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Background Simple, affordable diagnostic tools are essential to facilitate global hepatitis C virus (HCV) elimination efforts. Objectives This study evaluated the clinical performance of core antigen (HCVcAg) assay from plasma samples to monitor HCV treatment efficacy and HCV viral recurrence. Study design Plasma samples from a study of response-guided pegylated-interferon/ribavirin therapy for people who inject drugs with chronic HCV genotype 2/3 infection were assessed for HCV RNA (AmpliPrep/COBAS Taqman assay, Roche) and HCVcAg (ARCHITECT HCV Ag, Abbott Diagnostics) during and after therapy. The sensitivity and specificity of the HCVcAg assay was compared to the HCV RNA assay (gold standard). Results A total of 335 samples from 92 enrolled participants were assessed (mean 4 time-points per participant). At baseline, end of treatment response (ETR) and sustained virological response (SVR) visits, the sensitivity of the HCVcAg assay with quantifiable HCV RNA threshold was 94% (95% CI: 88%, 98%), 56% (21%, 86%) and 100%, respectively. The specificity was between 98 to 100% for all time-points assessed. HCVcAg accurately detected all six participants with viral recurrence, demonstrating 100% sensitivity and specificity. One participant with detectable (non-quantifiable) HCV RNA and non-reactive HCVcAg at SVR12 subsequently cleared HCV RNA at SVR24. Conclusions HCVcAg demonstrated high sensitivity and specificity for detection of pre-treatment and post-treatment viraemia. This study indicates that confirmation of active HCV infection, including recurrent viraemia, by HCVcAg is possible. Reduced on-treatment sensitivity of HCVcAg may be a clinical advantage given the moves toward simplification of monitoring schedules. [ABSTRACT FROM AUTHOR]

Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652–654 and 752–754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652–654 and 752–754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg 2 + - and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function. [ABSTRACT FROM AUTHOR]

Introduction HIV diagnoses among gay and bisexual men have increased over the past decade in Australia. HIV point‐of‐care testing (POCT) was introduced in Australia in 2011 as a strategy to increase HIV testing by making the testing process more convenient. We surveyed gay and bisexual men undergoing POCT to assess barriers to HIV testing and characteristics associated with not having previously tested for HIV (never testing). Methods During 2011 and 2012, gay and bisexual men who were undergoing POCT at four Sydney sexual health clinics self‐completed questionnaires assessing testing history and psychological and structural barriers to HIV testing. Bivariate and multivariate logistic regression was used to assess associations between patient characteristics and never testing. Results Of 1093 participants, 981 (89.9%) reported ever testing for HIV and 110 (10.1%) never testing. At least one barrier to testing was reported by 1046 men (95.7%), with only 47 men (4.3%) not reporting any barrier to testing. The most commonly reported barriers to testing were annoyance at having to return for results (30.2%), not having done anything risky (29.6%), stress in waiting for results (28.4%), being afraid of testing positive (27.5%) and having tested recently (23.2%). Never testing was independently associated with being non‐gay‐identified (adjusted odds ratio [AOR]: 1.9; 95% confidence interval [CI]: 1.1–3.2), being aged less than 25 years (AOR: 2.4; 95% CI: 1.6–3.8), living in a suburb with few gay couples (AOR: 1.9; 95% CI: 1.2–3.0), being afraid of testing HIV‐positive (AOR: 1.6; 95% CI: 1.0–2.4), not knowing where to test (AOR: 3.8; 95% CI: 1.3–11.2) and reporting one or no sexual partners in the last six months (AOR: 2.7; 95% CI: 1.2–6.2). Conclusions Barriers to HIV testing were commonly reported among the clinic‐based gay and bisexual men in this study. Our findings suggest further health promotion and prevention strategies are needed to address the knowledge, attitudes and behavioural factors associated with never testing. [ABSTRACT FROM AUTHOR]

Highlights: [•] Low costing and effective genotyping test for HIV-1 subtype is a practical and viable solution for resource-limiting countries. [•] Approximately 99% correlation when compare with commercial kit (Trugene). [•] Less time consuming for drug resistance testing. [ABSTRACT FROM AUTHOR]

Abstract: Background: Concordance in plasma HIV-1 viral load quantification at the lower limit of quantification (LLOQ) is crucial for current commercial assays. Objective: To compare the performance of three commercial viral load assays and carry out a correlation study with the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test, the Roche Cobas Amplicor HIV-1 MONITOR test, and the Abbott RealTime HIV-1 assay. Study design: Assay agreement was analyzed using linear regression and Bland–Altman plots. Concordance near the clinically critical LLOQ was measured by Cohen''s kappa statistics. Intra-assay precision was assessed, and assay reproducibility was measured at 50copies/mL across all three platforms. Results: While good overall correlation was observed between the assays (r ≥0.93), quantitative differences exceeded 0.5log10 copies/mL among paired results in 3.7 to 8.3% of specimens. The degree of concordance between the assays near the LLOQ was unsatisfactory, with Cohen''s kappa ranging from 0.14 to 0.38. The intra-assay precision of the Abbott RealTime HIV-1 assay ranged from 0.04 to 0.15 (SD log10) and 1.34% to 8.37% (CV). Reproducibility at 50copies/mL for RealTime HIV-1, TaqMan, and Amplicor was 10.05, 11.04 and 5.07 (% CV), respectively. Conclusion: Although good correlation was observed between the assays across their linear range, their concordance at the clinically critical LLOQ was poor. The accurate quantification of low-level viremia remains elusive, and the lack of correlation of these assays presents a challenge to the interpretation of such results and in the clinical management of HIV-infected patients. [Copyright &y& Elsevier]

