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Kim, Moon, Song, Song, Park, and Baek: Nucleotide Sequence and Phylogenetic Analysis of M and L Segment of Soochong Virus
Original Article

J Bacteriol Virol 2007;37(2):111-118.

Published online: 18 February 2007

DOI: https://doi.org/10.4167/jbv.2007.37.2.111

Nucleotide Sequence and Phylogenetic Analysis of M and L Segment of Soochong Virus

Eun Ju Kim, Sung Sil Moon, Ki-Joon Song, Jin-Won Song, Kwang Sook Park, Luck Ju Baek

Department of Microbiology, College of Medicine, Institute of Viral Diseases, Bank for Pathogenic Viruses, Korea University, Seoul 136-705, Korea

Received 6 February 2007       Accepted 27 April 2007

Copyright © 2007 Journal of Bacteriology and Virology

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Hantaan virus (HTNV) and Seoul virus (SEOV) have mainly been known as the cause of hemorrhagic fever with renal syndrome (HFRS) in Korea since HTNV has been isolated from Korean field mouse, Apodemus agrarius in 1976 and SEOV has been isolated from Rattus norvegicus in 1980. Soochong virus-1, –2, –3, –4 (SOOVs) were isolated from lung tissues of four Apodemus peninsulae captured on August 1997 at Mt. Gyebang in Hongcheon-gun, Mt. Gachil, Inje-gun, Gangwon Province, and in September 1998 at Mt. Deogyu, Muju-gun, Jeollabuk Province. Apodemus peninsulae is the second-most dominant field rodent species found throughout Korea. To determine phylogenetic analysis of SOOVs, we entirely identified nucleotide sequences of M and L segments. The length of M segment was 3,615 bp and L segment was 6,533 bp. SOOVs were diverged from HTNV by 22.7∼23.3% and SEOV by 36.3∼37.2%, in M segment. In addition, L segment was diverged from HTNV by 21.8∼22.0% and SEOV by 30.3∼30.5%. SOOVs sequence compared with Amur virus (AMRV) in M segment showed that SOOVs were different with AMRV about 14.6∼16.2% in nucleotide sequences. Neighbor-joining phylogenetic analysis based on entire sequences of the M and L segment indicated that the SOOVs sequences present a separate lineage with HTNV, SEOV and AMRV. SOOVs constituted an individual cluster on the phylogenetic tree and they composed a phylogenic lineage separately. According to these data, SOOVs could be classified as a new hantavirus.

