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1 The Korean Journal of Microbiology, Vol. 45, No. 2, June 2009, p Copyright 2009, The Microbiological Society of Korea w Hu/NLV/Gunpo/2006/KO w p 1,2 Á 1 Á 2 Á 3 Á 1 * w w w» w l s w w j Caliciviridae (family) w x w. ü RNA l 3 open reading frame (ORF)» wš, w m mw w p w. (Hu/NLV/Gunpo/2006/KO), 2 ƒ l. PCR s mw RNA 3 cdna r w w, w cdna» w. i Hu/NLV/Gunpo/2006/KO 3 ORF (ORF1, 5,100 bp; ORF2, 1,647 bp; ORF3, 765 bp). 35 w, ORF1 ORF2 ORF3 w» û, p ORF2 ORF3 C- w. w m w, Hu/NLV/Gunpo/2006/KO genogroup II w, Saitama U1, Gifu'96, Mc37, Vietnam 026 j l x w. m w Hu/NLV/Gunpo/2006/KO 3 ORF», w,»» w» œw» w. Key words ý genetic relationship, Hu/NLV/Gunpo/2006/KO, norovirus, sequencing l,,», yw w w, w wù. p 5 w 700 xw (15). w ƒ w wù, y» y w y. 5 w 21 w wš, 5 w š š (2, 13). w q - (fecal-to-oral) y m w x w q, l»¾ w ùkù, ƒ w wù (8) w ƒ, j ƒ w (8). w *To whom correspondence should be addressed. Tel: , Fax: ymlee@chungbuk.ac.kr w» w. w w, (institution), ev, w, (nursing home), w, ƒ w ³, mù ƒ ùkù 24~48» z w 1~2 (5, 9). Caliciviridae (family) Norovirus (genus) (6). s ƒ k human calicivirus. calicivirusƒ mw œm l, s ƒ Caliciviridae ü calicivirus w clade x w. w, d calicivirus. Caliciviridae w 2 Lagovirus Vesivirus w w ƒ., Lagovirus rabbit hemorrhagic disease virus european brown hare syndrome virusƒ sw, Vesivirus feline calicivirusƒ sw. (buoyant density) 1.33~1.41 g/ cm 3, 27~40 nm (envelope) ƒ š, ¼ ƒ 7.5 kb ƒ 105
2 106 Ah-Yong Jeong et al. Kor. J. Microbiol RNA ƒ š RNA (8). RNA 3 open reading frame (ORF),, w w cis-acting elementƒ 5 3 š (1~3, 6). (nonstructural protein) g w ORF1 2C-like helicase, VPg, 3C-like cysteine protease, 3D-like RNAdependent RNA polymerase domain ƒ š w 5 cleavage siteƒ w. ORF2 58 kda e (VP1) g wš, ORF3» y» g w. w 5 genogroup (GI~GV) ù, GI, GII, GIV š, GIII GV ƒƒ (23). j k» û ùkü [, ~45% (human norovirus), ~87% (murine norovirus)]. p, human norovirus w û ùkü (1, 3, 4, 14, 19, 21, 23). Calicivirus s, human calicivirus (HuCV) š f. genogroup ü genotype. e RNA-dependent RNA polymerase w genotype w. ù ¾ s l x ü w x w mw ƒ w. w d w w» œwš, w» w, w 35 w w ³ wš w. w Hu/NLV/Gunpo/2006/KO, 2 ƒ l, l s l w. y 1g ³ 10 w w z, d w -80 o C w. RNA 200 µl l Trizol LS (Invitrogen, USA) w z RNA w. RNA 20 µl dh 2 0 g. RNA -80 o C ¾ w. cdna w s RNA 3 cdna w sw. x š j k Table 1 w. cdna w w (reverse transcription, RT) ww. t RT r(50 mm Tris-HCl; ph 8.3, 75 mm KCl, 10 mm DTT, 3 mm MgCl 2, 0.5 mm dntp) 42 o C, 50 ww. RT w first-strand cdna r l doublestranded cdna» w PCR (polymerase chain reaction) ww. t PCR 20 mm Tris-HCl (ph 8.3), 2.0 mm MgCl 2, 10 mm KCl, 6 mm (NH 4 ) 2 SO 4, 0.1% Triton X-100, 0.001% BSA, 200 µm dntps, 20 µm primers, 2.5 U Pyrobest DNA polymerase (TaKaRa, Japan) sww 100 µl ww. s v denaturation (95 o C, 30 ), annealing (60 o C, 30 ), polymerization (72 o C, 3 ) 35 j ww š, extension 72 o C 10 ww. l j» cdna r, s cdna 1% ƒ» w z, ethidium bromide w w.» BigDye terminator cycle sequencing system (Applied Biosystems, USA) w, w w 3 cdna w» ü v w f w. composite sequence ww w Hu/NLV/Gunpo/2006/KO 3 ORF w» w.» œ. Table 1. Oligonucleotides used in this study Primer Sequence (5 to 3 ) Polarity Region AF ATA TTA ATT AAG TGA ATG AAG ATG GCG TCT AA AR-1 ATA CGG TCC GAA CTG AGT CTC TCA TTG TAG T BF CAT GAA CAT ACA AGA CCT CT BR ATA CGG TCC GTC ACT CGA CGC CAT CTT CAT T CF AGA CAA GAG CCA ATG TTC AG CR ATA CGG TCC GTT TTT TTT TTT TTT TTT TTT