Previous studies identified G791 in Escherichia coli 16S rRNA as an invariant residue for ribosome function. In order to establish the functional role of this residue in protein synthesis, we searched for multicopy suppressors of the mutant ribosomes that bear a G-to-U substitution at position 791. We identified relA, a gene whose product has been known to interact with ribosomes and trigger a stringent response. Overexpression of RelA resulted in the synthesis of approximately 1.5 times more chloramphenicol acetyltransferase (CAT) protein than could be synthesized by the mutant ribosomes in the absence of RelA overexpression. The ratio of mutant rRNA to the total ribosome pool was not changed, and the steady-state level of CAT mRNA was decreased by RelA overexpression. These data confirmed that the phenotype of RelA as a multicopy suppressor of the mutant ribosome did not result from the enhanced synthesis of mutant rRNA or CAT mRNA from the plasmid. To test whether the phenotype of RelA was related to the stringent response induced by the increased cellular level of (p)ppGpp, we screened for mutant RelA proteins whose overexpression enhances CAT protein synthesis by the mutant ribosomes as effectively as wild-type RelA overexpression and then screened for those whose overexpression does not produce sufficiently high levels of (p)ppGpp to trigger the stringent response under the condition of amino acid starvation. Overexpression of the isolated mutant RelA proteins resulted in the accumulation of (p)ppGpp in cells, which was amounted to approximately 18.2 to 38.9% of the level of (p)ppGpp found in cells that overexpress the wild-type RelA. These findings suggest that the function of RelA as a multicopy suppressor of the mutant ribosome does not result from its (p)ppGpp synthetic activity. We conclude that RelA has a previously unrecognized role in ribosome function. [ABSTRACT FROM AUTHOR]

Abstract: The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m2G966 and m5C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this ribosomal RNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Nonrandom nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m2G966 or m5C967 produce more protein in vivo than do wild-type ribosomes. Overexpression of initiation factor 3 specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for initiation factor 3 binding and for the proper initiation of protein synthesis. [Copyright &y& Elsevier]

Context-We previously developed a novel technology known as instant evolution for high-throughput analysis of mutations in Escherichia coli ribosomal RNA. Objective.-To develop a genetic platform for the isolation of new classes of antiinfectives that are not susceptible to drug resistance based on the instant evolution system. Design.-Mutation libraries were constructed in the 16S rRNA gene of E coli and analyzed. In addition, the rRNA genes from a number of pathogenic bacteria were cloned and expressed in E coli. The 16S rRNA genes were incorporated into the instant-evolution system in E coil. Setting.-The Department of Biological Sciences, Wayne State University, Detroit, Mich. Main Outcome Measures.-Ribosome function was assayed by measuring the amount of green fluorescent protein produced by ribosomes containing mutant or foreign RNA in vivo. Results.-We have developed a new combinatorial genetic technology (CGT) platform that allows high-through- put in vivo isolation and analysis of rRNA mutations that might lead to drug resistance. This information is being used to develop anti-infectives that recognize the wild type and all viable mutants of the drug target. CGT also provides a novel mechanism for identifying new drug targets. Conclusions.-Antimicrobials produced using CGT will provide new therapies for the treatment of infections caused by human pathogens that are resistant to current antibiotics. The new therapeutics will be less susceptible to de novo resistance because CGT identifies all mutations of the target that might lead to resistance during the earliest stages of the drug discovery process. [ABSTRACT FROM AUTHOR]

The 900 tetraloop that caps helix 27 of 16 S ribosomal RNA (rRNA) is amongst the most conserved regions of rRNA. This tetraloop forms a GNRA motif that docks into the minor groove of three base-pairs at the bottom of helix 24 of 16 S rRNA in the 30 S subunit. Both the tetraloop and its receptor in helix 24 contact the 23 S rRNA, forming the intersubunit bridge B2c. Here, we investigated the interaction between the 900 tetraloop and its receptor by genetic complementation. We used a specialized ribosome system in combination with an in vivo instant evolution approach to select mutations in helix 24 compensating for a mutation in the 900 tetraloop (A900G) that severely decreases ribosomal activity, impairing subunit association and translational fidelity. We selected two mutants where the G769-C810 base-pair of helix 24 was substituted with either U-A or C·A. When these mutations in helix 24 were investigated in the context of a wild-type 900 tetraloop, the C·A but not the U-A mutation severely impaired ribosome activity, interfering with subunit association and decreasing translational fidelity. In the presence of the A900G mutation, both mutations in helix 24 increased the ribosome activity to the same extent. Subunit association and translational fidelity were increased to the same level. Computer modeling was used to analyze the effect of the mutations in helix 24 on the interaction between the tetraloop and its receptor. This study demonstrates the functional importance of the interaction between the 900 tetraloop and helix 24. [Copyright &y& Elsevier]

