denv1 strain hawaii (ATCC)
ATCC is a verified supplier 
ATCC manufactures this product 
94
Structured Review
ATCC
denv1 strain hawaii
Denv1 Strain Hawaii, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/denv1+strain+hawaii/Dengue+virus+type+1/bio_rxiv__64898__2026__03__17__712358-109-12-15
Average 94 stars, based on 25 article reviews
Denv1 Strain Hawaii, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/denv1+strain+hawaii/Dengue+virus+type+1/bio_rxiv__64898__2026__03__17__712358-109-12-15
Average 94 stars, based on 25 article reviews
denv1 strain hawaii - by Bioz Stars,
2026-09
94/100 stars
Images
1) Product Images from "Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay"
Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay
Journal: bioRxiv
doi: 10.64898/2026.03.17.712358
Figure Legend Snippet: (A) The workflow is used to (i) verify dataset structure/QC; (ii) localize and rank conserved, feature-anchored windows; and (iii) guide MSA-based manual primer-probe design and specificity screening. Box colors indicate workflow phases; grey boxes denote intermediate artifacts/outputs; yellow boxes mark workflow components introduced in this study. (B) Family-level representation of dataset composition. Bars show the top 10 viral families by number of genomes, with Flaviviridae shown additionally for reference (highlighted), even though it falls outside the top 10. The cleaned dataset comprises 11,846 viral genomes, including 10,472 non-segmented and 1,374 segmented genomes. Most genomes fall into other taxa (6,292) and Unclassified (3,220), followed by Geminiviridae (591), Spinareoviridae (251), Sedoreoviridae (250), Phenuiviridae (219), Peribunyaviridae (205), Steitzviridae (204), Rhabdoviridae (180), Polydnaviriformidae (172), Fiersviridae (157), and Flaviviridae (105). (C) Genus-level composition of the family Flaviviridae in the RefSeq complete/near-complete genome dataset. Orthoflavivirus comprises the largest fraction (48.6%, n = 51), followed by Hepacivirus (8.1%, n = 19), unclassified Flaviviridae (16.2%, n = 17), Pestivirus (12.4%, n = 13), and Pegivirus (4.8%, n = 5). Genera are ranked by the number of complete/near-complete RefSeq genomes. (D) An alignment-free distance matrix was computed from preprocessed Orthoflavivirus genomes using a Mash-style transformed Jaccard metric (k = 11) and used to infer a neighbor-joining tree (rooted with a Pestivirus , orange branch in the bottom). The topology recapitulates expected intra-genus structure and coherent species-level clades, which we used to verify taxonomic assignments and flag outliers prior to conserved-signature analysis. The focused species within this study were labeled with their names on the tree. DENV1–4 = dengue virus serotype 1-4, JEV = Japanese encephalitis virus, WNV1,2 = West Nile virus linage 1,2, ZIKV_MR766 = Zika virus, ZIKV_ Natal_RGN = Zika virus
Techniques Used: Transformation Assay, Labeling, Virus
Figure Legend Snippet: (A) Average common feature shortest-unique k-mer (SUK) curves across k=9–51. Vertical guides highlight the onset of rapid feature loss from K17 and a sharper decline around K19, marking the transition from broadly shared to increasingly specific k-mer features. (B) SUK plot for the Orthoflavivirus considered genomes—dengue virus (DENV1–4), Japanese encephalitis virus (JEV), West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV)—showing the decay in shared k-mer features as k increases. We selected k = 19 for downstream conserved-signature discovery because at k ≥ 21 the number of shared k-mers dropped below the genus-level panel size (n = 51), limiting detection of features conserved across the full panel. (C) Genome-presence rank plot of 19-mers within Orthoflavivirus . Bars show the number of genomes containing each 19-mer sequence, ranked from highest to lowest; the top 2 highest-presence 19-mers are labeled. (D) Unitig summary after compacted de Bruijn graph (cDBG) consolidation of 19-mers filtered to those present in ≥3 genomes. Unitig length is plotted against the number of genomes supporting each unitig. Point size indicates k-mer support (number of distinct 19-mers per unitig). Highly conserved unitigs (supported by more genomes) are generally shorter, whereas longer unitigs are typically supported by fewer genomes. (E) Genome-wide conservation hotspot profile along a pseudo-genomic coordinate. Bars indicate the number of genomes contributing conserved hits per window, with color encoding conservation score. Prominent peaks coincide with the NS5 region; terminal repeat/UTR regions are indicated in gray (0–0.3 kbp and 10.5–11.1 kbp). The gray boxes indicate the terminal repeat/UTR regions.
Techniques Used: Virus, Sequencing, Labeling, Genome Wide
Figure Legend Snippet: (A) MAFFT multiple sequence alignment of 600 bps conserved windows from 51 Orthoflavivirus genomes, the red lines indicate the start and the end of the amplicon window used to place the primers and probe. The amplicon region shows high per-base identity, indicated by multiple, contiguous, or near-contiguous conserved bases at 100% identity, colored in forest green. (B) The top panel shows MSA of the considered genomes, including dengue virus (DENV1–4), Japanese encephalitis virus (JEV), West Nile virus (WNV1,2), yellow fever virus (YFV), and Zika virus (ZIKV) strains MR766 Natal RGN annotated with primer pair and probe position with mismatches in magenta underneath the genomes. The lower panel shows chemical properties of each oligonucleotide, including probe and primer concentration, Na+ concentration, length, degeneracy, GC content, salt-corrected T m , ΔG of the reaction, and product size.
