Evidence map›Paper›PMID 40862160›Full record

ArticleFrontiers in microbiology2025

Hairpin loop to hairpin loop: a full-length assembly of the ASFV genome using Oxford Nanopore long-read sequencing.

Poompat Phadphon, Chutima Sonthirod, Theeradej Thaweerattanasinp, Jeremy R Shearman, Sonicha U-Thoomporn, Janya Saenboonrueng, Asawin Wanitchang, Sithichoke Tangphatsornruang, Anan Jongkaewwattana, Wirulda Pootakham

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2025. 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
–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

1 citing paper in PubMed.

  1. Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027
    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

10 authors.

Poompat Phadphon *Genomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Chutima Sonthirod *Genomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Theeradej ThaweerattanasinpVirology and Vaccine Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Jeremy R ShearmanGenomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Sonicha U-ThoompornGenomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Janya SaenboonruengVirology and Vaccine Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Asawin WanitchangVirology and Vaccine Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Sithichoke TangphatsornruangGenomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Anan JongkaewwattanaVirology and Vaccine Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
Wirulda PootakhamGenomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Short-read assembly of the African swine fever virus (ASFV) genome is challenging due to the presence of inverted terminal repeat (ITR) and hairpin loop sequences, which often cause ambiguity in contig reconstruction. In this study, we employed Oxford Nanopore long-read sequencing to assemble a full-length ASFV genome from passage 50 of an ASFV strain adapted to MA-104 cells. We identified duplicated reverse complementary reads from the ITR and hairpin loop regions, which, if not properly analyzed, could lead to an inaccurate assembly that falsely represents these complex regions. Our findings highlight the power of long-read sequencing for resolving complex viral genomes and reveal potential challenges for other viruses with similar terminal structures.

Indexed as

adaptationAfrican swine fever virusASFVhairpin loopMA-104 cells

Identifiers

PMID40862160
PMCPMC12370676

What OpenQuestion holds

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Registered trials

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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.