The 900 tetraloop (positions 898–901) of Escherichia coli 16 S rRNA caps helix 27, which is involved in a conformational switch crucial for the decoding function of the ribosome. This tetraloop forms a GNRA motif involved in intramolecular RNA–RNA interactions with its receptor in helix 24 of 16 S rRNA. It is involved also in an intersubunit bridge, via an interaction with helix 67 in domain IV of 23 S rRNA. Using a specialized ribosome system and an instant-evolution procedure, the four nucleotides of this loop were randomized and 15 functional mutants were selected in vivo. Positions 899 and 900, responsible for most of the tetraloop/receptor interactions, were found to be the most critical for ribosome activity. Functional studies showed that mutations in the 900 tetraloop impair subunit association and decrease translational fidelity. Computer modeling of the mutations allows correlation of the effect of mutations with perturbations of the tetraloop/receptor interactions. [Copyright &y& Elsevier]

Reports that the aerobic activity of Escherichia coli alcohol dehydrogenase is determined by a single amino acid. Aerobic activity of AdhE[sup *] from adhC mutants; Phenotypes of constructs containing hybrids of adhE[sup +] and adhE[sup *] on alcohol indicator medium; Phenotypes of EMS and site-directed AdhE mutants.

• HIV-1 viral load assays are essential tools for clinical management. • We evaluated the performance of 3 HIV-1 viral load assays including cobas® HIV-1. • The limit of detection was below 20 copies/mL for each assay. • The agreement between pairs of assays was 94.8–98.1% at the 50 copies/mL cutoff. • Agreement was as high as 99.0 % at higher thresholds. HIV-1 viral load assays are essential tools for clinical management of people living with HIV-1. We evaluated concordance between three assays: the cobas ® HIV-1 test for use on the cobas ® 6800 and cobas ® 8800 systems (cobas HIV-1); the COBAS ® TaqMan ® HIV-1 Test, v2.0 for use with the High Pure System and the COBAS ® AmpliPrep/COBAS ® TaqMan ® HIV-1 test, v2.0. Analytical sensitivity, precision and accuracy of all three methods were assessed using the WHO 2nd International Standard for HIV-1, with concentrations from 5 to 1000 copies/mL. Accuracy and concordance were evaluated using 212 clinical specimens. Overall percent agreement (OPA) was determined using three different thresholds used as medical decision points. The limit of detection was below 20 copies/mL for each assay. The hit rate for each assay was 100 % for concentrations ≥ 50 copies/mL. Only the cobas HIV-1 test generated quantifiable data for all replicates at 50 copies/mL. Between 50 and 400 copies/mL, results for all assays were accurate within 0.09 log 10 copies/mL, with standard deviation less than 0.14 log 10 copies/mL. The mean difference between paired results in clinical specimens ranged from −0.050 to 0.107 log 10 copies/mL across all assay comparisons. The OPA between pairs of assays ranged from 94.8 to 98.1% at the 50 copies/mL cutoff, and improved to a range of 97.6–99.0% at the 200 copies/mL cutoff. At the 1000 copies/mL cutoff, OPA between assays was 98.5–99.0%. The cobas HIV-1 assay is highly sensitive, accurate and suitable for use in clinical practice. [ABSTRACT FROM AUTHOR]

Background Monitoring the hepatitis C virus (HCV) cascade of care (CoC) among people who inject drugs (PWID) is an essential component of the response to World Health Organisation's (WHO) hepatitis elimination goals. This study aimed to estimate the Consensus hepatitis C CoC among PWID using data collected in Australia prior to and after the introduction of unrestricted direct-acting antiviral (DAA) therapy in March 2016. Methods The Australian Needle Syringe Program Survey is a cross-sectional bio-behavioural surveillance system that recruits >2000 PWID annually. Using data from 2015 and 2019, HCV antibody and ribonucleic acid (RNA) test results from dried blood spots were combined with self-reported data on HCV diagnostic testing and treatment to project HCV Consensus CoC indicators at a population-level among Australian PWID. Results Among an estimated 75,000 people who inject drugs on a regular basis in Australia, the number with active HCV infection declined from 32,619 (44%) in October 2015 to 12,679 (17%) in October 2019. The majority (78% in 2015 and 2019) of PWID reported HCV diagnosis, while the proportion of those diagnosed who were treated increased from 3% in 2015 to 47% in 2019. Among those treated, the proportion who were HCV RNA negative and assumed to have been successfully treated (cured), increased from 27% in 2015 to 88% in 2019. Conclusion This study demonstrates remarkable HCV CoC progress among PWID in Australia following availability of DAA therapy. There was a substantial increase in the proportion of HCV diagnosed PWID who initiated treatment and were cured, while the number of PWID with active HCV infection more than halved over a 3.5 year period. Estimates of the Consensus hepatitis C CoC among PWID is required to monitor progress toward WHO HCV elimination goals. [ABSTRACT FROM AUTHOR]

