| Literature DB >> 26421289 |
Jae-Seok Kim1, Hyun Soo Kim1, Jungwon Hyun1, Han-Sung Kim1, Wonkeun Song1.
Abstract
Norovirus is a major cause of acute gastroenteritis. The molecular epidemiology of norovirus exhibits temporal and geographical fluctuations, and new variants of the GII.4 genotype emerge every 2-3 years to cause global epidemics of acute gastroenteritis. We investigated GI and GII genotypes of human norovirus strains isolated from patients with acute gastroenteritis in Korea in 2013. Norovirus antigen test was performed on 2,980 fecal specimens from January to December 2013. RNA was extracted from norovirus antigen-positive fecal suspensions, and the norovirus capsid (VP1) and polymerase (RdRp) genes were characterized by RT-PCR and sequencing. Of the 230 genotyped strains, GII.4 (77.3%) was the most frequently observed capsid genotype, followed by GII.3 (6.1%) and GII.13 (3.9%). A norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the most frequently found polymerase/capsid genotype (65.7%), followed by GII.P17/GII.17 (2.1%) and GII.P21/GII.3 (2.1%). Phylogenetic, similarity, and capsid epitope analyses of GII.Pe/GII.4 Sydney 2012 strains were performed. We concluded that the norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the main cause of norovirus-related gastroenteritis in Korea in 2013.Entities:
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Year: 2015 PMID: 26421289 PMCID: PMC4572438 DOI: 10.1155/2015/468304
Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411
Primers used in this study for the RT-PCR and sequencing of norovirus.
| Targeted gene | Reaction type | Primer name | Primer orientation | Primer sequence (5′ to 3′) | Annealing position | PCR product size | |
|---|---|---|---|---|---|---|---|
| ORF1 | 1 | One-step RT-PCR | JV12 | F | ATA CCA CTA TGA TGC AGA TTA | nt 4552 | 327 bp |
| JV13 | R | TCA TCA TCA CCA TAG AAA GAG | nt 4878 | ||||
| 2 | 1st PCR | NV32 | F | ATG AAT ATG AAT GAA GAT GG | nt 4226 | 501 bp | |
| NV36 | R | ATT GGT CCT TCT GTT TTG TC | nt 4726 | ||||
| Nested PCR | NV33 | F | TAC CAC TAT GAT GCA GAT TA | nt 4280 | 357 bp | ||
| NV35 | R | GTT GAC ACA ATC TCA TCA TC | nt 4636 | ||||
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| ORF2 | 1 (GI) | 1st PCR | GI-F1M | F | CTG CCC GAA TTY GTA AAT GAT GAT | nt 5342 | 330 bp |
| GI-R1M | R | CCA ACC CAR CCA TTR TAC ATY TG | nt 5671 | ||||
| Nested PCR | GI-F2 | F | ATG ATG ATG GCG TCT AAG GAC GC | nt 5357 | 315 bp | ||
| GI-R1M | R | CCA ACC CAR CCA TTR TAC ATY TG | nt 5671 | ||||
| 2 (GII) | 1st PCR | GII-F1M | F | GGG AGG GCG ATC GCA ATC | nt 5058 | 344 bp | |
| GII-R1M | R | CCR CCT GCA TRI CCR TTR TAC AT | nt 5401 | ||||
| Nested PCR | GII-F3 | F | TTG CCR GCA TRI CCR TTR TAC AT | nt 5088 | 314 bp | ||
| GII-R1M | R | CCR CCT GCA TRI CCR TTR TAC AT | nt 5401 | ||||
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| ORF1-ORF2 junction | One-step RT-PCR | NV33 | F | TAC CAC TAT GAT GCA GAT TA | nt 4280 | 1110 bp | |
| G2SKR | R | CCR CCN GCA TRH CCR TTR TAC AT | nt 5389 | ||||
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| ORF2 (capsid, VP1) | One-step RT-PCR | GII-F1M | F | GGG AGG GCG ATC GCA ATC | nt 5049 | 1681 bp | |
| GV132 | R | CCR GCR AAG AAA GCR CCA GCC AT | nt 6729 | ||||
F, forward; R, reverse.
Norovirus antigen positivity and GII.4 strain frequencies by month.
| Date | Number (No.) of specimens tested | Number (%) of norovirus antigen-positive specimens | Number of genotyped specimens | Number (%) of GII.4 strains of genotyped specimens | Number (%) of GII.4 Sydney 2012 strains of genotyped specimens |
|---|---|---|---|---|---|
| Jan. 2013 | 225 | 53 (23.6%) | 33 | 25 (75.8%) | 22 (66.7%) |
| Feb. | 300 | 38 (12.7%) | 28 | 19 (67.9%) | 14 (50.0%) |
| Mar. | 252 | 27 (10.7%) | 17 | 8 (47.1%) | 7 (41.2%) |
| Apr. | 256 | 16 (6.3%) | 10 | 3 (30.0%) | 3 (30.0%) |
| May | 247 | 11 (4.5%) | 2 | 1 (50.0%) | 1 (50.0%) |
| Jun. | 218 | 6 (2.8%) | 1 | 0 (0%) | 0 (0%) |
| Jul. | 237 | 5 (2.1%) | 2 | 0 (0%) | 0 (0%) |
| Aug. | 225 | 4 (1.8%) | 1 | 1 (100%) | 1 (100%) |
| Sep. | 260 | 11 (4.2%) | 8 | 8 (100%) | 7 (87.8%) |
| Oct. | 138 | 8 (5.8%) | 5 | 3 (60.0%) | 3 (60.0%) |
| Nov. | 284 | 62 (21.8%) | 49 | 47 (95.9%) | 47 (95.9%) |
| Dec. | 338 | 108 (32.0%) | 74 | 62 (83.4%) | 59 (79.7%) |
| Total | 2,980 | 349 (11.7%) | 230 | 177 (77.0%) | 164 (71.3%) |
Norovirus polymerase and capsid genotypes.
