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Enhanced virulence and neuroinvasion of contemporary <i>Oropouche</i> virus strains in the AG129 mouse model.

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1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 1 match
  1. [1] § Materials and methods › Production of viral stock and titration › OROV strains ↔ python-package/geobr/read_capitals.py, lines 1 to 38 · score 0.66 · Bras lia, Santa Catarina, Bel, Par, Acre, Sul · Report a mismatch

Paper

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The authors' code

Python · 69 lines · 2.2 KB · no license · 1 match

  1. """Download data of Brazilian state capitals."""
  3. from __future__ import annotations
  5. import pandas as pd
  7. from geobr.read_municipal_seat import read_municipal_seat
  8. from geobr._docstrings import docparams
  10. _CAPITALS = pd.DataFrame(
  11. {
  12. "name_muni": [
  13. "São Paulo", "Rio de Janeiro", "Belo Horizonte", "Salvador", "Fortaleza",
  14. "Vitória", "Goiânia", "Cuiabá", "São Luís", "Teresina", "Recife", "Aracaju",
  15. "João Pessoa", "Natal", "Maceió", "Porto Alegre", "Curitiba", "Florianópolis",
  16. "Belém", "Manaus", "Palmas", "Campo Grande", "Macapá", "Rio Branco",
  17. "Boa Vista", "Brasília", "Porto Velho",
  18. ],
  19. "code_muni": [
  20. 3550308, 3304557, 3106200, 2927408, 2304400, 3205309, 5208707, 5103403,
  21. 2111300, 2211001, 2611606, 2800308, 2507507, 2408102, 2704302, 4314902,
  22. 4106902, 4205407, 1501402, 1302603, 1721000, 5002704, 1600303, 1200401,
  23. 1400100, 5300108, 1100205,
  24. ],
  25. "name_state": [
  26. "São Paulo", "Rio de Janeiro", "Minas Gerais", "Bahia", "Ceará",
  27. "Espírito Santo", "Goiás", "Mato Grosso", "Maranhão", "Piauí", "Pernambuco",
  28. "Sergipe", "Paraíba", "Rio Grande do Norte", "Alagoas", "Rio Grande do Sul",
  29. "Paraná", "Santa Catarina", "Pará", "Amazonas", "Tocantins",
  30. "Mato Grosso do Sul", "Amapá", "Acre", "Roraima", "Distrito Federal",
  31. "Rondônia",
  32. ],
  33. "code_state": [
  34. 35, 33, 31, 29, 23, 32, 52, 51, 21, 22, 26, 28, 25, 24, 27, 43, 41, 42,
  35. 15, 13, 17, 50, 16, 12, 14, 53, 11,
  36. ],
  37. }
  38. ).sort_values("code_muni")
  41. @docparams
  42. def read_capitals(
  43. year: int = 2010,
  44. output: str = "gpd",
  45. show_progress: bool = True,
  46. cache: bool = True,
  47. verbose: bool = False,
  48. ):
  49. """Download spatial or tabular data for the 27 state capitals.
  51. Parameters
  52. ----------
  53. {year}
  54. {output}
  55. {show_progress}
  56. {cache}
  57. {verbose}
  59. """
  60. codes = _CAPITALS["code_muni"].tolist()
  62. return read_municipal_seat(
  63. year=year,
  64. code_muni=codes,
  65. output=output,
  66. show_progress=show_progress,
  67. cache=cache,
  68. verbose=verbose
  69. )

read_capitals.py at commit 0969f92, no license · at the source

Overview

Authors: Ellen Caroline Nobre Santos1, Nathália Costa Silva2, Luiza Godoy Rodrigues Pinto2, Luiz Gustavo Pontes Santos2, Juliana da Silva Brandi Oliveira2, Melissa Teixeira Goulart2, Marcele Neves Rocha2, Isaque João da Silva de Faria2, Renan Pedra de Souza1,3, Silvana F. de Mendonça1, Livia Baldon1, Yaovi M. H. Todjiro1,2, Amanda C. de Freitas1, Rafaela L. Moreira1,4, Maria E. C. Rodrigues1, Siad Amadou1, José M. G. Fernandes1,2, Natália R. Guimarães1,5, Talita E. R. Adelino1,5, Sara C. F. dos Santos1,4,5
and 7 other authorsFelipe C. M. Iani5, Keldenn M. F. Moreno1,4,5, João P. P. de Almeida2, Luiz Alcantara1,5, Marta Giovanetti1,6,7, Fabíola Mara Ribeiro2, Álvaro G. A. Ferreira1
  1. Mosquitos Vetores, Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou-Fiocruz, Belo Horizonte, Brazil
  2. Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
  3. Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
  4. Departamento de Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
  5. Fundação Ezequiel Dias, Belo Horizonte, Brazil
  6. Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
  7. Department of Science and Bio-Technology, Universita Campus Bio-Medico di Roma, Rome, Italy
Institutions: Fundação Oswaldo Cruz (Brazil); Universidade Federal de Minas Gerais (Brazil); Ezequiel Dias Foundation (Brazil); Università Campus Bio-Medico (Italy)
Journal: Frontiers in microbiology, volume 17, article 1771021
Dates: received 18 December 2025; accepted 17 April 2026; published online 19 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3389/fmicb.2026.1771021 · PMID 42238877 · PMCID PMC13226609 · OpenAlex W7161633292
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: mouse (organism)
Methods: Statistics, fMRI & imaging
Keywords: Oropouche virus, AG129 strain mice, neuroinvasion, central nervous system, viremia, tissue tropism, arthropod-borne viroses
Topic: Viral Infections and Vectors (Infectious Diseases, Medicine), according to OpenAlex
Funding: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Conselho Nacional de Desenvolvimento Científico e Tecnológico (NNF24OC0094346); Novo Nordisk (NNF24OC0094346); Fundação de Amparo à Pesquisa do Estado de Minas Gerais; Fundação Oswaldo Cruz; Universidade Federal de Minas Gerais; National Institutes of Health; National Institute of Allergy and Infectious Diseases
Citations: not cited yet (Europe PMC); 64 references in the paper

