Development and Optimization of Oligonucleotide Ligation Assay (OLA) Probes for Detection of HIV-1 Resistance to Dolutegravir DOI Creative Commons
Ingrid A. Beck, Ceejay L. Boyce, M. Bishop

и другие.

Viruses, Год журнала: 2024, Номер 16(7), С. 1162 - 1162

Опубликована: Июль 19, 2024

The WHO currently recommends dolutegravir (DTG)-based ART for persons living with HIV infection in resource-limited-settings (RLS). To expand access to testing drug resistance (DR) DTG RLS, we developed probes use the oligonucleotide ligation assay (OLA)-Simple, a near-point of care DR kit. Genotypic data from clinical trials and case reports were used determine mutations HIV-1 integrase critical identifying individuals DTG-resistance at virologic failure DTG-based ART. Probes detect G118R, Q148H/K/R, N155H R263K subtypes A, B, C, D CRF01_AE designed using sequence alignments Los Alamos database validated 61 samples D, genotyped by PacBio (n = 15) or Sanger 46). Initial OLA failed ligate 16/244 (6.5%) codons (9 G118R 7 Q148H/K/R). revised accommodate polymorphisms interfering Q148R reduced indeterminates 3.7% (5 4 Q148H/K/R) detected DTG-mutations sensitivity 96.5% 100% specificity. These appear highly sensitive specific across common RLS high burden infection.

Язык: Английский

Brief Histories of Retroviral Integration Research and Associated International Conferences DOI Creative Commons
Duane P. Grandgenett, Alan Engelman

Viruses, Год журнала: 2024, Номер 16(4), С. 604 - 604

Опубликована: Апрель 13, 2024

The field of retroviral integration research has a long history that started with the provirus hypothesis and subsequent discoveries reverse transcriptase integrase enzymes. Because both enzymes are essential for replication, they became valued targets in effort to discover effective compounds inhibit HIV-1 replication. In 2007, first strand transfer inhibitor was licensed clinical use, subsequently approved second-generation inhibitors now commonly co-formulated treat people living HIV. International meetings specifically focused on convened 1995, this paper is part Viruses Special Issue 7th Conference Retroviral Integration, which held Boulder Colorado summer 2023. Herein, we overview key historical developments field, especially as pertain development drug class. Starting from mid-1990s, advancements presented through lens international conferences. Our highlights impact regularly scheduled, subject-specific can have community-building and, result, field-specific collaborations scientific advancements.

Язык: Английский

Процитировано

4
Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations DOI Creative Commons
Hirotaka Ode,

Masakazu Matsuda,

Urara Shigemi

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Май 27, 2024

HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different target proteins. Since the number targets has increased with addition a new class antiretroviral drugs, simple high-throughput system for assessing nucleotide sequences throughout genome is required. Here, we developed solution using nanopore viral pangenomes amplified PCR. Benchmark molecular clones demonstrated an accuracy up to 99.9%. In addition, validation our protocol in 106 clinical samples high concordance and tropism genotypes (92.5% 98.1%, respectively) between sequencing-based results archived determinations made based on data. These suggest that approach will be powerful comprehensive survey mutations settings.

Язык: Английский

Процитировано

3
Comprehensive Database of HIV Mutations Selected During Antiretroviral In Vitro Passage Experiments DOI Creative Commons
Kaiming Tao,

Jinru Zhou,

Pavithra Nagarajan

и другие.

Antiviral Research, Год журнала: 2024, Номер 230, С. 105988 - 105988

Опубликована: Авг. 16, 2024

In vitro passage experiments are crucial to the development of antiretroviral (ARV) drugs.

Язык: Английский

Процитировано

3
The miRNomics of antiretroviral therapy-induced obesity DOI Creative Commons

Niska Majumdar,

Bishwa Raj Pokharel,

Anne E. Dickerson

и другие.

