Detection of diverse HIV strains by the m-PIMATM HIV-1/2 detect point-of-care assay

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology Pub Date : 2025-02-07 DOI:10.1016/j.jcv.2025.105771

Mark Anderson , Lara Teodoro , Fiona Harley , Eduardo Almaraz , Ana Vallari , Carolyn Strobel , Barbara Harris , Todd V. Meyer , Nicaise Ndembi , Dora Mbanya , Linda James , Souleymane Mboup , Jean-Christophe Plantier , Gavin Cloherty , Mary Rodgers

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引用次数: 0

Abstract

Background

HIV displays exceptionally high virus diversity that can impact detection by diagnostic assays, which rely on sequence conservation.

Methods

We tested the m-PIMA HIV-1/2 Detect point-of-care (POC) assay (Abbott Rapid Diagnostics) against a diverse HIV panel of 340 serum/plasma specimens and diluted cultured virus isolates for which viral load (VL) and classified sequences were known, including HIV-1 groups M, N, O, P, Circulating Recombinant Forms (CRF), and Unique Recombinant Forms (URF), and HIV-2. An in silico inclusivity analysis of 53,503 HIV-1 and 68 HIV-2 sequences from NCBI was performed to predict performance of m-PIMA HIV-1/2 Detect against a broader range of circulating strains.

Results

m-PIMA HIV-1/2 Detect detected HIV in 329/340 (96.8 %) tested samples. The mean VL was 3.80 (2.09–6.14) log copies/mL. Among samples with HIV VL >4000 copies/mL (3.60 log copies/mL; m-PIMA HIV-1/2 Detect design sensitivity), 181/181 (100 %) were detected. Among samples with VL between 3.0 and 3.6 log copies/mL, m-PIMA HIV-1/2 Detect detected 93/96 (96.9 %), and 55/63 (87.3 %) samples with VL below 3.0 log copies/mL were detected. At least one member from each subtype/CRF and all URFs were detected. In silico analysis identified 2/53,503 (0.0037 %) HIV-1 (both group O) and 1/68 (1.47 %) HIV-2 (subtype F) sequences with target region mutations that decreased identity below a 90 % threshold.

Conclusions

The m-PIMA HIV-1/2 Detect assay detected each of the major circulating HIV strains, including rare divergent strains. In silico analysis predicted that m-PIMA HIV-1/2 Detect would detect the majority of HIV-1 and HIV-2 strains indicating that this assay can detect the full range of HIV viral diversity.

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m-PIMATM HIV-1/2检测点护理试验检测多种HIV毒株

hiv表现出异常高的病毒多样性，这可能影响依赖于序列保守的诊断分析的检测。方法我们测试了M - pima HIV-1/2检测点护理（POC）测定（雅培快速诊断）对340个不同HIV组的血清/血浆样本和已知病毒载量（VL）和分类序列的稀释培养病毒分离物，包括HIV-1组M、N、O、P、循环重组形式（CRF）和独特重组形式（URF），以及HIV-2。对来自NCBI的53,503个HIV-1和68个HIV-2序列进行了计算机包容性分析，以预测m-PIMA HIV-1/2检测对更广泛的循环菌株的性能。结果sm- pima HIV-1/2检测阳性率为329/340（96.8%）。平均VL为3.80（2.09-6.14）个log拷贝/mL。HIV样本中VL >；4000 copies/mL (3.60 log copies/mL；m-PIMA HIV-1/2检测设计灵敏度为181/181（100%）。在VL在3.0 ~ 3.6 log copies/mL之间的样本中，m-PIMA HIV-1/2 Detect检出93/96 (96.9%)，VL在3.0 log copies/mL以下的样本中检出55/63（87.3%）。从每个subtype/CRF和所有urf中至少检测到一个成员。计算机分析鉴定出2/53,503 (0.0037%)HIV-1 （O组）和1/68 (1.47%)HIV-2 （F亚型）序列，其靶区突变使身份降低到90%以下的阈值。结论m-PIMA HIV-1/2检测方法可检出各主要流行HIV毒株，包括罕见的分化毒株。计算机分析预测m-PIMA HIV-1/2检测方法可以检测出大多数HIV-1和HIV-2毒株，表明该方法可以检测出全范围的HIV病毒多样性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Clinical Virology 医学-病毒学

CiteScore

22.70

自引率

1.10%

发文量

149

审稿时长

24 days

期刊介绍： The Journal of Clinical Virology, an esteemed international publication, serves as the official journal for both the Pan American Society for Clinical Virology and The European Society for Clinical Virology. Dedicated to advancing the understanding of human virology in clinical settings, the Journal of Clinical Virology focuses on disseminating research papers and reviews pertaining to the clinical aspects of virology. Its scope encompasses articles discussing diagnostic methodologies and virus-induced clinical conditions, with an emphasis on practicality and relevance to clinical practice. The journal publishes on topics that include: • new diagnostic technologies • nucleic acid amplification and serologic testing • targeted and metagenomic next-generation sequencing • emerging pandemic viral threats • respiratory viruses • transplant viruses • chronic viral infections • cancer-associated viruses • gastrointestinal viruses • central nervous system viruses • one health (excludes animal health)