Abstract

Oropouche virus (OROV) is an orthobunyavirus undergoing dramatic re-emergence and rapid geographic expansion across Central and South America, coinciding with the emergence of reassortant lineages carrying novel segment combinations and adaptive mutations. Despite extensive genomic and epidemiological characterization, the biological mechanisms driving OROV resurgence during 2023–2024 remain unclear. Here, we show that contemporary reassortant OROV isolates exhibit markedly enhanced virulence in the AG129 mouse model compared with the historical prototype strain OROVBeAn19991. Two reassortant 2024 isolates—OROVSC2024 from a non-Amazonian region and OROVAC2024 from the Amazon Basin—produced significantly higher viremia, accelerated disease progression, and increased mortality. These isolates disseminated widely, generating substantially elevated viral loads across multiple organs, including the spleen, kidney, liver, lung, uterus, and testes, and—most notably—demonstrated a heightened capacity for the brain. Infection with contemporary reassortant lineages also induced pro-inflammatory responses, characterized by consistent upregulation of IL-1β across tissues. Together, these findings provide experimental evidence that ongoing viral evolution is likely driving a measurable increase in OROV pathogenicity, providing a biological framework to better understand the increased severity of clinical cases reported in recent outbreaks. This work underscores the urgent need for enhanced surveillance, real-time genomic monitoring, and development of targeted countermeasures against this rapidly spreading arbovirus.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

ipeaGIT/geobr

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 0969f9279275d28b0e9f2f4fa0e21169a6033854, 27 September 2026
Languages: Python (116), R (99), JavaScript (11), Jupyter (4), Shell (1)
Size: 473 files, 231 scripts
Software Heritage: not archived
Found in: the references
Holds: README, environment (python-package/pyproject.toml, python-package/uv.lock, r-package/DESCRIPTION, qgis-plugin/geobr_qgis/requirements.txt), tests, continuous integration, documentation, 7 notebooks
Not found: license file, CITATION.cff
Tools: pandas (14 files), tidyverse (14 files), ggplot2 (5 files), Matplotlib (3 files), data.table (2 files), reticulate (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
232 files
At the source: github.com/ipeaGIT/geobr

Tracing map

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What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 231 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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

No dataset and no data link were found in the paper.

Data availability statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.

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

Versions

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Version 2, 28 September 2026

  • Funding: added Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Conselho Nacional de Desenvolvimento Científico e Tecnológico: NNF24OC0094346; Novo Nordisk: NNF24OC0094346; Fundação de Amparo à Pesquisa do Estado de Minas Gerais; Fundação Oswaldo Cruz; Universidade Federal de Minas Gerais; National Institutes of Health; National Institute of Allergy and Infectious Diseases

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 27 authors, 7 keywords, 59 references.

Cite

This paper

Nobre Santos, E. C., Costa Silva, N., Godoy Rodrigues Pinto, L., Pontes Santos, L. G., da Silva Brandi Oliveira, J., Teixeira Goulart, M., Neves Rocha, M., de Faria, I. J. d. S., de Souza, R. P., de Mendonça, S. F., Baldon, L., Todjiro, Y. M. H., de Freitas, A. C., Moreira, R. L., Rodrigues, M. E. C., Amadou, S., Fernandes, J. M. G., Guimarães, N. R., Adelino, T. E. R., . . . Ferreira, Á. G. A. (2026). Enhanced virulence and neuroinvasion of contemporary <i>Oropouche</i> virus strains in the AG129 mouse model. Frontiers in microbiology, 17, 1771021. https://doi.org/10.3389/fmicb.2026.1771021