| Polymerase (RdRp) genotype | Capsid (VP1) genotype | Number (%) |
|---|---|---|
| Nontyped | GI.3 | 1 (0.4%) |
| GI.P4 | GI.4 | 1 (0.4%) |
| Nontyped | GI.6 | 2 (0.9%) |
| GII.P16 | GII.2 | 4 (1.7%) |
| Nontyped | GII.2 | 2 (0.9%) |
| GII.P21 | GII.3 | 5 (2.1%) |
| GII.P12 | GII.3 | 1 (0.4%) |
| GII.Pe | GII.3 | 1 (0.4%) |
| Nontyped | GII.3 | 7 (3%) |
| GII.P4 Den Haag 2006b | GII.4 Den Haag 2006b | 2 (0.9%) |
| Nontyped | GII.4 Den Haag 2006b | 2 (0.9%) |
| GII.Pe | GII.4 Sydney 2012 | 151 (65.7%) |
| Nontyped | GII.4 Sydney 2012 | 14 (6.1%) |
| GII.Pe | GII.4 | 5 (2.1%) |
| Nontyped | GII.4 | 4 (1.7%) |
| Nontyped | GII.5 | 1 (0.4%) |
| Nontyped | GII.6 | 6 (2.6%) |
| GII.P8 | GII.8 | 1 (0.4%) |
| Nontyped | GII.8 | 1 (0.4%) |
| GII.P16 | GII.13 | 3 (1.3%) |
| Nontyped | GII.13 | 6 (2.6%) |
| GII.P17 | GII.17 | 5 (2.1%) |
| Nontyped | GII.17 | 1 (0.4%) |
| GII.P21 | GII.21 | 2 (0.9%) |
| Nontyped | GII.21 | 2 (0.9%) |
| Total | 230 (100%) |
Figure 1Phylogenetic tree based on partial nucleotide sequences of norovirus GII.4 ORF1 and ORF2. Seven samples of GII.Pe/GII.4 Sydney 2012 genotype in this study were compared to other representative GII.4 reference strains. The sequences of the region comprising nucleotide 4331-6660 were compared. The scale bar represents genetic distance (expressed as nucleotide substitutions per site).
Figure 2SimPlot analysis for nucleotide similarity between the GII.4 Sydney strains in this study and other previously reported GII.4 Sydney strains and other GII.4 variants causing pandemics. The sequence of one strain in this study served as a query strain. The sequences of the regions comprising nucleotide 4331-6660 were compared.
Deduced amino acid sequence of capsid antigen epitopes A to E of the norovirus GII.4 variants.
| GII.4 variant | Epitope A | Epitope B | Epitope C | Epitope D | Epitope E | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 294 | 296 | 297 | 298 | 368 | 372 | 373 | 333 | 382 | 340 | 376 | 393 | 394 | 395 | 407 | 412 | 413 | |
| Farmington Hills 2002/USA/AY502023 | A | T | H | N | N | N | N | M | K | G | E | N | G | A | S | T | G |
| Hunter 2004/AU/DQ078814 | A | A | Q | N | S | S | N | V | R | R | E | S | T | T | D | D | S |
| Den Haag 2006b/NL/EF126965 | A | S | R | N | S | E | N | V | K | G | E | S | T | T | S | N | V |
| Apeldoorn 2007/NL/AB445395 | T | S | R | N | A | D | N | V | K | T | D | D | T | A | S | N | N |
| New Orleans 2009/USA/GU445325 | P | S | R | N | A | D | N | V | K | T | E | S | T | T | S | N | I |
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| Sydney 2012/AU/JX459908_2012.03 |
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| Sydney 2012/KR/KM272334_12.08.04 |
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| Sydney 2012/Hong Kong/KC631827_12.12.10 |
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| Sydney 2012/Taiwan/KJ533134_13.02 |
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| Sydney 2012 in this study #88_13.01.18 |
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| Sydney 2012 in this study #280_13.02.08 |
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| Sydney 2012 in this study #327_13.02.12 |
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| Sydney 2012 in this study #1487_13.11.01 |
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| Sydney 2012 in this study #1497_13.11.04 |
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| Sydney 2012 in this study #1682_13.12.26 |
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| Sydney 2012 in this study #1696_13.12.27 |
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