Evidence map›Paper›PMID 40232684›Full record

ArticleEmerging microbes & infections2025

Development and validation of a new mpox virus sequencing and bioinformatic analysis pipeline.

Missiani Ochwoto, Skyler Kuhn, Paul Schaughency, Ben Greene, Kailin Hawes, Felix Koukouikila-Koussounda, Reiche Golmard Elenga, Dachel Aymard Eyenet Boussam, Pembe Issamou Mayangue, Jonathan Schulz and 6 more

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Emerging microbes & infections, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Missiani OchwotoDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Skyler KuhnResearch Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Paul SchaughencyResearch Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Ben GreeneDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Kailin HawesDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Felix Koukouikila-KoussoundaLaboratoire National de Santé Publique, Brazzaville, Republic of the Congo.
Reiche Golmard ElengaLaboratoire National de Santé Publique, Brazzaville, Republic of the Congo.
Dachel Aymard Eyenet BoussamLaboratoire National de Santé Publique, Brazzaville, Republic of the Congo.
Pembe Issamou MayangueLaboratoire National de Santé Publique, Brazzaville, Republic of the Congo.
Jonathan SchulzDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Craig MartensResearch Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Fabien Roch NiamaLaboratoire National de Santé Publique, Brazzaville, Republic of the Congo.
Justin LackResearch Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
Ryan F RelichDepartment of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
Vincent J MunsterDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.ORCID 0000-0002-2288-3196
Claude Kwe YindaDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Sequencing and bioinformatic analysis of mpox virus (MPXV) remain challenging in resource-limited settings. We developed and validated a PCR-based sequencing assay that targets a 12.5 kilobase (kb) region that is phylogenetically representative of the whole ∼ 200 kb MPXV genome. We combined this sequencing assay with a lightweight, downloadable, on-and-off-grid-bioinformatics pipeline for rapid phylogenetic analysis. Our findings demonstrate that this simplified sequencing method, and the associated bioinformatics pipeline accurately distinguished clades, subclades, and clusters of MPXV. Therefore, this assay will provide rapid sequence information for understanding transmission patterns and sources of outbreaks in resource-limited settings. In addition, this assay provides a unique opportunity to decentralize mpox molecular surveillance capacities that are needed to contain the ongoing outbreak.

Indexed as

Computational BiologyMonkeypox virusSequence Analysis, DNAGenome, ViralHigh-Throughput Nucleotide SequencingPhylogenyPolymerase Chain Reactionbioinformatics pipelinecladesMpoxMPXVPCRphylogeneticssequencing

Identifiers

PMID40232684
PMCPMC12051528

What OpenQuestion holds

Textmetadata
LicenceCC0
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.