Keywords: Hantavirus, Soochong virus, Apodemus peninsulae

References

1). 백락주, 강주일, 송기준, 송진원, 양병국, 이용주. 1995 년 계방산에서 채집한 들쥐의 한타바이러스 감염에 대 한 혈청학적 연구. 대한바이러스학회지. 27(2):177–183. 1997.
2). 송기준, 윤형선, 고은영, 정기모, 박광숙, 이용주, 송진 원, 백락주. Isolation of Apodemus peninsulae-borne Hantanvirus and comparison of molecular biological characteristics. 대한바이러스학회지 30권 1호. 19–28. 2000.
3). 정수용, 송기준, 송진원, 문성실, 김은주, 박광숙, 기선 호, 백락주. 신종 수청바이러스와 무주바이러스의 혈 청학적 특성. 대한바이러스학회지. 35(3):249–225. 2005.
4). Avsic-Zupanc T, Xiao SY, Stojanovic R, Gligic A, van der Groen G, LeDuc JW. Characterization of Dobrava virus: a Hantavirus from Slovenia, Yugoslavia. J Med Virol. 38:132–137. 1992.
crossref
5). Baek LJ, Kariwa H, Lokugamage K, Yoshimatsu K, Arikawa J, Takashima I, Kang JI, Moon SS, Chung SY, Kim EJ, Kang HJ, Song KJ, Klein TA, Yanagihara R, Song JW. Soochong virus: An antigenically and genetically distinct hantavirus isolated from Apodemus peninsulae in Korea. J Med Virol. 78(2):290–297. 2006.
6). Elliott LH, Ksiazek TG, Rollin PE, Spiropoulou CF, Morzunov S, Monroe M, Goldsmith CS, Humphrey CD, Zaki SR, Krebs JW, et al. Isolation of the causative agent of hantavirus pulmonary syndrome. Am J Trop Med Hyg. 51:102–108. 1994.
crossref
7). Hughes AL, Friedman R. Evolutionary diversification of protein-coding genes of hantaviruses. Mol Biol Evol. 17:1558–1568. 2000.
crossref
8). Lee HW, Baek LJ, Johnson KM. Isolation of Hantaan virus, the etiologic agent of Korean hemorrhagic fever, from wild urban rats. J Infect Dis. 146:638–644. 1982.
crossref
9). Lee PW, Amyx HL, Gajdusek DC, Yanagihara RT, Goldgaber D, Gibbs CJ Jr. New hemorrhagic fever with renal syndrome-related virus in rodents in the United States. Lancet. 2:1405. 1982.
10). Lopez N, Padula P, Rossi C, Miguel S, Edelstein A, Ramirez E, Franze-Fernandez MT. Genetic characterization and phylogeny of Andes virus and variants from Argentina and Chile. Virus Res. 50:77–84. 1997.
11). Brummer-Korvenkontio M, Vaheri A, Hovi T, von Bonsdorff CH, Vuorimies J, Manni T, Penttinen K, Oker-Blom N, Lahdevirta J. Nephropathia epidemica: detection of antigen in bank voles and serologic diagnosis of human infection. J Infect Dis. 141:131–134. 1980.
crossref
12). Nowak RM. Walker's mammals of the world. Baltimore: Johns Hopkins University: 1499. 1999.
13). Ogino M, Yoshimatsu K, Ebihara H, Araki K, Lee BH, Okumura M, Arikawa J. Cell fusion activities of Hantaan virus envelope glycoproteins. J Virol. 78:10776–10782. 2004.
crossref
14). Rollin PE, Ksiazek TG, Elliott LH, Ravkov EV, Martin ML, Morzunov S, Livingstone W, Monroe M, Glass G, Ruo S, et al. Isolation of black creek canal virus, a new hantavirus from Sigmodon hispidus in Florida. J Med Virol. 46:35–39. 1995.
15). Schmalhohn CS. Bunyaviridae: The Virus and Their Replication. Fields virology, Third Edition: 1447–1472. 1996.
16). Schmaljohn CS, Dalrymple JM. Analysis of Hantaan virus RNA: evidence for a new genus of bunyaviridae. Virology. 131:482–491. 1983.
crossref
17). Shi X, Elliott RM. Golgi localization of Hantaan virus glycoproteins requires coexpression of G1 and G2. Virology. 300:31–38. 2002.
crossref
18). Song JW, Baek LJ, Gajdusek DC, Yanagihara R, Gavrilovskaya I, Luft BJ, Mackow ER, Hjelle B. Isolation of pathogenic hantavirus from white-footed mouse (Peromyscus leucopus). Lancet. 344:1637. 1994.
crossref
19). Song JW, Song KJ, Baek LJ, Frost B, Poncz M, Park K. In vivo characterization of the integrin beta3 as a receptor for Hantaan virus cellular entry. Exp Mol Med. 37:121–127. 2005.
20). Yashina L, Mishin V, Zdanovskaya N, Schmaljohn C, Ivanov L. A newly discovered variant of a hantavirus in Apodemus peninsulae, far Eastern Russia. Emerg Infect Dis. 7:912–913. 2001.

