Evidence map›Paper›PMID 35151353›Full record

ArticleBMC research notes2022

Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing.

Lucky R Runtuwene, Nuankanya Sathirapongsasuti, Raweewan Srisawat, Narumon Komalamisra, Josef S B Tuda, Arthur E Mongan, Gabriel O Aboge, Victoria Shabardina, Wojciech Makalowski, Dela Ria Nesti and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.6field-weighted citation impact, top 25% of its field
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

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Article
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

20 authors at 14 institutions in 11 countries.

Lucky R RuntuweneDivision 1, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan. luckyron@niid.go.jp.ORCID http://orcid.org/0000-0003-3782-3628
Nuankanya SathirapongsasutiSection of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
Raweewan SrisawatDepartment of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
Narumon KomalamisraDepartment of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
Josef S B TudaFaculty of Medicine, Sam Ratulangi University, Manado, Indonesia.
Arthur E MonganFaculty of Medicine, Sam Ratulangi University, Manado, Indonesia.
Gabriel O AbogeDepartment of Public Health, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya.
Victoria ShabardinaInstitute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
Wojciech MakalowskiInstitute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany.
Dela Ria NestiDepartment of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia.
Wayan T ArtamaDepartment of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
Lan Anh Nguyen-ThiCenter of Biomedical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
Kiew-Lian WanDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
Byoung-Kuk NaDepartment of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju, South Korea.
William HallCentre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland.
Arnab PainPathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Yuki EshitaDivision of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Ryuichiro MaedaDivision of Biomedical Science, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary, Obihiro, Japan.
Junya YamagishiDivision of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Yutaka SuzukiDepartment of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
Hokkaido University · JPMahidol University · THSam Ratulangi University · IDUniversitas Gadjah Mada · IDGyeongsang National University · KRNational Institute Of Hygiene And Epidemiology · VNNational Institute of Infectious Diseases · JPNational University of Malaysia · MYObihiro University of Agriculture and Veterinary Medicine · JPThe University of Tokyo · JPUniversitat Pompeu Fabra · ESUniversity College Dublin · IEUniversity of Münster · DEUniversity of Nairobi · KE

Funding

Japan Society for the Promotion of Science JPJSCCB20190006
6 · The paper itself

Abstract

objectiveTo disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION's operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.

resultsOne of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country.

Indexed as

Communicable DiseasesHigh-Throughput Nucleotide SequencingAnimalsCattleGenomeMetagenomicsSequence Analysis, DNAField sequencingInternational collaborationMinIONPortable sequencing

Identifiers

PMID35151353
PMCPMC8840504
OpenAlexW4211135332

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.