A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species.

Code ↔ Paper

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Paper

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The authors' code

R · 245 lines · 7.4 KB · MIT

# ===============================================================
# 🧪 Table Analyzer — One-way ANOVA Module (Validated Version)
# ===============================================================
one_way_anova_ui <- function(id) {
ns <- NS(id)
list(
config = tagList(
uiOutput(ns("inputs")),
uiOutput(ns("level_order")),
tags$details(
tags$summary(strong("Advanced options")),
stratification_ui("strat", ns)
),
br(),
fluidRow(
column(
6,
with_help_tooltip(
actionButton(ns("run"), "Run analysis", width = "100%"),
"Run the ANOVA using the selected response and group variable."
)
),
column(
6,
with_help_tooltip(
downloadButton(ns("download_all"), "Download results", style = "width: 100%;"),
"Export the ANOVA summaries, post-hoc tests, and diagnostics."
)
)
)
),
results = uiOutput(ns("summary_ui"))
)
}
one_way_anova_server <- function(id, filtered_data) {
moduleServer(id, function(input, output, session) {
ns <- session$ns
responses <- multi_response_server("response", filtered_data)
strat_info <- stratification_server("strat", filtered_data)
# -----------------------------------------------------
# UI inputs
# -----------------------------------------------------
output$inputs <- renderUI({
req(filtered_data())
data <- filtered_data()
cat_cols <- names(data)[sapply(data, is.factor) | sapply(data, is.character)]
validate(
need(length(cat_cols) > 0,
"No categorical predictor available. Please upload a factor or character variable.")
)
tagList(
multi_response_ui(ns("response")),
with_help_tooltip(
selectInput(
ns("group"),
"Categorical predictor",
choices = cat_cols,
selected = cat_cols[1]
),
"Choose the grouping variable that defines the comparison categories."
)
)
})
# -----------------------------------------------------
# Order of levels
# -----------------------------------------------------
output$level_order <- renderUI({
req(filtered_data(), input$group)
levels <- resolve_order_levels(filtered_data()[[input$group]])
with_help_tooltip(
selectInput(
ns("order"),
"Order of levels (first = post-hoc reference)",
choices = levels,
selected = levels,
multiple = TRUE
),
"Arrange the group levels; the first level is used as the reference for post-hoc comparisons."
)
})
# -----------------------------------------------------
# Run models
# -----------------------------------------------------
models <- eventReactive(input$run, {
df <- filtered_data()
req(df, input$group)
resp_vals <- responses()
# ------------------------
# Validations
# ------------------------
validate(
need(length(resp_vals) > 0,
"Select at least one response variable.")
)
validate(
need(all(sapply(df[resp_vals], is.numeric)),
"All selected response variables must be numeric.")
)
# Response variance
for (r in resp_vals) {
validate(
need(stats::var(df[[r]], na.rm = TRUE) > 0,
paste("Response", r, "has zero variance and cannot be analyzed."))
)
}
# Group must have >= 2 levels
grp <- df[[input$group]]
validate(
need(dplyr::n_distinct(grp, na.rm = TRUE) > 1,
paste0("Categorical predictor '", input$group, "' must contain at least two levels."))
)
# Order must have >= 2 items
validate(
need(length(input$order) > 1,
paste0("The level order for '", input$group, "' must contain at least two levels."))
)
# Order must match data
actual_levels <- unique(grp)
missing_levels <- setdiff(input$order, actual_levels)
validate(
need(length(missing_levels) == 0,
paste0("Invalid level order for '", input$group,
"'. Some selected levels are not present in the filtered data: ",
paste(missing_levels, collapse = ", ")))
)
# Stratification checks
s_info <- strat_info()
if (!is.null(s_info$var)) {
validate(
need(!identical(s_info$var, input$group),
paste0("Stratification variable '", s_info$var,
"' cannot be the same as the categorical predictor."))
)
for (lev in s_info$levels) {
sub_df <- df[df[[s_info$var]] == lev, ]
k <- dplyr::n_distinct(sub_df[[input$group]], na.rm = TRUE)
validate(
need(k > 1,
paste0("In stratum '", lev, "', categorical predictor '", input$group,
"' contains fewer than two levels."))
)
}
}
# -----------------------------------------------------
# Run the main stratified ANOVA preparation
# -----------------------------------------------------
prepare_stratified_anova(
df = df,
responses = resp_vals,
model = "oneway_anova",
factor1_var = input$group,
factor1_order = input$order,
stratification = strat_info()
)
})
# -----------------------------------------------------
# Download handler
# -----------------------------------------------------
output$download_all <- downloadHandler(
filename = function() {
info <- models()
n_resp <- length(info$responses)
label <- if (!is.null(info$strata$var)) {
paste0("stratified_by_", janitor::make_clean_names(info$strata$var))
} else {
NULL
}
response_tag <- if (n_resp == 1) {
janitor::make_clean_names(info$responses[1])
} else {
paste0(n_resp, "resp")
}
build_export_filename(
analysis = "anova",
scope = "all",
extra = c(response_tag, label)
)
},
content = function(file) download_all_anova_results(models(), file)
)
# -----------------------------------------------------
# Summary UI
# -----------------------------------------------------
output$summary_ui <- renderUI({
render_anova_results(ns, models(), "One-way ANOVA")
})
# Forwarding other outputs
bind_anova_outputs(ns, output, models)
# -----------------------------------------------------
# Exportable ANOVA results object
# -----------------------------------------------------
anova_results <- reactive({
mod <- models()
req(mod)
res <- compile_anova_results(mod)
list(
analysis_type = "ANOVA",
type = "oneway_anova",
data_used = mod$data_used,
model = mod$models,
summary = res$summary,
posthoc = res$posthoc,
effects = res$effects,
stats = list(
n = nrow(mod$data_used),
vars = names(mod$data_used)
),
errors = res$errors,
responses = mod$responses,
strata = mod$strata,
factors = mod$factors,
orders = mod$orders
)
})
return(anova_results)
})
}