Techniques Used: Sequencing, Amplification, Virus, Concentration Assay
![(A) Faceted bar charts show Ct values measured across input copy numbers (copies per µL) for each virus—dengue virus (DENV1–4), Japanese encephalitis virus (JEV), West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV). Bars summarize Ct at each concentration, with points indicating individual reactions (technical replicates); red diamonds denote the mean (error bars, where shown, indicate variability across replicates). Across DENV1–4, ZIKV, and JEV (triplicates), Ct values generally decrease as input concentration increases. ZIKV shows greater replicate-to-replicate variation at some concentrations, reflected by wider error bars compared to other targets. WNV and YFV were detected at 1,000 copies per µL; only a single concentration was tested for these viruses due to limited sample material. Together, these results indicate broad target coverage and reliable amplification across a wide input range for the main panel members. (B) Limit of detection (LOD) assessment of the designed primer-probe set. Prior to testing clinical specimens, LOD was evaluated using nucleic acids from 6 arboviruses (DENV1–4, ZIKV, and JEV) at 1, 10, 1000 copies per µL, with 12 technical replicates per dilution. The assay detected DENV3, DENV4, and JEV down to 1 copy per µL, whereas DENV1, DENV2, and ZIKV were consistently detected down to 10 copies per µL. Points represent individual reaction; a diamond indicates the mean Ct, and error bars indicate ±SD. ND indicates not detected (did not meet the ≥95% positivity criterion and therefore did not qualify as the LOD). (C) Paired comparison of Ct values between assays in clinical samples. Ct values obtained with the commercial kit (Com; circles) and the designed primer–probe set (Des; triangles) are shown for each target, with paired measurements from the same sample connected by dashed lines, for 100 positive samples and 50 positive samples (20 positive with Chikungunya virus [CHIKV] and 30 others). Box plots summarize the distributions (center line, median; box, interquartile range; whiskers, range). Relative to the commercial kit, the designed primer–probe set detected DENV1–4 significantly earlier (lower Ct; p = 0.0004 [n = 25], 0.0013 [n=25], <0.0001 [n=11] and <0.0001 [n=25] for DENV1–4, respectively) but detected ZIKV later (higher Ct; p < 0.0001 [n =14]). P values were calculated using a two-sided paired t-test on matched Com–Des Ct values for each target. Overall diagnostic performance is reported in Tables 1,2 .](https://bio-rxiv-images-cdn.bioz.com/dois_ending_with_58/10__64898_slash_2026__03__17__712358/10__64898_slash_2026__03__17__712358___F4.large.jpg "... numbers (copies per µL) for each virus—dengue virus (DENV1–4), Japanese encephalitis virus (JEV), West Nile virus (WNV), ...")
Figure Legend Snippet: (A) Faceted bar charts show Ct values measured across input copy numbers (copies per µL) for each virus—dengue virus (DENV1–4), Japanese encephalitis virus (JEV), West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV). Bars summarize Ct at each concentration, with points indicating individual reactions (technical replicates); red diamonds denote the mean (error bars, where shown, indicate variability across replicates). Across DENV1–4, ZIKV, and JEV (triplicates), Ct values generally decrease as input concentration increases. ZIKV shows greater replicate-to-replicate variation at some concentrations, reflected by wider error bars compared to other targets. WNV and YFV were detected at 1,000 copies per µL; only a single concentration was tested for these viruses due to limited sample material. Together, these results indicate broad target coverage and reliable amplification across a wide input range for the main panel members. (B) Limit of detection (LOD) assessment of the designed primer-probe set. Prior to testing clinical specimens, LOD was evaluated using nucleic acids from 6 arboviruses (DENV1–4, ZIKV, and JEV) at 1, 10, 1000 copies per µL, with 12 technical replicates per dilution. The assay detected DENV3, DENV4, and JEV down to 1 copy per µL, whereas DENV1, DENV2, and ZIKV were consistently detected down to 10 copies per µL. Points represent individual reaction; a diamond indicates the mean Ct, and error bars indicate ±SD. ND indicates not detected (did not meet the ≥95% positivity criterion and therefore did not qualify as the LOD). (C) Paired comparison of Ct values between assays in clinical samples. Ct values obtained with the commercial kit (Com; circles) and the designed primer–probe set (Des; triangles) are shown for each target, with paired measurements from the same sample connected by dashed lines, for 100 positive samples and 50 positive samples (20 positive with Chikungunya virus [CHIKV] and 30 others). Box plots summarize the distributions (center line, median; box, interquartile range; whiskers, range). Relative to the commercial kit, the designed primer–probe set detected DENV1–4 significantly earlier (lower Ct; p = 0.0004 [n = 25], 0.0013 [n=25], <0.0001 [n=11] and <0.0001 [n=25] for DENV1–4, respectively) but detected ZIKV later (higher Ct; p < 0.0001 [n =14]). P values were calculated using a two-sided paired t-test on matched Com–Des Ct values for each target. Overall diagnostic performance is reported in Tables 1,2 .
Techniques Used: Virus, Concentration Assay, Amplification, Comparison, Diagnostic Assay
Related Articles
Transformation Assay:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Labeling:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Virus:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Sequencing:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Genome Wide:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Amplification:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Concentration Assay:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Comparison:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including Diagnostic Assay:Article Title: Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay Article Snippet: standard panel included DENV serotypes 1–4 (DENV1–4), ZIKV, chikungunya virus (CHIKV), JEV, WNV, and YFV. .. Reference viruses were obtained from the American Type Culture Collection (ATCC), including |