Rapid antigen diagnostic tests (Ag-RDTs) that quickly and accurately identify SARS-CoV-2 are an essential part of the COVID-19 response, but multiple factors can affect the validity of Ag-RDTs results. In Cambodia, several commercial Ag-RDTs have become available since the COVID-19 outbreak, but quality control (QC) and external quality assurance (EQA) of these rapid tests have yet to be fully and systematically implemented. We collaborated with laboratory experts in Australia and piloted an EQA programme of the commonly used COVID-19 Ag-RDTs at the University of Health Sciences' MERIEUX Laboratory (Tier 1 site-responsible for the in-country receipt and distribution of QA material) and four other participating laboratories (Tier 2-healthcare facility based) between November 2021 and November 2022. The preimplementation training including the Khmer-translated documentation was conducted virtually for Tier 1 laboratories and in-person for Tier 2 laboratories. All QC (n=290) and EQA (n=60) specimens were distributed to the laboratories and testing was performed according to the frequency of Ag-RDTs use in each laboratory. All National Reference Laboratory-provided EQA and QC specimens were tested and results were submitted via the EDCNet portal using QR code scanning. The Tier 1 laboratory reported 100% concordance with the EQA reference result, while some of Tier 2 laboratories' results were discordant. While continued capacity building and support with troubleshooting have been key to the successful EQA piloting at the UHS laboratory, the programme experienced delays in the shipping/delivery of EQA and QC panels due to customs and border requirements, which could have hindered implementation and potentially impacted the quality of the QA materials. The pilot EQA programme demonstrated potential scalability and provided data on the reliability of test results at the site. However, to ensure sustainability and practicability of this activity, in-country EQA panel preparation may need to be considered., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2025. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ Group.)

Background: Quality assurance programs (QAPs) are used to evaluate the analytical quality of a diagnostic test and provide feedback to improve quality processes in testing. Rapid diagnostic tests were used in both laboratory and non-laboratory settings to diagnose COVID-19, although varied in reported performance. We aimed to design and implement a QAP for antigen rapid diagnostic tests (Ag-RDTs) for COVID-19 in Cambodia, Lao PDR, and Papua New Guinea., Methods: Inactivated SARS-CoV-2 material derived from cell culture of Wildtype, Delta, and Omicron isolates were used to manufacture 435 quality control (QC) panels (consisting of a single positive and negative sample) and 36 external quality assessment (EQA) panels for use across 15 sites in accordance with provided training and protocols., Results: In total, 369 QC results and 112 EQA results were submitted by electronic reporting or paper forms by two countries. 19·3 % (34/176) positive and 99·5 % (192/193) negative samples were correctly reported in the QC, and 37·5 % (30/80) positive and 97·5 % (39/40) negative samples were correctly reported in the EQA., Conclusion: This QAP demonstrates the importance of operator training and the design of QAP materials, which may have contributed to the high rate of false-negative interpretations in known COVID-19 positive samples. The implementation of this project, to our knowledge the first of its kind in the region and one of only a few globally, emphasised the importance of quality assurance principles, including non-laboratory community testing sites, to promote diagnostic quality for COVID-19 testing., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Introduction: Decentralized molecular testing for infectious disease diagnosis at the point-of-care (POC) is critical to address inequities in access to timely, informed health care. The COVID-19 pandemic accelerated the demand, development and adoption of POC tests for infectious diseases globally. This has provided opportunities to maximize the individual benefits and public health impact of POC testing, particularly in remote and resource-limited primary care settings. Despite this, there remains a lack of harmonized, regulatory compliance and quality management frameworks for the delivery of molecular POC testing networks outside the laboratory setting., Areas Covered: This Perspective describes real-world lessons and experiences of delivering a fit-for-purpose, quality framework for one of the world's largest decentralized molecular POC testing programs for infectious disease across rural and remote Australian communities. Here we detail unique, key considerations to ensure the quality of POC testing in primary health settings with global application., Expert Opinion: There is an ethical and public health imperative to provide sustained access to decentralized POC testing for infectious disease in primary care. Genuine partnerships across stakeholders and disciplines are essential to deliver well governed, fit-for-purpose quality management POC testing frameworks and increase equitable access to timely, high-quality person-centered care.