Figure 1.
Phylogenetic tree of the hantavirus entire M segments. (AMRV: amur virus, SOOV: soochong virus, HTNV: hantaan virus, SEOV: seoul virus, SAAV: saaremaa virus, DOBV: dobrava virus)
jbv-37-111f1.tif
Figure 2.
Phylogenetic tree of the hantavirus entire L segments. (AMRV: amur virus, SOOV: soochong virus, HTNV: hantaan virus, SEOV: seoul virus, SAAV: saaremaa virus, DOBV: dobrava virus, TULV: tula virus, PUUV: puumala virus, CCV: creek canal virus, SNV: sin nombre virus, ANDV: andes virus)
jbv-37-111f2.tif
Table 1.
Oligonucleotide primers of M segment for PCR amplification
Primer name Position (bp) Primer sequence (5′-3′)
OSV 146(+) HTNV: 1∼22 5′-TAG TAG TAG ACA CCG CAA AAG A-3′
SCVM(+) 256 SCV1M: 256∼278 5′-CAC AAT CAC (G/A)AA GTA CAC TCA (G/A)G-3′
HTM F548(+) HTNV: 548∼564 5′-TAT GAG AGA AGT TAC TGT-3′
SCVM(–) 837 SCV1M: 815∼837 5′-GAT CTA AAG TCA TCA AGG GTT GG-3′
SCVM 931(+) SCV1M: 906∼930 5′-TTG CCT CTT CTT ATT CCA TTG TAG GAC C-3′
HTM3(+) HTNV: 1129∼1152 5′-GAT TGA TTT ACC TGG ATA CTA CGA-3′
SCVM(+) 1435 SCV1M: 1410∼1434 5′-CTA GCC TGT TTT CAC TTC TTC CTG G-3′
SCVM(–) 1572 SCV1M: 1573∼1597 5′-GCT TGT GTG GAA AAT GTT TGC AAT A-3′
HTM4(–) HTNV: 1671∼1694 5′-ACT CAT TCA TGC AGA CAT CAC ATA-3′
G2–1(+) HTNV: 1970∼1990 5′-TGG GCT GCA AGT GCA TCA GAG-3′
SCVM(–) 2095 SCV1M: 2096∼2120 5′-GGT TTG TAA GCC TTC TTC GGT AAG T-3′
HTMF(+) F2270 HTNV: 2270∼2286 5′-TAC CCT TGG CAT ACT GC-3′
G2–2(–) HTNV: 2360∼2380 5′-ACA TGC TGT ACA GCC TGT GCC-3′
SCVM(+) 2602 SCV1M: 2577∼2601 5′-TAT TGT TTT TTG GAC CGT TAG AGG G-3′
SCVM(–) 2665 SCV1M: 2666∼2690 5′-GGA AGC CTC TAT CTC TTG GAC TCA T-3′
SCVM(+) 3151 SCV1M: 3126∼3150 5′-CTG TTA AAG TCT CAG GGA AAG GAG G-3′
SCVM(–) 3185 SCV1M: 3186∼3210 5′-TGA AGA CCA ATT TGT GAG CAC TCT T-3′
HTM2(–) HTNV: 3594∼3616 5′-TAG TAG TAG ACA CCG CAA GAT GT-3′
Table 2.
Oligonucleotide primers of L segment for PCR amplification
Primer name Position (bp) Primer sequence (5′-3′)
SCV2L 5′ Terminal(+) SCV2L: 1∼14 5′-TAG TAG TAG ACT CC-3′
