Complete genome sequence and phylogenetic analysis of a recombinant Korean norovirus, CBNU1, recovered from a 2006 outbreak.
We have determined the complete nucleotide and deduced amino acid sequences of the RNA genome of CBNU1, a human norovirus (NoV) recovered from a 2006 outbreak in South Korea. The genome of 7547 nucleotides, excluding a 3'-poly(A) tail of 11-105 nucleotides, encodes three overlapping open reading frames (ORFs): ORF1 (nucleotides 5-5104), ORF2 (nucleotides 5085-6731), and ORF3 (nucleotides 6731-7495). In a comparison to 108 other currently available completely sequenced NoVs representing all five genogroups (GI-GV) except GIV, the CBNU1 strain was highly similar to GII.3 NoVs. Multiple sequence alignments of the completely sequenced NoV genomes revealed five hypervariable regions throughout their genomes: two in ORF1, one in ORF2, and two in ORF3. At both the nucleotide and amino acid levels, genome-based phylogenetic analyses invariably showed that the CBNU1 strain was most closely related to three GII.3 NoVs: the American Texas/TCH04-577 and the two Japanese Saitama U18 and Saitama U201 strains; furthermore, these genome-based phylogenetic topologies corresponded most closely to those based on the ORF2 genes, as compared to those based on the ORF1 and ORF3 genes. Subsequent ORF2-based phylogenetic analyses of a selection of 126 other NoVs representing all 19 GII genotypes, in combination with genome-based Simplot analyses, showed that the CBNU1 strain was a recombinant GII.3 NoV with a breakpoint at the ORF1/ORF2 junction between two putative parent-like strains, Guangzhou/NVgz01 and Texas/TCH04-577. Overall, the CBNU1 strain represents the first Korean human NoV whose genome has been completely sequenced and for which its relationship with a large panel of genetically diverse NoVs has been extensively characterized.
Yun
Sang-Im
SI
Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong, Heungduk-Ku, Cheongju, Chungbuk, South Korea.
Kim
Jin-Kyoung
JK
Song
Byung-Hak
BH
Jeong
Ah-Yong
AY
Jee
Young-Mee
YM
Lee
Chan-Hee
CH
Paik
Soon-Young
SY
Koo
Yongbum
Y
Jeon
Iksoo
I
Byun
Sung-June
SJ
Lee
Young-Min
YM
D000818:Animals; D001483:Base Sequence; D017250:Caliciviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology*; D002417:Cattle; D002418:Cattle Diseases / Q000821:virology; D002675:Child, Preschool; D004196:Disease Outbreaks; D005260:Female; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D029322:Norovirus / Q000737:chemistry / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016366:Open Reading Frames; D010802:Phylogeny; D056910:Republic of Korea / Q000453:epidemiology; D016415:Sequence Alignment; D017385:Sequence Homology; D013552:Swine; D013553:Swine Diseases / Q000821:virology