Diversity of Noroviruses throughout Outbreaks in Germany 2018
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection
2.3. PCR and Sequence Analysis
2.4. Surveillance Data
3. Results
3.1. Epidemiology
3.2. Distribution of Norovirus Genotypes in Germany and Brandenburg
3.3. Correlation of Norovirus GII.4 Surveillance Data and Phylogenetic Analyses in Märkisch-Oderland (Brandenburg) and Germany in 2018
3.4. Amino Acid Changes in GII.P16 Variants
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Genogroup | Primer/Probe | Sequence | Localization a |
---|---|---|---|
RT-qPCR | |||
I | 192 (sense) | 5’-GCYATGTTCCGCTGGATGC | 5321–5340 |
192a (sense) | 5´-GCAATGTTYCGCTGGATGC | 5321–5340 | |
193 (antisense) | 5´-CGTCCTTAGACGCCATCATCA | 5593–5574 | |
TM9-MGB probe (sense) | 5´-VIC-TGGACAGGAGATCGC-MGB-NFQ | 5345–5359 | |
II | NV107e (sense) | 5´-AACCAATGTTYAGMTGGATGAG | 5007–5026 |
NV107f (sense) | 5´-AACCCATGTTCAGATGGATGAG | 5007–5026 | |
NV107g (sense) | 5′-AGGCCATGTTYAGRTGGATGAG | 5007–5026 | |
NV107h (sense) | 5′-AGCCAATGTTCAGATGGATGAG | 5007–5026 | |
NV359 (antisense) | 5′-TCGACGCCATCTTCATTCACA | 5100–5080 | |
TM15-MGB probe (antisense) | 5′-FAM-TCGATCGCCCTCCCA-MGB-NFQ | 5048–5062 | |
MS-2 phage | MS2-fwd_KL (sense) | 5′-GGCTGCTCGCGGATAC | 3166–3181 |
MS2-rev_KL (antisense) | 5′-AACTTGCGTTCTCGAGCGAT | 3210–3229 | |
MS2 probe (sense) | 5′-Cy5-ACCTCGGGTTTCCGTCTTGCTCGT-BQH2 | 3186–3209 | |
ORF1 genotyping RT-PCR | |||
Genogroup | Primer/Probe | Sequence | localization a |
I and II | NV1c (sense) | 5′-ATG AAC ATG AAT GAG GAT GG | 4499–4518 |
NV1d (sense) | 5′-ATG AAT ATG AAT GAR GAT GG | 4499–4518 | |
NV1e (sense) | 5′-ATG AAT TCA ATT GAG GAT GG | 4499–4518 | |
NV1f (sense) | 5′-ATG AAT GCA ATT GAA GAT GG | 4499–4518 | |
NV7b (antisense) | 5′-GGD CCH TCA STY TTA TC | 4977–4961 | |
NV7c (antisense) | 5′-GGR CCY TCR CTY TTG TC | 4977–4961 | |
NV7d (antisense) | 5′-GGT CCT TCT GAT TTG TC | 4977–4961 | |
NV7e (antisense) | 5′-GGC CCC TCR GTT TTG TC | 4977–4961 | |
NV7f (antisense) | 5′-GGY CCT TCA GTY TTG TC | 4977–4961 | |
NV6e (sense) | 5′-ACC AYT WTG ATG CAG ACT A | 4554–4572 | |
NV6f (sense) | 5′-ACC AYT ATG ATG CTG ATT A | 4554–4572 | |
NV6g (sense) | 5′-ATC AYT ATG ATG CWG AYT A | 4554–4572 | |
NV4d (antisense) | 5′-ACY ATC TCA TCA TCA CCA | 4884–4866 | |
NV4e (antisense) | 5′-ACG ATC TCG TCR TCA CCG | 4884–4866 | |
NV4f (antisense) | 5′-ACT ATY TCA TCA TCA CCA | 4884–4866 | |
NV4g (antisense) | 5′-ACG ATC TCA TCG TCC CCA | 4884–4866 | |
ORF2 genotyping RT-PCR | |||
Genogroup | Primer/Probe | Sequence | Localization a |
