Journal: medRxiv

Article Title: Development and Evaluation of an ARTIC-Based Amplicon Sequencing Assay for Whole-Genome Characterization of Respiratory Syncytial Virus

doi: 10.64898/2026.04.06.26350258

Figure Lengend Snippet: A custom, in-house bioinformatics pipeline was used to detect, subtype, and generate high-quality consensus sequences for RSV-A and RSV-B.

Article Snippet: Intact synthetic RNA transcripts of RSV-A and RSV-B (ZeptoMetrix: RSV-A Cat. No. NATRSVA-STQ, RSV-B Cat. No. NATFRC-ERC; ATCC: RSV-A Cat. No. VR-3418, RSV-B Cat. No. VR-1400) were run in duplicate as positive controls, while nuclease-free water served as a negative extraction control.

Techniques:

Journal: medRxiv

Article Title: Development and Evaluation of an ARTIC-Based Amplicon Sequencing Assay for Whole-Genome Characterization of Respiratory Syncytial Virus

doi: 10.64898/2026.04.06.26350258

Figure Lengend Snippet: A) Genomic coverage and B) mean depth of coverage plots of high-quality RSV-A (75) samples and RSV-B samples (76). The boxplot values indicate the overall median percent coverage and depth: 98% and 53,434x for RSV-A, and 98% and 48,585x for RSV-B. C) Genomic coverage map for RSV-A; (Genomic coordinates: NS1 70-489, NS2 599-973, N 1111-2286, P 2318-3043, M 3226-3996, SH 4266-4460, G 4652-5617, F 5697-7421, M2-1 7640-8224, M2-2 8199-8465, L 8532-15029). D) Genomic coverage map for RSV-B; (Genomic coordinates: NS1 57-475, NS2 584-958, N 1097-2272, P 2305-3030, M 3154-3990, SH 4259-4456, G 4645-5578, F 5676-7400, M2-1 7627-8214, M2-2 8180-8452, L 8518-15018), showing all passing samples and primer pair positions. The dotted line indicates the median depth of coverage.

Article Snippet: Intact synthetic RNA transcripts of RSV-A and RSV-B (ZeptoMetrix: RSV-A Cat. No. NATRSVA-STQ, RSV-B Cat. No. NATFRC-ERC; ATCC: RSV-A Cat. No. VR-3418, RSV-B Cat. No. VR-1400) were run in duplicate as positive controls, while nuclease-free water served as a negative extraction control.

Techniques:

Journal: medRxiv

Article Title: Development and Evaluation of an ARTIC-Based Amplicon Sequencing Assay for Whole-Genome Characterization of Respiratory Syncytial Virus

doi: 10.64898/2026.04.06.26350258

Figure Lengend Snippet: Probit regression analysis estimating the lower limit of detection as 4.4 TCID 50 /mL for (A) RSV-A and 18.6 TCID 50 /mL for (B) RSV-B. Data points at the top of each panel represent infinitive values.

Article Snippet: Intact synthetic RNA transcripts of RSV-A and RSV-B (ZeptoMetrix: RSV-A Cat. No. NATRSVA-STQ, RSV-B Cat. No. NATFRC-ERC; ATCC: RSV-A Cat. No. VR-3418, RSV-B Cat. No. VR-1400) were run in duplicate as positive controls, while nuclease-free water served as a negative extraction control.

Techniques:

Journal: medRxiv

Article Title: Development and Evaluation of an ARTIC-Based Amplicon Sequencing Assay for Whole-Genome Characterization of Respiratory Syncytial Virus

doi: 10.64898/2026.04.06.26350258

Figure Lengend Snippet: B) Pie charts show the distribution of clades in the sample sets. For RSV-A, the dominant clades were A.D.3.1 (n = 26) and A.D.5.2 (n = 21), together comprising 63% (47/75) of the passing samples. For RSV-B, the dominant clade is B.D.E.1 (n = 69), representing 91% (69/76) of passing samples. The maximum likelihood phylogenetic trees of (C) RSV-A and (D) RSV-B genomes generated in Nextclade.

Article Snippet: Intact synthetic RNA transcripts of RSV-A and RSV-B (ZeptoMetrix: RSV-A Cat. No. NATRSVA-STQ, RSV-B Cat. No. NATFRC-ERC; ATCC: RSV-A Cat. No. VR-3418, RSV-B Cat. No. VR-1400) were run in duplicate as positive controls, while nuclease-free water served as a negative extraction control.

