KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
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| ||
| DENV-443 (hybridoma produced) | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | RRID:AB_2943662 |
| DENV-115 (hybridoma produced) | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | RRID:AB_2943663 |
| DENV-290 (hybridoma produced) | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | RRID:AB_2943664 |
| DENV-419 (hybridoma produced) | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | RRID:AB_2943665 |
| DENV-P7C07 | Magnani et al.64/JVI.00867–17 | RRID:AB_2943666 |
| DENV-P3D05 | Magnani et al.64/JVI.00867–17 | RRID:AB_2943667 |
| DENV-66 (hybridoma produced) | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | RRID:AB_2943668 |
| DENV-5J7 (plasmid produced Ig) | Beltramello et al.92; https://doi.org/10.1016/j.chom.2010.08.007 | RRID:AB_2943669 |
| DENV-1F4 (hybridoma produced) | Fibriansah et al.63 | RRID:AB_2943670 |
| DENV-14C10 (plasmid produced Ig) | Teoh et al.62 | RRID:AB_2943671 |
| Goat anti-human IgG (Fc)-AP | Meridian Life Science, Inc | Cat#W99008A; RRID: AB_151913 |
| DENV-4G2 (hybridoma produced Ig) | ATCC HB-112 | D1–4G2–4-15; RRID: AB-2722738 |
| DENV-2H2 (hybridoma produced Ig) | ATCC HB-114 | D3–2H2–9-21; RRID: AB-95338 |
|
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| Bacterial and Virus Strains | ||
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| ||
| DENV1ic West Pac 74 | Gallichotte et al., 201793; https://doi.org/10.1128/mSphere.00380–16 | N/A |
| DENV2ic 16803 | Gallichotte et al., 201594; https://doi.org/10.1128/mBio.01461–15 | N/A |
| DENV3 Thailand/CH53489/1973 | Wahala et al.95; https://doi.org/10.1371/journal.ppat.1000821 | N/A |
| DENV3ic Sri Lanka 89 G-III | Messer et al.61 | N/A |
| DENV3 Indonesia 1982, G-I | Messer et al.41 | N/A |
| DENV3 Thailand 1995, G-II | Messer et al.41 | N/A |
| DENV3 Cuba 2002, G-III | Messer et al.41 | N/A |
| DENV3 Puerto Rico 1977, G-IV | Messer et al.41 | N/A |
| DENV4ic Sri Lanka 92 | Widman et al.96; https://10.1586/14760584.2015.961431 | N/A |
| DENV1/3 EDI B | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | NCBI accession #:SRR23674710 |
| DENV1/3 EDII A | This Manuscript | NCBI accession #: SRR23675053 |
| DENV1/3 EDII B | This Manuscript | N/A |
| DENV1/3 EDII C | This Manuscript | N/A |
| DENV1/3 EDII D | This Manuscript | N/A |
| DENV1/3 EDIIIa | This Manuscript | N/A |
| DENV1/3 EDIIIb | This Manuscript | NCBI accession #: SRR23675073 |
| DENV1/3 EDIIIc | This Manuscript | N/A |
| DENV1/3 EDIIId | This Manuscript | N/A |
| DENV3/3 C1 | This Manuscript | N/A |
| DENV3/3 C2 | This Manuscript | N/A |
| DENV3/3 C3 | This Manuscript | N/A |
| DENV3/3 C4 | This Manuscript | N/A |
|
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| Biological Samples | ||
|
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| Serum Samples from DENV3 Primary Infection Survivors | This Manuscript | Adult Arbovirus Travelers Cohort, UNC; DT103/ATC A, DT133/ATC B, DT226/ATC C |
| Serum Samples from DENV3 Primary Infection Survivors | This Manuscript | Nicaraguan Pediatric Dengue Cohort Study, Donor IDs: 4082.7/NPDCS A, 4862.7/NPDCS B, 5862.7/NPDCS C |