Functional & Integrative Genomics, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 5, 2025

Язык: Английский

Процитировано

0
Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity DOI Creative Commons
Long Chen, Yuta Hikichi, Juan S. Rey

и другие.

Science Advances, Год журнала: 2025, Номер 11(19)

Опубликована: Май 9, 2025

During HIV-1 maturation, the matrix (MA) lattice underlying viral membrane undergoes a structural rearrangement, and newly released capsid (CA) protein forms mature CA. While it is well established that CA formation essential for particle infectivity, functional role of MA maturation remains unclear. Here, we examine an triple mutant, L20K/E73K/A82T, which, despite replicating similarly to wild-type (WT) in some cell lines, exhibits distinct biochemical behaviors suggest altered MA-MA interactions. Cryo–electron tomography with subtomogram averaging reveals that, although immature L20K/E73K/A82T virions closely resembles WT, lack detectable lattice. All-atom molecular dynamics simulations this absence results from destabilized inter-trimer interactions mutant virions. These findings ordered, membrane-associated not providing insights into requirements generation infectious particles.

Язык: Английский

Процитировано

0
Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity DOI Open Access
Long Chen, Yuta Hikichi, Juan S. Rey

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 23, 2024

Abstract HIV-1 assembly is initiated by the binding of Gag polyproteins to inner leaflet plasma membrane, mediated myristylated matrix (MA) domain Gag. Subsequent membrane binding, oligomerizes and buds as an immature, non-infectious virus particle, which, upon cleavage precursor viral protease, transforms into a mature, infectious virion. During maturation, MA lattice underlying undergoes structural rearrangement newly released capsid (CA) protein forms mature that encloses genome. While it well established formation essential particle infectivity, functional role maturation remains unclear. Here, we examine triple mutant, L20K/E73K/A82T, which exhibits distinct biochemical behaviours. The L20K/E73K/A82T mutant revertant derived propagating L20K reduced infectivity increased association polyprotein with membranes. replicates similarly wild type but retains properties L20K. also sediments high-density fractions in sucrose gradients after detergent treatment under conditions fully solubilize WT MA, suggesting enhanced MA-MA interactions. Cryo-electron tomography subtomogram averaging reveals immature closely resembles type. However, virions lack detectable lattice, stark contrast both mutant. All-atom molecular dynamics simulations suggest this absence results from destabilized inter-trimer interactions MA. Furthermore, introducing additional mutations designed disrupt does not impair infectivity. These findings ordered, membrane-associated for providing new insights plasticity during its lifecycle.

Язык: Английский

Процитировано

1
Development and Optimization of Oligonucleotide Ligation Assay (OLA) Probes for Detection of HIV-1 Resistance to Dolutegravir DOI Creative Commons
Ingrid A. Beck, Ceejay L. Boyce, M. Bishop

и другие.

Viruses, Год журнала: 2024, Номер 16(7), С. 1162 - 1162

Опубликована: Июль 19, 2024

The WHO currently recommends dolutegravir (DTG)-based ART for persons living with HIV infection in resource-limited-settings (RLS). To expand access to testing drug resistance (DR) DTG RLS, we developed probes use the oligonucleotide ligation assay (OLA)-Simple, a near-point of care DR kit. Genotypic data from clinical trials and case reports were used determine mutations HIV-1 integrase critical identifying individuals DTG-resistance at virologic failure DTG-based ART. Probes detect G118R, Q148H/K/R, N155H R263K subtypes A, B, C, D CRF01_AE designed using sequence alignments Los Alamos database validated 61 samples D, genotyped by PacBio (n = 15) or Sanger 46). Initial OLA failed ligate 16/244 (6.5%) codons (9 G118R 7 Q148H/K/R). revised accommodate polymorphisms interfering Q148R reduced indeterminates 3.7% (5 4 Q148H/K/R) detected DTG-mutations sensitivity 96.5% 100% specificity. These appear highly sensitive specific across common RLS high burden infection.

Язык: Английский

Процитировано

0