3 Vol. 45, No. 2 NLV w 107 Table 2. Noroviruses used in this study Virus strain Place and year of isolation GenBank assession no. SzUG1 Japan, ? AB Saitama U1 Japan, ? AB Saitama U3 Japan, 1997 AB Saitama U4 Japan, 1997 AB Saitama U16 Japan, 1997 AB Saitama U17 Japan, 1997 AB Saitama U25 Japan, ? AB Saitama U18 Japan, ? AB Saitama U201 Japan, 1998 AB Gifu 96 Japan, IU AB WUG1 Japan, 2000 AB Hu/Gl/otofuke/1979/JP Japan, 1979 AB Chiba (Hu/NLV/Chiba 407/1987/JP) Japan, 1987 AB Hu/Chiba/ /2005/JP) Japan, 2005 AB BS5 IU AF Vietnam 026 Vietnam, IU AF Hu/NLV/GII/MD145-12/1987/US USA, 1987 AY Snow Mountain USA, IU AY Mc37 Thailand, IU AY Hu/NLV/GII/Langen1061/2002/DE Germany, 2002 AY Hu/NLV/Oxford/B5S22/2003/UK UK, 2003 AY Hu/NLV/Oxford/B4S2/2002/UK UK, 2002 AY Hu/NLV/Oxford/B4S5/2002/UK UK, 2002 AY Hu/NLV/Oxford/B4S6/2002/UK UK, 2002 AY Hu/NLV/Oxford/B4S4/2002/UK UK, 2002 AY Hu/NLV/Oxford/B4S7/2002/UK UK, 2002 AY Hu/NLV/Oxford/B4S1/2002/UK UK, 2002 AY Hu/NLV/Oxford/B2S16/2002/UK UK, 2002 AY Hu/NLV/Dresden174/pUS-NorII/1997/GE Germany, 1997 AY Hu/NLV/GII/Neustrelitz260/2000/DE Germany, 2000 AY Hu/Guangzhou/NVgz01/CHN China, IU DQ Southampton UK, IU L07418 Norwalk(M87661) IU M87661 Norwalk(NC_001959) USA, IU NC_ Lordsdale IU X86557 HU/NLV/Seoul/2006/KO Korea, 2006 This study IUS information unavailable Multiple sequence alignment phylogenetic analysis Multiple sequence alignment phylogenetic analysis w Hu/NLV/Gunpo/2006/KO sww GenBank z 35» w. w w GenBank accession no. Table 2 w. w w, CLUSTAL X (22) v w default w multiple sequence alignment
4 108 Ah-Yong Jeong et al. Kor. J. Microbiol ww. q l e l neighbor-joining method (18) w m w. w TREEVIEW software (16) w m ƒyw. w Hu/NLV/Gunpo/2006/KO» 2006» s w y RNA w» w w, Hu/NLV/Gunpo/2006/KO w. 5 3 w» w» w, 3 cdna r sw. cdna w PCR s š j k Table 1 w. w 3 kb j» s cdna» w.» r», DNA strider v w wù composite sequence w.», ü Hu/NLV/Gunpo/2006/KO 3 ORF ƒƒ 5,100 bp (ORF1), 1,647 bp (ORF2), 765 bp (ORF3). w ¾ ƒ 3 poly(a) tail óù y w. w Hu/NLV/Gunpo/2006/KO w p Multiple sequence alignment mw Hu/NLV/Gunpo/2006/KO sww ü 36 (Table 2) consensus sequence wš,» w. mw 3 ORF ORF2 ORF3ƒ» yƒ j (Fig. 1). p, ORF2 C- ƒ virus-like particle 3D mw ƒ Á e š (17)., ORF1 ORF2 ùkü (Fig. 1). w ORF2 upstream sequenceƒ packaging ù y g wš ew (13). w, consensus sequence 5,071 bp~5,090 bp 20 j k, 5,103 bp~5,123 bp 2 w 20 j k ƒ ew w (Fig. 2). ƒ š RNA-dependent RNA polymerase C- PCR s v w». w Hu/NLV/Gunpo/2006/KO w m w Hu/NLV/Gunpo/2006/KO 35 w w» w,» m multiple sequence alignment ww, ƒ š neighbor joining method (18) w Fig. 1. Nucleotide variability of the ORF1 (A), ORF2 (B), and ORF3 (C) of 36 norovirus genomes. The number of nucleotide differences was plotted at each residue throughout the 36 norovirus genomes after multiple sequence alignments.