Introduction: Progress toward hepatitis C virus (HCV) elimination is impeded by low testing and treatment due to the current diagnostic pathway requiring multiple visits leading to loss to follow-up. Point-of-care testing technologies capable of detecting current HCV infection in one hour are a 'game-changer.' These tests enable diagnosis and treatment in a single visit, overcoming the barrier of multiple visits that frequently leads to loss to follow-up. Combining point-of-care HCV antibody and RNA tests should improve cost-effectiveness, patient/provider acceptability, and testing efficiency. However, implementing HCV point-of-care testing programs at scale requires multiple considerations., Areas Covered: This commentary explores the need for point-of-care HCV tests, diagnostic strategies to improve HCV testing, key considerations for implementing point-of-care HCV testing programs, and remaining challenges for point-of-care testing (including operator training, quality management, connectivity and reporting systems, regulatory approval processes, and the need for more efficient tests)., Expert Opinion: It is exciting that single-visit testing, diagnosis, and treatment for HCV infection have been achieved. Innovations afforded through COVID-19 should facilitate the accelerated development of low-cost, rapid, and accurate tests to improve HCV testing. The next challenge will be to address barriers and facilitators for implementing point-of-care testing to deliver them at scale.

Background: Long-term immunity to SARS-CoV-2 infection, including neutralizing antibodies and T cell-mediated immunity, is required in a very large majority of the population in order to reduce ongoing disease burden., Methods: We have investigated the association between memory CD4 and CD8 T cells and levels of neutralizing antibodies in convalescent COVID-19 subjects., Findings: Higher titres of convalescent neutralizing antibodies were associated with significantly higher levels of RBD-specific CD4 T cells, including specific memory cells that proliferated vigorously in vitro . Conversely, up to half of convalescent individuals had low neutralizing antibody titres together with a lack of receptor binding domain (RBD)-specific memory CD4 T cells. These low antibody subjects had other, non-RBD, spike-specific CD4 T cells, but with more of an inhibitory Foxp3+ and CTLA-4+ cell phenotype, in contrast to the effector T-bet+, cytotoxic granzymes+ and perforin+ cells seen in RBD-specific memory CD4 T cells from high antibody subjects. Single cell transcriptomics of antigen-specific CD4+ T cells from high antibody subjects similarly revealed heterogenous RBD-specific CD4+ T cells that comprised central memory, transitional memory and Tregs, as well as cytotoxic clusters containing diverse TCR repertoires, in individuals with high antibody levels. However, vaccination of low antibody convalescent individuals led to a slight but significant improvement in RBD-specific memory CD4 T cells and increased neutralizing antibody titres., Interpretation: Our results suggest that targeting CD4 T cell epitopes proximal to and within the RBD-region should be prioritized in booster vaccines., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Phetsouphanh, Khoo, Jackson, Klemm, Howe, Aggarwal, Akerman, Milogiannakis, Stella, Rouet, Schofield, Faulks, Law, Danwilai, Starr, Munier, Christ, Singh, Croucher, Brilot-Turville, Turville, Phan, Dore, Darley, Cunningham, Matthews, Kelleher and Zaunders.)

New South Wales has the greatest burden of HIV in Australia, with 2012 and 2013 recording the highest rates of new diagnoses in 20 years. Concurrently, there has been significant changes in antiretroviral treatments and testing paradigms. We compiled a statewide resistance database to characterize changes in HIV-1 resistance mutations over time. Genotypic antiretroviral resistance testing (GART) was performed on request at three reference laboratories using commercial and in-house methods. In total, 7629 HIV-1 polymerase sequences obtained from GART from 2004 to 2013 were retrospectively collated, reformatted, de-identified, and analyzed using Stanford HIVdb program 7.0 and the 2009 World Health Organization (WHO) surveillance drug resistance mutations (SDRMs). Analyses were performed on subgroups of known treatment naives, treatment experienced, and seroconverters. There has been a decrease in overall rates of prevalent drug resistance mutations from 57.8% in 2004 to 21% in 2013. Dual and triple class resistance mutations have decreased from 32.7% in 2004 to 5.8% in 2013 and 16.4% to 1.2%, respectively. In treatment-naive individuals ( n  = 450), the frequency of protease inhibitor (PI) mutations remains low at 2.7%. In seroconverters, rates of transmitted drug resistance (TDR) are 6.6%, 3%, 3%, and 1.5% for overall, PI, non-nucleoside reverse transcription inhibitor (NNRTI), and NRTI, respectively. In treatment experienced, rates remain stable with 36.0%, 18.9%, 29.1%, and 6.4% for overall, NNRTI, NRTI, and PI mutations. The most common mutations in treatment experienced occurred at position M184, T215 (NRTI); K103 (NNRTI); I54 (PI). Apparent decreases in prevalent SDRMs can be attributed to changes in GART testing indications over time. In treatment-naive and -experienced subgroups, rates have been stable with low rates of TDR in seroconverters.

