Evidence map›Paper›PMID 41990403›Full record

ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2026

Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.

Jiangqin Zhao, Tianxiong Li, Hanxia Huang, Venice Servellita, Alicia Sotomayor-Gonzalez, Oksana Yakovleva, Xue Wang, Viswanath Ragupathy, Santanu Biswas, Patricia Barilko and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

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

22 authors.

Jiangqin ZhaoLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States. Electronic address: Jiangqin.Zhao@fda.hhs.gov.
Tianxiong LiLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Hanxia HuangLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Venice ServellitaDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.
Alicia Sotomayor-GonzalezDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.
Oksana YakovlevaLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Xue WangLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Viswanath RagupathyLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Santanu BiswasLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.
Patricia BarilkoRoche Diagnostics Solutions, Clinical Development and Medical Affairs (CDMA), Pleasanton, CA, United States.
Ethan SunRoche Diagnostics Solutions, Clinical Development and Medical Affairs (CDMA), Pleasanton, CA, United States.
Samantha HuynhRoche Diagnostics Solutions, Clinical Development and Medical Affairs (CDMA), Pleasanton, CA, United States.
Melissa HunsickerHologic, Inc., San Diego, CA, United States.
Jessica DeQuachHologic, Inc., San Diego, CA, United States.
Jose D MoralesHologic, Inc., San Diego, CA, United States.
Helene HighbargerVirus Isolation and Serology Laboratory (VISL), Frederick National Laboratory, Frederick, MD, United States.
Robin L DewarVirus Isolation and Serology Laboratory (VISL), Frederick National Laboratory, Frederick, MD, United States.
Cassie PorthEQAPOL, Duke University, Durham, NC, United States. Electronic address: Cassandra.Porth@duke.edu.
Thomas N DennyEQAPOL, Duke University, Durham, NC, United States.
David R McGivernLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States. Electronic address: David.McGivern@fda.hhs.gov.
Charles Y ChiuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.
Indira HewlettLaboratory of Molecular Virology, DETTD, OBRR, CBER, FDA, 10903 New Hampshire Ave, Silver Spring, MD, United States.

Funding

WORK ORDER 126643 B539 EXPAND IC SUITE75N91019D00024 · NIAID · LEIDOS BIOMEDICAL RESEARCH, INC. · PI BRISCOE, LYNN · 2019 to 2025
$3932.6M
FDA HHS U01 FD005978Intramural FDA HHS FD999999NCI NIH HHS 75N91019D00024NIH HHS 75N91019D00024
6 · The paper itself

Abstract

backgroundThe high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.

objectiveTo develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains. STUDY

designHIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.

resultsNear full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n = 18, 2.53 log10 copies/mL), medium (n = 18, 3.61 log10 copies/mL), and high viral loads (n = 15, 4.66 log10 copies/mL), yielding 51 panel members in total.

conclusionThis diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.

Indexed as

Genetic VariationGenome, ViralHIV-1HIV InfectionsCameroonHigh-Throughput Nucleotide SequencingHumansReference StandardsRNA, ViralSequence Analysis, DNAViral LoadRNA, Viraldiagnosticsgenetic diversityhuman immunodeficiency virusNATp24PCRrecombinantsubtypeviral load

Identifiers

PMID41990403
PMCPMC13155410

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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.