anova_oneway_analysis.R at commit 39ca8fe, under MIT · at the source

Overview

Authors: Miguel Matos¹, Ivana Bilic¹, Nicolas Viloux², Barbara Jaskulska¹, Fatou Geißler¹, Yasamin Vali³, Eberhard Ludewig³, Olivier Albaric⁴, Susanne Richter⁵, Dieter Liebhart¹, Nicola Palmieri¹, Michael Hess^1,6

ORCID iDs: Miguel Matos, Fatou Geißler, Yasamin Vali, Dieter Liebhart, Michael Hess

Clinical Unit for Poultry Medicine, University of Veterinary Medicine,Vienna, Austria
Labovet Conseil, Les Herbiers, France
Diagnostic Imaging - Clinical Center for Small Animal Health and Research, University of Veterinary Medicine,Vienna, Austria
Independent Pathologist, Lasseube, France
Institute for Veterinary Disease Control, Division for Animal Health, Austrian Agency for Health and Food Safety,Mödling, Austria
Present Address: Histovac GmbH, Klosterneuburg, Austria

Institutions: University of Veterinary Medicine Vienna (Austria); Austrian Agency for Health and Food Safety (Austria)

Journal: Nature communications, volume 17, issue 1, article 7200

Dates: received 13 June 2025; accepted 13 May 2026; published online 5 June 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1038/s41467-026-73858-8 · PMID 42248885 · PMCID PMC13396197 · OpenAlex W7163668803

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: histology / microscopy (modality), other (organism), other condition (population)

Methods: Statistics

Keywords: Viral pathogenesis, Virus-host interactions, Infection, Pathogens

MeSH: Bird Diseases*, Encephalitis, Viral*, Flaviviridae Infections*, Galliformes*, Pegivirus*, Poultry Diseases*, Viral Tropism*, Animals, Brain, Chickens, Neurons, Phylogeny, RNA, Viral, Virus Replication (* major topic)

Topic: Mosquito-borne diseases and control (Public Health, Environmental and Occupational Health, Medicine), according to OpenAlex