Techniques: Generated

Journal: Nature Communications

Article Title: Interleukin-27 is antiviral against Zika virus at the maternal-fetal interface

doi: 10.1038/s41467-025-67378-0

Figure Lengend Snippet: Representative brightfield images of single trophoblast organoid (TO) culture at 1-, 3-, and 6-days post-passage. 5X magnification, scale bar 1000 μm (top). Insets denote area captured at 10X magnification, scale bar 200μm (bottom). For all 4 biological TO donors, experiment was repeated independently >4 times with similar results. B Expression of IL-27 cytokine ( p28, EBI3 ) and receptor ( WSX1, gp130 ) subunit genes by decidual organoids (DOs) and TOs at day 6 post-passage as determined by quantitative RT-PCR, relative to housekeeping gene HPRT1 . Graphs represent 3 experimental replicates from 4 biological donors of TOs (circles, squares, triangles, and diamonds) and 3 biological donors of DOs (circles, squares, and triangles). Data presented as mean values ± SEM. C Conditioned media were collected from TO cultures from 3 biological donors at 1-, 24-, 48-, and 72-h post-passage and secreted IL-27 was measured via human IL-27 ELISA. Graph represents 5 experimental replicates per timepoint for donor 1 TOs (circles); Graph represents 3 experimental replicates per timepoint for donor 2 and 3 TOs (squares, triangles). Data presented as mean values ± SD. D Representative immunofluorescent images of TOs at day 6 post-passage. 10 μm TO cross-sections were stained for DAPI (blue), Ki67 for cytotrophoblasts (white), SDC1 for syncytiotrophoblasts (green), and IL27RA (magenta). White box indicates zoom inset and white dashed line demarcates regions of cytotrophoblasts (CTB) and syncytiotrophoblasts (STB). 20X magnification, Z-stack, merged. Scale bar, 100μm. Images representative experiments independently repeated in 4 biological TO donors with similar results. E. TOs from 2 biological donors (circles, diamonds) were pre-treated with neutralizing antibodies prior to infection with ZIKV-CAM, as described in Supplementary Fig. , . TO cultures were then collected at 1-, 24-, or 48-h post-infection (hpi) for RNA analysis. Graph displays ZIKV viral RNA expression in TOs as determined by quantitative RT-PCR relative to housekeeping gene HPRT1 , normalized to isotype control-treated organoids. Graph represents 4 independent infections preformed in first TO donor (circles) and 3 independent infections preformed in second TO donor (diamonds). Data presented as mean values ± SEM.

Article Snippet: ZIKV-CAM stocks were propagated in C6/36 mosquito cells ( Aedes albopictus ) (ATCC, CRL-1660), while ZIKV DAKAR stocks were grown in Vero cells (ATCC, CCL-81).

Techniques: Expressing, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay, Staining, Infection, RNA Expression, Control

Journal: Nature Communications

Article Title: Interleukin-27 is antiviral against Zika virus at the maternal-fetal interface

doi: 10.1038/s41467-025-67378-0

Figure Lengend Snippet: A Table of experimental conditions for antiviral gene expression analyses in ( B , C ). B TO antiviral gene expression as determined by quantitative RT-PCR, relative to housekeeping gene HPRT1 . Graphs display 5 experimental replicates from 1 TO donor. Statistical analysis performed with multiple unpaired t-tests (two-sided Mann-Whitney), *p < 0.05 (adjusted p values = 0.023621). Data presented as mean values ± SEM. C TO antiviral gene expression as determined by quantitative RT-PCR, relative to Rux. Graphs display 5 experimental replicates from 1 TO donor. Statistical analysis performed with ordinary one-way Kruskal-Wallis ANOVA *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns=not significant ( MX1 from left, p = 0.0125, <0.0001, 0.0003, 0.2709; IFIT1 from left, p = 0.0031, <0.0001, 0.0001, 0.3945; OAS2 from left, p = 0.0141, <0.0001, 0.0012, 0.6252). Data presented as mean values ± SEM. D Left: Volcano plots depicting differentially expressed genes (DEGs) in IL-27-stimulated TOs and IFNλ-stimulated TOs. Statistical analysis performed via two-sided t-test with Benjamini-Hochberg False Discovery Rate correction. Vertical dashed lines: 0.5 log fold-change cutoffs; Horizontal dashed line: 0.05 adjusted p-value cutoff. Right: Venn diagram depicts total upregulated DEGs in IL-27- and IFNλ-stimulated conditions, with the 5 shared genes highlighted in red text on volcano plots. E Select upregulated pathways from gene set enrichment analysis (GSEA). Figure displays top 8 pathways by order of normalized enrichment score (NES). Numbers at end of bars indicate total number of genes associated with each term. Red asterisks indicate pathways that were enriched in both IL-27- and IFNλ-stimulated TOs. F ZIKV viral RNA expression in TOs at 24-h post-infection, as determined by quantitative RT-PCR relative to housekeeping gene HPRT1 , normalized to isotype control-treated organoids. Graph represents 6 independent infections in single TO donor. Statistical analysis performed with Kruskal-Wallis ANOVA, *p < 0.05, ***p < 0.001 (From left, p = 0.0383, 0.0480, 0.0003). Data presented as mean values ± SD. G Antiviral gene expression in ZIKV-infected TOs as determined by quantitative RT-PCR, relative to Isotype. Graphs display 5 experimental replicates from single TO donor. Statistical analysis performed with Kruskal-Wallis ANOVA *p < 0.05, **p < 0.01 ( IFIT1 from left, p = 0.0119, 0.0039; MX1 from left, p = 0.0484, 0.0019; PARP9 from left, p = 0.0033, 0.0163). Data presented as mean values ± SEM.