Objective: Some HIV+ patients, virally suppressed on ART, show occasional 'blips' of detectable HIV-1 plasma RNA. We used a new highly sensitive assay of cell-associated HIV-1 RNA to measure transcriptional activity in PBMCs and production of infectious virus from the viral reservoir, in patients with and without 'blips'., Design/methods: RNA and DNA extracted from cells in 6 ml of peripheral blood, from suppressed patients with one to two 'blip' episodes over the past 2 years of ART (n = 55), or no 'blips' (n = 52), were assayed for HIV-1 RNA transcripts and proviral DNA targeting the highly conserved 'R' region of the LTR. Follow-up samples were also collected. Purified CD4+ T cells were cultured with anti-CD3/CD28/CD2 T-cell activator to amplify transcription and measure replication competent virus., Results: HIV-1 RNA transcripts ranged from 1.3 to 5415 copies/106 white blood cells. 'Blip' patients had significantly higher levels vs. without blips (median 192 vs. 49; P = 0.0007), which correlated with: higher levels of inducible transcripts after activation in vitro, sustained higher HIV-1 transcription levels in follow-up samples along with increasing HIV-1 DNA in some, and production of replication-competent HIV-1., Conclusion: Viral 'blips' are significant reflecting higher transcriptional activity from the reservoir and contribute to the reservoir over time. This sensitive assay can be used in monitoring the size and activity of the HIV-1 reservoir and will be useful in HIV-1 cure strategies., (Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc.)

Peptides have important biomedical applications, but poor correlation between in vitro and in vivo activities can limit their development for clinical use. The ability to generate peptides and monitor their expression with new mass spectrometric methods and biological activities in vivo would be an advantage for the discovery and improvement of peptide-based drugs. In this study, a plasmid-based system was used to express the ribosome-targeting peptide oncocin (19 amino acids, VDKPPYLPRPRPPRRIYNR) and to determine its direct antibacterial effects on Escherichia coli. Previous biochemical and structure studies showed that oncocin targets the bacterial ribosome. The oncocin peptide generated in vivo strongly inhibits bacterial growth. In vivo dimethyl sulfate footprinting of oncocin on the rRNA gives results that are consistent with those of in vitro studies but reveals additional binding interactions with E. coli ribosomes. Furthermore, expression of truncated or mutated peptides reveals which amino acids are important for antimicrobial activity. Overall, the in vivo peptide expression system can be used to investigate biological activities and interactions of peptides with their targets within the cellular environment and to separate contributions of the sequence to cellular transport. This strategy has future applications for improving the effectiveness of existing peptides and developing new peptide-based drugs.

Simplified, affordable tools to diagnose active hepatitis C virus (HCV) infection are needed to scale up treatment. This study evaluated the analytical performance of HCV core antigen (HCVcAg) detection in samples of plasma and dried venous blood spots (DBSs). Paired plasma and DBS samples were prepared from remnant diagnostic samples, and plasma HCV RNA and HCVcAg were quantified. Sensitivity and specificity for HCVcAg (>3 fmol/L) at two HCV RNA thresholds (≥15 and ≥3000 IU/mL) were calculated. Of 120 paired samples tested, 25 had nonquantifiable HCV RNA and 95 had quantifiable HCV RNA. The median HCV RNA level in plasma was 5.6 log 10 IU/mL (interquartile range: 5.2 to 6.2). The median HCVcAg levels in plasma and DBS samples were 2.3 log 10 fmol/L (interquartile range: 0.1 to 3.1) and 1.1 log 10 fmol/L (interquartile range: 0.0 to 1.9), respectively. For diagnosing HCV RNA ≥3000 IU/mL, the sensitivity and specificity of HCVcAg in plasma were 97.7% (95% CI, 91%-100%) and 100% (95% CI, 87%-100%), respectively. The sensitivity and specificity of HCVcAg in DBS were 88.6% (95% CI, 80%-94%) and 97% (95% CI, 82%-100%), respectively. The data from this study demonstrate good sensitivity and specificity of HCVcAg in plasma at an HCV RNA threshold of ≥3000 IU/mL. The level of HCVcAg quantified in plasma was higher than that in DBS., (Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

Background: Point-of-care hepatitis C virus (HCV) RNA testing offers an advantage over antibody testing (which only indicates previous exposure), enabling diagnosis of active infection in a single visit. In this study, we evaluated the performance of the Xpert HCV Viral Load assay with venepuncture and finger-stick capillary whole-blood samples., Methods: Plasma and finger-stick capillary whole-blood samples were collected from participants in an observational cohort enrolled at five sites in Australia (three drug and alcohol clinics, one homelessness service, and one needle and syringe programme). We compared the sensitivity and specificity of the Xpert HCV Viral Load test for HCV RNA detection by venepuncture and finger-stick collection with the Abbott RealTime HCV Viral Load assay (gold standard)., Findings: Of 210 participants enrolled between Feb 8, 2016, and July 27, 2016, 150 participants had viral load testing results for the three assays tested. HCV RNA was detected in 45 (30% [95% CI 23-38]) of 150 participants based on Abbott RealTime. Sensitivity of the Xpert HCV Viral Load assay for HCV RNA detection in plasma collected by venepuncture was 100·0% (95% CI 92·0-100·0) and specificity was 99·1% (95% CI 94·9-100·0). Sensitivity of the Xpert HCV Viral Load assay for HCV RNA detection in samples collected by finger-stick was 95·5% (95% CI 84·5-99·4) and specificity was 98·1% (95% CI 93·4-99·8). No adverse events caused by the index test or the reference standard were observed., Implications: The Xpert HCV Viral Load test can detect active infection from a finger-stick sample, which represents an advance over antibody-based tests that only indicate past or previous exposure., Funding: National Health and Medical Research Council (Australia), Cepheid, South Eastern Sydney Local Health District (Australia), and Merck Sharp & Dohme (Australia)., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