Citations: not cited yet (Europe PMC); 41 references in the paper

Abstract

Pegiviruses are generally regarded as non-pathogenic viruses with controversial clinical significance. Here, we describe an avian pegivirus (partridge pegivirus, ParPgV) associated with field outbreaks of encephalitis in red-legged partridges (Alectoris rufa). Next-generation sequencing identified ParPgV in brain tissues, revealing two distinct avian-origin pegiviruses. Histopathology and electron microscopy revealed encephalitic lesions, neuronal degeneration, and viral particles within neurons. Field surveillance demonstrated widespread vertical transmission across multiple partridge flocks. Experimental inoculation of red-legged partridges, grey partridges, and specific-pathogen-free chickens demonstrated viral neurotropism and systemic distribution with differences in humoral immune response. Infected red-legged partridges developed cerebellar atrophy detectable by MRI. Detection of negative-strand RNA replication intermediates confirmed active viral replication across different experimental hosts, and RNAscope in situ hybridization and immunohistochemistry further confirmed viral RNA and antigen in neural and lymphoid tissues. Here, we show experimental evidence supporting an association between a pegivirus and encephalitis, and suggest underappreciated neuropathogenic potential.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

nicola-palmieri/TableAnalyzer

License: MIT

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 39ca8febd375f58353e7c8d0135f2adb4fd3eab1, 15 September 2026

Languages: R (60)

Size: 110 files, 60 scripts

Software Heritage: not archived

Found in: “Code availability”

Holds: README, tests, documentation

Not found: license file, CITATION.cff, environment file, continuous integration

Tools: tidyverse (20 files), patchwork (11 files), ggplot2 (9 files), car (5 files), lme4 (3 files), emmeans (2 files), lmerTest (2 files), broom (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

61 files

R/anova_oneway_analysis.R, R, 245 lines
R/anova_oneway_visualize.R, R, 342 lines
R/anova_shared_barplots.R, R, 665 lines
R/anova_shared_boxplots.R, R, 122 lines
R/anova_shared_data.R, R, 48 lines
R/anova_shared_lineplots.R, R, 465 lines
R/anova_shared_model.R, R, 218 lines
R/anova_shared_plot_context.R, R, 217 lines
R/anova_shared_results.R, R, 513 lines
R/anova_shared_ui.R, R, 301 lines
R/anova_shared_utils.R, R, 12 lines
R/anova_twoway_analysis.R, R, 279 lines
R/anova_twoway_visualize.R, R, 483 lines
R/descriptive_analysis.R, R, 509 lines
R/descriptive_visualize.R, R, 104 lines
R/descriptive_visualize_categorical_barplots.R, R, 520 lines
R/descriptive_visualize_numeric_boxplots.R, R, 683 lines
R/descriptive_visualize_numeric_histograms.R, R, 474 lines
R/helpers.R, R, 136 lines
R/lm_analysis.R, R, 7 lines
R/lmm_analysis.R, R, 36 lines
R/module_analysis.R, R, 316 lines
R/module_filter.R, R, 326 lines
R/module_home.R, R, 104 lines
R/module_upload.R, R, 396 lines
R/module_upload_helpers.R, R, 96 lines
R/module_visualize.R, R, 288 lines
R/pairwise_correlation_analysis.R, R, 359 lines
R/pairwise_correlation_visualize.R, R, 187 lines
R/pairwise_correlation_visualize_ggpairs.R, R, 303 lines
R/pca_analysis.R, R, 355 lines
R/pca_visualize.R, R, 1,000 lines
R/regression_analysis.R, R, 325 lines
R/regression_shared_export.R, R, 309 lines
R/regression_shared_formula.R, R, 29 lines
R/regression_shared_model.R, R, 347 lines
R/regression_shared_results.R, R, 330 lines
R/regression_shared_ui.R, R, 43 lines
R/regression_shared_utils.R, R, 37 lines
R/regression_shared_validation.R, R, 134 lines
R/submodule_base_size.R, R, 56 lines
R/submodule_colors.R, R, 350 lines
R/submodule_multiple_responses.R, R, 58 lines
R/submodule_plot_grid.R, R, 201 lines
R/submodule_stratification.R, R, 84 lines
R/submodule_subplot_size.R, R, 69 lines
R/submodule_theme.R, R, 34 lines
app.R, R, 141 lines
dev/lm_visualize.R, R, 375 lines
dev/new_graphics.R, R, 197 lines
tests/run_tests.R, R, 3 lines
tests/test_analysis_helpers.R, R, 63 lines
tests/test_analysis_invalidation.R, R, 56 lines
tests/test_convert_wide_to_long.R, R, 190 lines
tests/test_helpers.R, R, 46 lines
tests/test_plot_edge_cases.R, R, 82 lines
tests/test_preprocess_uploaded_table.R, R, 87 lines
tests/test_regression_helpers.R, R, 44 lines
tests/test_regression_model.R, R, 59 lines
tests/test_type3_contrasts.R, R, 44 lines
README.md, Text, 115 lines