SCV2L 5′ Terminal(–) SCV2L: 167∼186 5′-GTT GTC AGA CCA GTC ATC CT-3′
SCVL(+) 131 SCV2L: 131∼150 5′-TAT GCA GTC AGG CAT GA(T/C) AT-3′
SCVL (–) 1111 SCV2L: 1092∼1111 5′-ATT ATG CAC CAA GGA TTC AG-3′
SCL(+) H1012 SCV2L: 1012∼1031 5′-TCC AGA CAC ACC AGC ATC AT-3′
SCL(+) H1666 SCV2L: 1665∼1685 5′-GGA TAC TAT CTT GCT TGA TGG-3′
SCL(–) H1716 SCV2L: 1695∼1714 5′-TAA CTT TGG ATA CCC CCC AC-3′
HTL-F2099 HTNV: 2099∼2115 5′-TT(A/G) AC(A/T) GTT GAC CAA TC-3′
HTL-R 2262 HTNV: 2246∼2262 5′-TG(A/T/G) ATT TT(A/T) GC(C/T) TCT TC-3′
SCL(–) H2780 SCV2L: 2760∼2779 5′-TGG CAT CAT AGT AGT CCT CA-3′
SCL(+) H3012 SCV2L: 2991∼3010 5′-TCG GAG ATT TAC TGC TAT GT-3′
SCL(–) 1 SCV2L: 3193∼3215 5′-TTA CCT TGC AGC CAA TTT CCT TT-3′
SCL(+) H3690 SCV2L: 3570∼3587 5′-AGG TTG TGC TGT TTC GAT CCC A-3′
HTL-F4403 HTNV: 4403∼4419 5′-TG(C/T) ACA TTT TCT AAA GA-3′
HTL-R4518 HTNV: 4502∼4518 5′-TCT (C/T)T(G/C) ACT GTG AAT GT-3′
SCL(–) H4477 SCV2L: 4476∼4500 5′-TCT GCC CAC TTT TGC TCT CTG AAC T-3′
SCL(+) H4875 SCV2L: 4854∼4873 5′-AGT TCT CCA GGC AGT GTC GA-3′
SCL(–) 5 SCV2L: 5169∼5190 5′-ATT TGC TTT TAC ACC ATC TCC A-3′
SCL(–) H5527 SCV2L: 5503∼5525 5′-TGA TTG ATT GCC TGT GTT GTC CT-3′
SCL(+) H5768 SCV2L: 5744∼5766 5′-ACC TCC CTG CAG CTA TCC CAC CT-3′
SCL(–) 7 SCV2L: 5930∼5949 5′-AAA CTC ATC TCT TCA GAC CA-3′
SCV2L 3′ Terminal(+) SCV2L: 6162∼6182 5′-GGT ATC ACG AGG GTT ATC AAT-3′
SCV2L 3′ Terminal(+) Nested SCV2L: 6258∼6279 5′-GCA AGT GTC TTT ATT AGA TCC A-3′
HTL-R6533 HTNV: 6516∼6533 5′-TAG TAG TA(T/G) (G/A)CT CCG-3′
Table 3.
GenBank accession code of Soochong viruses
Virus Animal serial No. Virus isolated provinces GenBank accession No.
S-segment M-segment L-segment
SOOV-1 A.p 97–35 Gyebang Mt. Hongcheon-country, Gangwon-province, Korea AY675349 AY675353 DQ056292
SOOV-2 A.p 97–59 Gachil Mt. Inje-country, Gangwon-province, Korea AY675350 DQ056293 AY675354
SOOV-3 A.p 98–43 Deogyu Mt. Muju-country, Jeollabuk-province, Korea AY675351 DQ056294 –
SOOV-4 A.p 98–50 Deogyu Mt. Muju-country, Jeollabuk-province, Korea AY675352 DQ056295 –