In many countries, including Australia, policies have recently changed to support HIV self-testing. The decision has created much debate about the public health benefits of the strategy versus the risks. Self-testing for HIV was approved in the US on the basis that it would facilitate greater HIV testing uptake, despite having a lower sensitivity than laboratory HIV immunoassays. We calculated the frequency of self-testing that would be required among Australian gay and bisexual men at high-risk for there to be a public health benefit (detection of HIV infections that would have otherwise remained undiagnosed). At a population level, if access to HIV self-testing led to men supplementing their usual sexual health check-ups (involving a laboratory HIV immunoassay) with one or more self-tests at home, or self-tests led to untested gay and bisexual men having an HIV test for the first time, there would be a public health benefit. If men replaced their average of one laboratory HIV immunoassay per year with self-testing at home, then three self-tests would be needed to counteract the lower sensitivity of the self-test (so zero infections would be missed). If four self-tests were undertaken then additional infections would be detected (ie, there would be a public health benefit). Additional public health benefits include a reduction in the period of undiagnosed infection, which is known to be a period of relatively high infectiousness.

Structural changes and xylose docking to eight conformers of Escherichia Coli XylE, a xylose transporter similar to mammalian passive glucose transporters GLUTs, have been examined. Xylose docks to inward and outward facing conformers at a high affinity central site (K(i) 4-20 µM), previously identified by crystallography and additionally consistently docks to lower affinity sites in the external and internal vestibules (K(i) 12-50 µM). All these sites lie within intramolecular tunnels and cavities. Several local regions in the central transmembrane zone have large positional divergences of both skeleton carbon Cα positions and side chains. One such in TM 10 is the destabilizing sequence G388-P389-V390-C391 with an average RMSD (4.5 ± 0.4 Å). Interchange between conformer poses results in coalescence of tunnels with adjacent cavities, thereby producing a transitory channel spanning the entire transporter. A fully open channel exists in one inward-facing apo-conformer, (PDB 4ja4c) as demonstrated by several different tunnel-finding algorithms. The conformer interchanges produce a gated network within a branched central channel that permits staged ligand diffusion across the transporter during the open gate periods. Simulation of this model demonstrates that small-scale conformational changes required for sequentially opening gate with frequencies in the ns-μs time domain accommodate diffusive ligand flow between adjacent sites with association-dissociation rates in the μs-ms domain without imposing delays. This current model helps to unify the apparently opposing concepts of alternate access and multisite models of ligand transport.

The nucleotide at position 791(G791) of E. coli 16S rRNA was previously identified as an invariant residue for ribosomal function. In order to characterize the functional role of G791, base substitutions were introduced at this position, and mutant ribosomes were analyzed with regard to their protein synthesis ability, via the use of a specialized ribosome system. These ribosomal RNA mutations attenuated the ability of ribosomes to conduct protein synthesis by more than 65%. A transition mutation (G to A) exerted a moderate effect on ribosomal function, whereas a transversion mutation (G to C or U) resulted in a loss of protein synthesis ability of more than 90%. The sucrose gradient profiles of ribosomes and primer extension analysis showed that the loss of protein-synthesis ability of mutant ribosomes harboring a base substitution from G to U at position 791 stems partially from its inability to form 70S ribosomes. These findings show the involvement of the nucleotide at position 791 in the association of ribosomal subunits and protein synthesis steps after 70S formation, as well as the possibility of using 16S rRNA mutated at position 791 for the selection of second-site revertants in order to identify ligands that interact with G791 in protein synthesis.

Photoinduced cleavage reactions by the rhodium complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III) [Rh(DIP)(3)(3+)] with three RNA hairpins, r(GGGGU UCGCUC CACCA) (16 nucleotide, tetraloop(Ala2)), r(GGGGCUAUAGCUCUAGCUC CACCA) (24 nucleotide, microhelix(Ala)), and r(GGCGGUUAGAUAUCGCC) (17 nucleotide, 790 loop), and full-length (1542 nucleotide) 16S rRNA from Escherichia coli were investigated. The cleavage reactions were monitored by gel electrophoresis and the sites of cleavage by Rh(DIP)(3)(3+) were determined by comparisons with chemical or enzymatic sequencing reactions. In general, RNA backbone scission by the metal complex was induced at G.U mismatches and at exposed G residues. The cleavage activity was observed on the three small RNA hairpins as well as on the isolated 1542-nucleotide ribosomal RNA.