5 Vol. 45, No. 2 NLV 한국분리주 109 Fig. 2. Nucleotide sequence alignment of the conserved region in the C-terminus of ORF1 of the 28 fully sequenced GII norovirus strains including Hu/NLV/Gunpo/2006/KO. Two highly conserved regions were shown in dotted boxes. Fig. 3. A phylogenetic tree based on the 36 fully sequenced human noroviruses including Hu/NLV/Gunpo/2006/KO. The multiple sequence alignment was obtained by CLUSTAL X, and the phylogenetic tree was constructed by the neighbor-joining method. The scale bar represents the number of nucleotide substitutions per site.
6 110 Ah-Yong Jeong et al. Kor. J. Microbiol m w. w m 2 j j l(cluster) x w (Fig. 3). ¾ ƒ 2 genogroup (GI GII) ew (1, 3, 14, 19, 21). GI j l Hu/GI/Otofuke/1979/JP, BS5, Chiba, SzUG1, Southampton, WUG1, Norwalk (NC_001959), Norwalk (M87661) sww 8 ƒ sw. GII j l 2 cladeƒ x. 2 clade wù Saitama U25, U3, U4, U16, U17 swwš, wù Hu/NLV/Gunpo/2006/KO w Saitama U1, Gifu'96, Mc 37, Vietnam 026 sw. Cladeƒ ù,, ƒ j wù clade x w,,, pû, w ƒ clade x w w w. š, 2 ƒ l w Hu/NLV/Gunpo/2006/KO» w. l» m» 35 wš w m w, Hu/NLV/Gunpo/2006/KOƒ GII w Mc37, Vietnam 026, Saitama U1, Gifu'96 ƒ w ùkü. w, multiple sequence alignment ww j k ORF1 ORF2 ORF3 w ùkü. ORF1 ƒ packaging signal y transcription start signal g wš w ew, ƒ w e ƒ. ORF1 RNA-dependent RNA polymerase s ƒ w (12). ORF2ƒ g w e N- w w N/S ORF1 û ùkü. š e C- w w P2 ƒ û ù kü., human immunodeficiency virus (HIV) V3 loop (7) hepatitis C virus (HCV) E2/hypervariable (10) j k d ù kü. HIV HCV t, w wš vw (11, 20). w v e P2 w w w. P2 t y wš w w w w w ƒ. mw Hu/NLV/Gunpo/2006/KO»» w» w» y». w, w w w w w. yw, w, w, x w ƒ ü s l w w w w w. š x 1. Ando, T., S.S. Monroe, J.R. Gentsch, Q. Jin, D.C. Lewis, and R.I. Glass Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-pcr and southern hybridization. J. Clin. Microbiol. 33, Glass, R.I., J. Noel, T. Ando, R. Fankhauser, G. Belliot, A. Mounts, U.D. Parashar, J.S. Bresee, and S.S. Monroe The epidemiology of enteric caliciviruses from humans: a reassessment using new diagnostics. J. Infect. Dis. 181, Green, K.Y., T. Ando, M.S. Balayan, T. Berke, I.N. Clarke, M.K. Estes, D.O. Matson, S. Nakata, J.D. Neill, M.J. Studdert, and H-J. Thiel Taxonomy of the Caliciviruses. J. Infect. Dis. 181, Green, S.M., K.E. Dingle, P.R. Lambden, E.O. Caul, C.R. Ashley, and I.N. Clarke Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity. J. Gen. Virol. 75, Greenberg, H.B., J. Valdesuso, R.H. Yoken, E. Gangarosa, W. Gary, R.G. Wyatt, T. Konno, H. Suzuki, R.M. Chanock, and A.Z. Kapikian Role of Norwalk virus in outbreaks of nonbacterial gastroenteritis. J. Infect. Dis. 139, Hardy, M.E., S.F. Kramer, J.J. Treanor, and M.K. Estes Human calicivirus genogroup II capsid sequence diversity revealed by analyses of the prototype Snow Mountain agent. Arch. Virol. 142, Holmes, E.C., L.Q. Zhang, P. Simmonds, C.A. Ludlam, and A.J. Brown Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89, Kapikian, A.Z., R.G. Wyatt, R. Dolin, T.S. Thornhill, A.R. Kalica, and R.M. Chanock Visualization by immune electron microscopy of a 27-nm particle associated with acute infectious nonbacterial gastroenteritis. J. Virol. 10,
7 Vol. 45, No. 2 NLV w Kaplan, J.E., G.W. Gary, R.C. Baron, N. Singh, L.B. Schonberger, R. Feldman, and H.B. Greenberg Epidemiology of Norwalk gastroenteritis and the role of Norwalk virus in outbreaks of acute nonbacterial gastroenteritis. Ann. Intern. Med. 96, Kato, N., Y. Ootsuyama, S. Ohkoshi, T. Nakazawa, H. Sekiya, M. Hijikata, and K. Shimotohno Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus. Biochem. Biophys. Res. Commun. 189, Kato, N., H. Sekiya, Y. Ootsuyama, T. Nakazawa, M. Hijikata, S. Ohkoshi, and K. Shimotohno Humoral immune response to hyper-variable region 1 of the putative envelope glycoprotein (gp70) of hepatitis C virus. J. Virol. 