Article Snippet: ZIKV-CAM stocks were propagated in C6/36 mosquito cells ( Aedes albopictus ) (ATCC, CRL-1660), while ZIKV DAKAR stocks were grown in Vero cells (ATCC, CCL-81).

Techniques: Gene Expression, Quantitative RT-PCR, MANN-WHITNEY, RNA Expression, Infection, Control

Journal: Nature Communications

Article Title: Interleukin-27 is antiviral against Zika virus at the maternal-fetal interface

doi: 10.1038/s41467-025-67378-0

Figure Lengend Snippet: A Timeline for mating and treatment of human STAT2 knock-in (hSTAT2 KI) mice with high molecular weight polyinosinic-polycytidylic acid (HMW poly(I:C)). Created in BioRender. Jurado, K. (2025) https://BioRender.com/eegilr9 . B Serum IL-6 levels in PBS- and HMW Poly(I:C)-treated dams at 6 h post-injection as determined via ELISA. n = 3 dams per group. Statistical analysis performed via ordinary two-way ANOVA, **p < 0.01, ns= not significant (From left, p = >0.9999, 0.0013, 0.0011, 0.9896). Data presented as mean values ± SD. C Proportion of fetuses exhibiting healthy, early resorption, or total resorption phenotypes at E13.5 in PBS- and HMW Poly(I:C)-treated dams. Graph displays total number of fetuses from 3-4 litters per condition. D Representative images depicting fetal outcomes at E13.5. Phenotypes were determined for each fetus based on gross morphology and tissue integrity, as described in methods. E Timeline for mating and infection of hSTAT2 KI mice, as described in methods. Created in BioRender. Jurado, K. (2025) https://BioRender.com/m1xcoc2 . F Proportion of fetuses exhibiting healthy, early resorption, or total resorption phenotypes at E13.5 in PBS- and ZIKV-infected dams. Fetal outcomes were evaluated in 3 independent litters for all conditions except ZIKV-infected IL27RA −/− dams, for which 4 independent litters were evaluated. Graph displays total number of fetuses per condition. G–I ZIKV burdens at E13.5 as determined via quantitative RT-PCR. G Combined ZIKV burden of one matching fetus and placenta, normalized to combined tissue weight. Shape of data point represents observed fetal phenotype. Total number of fetal/placental units per condition plotted (see 4 F ). Statistical analysis performed via Kruskal-Wallis ANOVA, ***p < 0.001, ns=not significant (From left, p = >0.9999, 0.0006). H Left: Fetal ZIKV burdens, normalized to fetus weights. Viral burdens for subset of fetuses exhibiting “healthy” phenotypes plotted (Isotype n = 24, α-IL-27 n = 16, IL27RA −/− n = 28). Right: Placental ZIKV burdens, normalized to placental weights. Viral burdens of placentas matched to fetuses with “healthy” phenotypes plotted (Isotype n = 24, α-IL-27 n = 16, IL27RA −/− n = 28). Statistical analysis performed via Kruskal-Wallis ANOVA, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns=not significant (Fetal from left, p = >0.9999, 0.0374; Placental from left, p = 0.0378, <0.0001). I Maternal serum ZIKV burdens, normalized to serum weight. n = 3 dams for Isotype and α-IL-27-treated groups, n = 4 IL27RA −/− dams. Not significant via Kruskal-Wallis ANOVA.

Article Snippet: ZIKV-CAM stocks were propagated in C6/36 mosquito cells ( Aedes albopictus ) (ATCC, CRL-1660), while ZIKV DAKAR stocks were grown in Vero cells (ATCC, CCL-81).

Techniques: Knock-In, High Molecular Weight, Injection, Enzyme-linked Immunosorbent Assay, Infection, Quantitative RT-PCR