer than the full length genome segment 11 sequence reported previously. This paper reports the first complete consensus genome sequence for the tissue culture adapted DS-1 strain free from cloning bias and the limitations of Sanger sequencing. Sequence differences in previous publications reporting on DS-1 rotavirus genome segment sequencing, were identified and discussed.

► The DS-1 whole-genome consensus sequence was determined using 454® pyrosequencing.
► A novel I397 was found in a hydrophobic region in VP4.
► The additional 7 residues found in NSP1 suggest an alternative start codon.
► The first 34 and last 30 terminal nucleotides were identified for genome segment 10.
► Genome segment 11 is 821 bp long.