17 beta-Oestradiol (ED when subscript to K) and the phytoestrogen isoflavone genistein (GEN) inhibit glucose transport in human erythrocytes and erythrocyte ghosts. The selective oestrogen receptor modulators or anti-oestrogens, faslodex (ICI 182780) (FAS) and tamoxifen (TAM), competitively antagonize oestradiol inhibition of glucose exit from erythrocytes (K(i(ED/FAS))=2.84+/-0.16 microM and K(i(ED/TAM))=100+/-2 nM). Faslodex has no significant inhibitory effect on glucose exit, but tamoxifen alone inhibits glucose exit (K(i(TAM))=300+/-100 nM). In ghosts, ATP (1-4 mM) competitively antagonizes oestradiol, genistein and cytochalasin B (CB)-dependent inhibitions of glucose exit, (K(i(ATP/ED))=2.5+/-0.23 mM, K(i(ATP/GEN))=0.99+/-0.17 mM and K(i(ATP/CB))=0.76+/-0.08 mM). Tamoxifen and faslodex reverse oestradiol-dependent inhibition of glucose exit with ATP>1 mM (K(i(ED/TAM))=130+/-5 nM and K(i(ED/FAS))=2.7+/-0.9 microM). The cytoplasmic surface of the glucose transporter (GLUT)1 contains four sequences with close homologies to sequences in the ligand-binding domain of human oestrogen receptor beta (hesr-2). One homology is adjacent to the Walker ATP-binding motif II (GLUT1, residues 225-229) in the large cytoplasmic segment linking transmembrane helices 6 and 7; another GLUT (residues 421-423) contains the Walker ATP-binding motif III. Mapping of these regions on to a three-dimensional template of GLUT indicates that a possible oestrogen-binding site lies between His(337), Arg(349) and Glu(249) at the cytoplasmic entrance to the hydrophilic pore spanning GLUT, which have a similar topology to His(475), Glu(305) and Arg(346) in hesr-2 that anchor the head and tail hydroxy groups of oestradiol and genistein, and thus are suitably placed to provide an ATP-sensitive oestrogen binding site that could modulate glucose export.

The 900 tetraloop (positions 898-901) of Escherichia coli 16S rRNA caps helix 27, which is involved in a conformational switch crucial for the decoding function of the ribosome. This tetraloop forms a GNRA motif involved in intramolecular RNA-RNA interactions with its receptor in helix 24 of 16S rRNA. It is involved also in an intersubunit bridge, via an interaction with helix 67 in domain IV of 23S rRNA. Using a specialized ribosome system and an instant-evolution procedure, the four nucleotides of this loop were randomized and 15 functional mutants were selected in vivo. Positions 899 and 900, responsible for most of the tetraloop/receptor interactions, were found to be the most critical for ribosome activity. Functional studies showed that mutations in the 900 tetraloop impair subunit association and decrease translational fidelity. Computer modeling of the mutations allows correlation of the effect of mutations with perturbations of the tetraloop/receptor interactions.

Objective: Monocyte fibrinolytic activity may influence thrombus resolution. The balance between uPA and PAI-2 could determine the fibrinolytic activity of the monocyte. Inhibiting PAI-2 production using specific antisense sequences might alter this balance. Selecting effective sequences is a problem as prediction of the secondary structure of target mRNA is difficult. This study reports the modification of a cell free system for rapid antisense screening., Methods: Five 18-19 mer oligodeoxynucleotides (ODN), sequences A, B, K, T and Q, and their matched scrambled controls were designed and screened using a modified rabbit reticulocyte lysate transcription and translation system (RRL). Intracellular uptake of ODNs was confirmed by fluorescence microscopy, scanning laser confocal microscopy and fluorimetry. Monocytes were transfected with a liposome/ODN complex using sequences A, B, A + B combined, or T and PAI-2 levels measured by ELISA. Inhibition of PAI-2 production was calculated as a percentage of control levels (baseline and scrambled)., Results: (i) RRL System--Sequence A was the most effective inhibitor of PAI-2 production in this system (median 63%) compared with sequences, B median 9%, K median 14%, T median 11% and Q median -8% respectively (n = 3). Sequence A was the only sequence, which always inhibited PAI-2. This was confirmed using fluorescently labelled protein (n = 2). (ii) Monocyte transfection--Fluorescence microscopy and fluorimetry showed that intracellular delivery of labelled antisense was only achieved when a liposome was used. Transfection of monocytes extracted from 5 subjects showed that sequence A significantly reduced PAI-2 production (mean % 41.4, sem 9.1) compared with sequences B (mean% 3.4, sem 8.9, p = 0.04), A + B (mean % 0.4, sem 7.8, p = 0.04), and T (mean % 5.4, sem 4.9, p = 0.01). Further studies using sequence A on cells from 10 subjects showed a significant reduction in monocyte PAI-2 production (27.6 ng/ml, sem 3.9) compared with matched scrambled controls (mean 38.3 ng/ml, sem 4.5, p = 0.0112) and baseline (mean 51.4 ng/ml, sem 6.7, p = 0.0009)., Conclusion: Use of the RRL screening system allowed the selection of a novel antisense sequence, which significantly reduced PAI-2 production in monocytes.