At the source: github.com/nicola-palmieri/TableAnalyzer

Zenodo 19233119

License: CC-BY-4.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Size: 1 file

Software Heritage: not checked

Found in: the references

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: tidyverse (18 files), patchwork (11 files), ggplot2 (8 files), car (4 files), emmeans (2 files), lme4 (2 files), lmerTest (2 files), broom (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)

27 September 2026: the link answers (HTTP 200)

53 files

R/anova_oneway_analysis.R, R, 245 lines
R/anova_oneway_visualize.R, R, 342 lines
R/anova_shared_barplots.R, R, 654 lines
R/anova_shared_boxplots.R, R, 122 lines
R/anova_shared_data.R, R, 48 lines
R/anova_shared_lineplots.R, R, 442 lines
R/anova_shared_model.R, R, 211 lines
R/anova_shared_plot_context.R, R, 217 lines
R/anova_shared_results.R, R, 517 lines
R/anova_shared_ui.R, R, 301 lines
R/anova_shared_utils.R, R, 12 lines
R/anova_twoway_analysis.R, R, 279 lines
R/anova_twoway_visualize.R, R, 483 lines
R/descriptive_analysis.R, R, 509 lines
R/descriptive_visualize.R, R, 104 lines
R/descriptive_visualize_categorical_barplots.R, R, 520 lines
R/descriptive_visualize_numeric_boxplots.R, R, 683 lines
R/descriptive_visualize_numeric_histograms.R, R, 474 lines
R/helpers.R, R, 117 lines
R/lm_analysis.R, R, 7 lines
R/lmm_analysis.R, R, 36 lines
R/module_analysis.R, R, 296 lines
R/module_filter.R, R, 326 lines
R/module_home.R, R, 104 lines
R/module_upload.R, R, 396 lines
R/module_upload_helpers.R, R, 87 lines
R/module_visualize.R, R, 288 lines
R/pairwise_correlation_analysis.R, R, 359 lines
R/pairwise_correlation_visualize.R, R, 187 lines
R/pairwise_correlation_visualize_ggpairs.R, R, 303 lines
R/pca_analysis.R, R, 355 lines
R/pca_visualize.R, R, 1,000 lines
R/regression_analysis.R, R, 323 lines
R/regression_shared_export.R, R, 309 lines
R/regression_shared_formula.R, R, 29 lines
R/regression_shared_model.R, R, 344 lines
R/regression_shared_results.R, R, 330 lines
R/regression_shared_ui.R, R, 43 lines
R/regression_shared_utils.R, R, 37 lines
R/regression_shared_validation.R, R, 134 lines
R/submodule_base_size.R, R, 56 lines
R/submodule_colors.R, R, 350 lines
R/submodule_multiple_responses.R, R, 58 lines
R/submodule_plot_grid.R, R, 201 lines
R/submodule_stratification.R, R, 84 lines
R/submodule_subplot_size.R, R, 69 lines
R/submodule_theme.R, R, 34 lines
app.R, R, 141 lines
dev/lm_visualize.R, R, 375 lines
dev/new_graphics.R, R, 197 lines
tests/test_convert_wide_to_long.R, R, 186 lines
tests/test_preprocess_uploaded_table.R, R, 87 lines
README.md, Text, 106 lines

At the source:

Code availability

Serological data were assessed with Table Analyzer (Version 388 v1.10), an R Shiny web application publicly available on GitHub (https://github.com/nicola-palmieri/TableAnalyzer)41.