–: Sequences were determined completely, but un-published on the GenBank.

Table 4.
Percent similarity and divergency based on the nucleotide sequences of M segments
Percent Identity
    SOOV-1 SOOV-2 SOOV-3 SOOV-4 AMRV/B78 AMRV/H5 HTNV/76–118 HTNV/84FLi HTNV/8ao14 HTNV/A9 HTNV/Lee Hanta/HB55 Hanta/L99 Hanta/Liu Hanta/Z10 Hanta/Z37 HTNV/CUMC-B11 SEOV/80–39 SAAV DOBV
Divergence SOOV-1   98.6 89.8 87.4 87.0 87.0 80.7 80.6 80.2 79.6 80.3 72.2 72.1 87.0 79.9 72.1 80.7 71.9 70.8 71.6
SOOV-2 1.5   90.1 87.3 86.8 87.0 80.7 80.4 80.1 79.8 80.2 72.3 72.2 87.1 80.1 72.3 80.7 72.1 70.9 71.6
SOOV-3 11.1 10.8   96.9 86.3 86.0 81.1 80.7 80.8 80.1 80.8 72.0 72.1 86.0 80.4 71.9 81.1 72.0 71.5 71.3
SOOV-4 14.0 14.1 3.2   85.9 85.8 80.6 81.2 80.7 80.5 80.7 72.1 72.1 85.8 80.4 72.0 80.7 71.9 71.4 71.1
AMRV/B78 14.6 14.9 15.5 15.9   96.5 79.4 80.2 80.1 79.7 79.7 71.6 71.5 96.4 79.2 71.4 79.5 71.4 70.3 70.7
AMRV/H5 14.7 14.6 15.9 16.2 3.6   79.7 79.8 79.7 79.7 79.7 69.0 69.1 99.9 79.6 71.7 79.6 71.2 70.2 69.8
HTNV/76–118 23.1 23.1 22.7 23.3 24.8 24.3   84.0 87.8 84.7 95.0 71.9 71.8 79.6 84.2 71.5 99.9 71.8 71.3 71.4
HTNV/84FLi 22.9 23.5 22.7 22.1 23.4 23.8 18.4   84.6 85.4 84.1 71.4 71.4 80.2 85.2 72.1 84.0 72.1 71.8 72.0
HTNV/8ao14 23.2 23.4 22.8 22.8 23.4 24.0 13.7 17.6   84.4 87.7 69.0 69.1 79.6 84.8 70.4 87.8 69.9 69.2 71.3
HTNV/A9 24.6 24.4 23.5 23.0 24.3 24.0 17.6 16.6 18.0   84.2 71.6 71.6 80.0 87.3 71.9 84.7 71.6 70.6 71.1
HTNV/Lee 23.7 24.0 23.1 23.1 24.4 24.6 5.2 18.3 13.8 18.3   71.7 71.7 79.7 84.0 71.1 95.0 71.7 71.3 71.3
Hanta/HB55 36.9 36.5 36.4 36.5 37.3 37.6 36.6 38.0 37.0 37.4 37.2   99.5 71.9 71.8 95.8 72.1 95.6 70.6 71.3
Hanta/L99 36.9 36.6 36.3 36.4 37.3 37.6 36.7 37.9 37.0 37.4 37.1 0.5   71.9 71.9 95.7 72.1 95.5 70.6 71.3
Hanta/Liu 14.6 14.6 15.9 16.2 3.7 0.1 24.4 23.6 24.0 23.7 24.4 37.3 37.3   79.8 72.1 79.8 71.5 70.7 71.2
Hanta/Z10 24.0 23.9 23.5 23.6 24.9 24.3 18.2 16.8 17.3 14.3 18.4 37.0 36.9 24.1   71.8 84.1 71.8 70.9 71.0
Hanta/Z37 36.5 36.3 36.2 36.3 37.6 37.2 37.3 36.8 37.4 36.8 37.9 4.3 4.4 36.9 37.0   71.7 96.1 70.7 71.6
HTNV/CUMC-B11 23.2 23.2 22.7 23.3 24.7 24.6 0.1 18.4 13.7 17.6 5.2 36.6 36.7 24.5 18.3 37.3   72.0 71.5 71.5
SEOV/80–39 37.2 36.7 36.3 36.6 37.8 38.2 36.5 36.6 37.0 37.1 37.0 4.6 4.7 37.8 37.1 4.1 36.5   70.9 71.6
SAAV 39.3 39.3 38.5 38.6 40.3 40.3 37.9 38.6 38.9 38.7 38.3 40.1 40.0 40.1 39.4 40.0 37.9 39.3   82.4
DOBV 38.2 38.4 37.9 38.5 39.7 39.1 37.6 37.1 38.1 38.7 38.0 39.4 39.4 39.0 39.1 38.9 37.5 38.6 20.8  
Table 5.
Percent similarity and divergency based on the nucleotide sequences of L segments
Percent Identity
    SOOV-1 SOOV-2 SOOV-3 SOOV-4 HTNV/76–118 HTNV/84FLi Hanta/A9 Hanta/L99 Hanta/Z10 Hanta/Z37 SEOV/80–39 SAAV DOBV PUUV/sotkamo PUUV/CG1820 PUUV/Umeahu TULV SNV/NMH-10 SNV/NMR-11 ANDV/Chile-9717869 ANDV/CHI-7913 CCV
