Evidence map›Paper›PMID 40593980›Full record

ArticleScientific reports2025

Development and verification of a novel tiling PCR method for long-range HIV-1 sequencing in a diagnostic setting.

Bethany A Horsburgh, Arunasingam Abayasingam, Frances Jenkins, Hui Li, Charles S P Foster, Andrew Lloyd, Lachlan Coin, William Rawlinson, Anthony D Kelleher, Sebastiaan van Hal and 3 more

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Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

13 authors.

Bethany A HorsburghThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Arunasingam AbayasingamThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Frances JenkinsDepartment of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia.
Hui LiThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Charles S P FosterSchool of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Andrew LloydThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Lachlan CoinDepartment of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
William RawlinsonSchool of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Anthony D KelleherThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Sebastiaan van HalDepartment of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia.
Rowena A BullThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia. r.bull@unsw.edu.au.
Francesca Di GiallonardoThe Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
H2Seq Genome Sequencing Working Group

Funding

Department of Health and Aged Care, Australian Government FSPGN000047
6 · The paper itself

Abstract

New HIV-1 infections are genotyped as part of standard of care testing to ensure that antiretroviral treatment will be efficacious against the virus. Historically this has been performed by sequencing the pol region of the HIV-1 genome only. The popularity of next-generation sequencing (NGS) methods during the SARS-CoV-2 pandemic has resulted in a shift towards using NGS in diagnostic sequencing, but there remain limited methodologies utilising the strengths of NGS for robust diagnostic sequencing of longer regions of the HIV-1 genome. Given the acceptance and success of tiling PCR methodologies during the SARS-CoV-2 pandemic, we aimed to design and verify a novel tiling PCR method for routine HIV-1 sequencing. A set of tiling PCR primers was designed to amplify the 5' half of HIV-1 in six overlapping segments of 1,000 bp in only two PCR reactions. The assay can move from sample to sequencer in under a day. The tiling PCR was able to generate HIV-1 sequences from 90 (100%) samples in a comparison panel, and complete protease-reverse transcriptase and integrase regions were amplified in > 90% of samples with a viral load > 5000 copies/mL. Seven additional drug resistance mutations were identified when using this novel method. As such, this novel designer tiling PCR is a promising method for the routine NGS-based diagnostic sequencing of HIV-1.

Indexed as

HIV-1HIV InfectionsPolymerase Chain ReactionCOVID-19Genome, ViralHigh-Throughput Nucleotide SequencingHumansSARS-CoV-2Assay verificationClinical sequencingHIV-1Next-generation sequencingTiling PCR

Identifiers

PMID40593980
PMCPMC12214867

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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.