| Serum Samples from DENV3 NIH monovalent vaccine trial | Swanstrom et al.68; PMCID: PMC6581895 | Depeleted IDs: 257.01.02/NIH A, 257.01.16/NIH B, 257.03.47/NIH D, 257.03.50/NIH F; Undepleted IDs: 257.03.45/NIH C, 257.03.49/NIH E |
| Normal Human Serum (NHS) Sample | Henein et al.53; PMCID: PMC8245170 | DT236 |
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| Chemicals, Peptides, & Recombinant Proteins | ||
|
| ||
| DMEM, high glucose, GlutaMAX™ Supplement | Thermo Fisher Scientific | Cat# 10566–024 |
| Dulbecco’s modified Eagle’s/Ham’s F-12 50/50 Mix | Gibco | 10–092-CV |
| Opti-MEM I | Gibco | 31985–070 |
| TrueBlue substrate | KPL | 0510–0050 |
| TRIzol LS | Thermo Fisher Scientific | 10296028 |
| Non-fat dry milk | Bio Rad | Cat# 1706404 |
|
| ||
| Cell Lines | ||
|
| ||
| C6/36 cells | ATCC | CRL-1660; RRID: CV_CL_Z230 |
| Vero-81 cells | ATCC | CCL-81; RRID: CV-CL_0059 |
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| Critical Commercial Assays | ||
|
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| Illumina Stranded Total RNA Prep | Illumina | Ribozero Plus Protocol; 20040525 |
| MiSeq Reagent Kit v3 | Illumina | MS-102–3001 |
|
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| Deposited Data | ||
|
| ||
| DENV1/3 EDI B | Young et al.60; https://doi.org/10.1016/j.chom.2020.04.007 | NCBI accession #:SRR23674710 |
| DENV1/3 EDII A | This Manuscript | NCBI accession #: SRR23675053 |
| DENV1/3 EDIIIb | This Manuscript | NCBI accession #: SRR23675073 |
|
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| Recombinant DNA | ||
|
| ||
| Seq & PCR Primer: DENV3 (G-IV), 916F: GCC CAT TAC ATA GGC ACT TC | This Manuscript | Cluster 916F |
| Seq & PCR Primer: DENV3 (G-IV), 2143R: CGA GCT TCC TTT CTT GTA CC | This Manuscript | Cluster 2143R |
| Seq Primer, Cluster 935R: GAA GTG CCT ATG TAA TGG GC | This Manuscript | Cluster 935R |
| Seq Primer, Cluster 1420F: GTT CAC ACA GGA GAT CAA CAC C | This Manuscript | Cluster 1420F |
| Seq Primer, Cluster 1441R: GGT GTT GAT CTC CTG TGT GAA C | This Manuscript | Cluster 1441R |
| Seq Primer, Cluster 1735F: GTG GTT GTT CTT GGA TCG CAA G | This Manuscript | Cluster 1735F |
| Seq Primer, Cluster 1756R: CTT GCG ATC CAA GAA CAA CCA C | This Manuscript | Cluster 1756 R |
| PCR Primer: DENV1/3 Panel; A1F: CAT GCT CCT CAT GCT GCT GC | This Manuscript | A1F |
| PCR Primer: DENV1/3 Panel; U24R: GCC TTT CCA GTT GAT TAC AC | This Manuscript | U24R |
| Seq Primer: DENV1/3 Panel; 1215F: CGA TTC GAG ATG TCC AAC ACA AGG | This Manuscript | 1215 F |
| Seq Primer: DENV1/3 Panel; 1238R: CCT TGT GTT GGA CAT CTC GAA TCG | This Manuscript | 1238 R |
| Seq Primer: DENV1/3 Panel; 1765R: CTA GTA CGA CTA CTT CCT GC | This Manuscript | 1765 R |
| Seq Primer: DENV1/3 Panel; 1650F: CTT ACC ACT GCC TTG GAC CTC | This Manuscript | 1650 F |
| Seq Primer: DENV1/3 Panel; 1670R: GAG GTC CAA GGC AGT GGT AAG | This Manuscript | 1670R |
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| Software and Algorithms | ||
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| ||
| GraphPad Prism, v9.0 | GraphPad Software, Inc. | https://www.graphpad.com |
| PyMOL | Schrödinger, LLC | https://www.pymol.org/ |
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| Other | ||
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| MiSeq | Illumina | N/A |
| EL406 washer dispenser | BioTek | N/A |
| Biostack microplate stacker | BioTek | N/A |
| Immunospot | CTL | N/A |