67, Kojima, S., T. Kageyama, S. Fukushi, F.B. Hoshino, M. Shinohara, K. Uchida, K. Natori, N. Takeda, and K. Katayama Genogroup-specific PCR primers for detection of Norwalk-like viruses. J. Virol. Methods 100, Lambden, P.R., B. Liu, and I.N. Clarke A conserved sequence motif at the 5terminus of the Southampton virus genome is characteristic of the Caliciviridae. Virus Genes. 10, Liu, B., I.N. Clarke, and P.R. Lambden Polyprotein processing in Southamptonvirus: Identification of 3C-like protease cleavage sites by in vitro mutagenesis. J. Virol. 70, Murray, C.J. and A.D. Lopez Mortality by cause for eight regions of the world: Global burden of disease study. Lancet 349, Page, R.D TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, Prasad, B.V., M.E. Hardy, T. Dokland, J. Bella, M.G. Rossmann, and M.K. Estes X-ray crystallographic structure of the Norwalk virus capsid. Science 286, Saitou, N. and M. Nei The neighbor-joining methods: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, Seah, E.L., J.A. Marshall, and P.J. Wright Open reading frame 1 of the Norwalk-like virus Camberwell: Completion of sequence and expression in mammalian cells. J. Virol. 73, Shioda, T., J.A. Levy, and C. Cheng-Mayer Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc. Natl. Acad. Sci. USA 89, Someya, Y., N. Takeda, and T. Miyamura Complete nucleotide sequence of the chibavirus genome and functional expression of the 3C-like protease in Escherichia coli. Virology 278, Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality tools. Nucleic Acids Res. 25, Thornton, A.C., K.S. Jenning-Conklin, and M.I. McCormick Noroviruses: agents in outbreaks of acute gastroenteritis. Disaster Manag Res. 2, 4-9. (Received May 11, 2009/Accepted June 8, 2009) ABSTRACT : Molecular Characterization of a Korean Isolate of Human Norovirus, the Hu/NLV/ Gunpo/2006/KO Strain Ah-Yong Jeong 1,2, Sang-Im Yun 1, Young-Mee Jee 2, Yoonsung Kang 3, and Young-Min Lee 1 * ( 1 Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju , Republic of Korea, 2 Division of Viral Hepatitis and Poliovirus, Center for Infectious Diseases, National Institute of Health, Seoul , Republic of Korea, 3 Department of Bio-Material, DNA Repair Research Center, Graduate School, Chosun University, Gwangju , Republic of Korea) Norovirus (NV) with a variety of genotypes, a member of the family Caliciviridae, causes acute nonbacterial gastroenteritis in humans. We determined the nucleotide sequence of three open reading frames (ORFs) of a NV Korean strain and characterized the genetic relationship with others. The Korean strain designated Hu/NLV/ Gunpo/2006/KO was isolated from the stool specimen of a 2-year-old female suffering from gastroenteritis. By performing reverse transcription and PCR amplification, three overlapping cdnas were synthesized and used for direct sequencing. We found that like other NVs, this strain contains three ORFs: ORF1, 5,100 bp; ORF2, 1,647 bp; ORF3, 765 bp. Of 35 NVs, ORF1 had a level of genetic diversity lower than ORF2 and ORF3, of which the C-termini of the ORF2 and ORF3 showed a relatively high degree of genetic diversity. Phylogenetic analyses indicated that the Korean strain belonged to genogroup II, with Saitama U1, Gifu 96, Mc37, and Vietnam 026 being formed a single genetic cluster. The nucleotide sequence information of three ORFs of a NV Korean isolate will be useful not only for the development of a diagnostic tool and understanding of genetic relationship, but also provide important basic information for the functional analysis of their gene products.
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