Divergence SOOV-1   98.6 86.3 86.1 81.4 81.8 81.2 75.2 81.5 75.3 75.5 75.0 75.0 68.4 68.5 67.7 68.1 67.8 67.7 67.6 67.8 67.6
SOOV-2 1.4   86.2 86.0 81.3 81.7 81.2 75.5 81.4 75.5 75.7 75.0 75.1 68.3 68.5 67.4 68.3 67.7 67.7 67.6 67.6 67.6
SOOV-3 15.4 15.6   99.6 81.2 81.4 80.8 75.3 81.1 75.3 75.5 74.9 75.5 68.5 68.1 67.0 67.8 67.7 67.7 67.1 67.7 67.3
SOOV-4 15.8 15.9 0.4   81.2 81.2 80.7 75.3 81.1 75.3 75.4 74.9 75.5 68.4 68.1 66.9 67.8 67.7 67.7 67.0 67.7 67.3
HTNV/76–118 21.8 21.9 22.0 22.1   83.7 83.8 74.4 83.7 74.5 74.7 74.6 74.9 67.9 68.0 67.6 67.5 67.6 67.6 67.4 67.8 67.5
HTNV/84FLi 21.2 21.4 21.8 22.0 18.8   97.9 75.8 86.4 75.5 75.7 74.9 75.0 68.6 68.3 67.1 67.9 67.7 67.7 67.6 67.3 67.6
Hanta/A9 22.1 22.1 22.6 22.7 18.7 2.2   75.1 85.6 74.8 75.1 74.6 74.8 68.5 68.0 66.8 67.7 67.5 67.5 67.3 67.1 67.5
Hanta/L99 31.1 30.7 30.7 30.7 32.3 30.1 31.1   75.5 95.7 95.9 75.1 75.3 68.7 67.6 67.3 67.7 67.9 67.9 67.3 67.7 68.1
Hanta/Z10 21.7 21.8 22.2 22.3 18.9 15.4 16.5 30.6   74.8 75.0 75.1 75.2 68.3 67.9 67.5 67.9 67.6 67.6 67.8 67.6 67.5
Hanta/Z37 30.8 30.6 30.5 30.5 32.0 30.3 31.3 4.4 31.3   96.2 74.9 75.4 68.7 68.0 67.4 67.9 67.7 67.7 67.5 67.8 68.1
SEOV/80–39 30.6 30.4 30.3 30.4 31.9 30.2 31.2 4.3 31.0 3.9   74.9 75.4 68.5 67.8 67.5 67.6 67.8 67.8 67.0 67.5 67.9
SAAV 31.2 31.2 31.2 31.3 31.6 31.5 31.9 31.0 31.1 31.4 31.4   85.7 68.1 68.6 67.6 67.4 67.2 67.3 67.3 67.0 68.1
DOBV 31.1 31.0 30.5 30.6 31.1 31.0 31.4 30.9 30.8 30.6 30.7 16.3   68.5 68.2 68.1 67.9 68.2 68.2 67.9 67.5 67.3
PUUV/sotkamo 44.9 45.1 44.9 45.0 45.3 44.4 45.0 44.5 44.8 44.4 44.3 44.8 44.3   84.6 82.4 75.6 71.8 71.8 71.9 71.9 72.7
PUUV/CG1820 45.1 45.2 45.3 45.3 45.1 44.9 46.0 45.8 45.7 44.9 45.3 44.7 44.9 17.6   81.7 75.3 71.5 71.5 71.2 71.4 71.4
PUUV/Umea-hu 45.4 45.7 47.2 47.2 45.8 45.8 47.0 47.1 46.5 46.4 46.5 45.5 44.2 20.3 21.3   74.7 71.0 71.0 71.4 71.0 71.1
TULV 44.7 44.5 45.8 45.9 46.7 45.1 46.0 45.6 46.0 45.4 45.6 46.4 45.2 30.5 30.8 31.5   71.9 71.9 72.2 71.8 72.0
SNV/NMH10 45.6 45.8 45.6 45.7 45.9 45.2 45.6 44.6 45.5 44.4 44.7 45.5 44.2 36.8 37.0 38.3 36.1   100.0 75.6 75.4 88.0
SNV/NMR11 45.6 45.9 45.6 45.7 45.9 45.3 45.7 44.6 45.5 44.5 44.7 45.5 44.2 36.8 37.1 38.3 36.1 0.0   75.6 75.4 88.0
ANDV/Chile-9717869 45.1 45.1 46.7 46.8 45.5 45.1 45.9 45.7 45.4 45.4 45.6 45.7 45.1 36.0 36.7 37.2 46.2 30.3 30.3   93.9 74.9
ANDV/CHI-7913 46.0 46.2 46.4 46.4 45.8 45.8 46.6 45.8 45.5 45.6 45.9 46.5 45.8 36.2 37.0 37.8 36.4 30.5 30.5 6.4   75.3
CCV 45.7 45.5 46.2 46.3 45.4 44.9 45.1 43.8 45.4 43.8 44.0 45.0 45.6 35.1 37.1 37.6 36.1 13.5 13.4 31.1 30.5  
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