GI | NV351 a (sense) | CCI CAT GTI ATT GCT GAT GT | 5793–5812 |
NV351 b (sense) | CCI CAC GTI ATM GCA GAT GT | 5793–5812 | |
NV352 a (antisense) | TTC CCA CAG GCT TIA AYT G | 6909–6891 | |
NV352 b (antisense) | TTC CCA CAG GCT TIA GYT G | 6909–6891 | |
NV354 (sense) | ATG ATG ATG GCG TCT AAG GAC | 5358–5378 | |
GII | NV347 a (sense) | GAI GAT GTC TTC ACA GTY TCT T | 5661–5682 |
NV347 b (sense) | GAT GAT GTK TTC ACW GTI TCT T | 5661–5682 | |
NV347 c (sense) | GAT GAY GTI TTC ACI GTI TCM T | 5661–5682 | |
NV348 a (antisense) | GGT TRA CCC ARG AAT CAA A | 6648–6630 | |
NV348 b (antisense) | GRT TMA CCC AAG AIT CAA A | 6648-6630 | |
NV348 c (antisense) | GRT TRA CCC AIA CTT CAA A | 6648-6630 |
Detected Genotype | Number of Outbreaks in Germany 2018 | % of Outbreaks in Germany | Number of Outbreaks in Märkisch-Oderland 2018 | % of Outbreaks in Märkisch-Oderland |
---|---|---|---|---|
GI.P1-GI.1 | 8 | 3.2 | ||
GI.P2-GI.2 | 8 | 3.2 | 1 | 2.6 |
GI.P2 | 2 | 0.8 | ||
GI.P3-GI.3 | 3 | 1.2 | ||
GI.P3 | 1 | 0.4 | ||
GI.P4-GI.4 | 10 | 4.0 | 1 | 2.6 |
GI.P4 | 1 | 0.4 | ||
GI.P6-GI.6 | 2 | 0.8 | 1 | 2.6 |
GI.P6 | 1 | 0.4 | ||
GI.P6-GI.2 | 1 | 0.4 | ||
GI.P7-GI.7 | 2 | 0.8 | ||
GI.P9-GI.7 | 1 | 0.4 | ||
GI.P11-GI.6 | 7 | 0.4 | ||
GI.P11 | 1 | 1.6 | 1 | 2.6 |
GI.P13-GI.3 | 1 | 1.2 | ||
GI.P13 | 1 | 0.8 | ||
GII.P4-GII.4 Sydney | 2 | 0.8 | ||
GII.P4 2009-GII.4 Sydney | 7 | 2.8 | ||
GII.P6-GII.6 | 4 | 0.4 | ||
GII.P7-GII.6 | 24 | 9.6 | 1 | 2.6 |
GII.P7-GII.7 | 3 | 2.8 | 1 | 2.6 |
GII.P7-GII.14 | 5 | 2.0 | ||
GII.P7 | 5 | 2.0 | ||
GII.P8-GII.8 | 2 | 0.4 | ||
GII.P12-GII.3 | 1 | 0.4 | ||
GII.P16-GII.12 | 3 | 1.2 | ||
GII.P16-GII.2 | 16 | 6.4 | 10 | 25.6 |
GII.P16-GII.3 | 1 | 0.4 | 1 | 2.6 |
GII.P16-GII.4 Sydney | 72 | 28.8 | 3 | 7.7 |
GII.P16 | 10 | 4.0 | ||
GII.P17-GII.17 | 1 | 0.4 | ||
GII.P21-GII.3 | 10 | 4.0 | 6 | 15.4 |
GII.P30-GII.3 | 1 | 0.4 | ||
GII.P31-GII.4 Sydney | 32 | 12.8 | 13 | 33.3 |
GII.P31 | 1 | 0.4 | ||
total | 250 | 39 |
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Niendorf, S.; Faber, M.; Tröger, A.; Hackler, J.; Jacobsen, S. Diversity of Noroviruses throughout Outbreaks in Germany 2018. Viruses 2020, 12, 1157. https://doi.org/10.3390/v12101157
Niendorf S, Faber M, Tröger A, Hackler J, Jacobsen S. Diversity of Noroviruses throughout Outbreaks in Germany 2018. Viruses. 2020; 12(10):1157. https://doi.org/10.3390/v12101157
Chicago/Turabian StyleNiendorf, Sandra, Mirko Faber, Andrea Tröger, Julian Hackler, and Sonja Jacobsen. 2020. "Diversity of Noroviruses throughout Outbreaks in Germany 2018" Viruses 12, no. 10: 1157. https://doi.org/10.3390/v12101157