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
112 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

bioproject:PRJNA1314175, at NCBI BioProject; found in “Data availability”

Data availability

The complete genome sequences of ParPgV-A and ParPgV-C have been deposited in the NCBI GenBank under accession numbers PV472371 (https://www.ncbi.nlm.nih.gov/nuccore/PV472371.1/) and PV472372 (https://www.ncbi.nlm.nih.gov/nuccore/PV472372.1/), respectively. The raw sequencing data from all field samples used as inocula were submitted into the NCBI SRA database, under the BioProject PRJNA1314175 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1314175/). Data under accessions SAMN50922524 (https://www.ncbi.nlm.nih.gov/biosample/SAMN50922524/) and SAMN50922527 (https://www.ncbi.nlm.nih.gov/biosample/SAMN50922527/) correspond to the inoculum used for animal experiment in grey partridges, whereas data with accessions SAMN50922526 (https://www.ncbi.nlm.nih.gov/biosample/SAMN50922526/) and SAMN50922529 (https://www.ncbi.nlm.nih.gov/biosample/SAMN50922529/) are from the inoculum used in animal experiments performed in red-legged partridges and SPF chickens. All other data supporting the findings of this study, including viral load measurements, histopathology evaluations, serological data, statistical source data, primers, probes, cycling conditions, and amino acid identity matrix, are available within the manuscript and its Supplementary files/Source data file. Source data are provided with this paper.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 4 keywords, 14 MeSH terms, 41 references.

Cite

This paper

Matos, M., Bilic, I., Viloux, N., Jaskulska, B., Geißler, F., Vali, Y., Ludewig, E., Albaric, O., Richter, S., Liebhart, D., Palmieri, N., & Hess, M. (2026). A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species. Nature communications, 17(1), 7200. https://doi.org/10.1038/s41467-026-73858-8

BibTeX

@article{matos2026pegivirus, author = {Matos, Miguel and Bilic, Ivana and Viloux, Nicolas and Jaskulska, Barbara and Geißler, Fatou and Vali, Yasamin and Ludewig, Eberhard and Albaric, Olivier and Richter, Susanne and Liebhart, Dieter and Palmieri, Nicola and Hess, Michael}, title = {{A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species}}, journal = {Nature communications}, year = {2026}, month = jun, volume = {17}, number = {1}, pages = {7200}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-026-73858-8}, url = {https://doi.org/10.1038/s41467-026-73858-8}, pmid = {42248885}, pmcid = {PMC13396197} }

RIS

TY - JOUR AU - Matos, Miguel AU - Bilic, Ivana AU - Viloux, Nicolas AU - Jaskulska, Barbara AU - Geißler, Fatou AU - Vali, Yasamin AU - Ludewig, Eberhard AU - Albaric, Olivier AU - Richter, Susanne AU - Liebhart, Dieter AU - Palmieri, Nicola AU - Hess, Michael TI - A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species T2 - Nature communications J2 - Nat Commun PY - 2026 DA - 2026/06/05 VL - 17 IS - 1 SP - 7200 SN - 2041-1723 PB - Nature Publishing Group DO - 10.1038/s41467-026-73858-8 UR - https://doi.org/10.1038/s41467-026-73858-8 LA - en ER -

CSL-JSON

{ "id": "10.1038/s41467-026-73858-8", "type": "article-journal", "title": "A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species", "container-title": "Nature communications", "author": [ { "family": "Matos", "given": "Miguel" }, { "family": "Bilic", "given": "Ivana" }, { "family": "Viloux", "given": "Nicolas" }, { "family": "Jaskulska", "given": "Barbara" }, { "family": "Geißler", "given": "Fatou" }, { "family": "Vali", "given": "Yasamin" }, { "family": "Ludewig", "given": "Eberhard" }, { "family": "Albaric", "given": "Olivier" }, { "family": "Richter", "given": "Susanne" }, { "family": "Liebhart", "given": "Dieter" }, { "family": "Palmieri", "given": "Nicola" }, { "family": "Hess", "given": "Michael" } ], "container-title-short": "Nat Commun", "volume": "17", "issue": "1", "page": "7200", "DOI": "10.1038/s41467-026-73858-8", "PMID": "42248885", "PMCID": "PMC13396197", "ISSN": "2041-1723", "publisher": "Nature Publishing Group", "URL": "https://doi.org/10.1038/s41467-026-73858-8", "language": "en", "issued": { "date-parts": [ [ 2026, 6, 5 ] ] } }

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A pegivirus associated with encephalitis in red-legged partridges shows neurotropism across avian species.

Code ↔ Paper

Paper

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Overview

Abstract

Repositories

nicola-palmieri/TableAnalyzer

Zenodo 19233119

Code availability

Tracing map

Data

Datasets cited

Data availability

Versions

Version 1, 27 September 2026: the first record

Cite

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