BibTeX

@article{nobresantos2026enhanced,
author = {Nobre Santos, Ellen Caroline and Costa Silva, Nathália and Godoy Rodrigues Pinto, Luiza and Pontes Santos, Luiz Gustavo and da Silva Brandi Oliveira, Juliana and Teixeira Goulart, Melissa and Neves Rocha, Marcele and de Faria, Isaque João da Silva and de Souza, Renan Pedra and de Mendonça, Silvana F. and Baldon, Livia and Todjiro, Yaovi M. H. and de Freitas, Amanda C. and Moreira, Rafaela L. and Rodrigues, Maria E. C. and Amadou, Siad and Fernandes, José M. G. and Guimarães, Natália R. and Adelino, Talita E. R. and dos Santos, Sara C. F. and Iani, Felipe C. M. and Moreno, Keldenn M. F. and de Almeida, João P. P. and Alcantara, Luiz and Giovanetti, Marta and Ribeiro, Fabíola Mara and Ferreira, Álvaro G. A.},
title = {{Enhanced virulence and neuroinvasion of contemporary \<i\>Oropouche\</i\> virus strains in the AG129 mouse model}},
journal = {Frontiers in microbiology},
year = {2026},
month = may,
volume = {17},
pages = {1771021},
publisher = {Frontiers Media SA},
issn = {1664-302X},
doi = {10.3389/fmicb.2026.1771021},
url = {https://doi.org/10.3389/fmicb.2026.1771021},
pmid = {42238877},
pmcid = {PMC13226609}
}

RIS

TY - JOUR
AU - Nobre Santos, Ellen Caroline
AU - Costa Silva, Nathália
AU - Godoy Rodrigues Pinto, Luiza
AU - Pontes Santos, Luiz Gustavo
AU - da Silva Brandi Oliveira, Juliana
AU - Teixeira Goulart, Melissa
AU - Neves Rocha, Marcele
AU - de Faria, Isaque João da Silva
AU - de Souza, Renan Pedra
AU - de Mendonça, Silvana F.
AU - Baldon, Livia
AU - Todjiro, Yaovi M. H.
AU - de Freitas, Amanda C.
AU - Moreira, Rafaela L.
AU - Rodrigues, Maria E. C.
AU - Amadou, Siad
AU - Fernandes, José M. G.
AU - Guimarães, Natália R.
AU - Adelino, Talita E. R.
AU - dos Santos, Sara C. F.
AU - Iani, Felipe C. M.
AU - Moreno, Keldenn M. F.
AU - de Almeida, João P. P.
AU - Alcantara, Luiz
AU - Giovanetti, Marta
AU - Ribeiro, Fabíola Mara
AU - Ferreira, Álvaro G. A.
TI - Enhanced virulence and neuroinvasion of contemporary <i>Oropouche</i> virus strains in the AG129 mouse model
T2 - Frontiers in microbiology
J2 - Front Microbiol
PY - 2026
DA - 2026/05/19
VL - 17
SP - 1771021
SN - 1664-302X
PB - Frontiers Media SA
DO - 10.3389/fmicb.2026.1771021
UR - https://doi.org/10.3389/fmicb.2026.1771021
LA - en
ER -

CSL-JSON

{
"id": "10.3389/fmicb.2026.1771021",
"type": "article-journal",
"title": "Enhanced virulence and neuroinvasion of contemporary <i>Oropouche</i> virus strains in the AG129 mouse model",
"container-title": "Frontiers in microbiology",
"author": [
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"family": "Nobre Santos",
"given": "Ellen Caroline"
},
{
"family": "Costa Silva",
"given": "Nathália"
},
{
"family": "Godoy Rodrigues Pinto",
"given": "Luiza"
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{
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{
"family": "da Silva Brandi Oliveira",
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{
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{
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{
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{
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"given": "Yaovi M. H."
},
{
"family": "de Freitas",
"given": "Amanda C."
},
{
"family": "Moreira",
"given": "Rafaela L."
},
{
"family": "Rodrigues",
"given": "Maria E. C."
},
{
"family": "Amadou",
"given": "Siad"
},
{
"family": "Fernandes",
"given": "José M. G."
},
{
"family": "Guimarães",
"given": "Natália R."
},
{
"family": "Adelino",
"given": "Talita E. R."
},
{
"family": "dos Santos",
"given": "Sara C. F."
},
{
"family": "Iani",
"given": "Felipe C. M."
},
{
"family": "Moreno",
"given": "Keldenn M. F."
},
{
"family": "de Almeida",
"given": "João P. P."
},
{
"family": "Alcantara",
"given": "Luiz"
},
{
"family": "Giovanetti",
"given": "Marta"
},
{
"family": "Ribeiro",
"given": "Fabíola Mara"
},
{
"family": "Ferreira",
"given": "Álvaro G. A."
}
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"container-title-short": "Front Microbiol",
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"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
19
]
]
}
}

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