A new type of human calicivirus (HuCV) showing the classic cup-shaped surface morphology was identified in the stool sample from a child with symptoms of acute gastroenteritis in Seoul, Korea (SK virus). Genomic RNA was extracted directly from the stool sample, and the nucleotide sequence of 3.2 kb of the 3' end of SK virus was determined from cDNA. This region spanned sequences from the RNA-dependent RNA polymerase (RDRP) region in the open reading frame 1 (ORF1) to the 3' poly A tail. The non-structural and capsid protein coding sequences were fused in a single ORF as observed in Manchester type (Genogroup III). However, ORF2 of Manchester virus was missing in SK virus. In RDRP region, SK virus showed amino acid and nucleotide identities of 74-75% and 68-69% respectively, with those of Manchester virus, while showed 34-46% and 55-60% identities respectively with those of other human caliciviruses. However, capsid protein of SK virus showed a partial (29-46%) amino acid identity with those of other caliciviruses including Manchester type. The closest resemblance in amino acid (97-99%) and nucleotide sequence (85-86%) identities were found in RDRP region with Vanderbijlpark and Pretoria isolates recently found in South Africa. These results suggest that SK virus together with Vanderbijlpark and Pretoria isolates belong to a new type different from Manchester virus.
Amino Acid Sequence ; Base Sequence ; Calicivirus/ultrastructure ; Calicivirus/isolation & purification* ; Calicivirus/genetics* ; Child ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA, Complementary/chemistry ; Feces/virology ; Genome, Viral ; Genotype ; Human ; Korea ; Microscopy, Electron ; Molecular Sequence Data ; Open Reading Frames ; RNA, Viral/isolation & purification ; RNA, Viral/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid