Pub Date : 2024-02-15DOI: 10.1016/j.jcv.2024.105654
Matthias E. Futschik , Samuel Johnson , Elena Turek , David Chapman , Simon Carr , Zareen Thorlu-Bangura , Paul E. Klapper , Malur Sudhanva , Andrew Dodgson , Joanna R. Cole-Hamilton , Nick Germanacos , Raghavendran Kulasegaran-Shylini , Edward Blandford , Sarah Tunkel , Timothy Peto , Susan Hopkins , Tom Fowler
Background
The advent of lateral flow devices (LFDs) for SARS-CoV-2 detection enabled widespread use of rapid self-tests during the pandemic. While self-testing using LFDs is now common, whether self-testing provides comparable performance to professional testing was a key question that remained important for pandemic planning.
Methods
Three prospective multi-centre studies were conducted to compare the performance of self- and professional testing using LFDs. Participants tested themselves or were tested by trained (professional) testers at community testing sites in the UK. Corresponding qRT-PCR test results served as reference standard. The performance of Innova, Orient Gene and SureScreen LFDs by users (self) and professional testers was assessed in terms of sensitivity, specificity, and kit failure (void) rates. Impact of age, sex and symptom status was analysed using logistic regression modelling.
Results
16,617 participants provided paired tests, of which 15,418 were included in the analysis. Self-testing with Innova, Orient Gene or SureScreen LFDs achieved sensitivities of 50 %, 53 % or 72 %, respectively, compared to qRT-PCR. Self and professional LFD testing showed no statistically different sensitivity with respect to corresponding qRT-PCR testing. Specificity was consistently equal to or higher than 99 %. Sex and age had no or only marginal impact on LFD performance while sensitivity was significantly higher for symptomatic individuals. Sensitivity of LFDs increased strongly to up to 90 % with higher levels of viral RNA measured by qRT-PCR.
Conclusions
Our results support SARS-CoV-2 self-testing with LFDs, especially for the detection of individuals whose qRT-PCR tests showed high viral concentrations.
{"title":"Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites","authors":"Matthias E. Futschik , Samuel Johnson , Elena Turek , David Chapman , Simon Carr , Zareen Thorlu-Bangura , Paul E. Klapper , Malur Sudhanva , Andrew Dodgson , Joanna R. Cole-Hamilton , Nick Germanacos , Raghavendran Kulasegaran-Shylini , Edward Blandford , Sarah Tunkel , Timothy Peto , Susan Hopkins , Tom Fowler","doi":"10.1016/j.jcv.2024.105654","DOIUrl":"10.1016/j.jcv.2024.105654","url":null,"abstract":"<div><h3>Background</h3><p>The advent of lateral flow devices (LFDs) for SARS-CoV-2 detection enabled widespread use of rapid self-tests during the pandemic. While self-testing using LFDs is now common, whether self-testing provides comparable performance to professional testing was a key question that remained important for pandemic planning.</p></div><div><h3>Methods</h3><p>Three prospective multi-centre studies were conducted to compare the performance of self- and professional testing using LFDs. Participants tested themselves or were tested by trained (professional) testers at community testing sites in the UK. Corresponding qRT-PCR test results served as reference standard. The performance of Innova, Orient Gene and SureScreen LFDs by users (self) and professional testers was assessed in terms of sensitivity, specificity, and kit failure (void) rates. Impact of age, sex and symptom status was analysed using logistic regression modelling.</p></div><div><h3>Results</h3><p>16,617 participants provided paired tests, of which 15,418 were included in the analysis. Self-testing with Innova, Orient Gene or SureScreen LFDs achieved sensitivities of 50 %, 53 % or 72 %, respectively, compared to qRT-PCR. Self and professional LFD testing showed no statistically different sensitivity with respect to corresponding qRT-PCR testing. Specificity was consistently equal to or higher than 99 %. Sex and age had no or only marginal impact on LFD performance while sensitivity was significantly higher for symptomatic individuals. Sensitivity of LFDs increased strongly to up to 90 % with higher levels of viral RNA measured by qRT-PCR.</p></div><div><h3>Conclusions</h3><p>Our results support SARS-CoV-2 self-testing with LFDs, especially for the detection of individuals whose qRT-PCR tests showed high viral concentrations.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105654"},"PeriodicalIF":8.8,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000167/pdfft?md5=daa73e614638408a001b9967885ab74a&pid=1-s2.0-S1386653224000167-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139892936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-12DOI: 10.1016/j.jcv.2024.105655
Mikayla Quinton , Duane W. Newton , Becky Neil , Sondra Mitchell , Heba H. Mostafa
Introduction
Quality control (QC) is one component of an overarching quality management system (QMS) that aims at assuring laboratory quality and patient safety. QC data must be acceptable prior to reporting patients’ results. Traditionally, QC statistics, records, and corrective actions were tracked at the Johns Hopkins Molecular Virology Laboratory using Microsoft Excel. Unity Real-Time (UnityRT), a QMS software (Bio-Rad Laboratories), which captures and analyzes QC data by instrument and control lot per assay, was implemented and its impact on the workflow was evaluated. The clinical utility of real-time QC monitoring using UnityRT is highlighted with a case of subtle QC trending of HIV-1 quantitative control results.
Methods
A comprehensive workflow analysis was performed, with a focus on Epstein Barr Virus (EBV) and BKV quantitative viral load testing (Roche cobas 6800). The number of QC steps and time to complete each step were assessed before and after implementing UnityRT.
Results
Our assessment of monthly QC data review revealed a total of 10 steps over 57 min when using Microsoft Excel, versus 6 steps over 11 min when using UnityRT. HIV-1 QC monitoring revealed subtle trending of the low positive control above the mean from November to December 2022, correlating with a change in the reagent kit lot. This associated with a shift in patients’ results from positives below the lower limit of quantification to positives between 20 and 100 copies/mL.
Conclusions
UnityRT consolidated QC analyses, monitoring, and tracking corrective actions. UnityRT was associated with significant time savings, which along with the interfaced feature of the QC capture and data analysis, have improved the workflow and reduced the risk of laboratory errors. The HIV-1 case revealed the value of the real-time monitoring of QC.
{"title":"Quality control data management with unity real-time in molecular virology","authors":"Mikayla Quinton , Duane W. Newton , Becky Neil , Sondra Mitchell , Heba H. Mostafa","doi":"10.1016/j.jcv.2024.105655","DOIUrl":"https://doi.org/10.1016/j.jcv.2024.105655","url":null,"abstract":"<div><h3>Introduction</h3><p>Quality control (QC) is one component of an overarching quality management system (QMS) that aims at assuring laboratory quality and patient safety. QC data must be acceptable prior to reporting patients’ results. Traditionally, QC statistics, records, and corrective actions were tracked at the Johns Hopkins Molecular Virology Laboratory using Microsoft Excel. Unity Real-Time (UnityRT), a QMS software (Bio-Rad Laboratories), which captures and analyzes QC data by instrument and control lot per assay, was implemented and its impact on the workflow was evaluated. The clinical utility of real-time QC monitoring using UnityRT is highlighted with a case of subtle QC trending of HIV-1 quantitative control results.</p></div><div><h3>Methods</h3><p>A comprehensive workflow analysis was performed, with a focus on Epstein Barr Virus (EBV) and BKV quantitative viral load testing (Roche cobas 6800). The number of QC steps and time to complete each step were assessed before and after implementing UnityRT.</p></div><div><h3>Results</h3><p>Our assessment of monthly QC data review revealed a total of 10 steps over 57 min when using Microsoft Excel, versus 6 steps over 11 min when using UnityRT. HIV-1 QC monitoring revealed subtle trending of the low positive control above the mean from November to December 2022, correlating with a change in the reagent kit lot. This associated with a shift in patients’ results from positives below the lower limit of quantification to positives between 20 and 100 copies/mL.</p></div><div><h3>Conclusions</h3><p>UnityRT consolidated QC analyses, monitoring, and tracking corrective actions. UnityRT was associated with significant time savings, which along with the interfaced feature of the QC capture and data analysis, have improved the workflow and reduced the risk of laboratory errors. The HIV-1 case revealed the value of the real-time monitoring of QC.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105655"},"PeriodicalIF":8.8,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000179/pdfft?md5=9735fc96bfffc3d03b339cd08608d485&pid=1-s2.0-S1386653224000179-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139749129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-12DOI: 10.1016/j.jcv.2024.105652
Eeva Auvinen , Anni Honkimaa , Pia Laine , Sara Passerini , Ugo Moens , Valeria Pietropaolo , Mika Saarela , Leena Maunula , Laura Mannonen , Olli Tynninen , Hannu Haapasalo , Tuomas Rauramaa , Petri Auvinen , Hanna Liimatainen
Background
JC polyomavirus (JCPyV) persists asymptomatic in more than half of the human population. Immunocompromising conditions may cause reactivation and acquisition of neurotropic rearrangements in the viral genome, especially in the non-coding control region (NCCR). Such rearranged JCPyV strains are strongly associated with the development of progressive multifocal leukoencephalopathy (PML).
Methods
Using next-generation sequencing (NGS) and bioinformatics tools, the NCCR was characterized in cerebrospinal fluid (CSF; N = 21) and brain tissue (N = 16) samples from PML patients (N = 25), urine specimens from systemic lupus erythematosus patients (N = 2), brain tissue samples from control individuals (N = 2) and waste-water samples (N = 5). Quantitative PCR was run in parallel for diagnostic PML samples.
Results
Archetype NCCR (i.e. ABCDEF block structure) and archetype-like NCCR harboring minor mutations were detected in two CSF samples and in one CSF sample and in one tissue sample, respectively. Among samples from PML patients, rearranged NCCRs were found in 8 out of 21 CSF samples and in 14 out of 16 brain tissue samples. Complete or partial deletion of the C and D blocks was characteristic of most rearranged JCPyV strains. From ten CSF samples and one tissue sample NCCR could not be amplified.
Conclusions
Rearranged NCCRs are predominant in brain tissue and common in CSF from PML patients. Extremely sensitive detection and identification of neurotropic viral populations in CSF or brain tissue by NGS may contribute to early and accurate diagnosis, timely intervention and improved patient care.
{"title":"Differentiation of highly pathogenic strains of human JC polyomavirus in neurological patients by next generation sequencing","authors":"Eeva Auvinen , Anni Honkimaa , Pia Laine , Sara Passerini , Ugo Moens , Valeria Pietropaolo , Mika Saarela , Leena Maunula , Laura Mannonen , Olli Tynninen , Hannu Haapasalo , Tuomas Rauramaa , Petri Auvinen , Hanna Liimatainen","doi":"10.1016/j.jcv.2024.105652","DOIUrl":"https://doi.org/10.1016/j.jcv.2024.105652","url":null,"abstract":"<div><h3>Background</h3><p>JC polyomavirus (JCPyV) persists asymptomatic in more than half of the human population. Immunocompromising conditions may cause reactivation and acquisition of neurotropic rearrangements in the viral genome, especially in the non-coding control region (NCCR). Such rearranged JCPyV strains are strongly associated with the development of progressive multifocal leukoencephalopathy (PML).</p></div><div><h3>Methods</h3><p>Using next-generation sequencing (NGS) and bioinformatics tools, the NCCR was characterized in cerebrospinal fluid (CSF; <em>N</em> = 21) and brain tissue (<em>N</em> = 16) samples from PML patients (<em>N</em> = 25), urine specimens from systemic lupus erythematosus patients (<em>N</em> = 2), brain tissue samples from control individuals (<em>N</em> = 2) and waste-water samples (<em>N</em> = 5). Quantitative PCR was run in parallel for diagnostic PML samples.</p></div><div><h3>Results</h3><p>Archetype NCCR (i.e. ABCDEF block structure) and archetype-like NCCR harboring minor mutations were detected in two CSF samples and in one CSF sample and in one tissue sample, respectively. Among samples from PML patients, rearranged NCCRs were found in 8 out of 21 CSF samples and in 14 out of 16 brain tissue samples. Complete or partial deletion of the C and D blocks was characteristic of most rearranged JCPyV strains. From ten CSF samples and one tissue sample NCCR could not be amplified.</p></div><div><h3>Conclusions</h3><p>Rearranged NCCRs are predominant in brain tissue and common in CSF from PML patients. Extremely sensitive detection and identification of neurotropic viral populations in CSF or brain tissue by NGS may contribute to early and accurate diagnosis, timely intervention and improved patient care.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105652"},"PeriodicalIF":8.8,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000143/pdfft?md5=4112f0302908005c9489e4d6d497a50c&pid=1-s2.0-S1386653224000143-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139737735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-12DOI: 10.1016/j.jcv.2024.105653
Pedro Pisa , Constance Wose Kinge , Charles Chasela , Eula Mothibi , Yin Min Thaung , Hnin T. Thwin , Nay M. Aung , Kara W. Chew , Malini M. Gandhi , Cavenaugh Clint , Thomas Minior , Aye A. Lwin , Morgan J. Freiman , Khin P. Kyi , Yi Y. Sein , Fadzai Marange , Charles van der Horst , Sofiane Mohamed , Matthieu Barralon , Ian Sanne
Background
Developing countries experience limited access to HCV laboratory tests for different reasons. Providing near to real–time HCV testing and results especially to at–risk populations including those in rural settings for timely initiation to treatment is key. Within a rural Myanmar setting, we compared HCV diagnostic detection and quantification of the GeneXpert, and Advanced Biological Laboratories UltraGene–HCV assays against the gold standard and reference method Roche real–time HCV in Myanmar.
Methods
Blood samples from 158 high–risk individuals were assessed using three different methods at baseline. Results were checked for normality and log transformed. Log differences and bias between methods were calculated and correlated. Pearson's correlation coefficient was used to determine the association of HCV viral loads across all methods. The level of agreement with the standard method (Roche real time HCV) was assessed using Bland–Altman analyses.
Results
There was a strong positive correlation coefficient between all three methods with GeneXpert and Roche having the strongest, r = 0.96, (p<0.001). Compared to Roche, ABL (mean difference, 95 % limits of agreement; -0.063 and -1.4 to 1.3 Log10IU/mL) and GeneXpert (mean difference, 95 % limits of agreement; -0.28 and -0.7 to 1.8 Log10IU/mL) showed a good level of agreement with the GeneXpert being slightly superior.
Conclusion
We demonstrate the excellent performance and no-inferiority, in terms of levels of agreements of both GeneXpert and ABL compared to the Roche platform and supporting the use of the POC assays as alternative a cost-effective methods in HCV detection and diagnosis in developing and low resource settings countries.
{"title":"Evaluation of GeneXpert and advanced biological laboratories UltraGene HCV diagnostic detection and performance against Roche real time PCR in Myanmar","authors":"Pedro Pisa , Constance Wose Kinge , Charles Chasela , Eula Mothibi , Yin Min Thaung , Hnin T. Thwin , Nay M. Aung , Kara W. Chew , Malini M. Gandhi , Cavenaugh Clint , Thomas Minior , Aye A. Lwin , Morgan J. Freiman , Khin P. Kyi , Yi Y. Sein , Fadzai Marange , Charles van der Horst , Sofiane Mohamed , Matthieu Barralon , Ian Sanne","doi":"10.1016/j.jcv.2024.105653","DOIUrl":"10.1016/j.jcv.2024.105653","url":null,"abstract":"<div><h3>Background</h3><p>Developing countries experience limited access to HCV laboratory tests for different reasons. Providing near to real–time HCV testing and results especially to at–risk populations including those in rural settings for timely initiation to treatment is key. Within a rural Myanmar setting, we compared HCV diagnostic detection and quantification of the GeneXpert, and Advanced Biological Laboratories UltraGene–HCV assays against the gold standard and reference method Roche real–time HCV in Myanmar.</p></div><div><h3>Methods</h3><p>Blood samples from 158 high–risk individuals were assessed using three different methods at baseline. Results were checked for normality and log transformed. Log differences and bias between methods were calculated and correlated. Pearson's correlation coefficient was used to determine the association of HCV viral loads across all methods. The level of agreement with the standard method (Roche real time HCV) was assessed using Bland–Altman analyses.</p></div><div><h3>Results</h3><p>There was a strong positive correlation coefficient between all three methods with GeneXpert and Roche having the strongest, <em>r</em> = 0.96, (<em>p</em><0.001). Compared to Roche, ABL (mean difference, 95 % limits of agreement; -0.063 and -1.4 to 1.3 Log10IU/mL) and GeneXpert (mean difference, 95 % limits of agreement; -0.28 and -0.7 to 1.8 Log10IU/mL) showed a good level of agreement with the GeneXpert being slightly superior.</p></div><div><h3>Conclusion</h3><p>We demonstrate the excellent performance and no-inferiority, in terms of levels of agreements of both GeneXpert and ABL compared to the Roche platform and supporting the use of the POC assays as alternative a cost-effective methods in HCV detection and diagnosis in developing and low resource settings countries.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105653"},"PeriodicalIF":8.8,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000155/pdfft?md5=09f425e484bdfe4e15922e598f5c3960&pid=1-s2.0-S1386653224000155-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139819700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1016/j.jcv.2024.105651
Raquel Fernández-Moreno , Aurora Páez-Vega , Diego Rodríguez-Cano , Ana Salinas , Fernando Rodríguez-Cantalejo , Aurora Jurado , Julián Torre-Cisneros , Sara Cantisán
Background
The QuantiFERONCMV (QF-CMV) assay is an interferon-gamma release assay (IGRA) used to monitor CMV-specific cell-mediated immunity (CMV-CMI) by ELISA in transplant patients. However, a chemiluminescent immunoassay (CLIA) has been developed to quantify IFNG in the QuantiFERON-Tuberculosis (TB) to detect latent TB infection.
Objectives
The aim of this work is to compare the results of QF-CMV by ELISA with those obtained by CLIA in an automated Liaison XL analyzer using the QuantiFERON-TB Gold Plus reagents.
Study Design
The QF-CMV assay had been performed by ELISA in kidney and lung transplant patients between July 2019-April 2023 at the IMIBIC/Reina Sofía Hospital (Cordoba, Spain). The remaining QF-CMV supernatants had been preserved at -80 ºC from then. Now, the IFNG levels in the same samples were determined by CLIA.
Results
One hundred and three QF-CMV supernatants from kidney (n = 50) and lung (n = 53) transplant patients were selected. An agreement of 87.4 % (kappa coefficient 0.788) between CLIA and ELISA was observed. Thirteen (12.6 %) discrepant results were detected. Some Indeterminate results by ELISA converted to Non-reactive by CLIA (0.53–0.92 IU/mL for Mitogen-Nil values). Likewise, borderline Non-reactive results by ELISA were above the 0.2 IU/mL cut-off by CLIA and then were Reactive (0.21–0.31 for CMV-Nil values).
Conclusion
CLIA shows substantial concordance with ELISA and acceptable discrepancies. The possible higher sensitivity of CLIA returns a higher number of Reactive results, which entails potential clinical consequences. Therefore, a new threshold to confer protection against CMV infection after transplantation needs to be defined.
{"title":"QuantiFERON–CMV assay by chemiluminescence immunoassay: Is it more suitable for real-live monitoring of transplant patients?","authors":"Raquel Fernández-Moreno , Aurora Páez-Vega , Diego Rodríguez-Cano , Ana Salinas , Fernando Rodríguez-Cantalejo , Aurora Jurado , Julián Torre-Cisneros , Sara Cantisán","doi":"10.1016/j.jcv.2024.105651","DOIUrl":"https://doi.org/10.1016/j.jcv.2024.105651","url":null,"abstract":"<div><h3>Background</h3><p>The QuantiFERON<img>CMV (QF-CMV) assay is an interferon-gamma release assay (IGRA) used to monitor CMV-specific cell-mediated immunity (CMV-CMI) by ELISA in transplant patients. However, a chemiluminescent immunoassay (CLIA) has been developed to quantify IFNG in the QuantiFERON-Tuberculosis (TB) to detect latent TB infection.</p></div><div><h3>Objectives</h3><p>The aim of this work is to compare the results of QF-CMV by ELISA with those obtained by CLIA in an automated Liaison XL analyzer using the QuantiFERON-TB Gold Plus reagents.</p></div><div><h3>Study Design</h3><p>The QF-CMV assay had been performed by ELISA in kidney and lung transplant patients between July 2019-April 2023 at the IMIBIC/Reina Sofía Hospital (Cordoba, Spain). The remaining QF-CMV supernatants had been preserved at -80 ºC from then. Now, the IFNG levels in the same samples were determined by CLIA.</p></div><div><h3>Results</h3><p>One hundred and three QF-CMV supernatants from kidney (<em>n</em> = 50) and lung (<em>n</em> = 53) transplant patients were selected. An agreement of 87.4 % (kappa coefficient 0.788) between CLIA and ELISA was observed. Thirteen (12.6 %) discrepant results were detected. Some Indeterminate results by ELISA converted to Non-reactive by CLIA (0.53–0.92 IU/mL for Mitogen-Nil values). Likewise, borderline Non-reactive results by ELISA were above the 0.2 IU/mL cut-off by CLIA and then were Reactive (0.21–0.31 for CMV-Nil values).</p></div><div><h3>Conclusion</h3><p>CLIA shows substantial concordance with ELISA and acceptable discrepancies. The possible higher sensitivity of CLIA returns a higher number of Reactive results, which entails potential clinical consequences. Therefore, a new threshold to confer protection against CMV infection after transplantation needs to be defined.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105651"},"PeriodicalIF":8.8,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139718601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hepatitis Delta virus (HDV) infection is a major cause of liver-related morbidity and mortality in patients infected with HBV, with a global HDV prevalence uncertain. In France, 2 to 5 % of HBs antigen (HBsAg) carriers present anti-HDV antibodies (anti-HDV). The EASL recommends testing for anti-HDV in all HBsAg-positive patients. Since January 2022, we have systematically carried out anti-HDV serology when a positive HBsAg is discovered (new HBsAg carriers).
Objectives
We evaluated the benefit of anti-HDV reflex testing after one year of practice by comparing anti-HDV and HBsAg serology data over the last six years, among the new HBsAg carriers and all the HBsAg carriers.
Study design
HBsAg and anti-HDV were screened using the Abbott Architect HBsAg quanti kit and the DIA.PRO HDVAb kit. Serological, demographic, virological, and clinical data were analyzed.
Results
Implementing anti-HDV reflex testing leads to more than a 2-fold increase in diagnoses of HDV infection among all HBsAg carriers. If the anti-HDV positive rate remains stable among the new HBsAg carriers, a significant increase in the anti-HDV positive rate from 6.8 % to 10.3 % was observed considering all HBsAg carriers. Interestingly, the discovery of anti-HDV carriage increased from 3.9 % to 6.5 % in 2022, allowing earlier identification of HBV-HDV-infected patients and a fast referral to hepatologists for adequate clinical management and, in some cases, the introduction of bulevirtide-based therapy.
Conclusions
Our preliminary results at one year seem promising and evaluating the cost-effectiveness of reflex tests in real life with feedback would be helpful.
{"title":"Impact of anti-HDV reflex testing at HBs antigen positive discovery in a single center France: Support for primary HDV screening in France","authors":"Assilina Parfut , Simona Tripon , Pierre Gantner , Fréderic Chaffraix , Elodie Laugel , Marie-Josée Wendling , Furkan Erol , Carine Wiedemer , Michel Doffoel , Antonio Saviano , Maude Royant , François Habersetzer , Samira Fafi-Kremer , Aurélie Velay","doi":"10.1016/j.jcv.2024.105650","DOIUrl":"10.1016/j.jcv.2024.105650","url":null,"abstract":"<div><h3>Background</h3><p>Hepatitis Delta virus (HDV) infection is a major cause of liver-related morbidity and mortality in patients infected with HBV, with a global HDV prevalence uncertain. In France, 2 to 5 % of HBs antigen (HBsAg) carriers present anti-HDV antibodies (anti-HDV). The EASL recommends testing for anti-HDV in all HBsAg-positive patients. Since January 2022, we have systematically carried out anti-HDV serology when a positive HBsAg is discovered (new HBsAg carriers).</p></div><div><h3>Objectives</h3><p>We evaluated the benefit of anti-HDV reflex testing after one year of practice by comparing anti-HDV and HBsAg serology data over the last six years, among the new HBsAg carriers and all the HBsAg carriers.</p></div><div><h3>Study design</h3><p>HBsAg and anti-HDV were screened using the Abbott Architect HBsAg quanti kit and the DIA.PRO HDVAb kit. Serological, demographic, virological, and clinical data were analyzed.</p></div><div><h3>Results</h3><p>Implementing anti-HDV reflex testing leads to more than a 2-fold increase in diagnoses of HDV infection among all HBsAg carriers. If the anti-HDV positive rate remains stable among the new HBsAg carriers, a significant increase in the anti-HDV positive rate from 6.8 % to 10.3 % was observed considering all HBsAg carriers. Interestingly, the discovery of anti-HDV carriage increased from 3.9 % to 6.5 % in 2022, allowing earlier identification of HBV-HDV-infected patients and a fast referral to hepatologists for adequate clinical management and, in some cases, the introduction of bulevirtide-based therapy.</p></div><div><h3>Conclusions</h3><p>Our preliminary results at one year seem promising and evaluating the cost-effectiveness of reflex tests in real life with feedback would be helpful.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105650"},"PeriodicalIF":8.8,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139677435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-01DOI: 10.1016/j.jcv.2024.105649
D.A.M. Heideman , J. Berkhof , L. Verhoef , C. Ouwerkerk , P.W Smit , A. Oštrbenk Valenčak , J. Mlakar , M. Poljak , R.D.M. Steenbergen , M.C.G. Bleeker
Background
Human papillomavirus (HPV) testing on self-samples is a valid tool for cervical cancer screening. HPV self-sample workflows need to be clinically validated to ensure safe use in screening.
Objective
This study evaluated the fully automated NeuMoDx HPV Assay self-sample workflow that is compiled of the NeuMoDx HPV assay and the NeuMoDx 96/288 Molecular Systems, for clinical performance and reproducibility on Evalyn Brush-collected self-samples.
Methods
The clinical performance of the NeuMoDx HPV Assay self-sample workflow for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and CIN3+ was evaluated on 987 self-samples obtained from women attending national organized HPV-based cervical cancer screening by a noninferiority analysis relative to reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR. Intra- and inter-laboratory reproducibility of the NeuMoDx HPV Assay self-sample workflow using both NeuMoDx 96 and 288 Molecular Systems was assessed on 520 self-samples in three laboratories.
Results
The clinical sensitivity and specificity of the NeuMoDx HPV Assay self-sample workflow for the detection of CIN2+ and CIN3+ were found to be non-inferior to the reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR, with all p-values <0.034. The NeuMoDx HPV Assay self-sample workflow exhibited an intra-laboratory reproducibility of 94.4 % (95 %CI:92.5–96.1 %) with kappa value 0.86 (95 %CI:0.81–0.91). Inter-laboratory agreement was high (all ≥93.4 % and all kappa values ≥0.83).
Conclusions
The NeuMoDx HPV Assay self-sample workflow demonstrated high clinical accuracy for CIN2+/3+ and high reproducibility. The NeuMoDx HPV Assay self-sample workflow can be considered suitable for cervical cancer screening purposes.
{"title":"Validation of the clinical performance and reproducibility of the NeuMoDx HPV assay self-sample workflow","authors":"D.A.M. Heideman , J. Berkhof , L. Verhoef , C. Ouwerkerk , P.W Smit , A. Oštrbenk Valenčak , J. Mlakar , M. Poljak , R.D.M. Steenbergen , M.C.G. Bleeker","doi":"10.1016/j.jcv.2024.105649","DOIUrl":"10.1016/j.jcv.2024.105649","url":null,"abstract":"<div><h3>Background</h3><p>Human papillomavirus (HPV) testing on self-samples is a valid tool for cervical cancer screening. HPV self-sample workflows need to be clinically validated to ensure safe use in screening.</p></div><div><h3>Objective</h3><p>This study evaluated the fully automated NeuMoDx HPV Assay self-sample workflow that is compiled of the NeuMoDx HPV assay and the NeuMoDx 96/288 Molecular Systems, for clinical performance and reproducibility on Evalyn Brush-collected self-samples.</p></div><div><h3>Methods</h3><p>The clinical performance of the NeuMoDx HPV Assay self-sample workflow for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and CIN3+ was evaluated on 987 self-samples obtained from women attending national organized HPV-based cervical cancer screening by a noninferiority analysis relative to reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR. Intra- and inter-laboratory reproducibility of the NeuMoDx HPV Assay self-sample workflow using both NeuMoDx 96 and 288 Molecular Systems was assessed on 520 self-samples in three laboratories.</p></div><div><h3>Results</h3><p>The clinical sensitivity and specificity of the NeuMoDx HPV Assay self-sample workflow for the detection of CIN2+ and CIN3+ were found to be non-inferior to the reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR, with all p-values <0.034. The NeuMoDx HPV Assay self-sample workflow exhibited an intra-laboratory reproducibility of 94.4 % (95 %CI:92.5–96.1 %) with kappa value 0.86 (95 %CI:0.81–0.91). Inter-laboratory agreement was high (all ≥93.4 % and all kappa values ≥0.83).</p></div><div><h3>Conclusions</h3><p>The NeuMoDx HPV Assay self-sample workflow demonstrated high clinical accuracy for CIN2+/3+ and high reproducibility. The NeuMoDx HPV Assay self-sample workflow can be considered suitable for cervical cancer screening purposes.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105649"},"PeriodicalIF":8.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000118/pdfft?md5=9d80c7da473343ba9efee10cb9790b11&pid=1-s2.0-S1386653224000118-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139677365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-22DOI: 10.1016/j.jcv.2024.105648
Or Kriger , Sarah Dovrat , Ilana S. Fratty , Eyal Leshem , Michal Tepperberg Oikawa , Danit Sofer , Sharon Amit
Background
Varicella zoster virus (VZV) is among the leading pathogens causing meningitis and encephalitis. While VZV-PCR-positive CSF is considered a gold-standard for diagnosis, it is not-uncommon to detect VZV-DNA in CSF of patients with other acute or chronic illness. Our goal was to determine the clinical relevance of VZV-PCR-positive CSF when investigating patients with neurological symptoms.
Methods
In this retrospective cohort from the largest hospital in Israel, we collected demographic, clinical and laboratory data of patients with VZV-PCR-positive CSF, analyzing the significance of various parameters.
Results
During a 5-years study, 125 patient-unique VZV-PCR-positive CSFs were recorded, in which only 9 alternative diagnoses were noted. The commonest symptoms were headache (N = 104, 83 %) and rash (N = 96, 76 %). PCR-cycle-threshold (Ct), a surrogate of viral burden, did not significantly vary across the clinical manifestations; however, patients with rash and Ct<35 were prone to develop stroke in the following year (N = 6, 7 %). Empiric nucleoside-analogue treatment was not associated with a better outcome compared to treatment administered upon a positive-PCR result.
Discussion
Our findings suggest that in patients with neurological symptoms, detection of VZV-DNA in CSF renders VZV the probable culprit. Nevertheless, a systematic evaluation of treatment and follow-up algorithms of patients with suspected or proved VZV meningitis and encephalitis is needed. The benefits of a prompt treatment should be weighed against the potential complications of nucleoside-analogue. Conversely, the propensity for stroke in patients with higher viral-burden, necessitates further studies assessing VZV causal role, directing additional workup, treatment and monitoring policy.
{"title":"Don't rash it! The clinical significance of positive Varicella zoster virus PCR in cerebrospinal fluid of patients with neurological symptoms","authors":"Or Kriger , Sarah Dovrat , Ilana S. Fratty , Eyal Leshem , Michal Tepperberg Oikawa , Danit Sofer , Sharon Amit","doi":"10.1016/j.jcv.2024.105648","DOIUrl":"10.1016/j.jcv.2024.105648","url":null,"abstract":"<div><h3>Background</h3><p>Varicella zoster virus (VZV) is among the leading pathogens causing meningitis and encephalitis. While VZV-PCR-positive CSF is considered a gold-standard for diagnosis, it is not-uncommon to detect VZV-DNA in CSF of patients with other acute or chronic illness. Our goal was to determine the clinical relevance of VZV-PCR-positive CSF when investigating patients with neurological symptoms.</p></div><div><h3>Methods</h3><p>In this retrospective cohort from the largest hospital in Israel, we collected demographic, clinical and laboratory data of patients with VZV-PCR-positive CSF, analyzing the significance of various parameters.</p></div><div><h3>Results</h3><p>During a 5-years study, 125 patient-unique VZV-PCR-positive CSFs were recorded, in which only 9 alternative diagnoses were noted. The commonest symptoms were headache (<em>N</em> = 104, 83 %) and rash (<em>N</em> = 96, 76 %). PCR-cycle-threshold (Ct), a surrogate of viral burden, did not significantly vary across the clinical manifestations; however, patients with rash and Ct<35 were prone to develop stroke in the following year (<em>N</em> = 6, 7 %). Empiric nucleoside-analogue treatment was not associated with a better outcome compared to treatment administered upon a positive-PCR result.</p></div><div><h3>Discussion</h3><p>Our findings suggest that in patients with neurological symptoms, detection of VZV-DNA in CSF renders VZV the probable culprit. Nevertheless, a systematic evaluation of treatment and follow-up algorithms of patients with suspected or proved VZV meningitis and encephalitis is needed. The benefits of a prompt treatment should be weighed against the potential complications of nucleoside-analogue. Conversely, the propensity for stroke in patients with higher viral-burden, necessitates further studies assessing VZV causal role, directing additional workup, treatment and monitoring policy.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105648"},"PeriodicalIF":8.8,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-11DOI: 10.1016/j.jcv.2024.105640
Emma Ann Davies , Laura Dutton , Malcolm Guiver
Background: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples.
Methods: Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices.
Results: Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species.
Conclusion: Overall performance of this modified SureSelectXT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.
背景:人类腺病毒是一种常见的致病病毒,可导致免疫力低下的患者严重发病和死亡。全基因组测序在其中发挥着至关重要的作用。本研究评估了基于 14 个腺病毒基因组定制设计的 SureSelectXT 目标富集测定的性能,该测定可直接对临床样本进行测序:方法: 对 SureSelectXT 低输入方案进行了修改,以提高病毒靶标的性能。使用内部设计的三阶段生物信息学管道生成共识序列。我们评估了目标读数百分比、平均覆盖深度和基因组覆盖百分比,以确定一系列样本基质的检测性能:结果:91.6%的评估样本成功生成了全基因组序列。腺病毒 DNA 浓度是富集成功与否的良好指标。只有 6% 的样本显示出 50%的目标读数,可见高度特异性富集。呼吸道样本和粪便样本表现良好,而血液样本的非特异性富集程度较高,这可能与腺病毒 DNA 浓度较低有关。该方案的性能似乎不受腺病毒类型或种类的影响:结论:尽管存在一些需要进一步研究的干扰因素,但改进后的 SureSelectXT 方案的总体性能与之前发表的论文一致。使用小型 RNA 诱饵集有可能降低相关成本,而这些成本可能会让人望而却步。
{"title":"Evaluation of a custom designed hybridisation assay for whole genome sequencing of human adenoviruses direct from clinical samples","authors":"Emma Ann Davies , Laura Dutton , Malcolm Guiver","doi":"10.1016/j.jcv.2024.105640","DOIUrl":"10.1016/j.jcv.2024.105640","url":null,"abstract":"<div><p><strong>Background:</strong> Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelect<sup>XT</sup> target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples.</p><p><strong>Methods:</strong> Modifications were made to the SureSelect<sup>XT</sup> low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices.</p><p><strong>Results:</strong> Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species.</p><p><strong>Conclusion:</strong> Overall performance of this modified SureSelect<sup>XT</sup> protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105640"},"PeriodicalIF":8.8,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139421390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-09DOI: 10.1016/j.jcv.2024.105639
Sung Yong Park , Gina Faraci , Kevin Ganesh , Michael P. Dubé , Ha Youn Lee
Background
Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care.
Methods
We developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals).
Results
A total of 472 HIV consensus sequences, each tagged with a unique molecular identifier, were produced from over 1.4 million bases acquired through portable Nanopore sequencing, which matched those obtained independently via Pacbio sequencing. With this desirable accuracy, we first documented the linkage of multidrug cross-resistance mutations across Integrase Strand Transfer inhibitors (INSTIs) and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from an individual failing a second-generation INSTI regimen. By producing more than 500 full-length HIV pol gene sequences in a single portable sequencing run, we detected Protease Inhibitor (PI), Nucleoside Reverse Transcriptase Inhibitor (NRTI), NNRTI and INSTI resistance mutations. All drug resistance mutations identified through portable sequencing were cross-validated using fixed-site Pacbio sequencing.
Conclusions
Our accurate and affordable HIV drug resistance testing solution is adaptable for both individual patient care and large-scale surveillance initiatives.
背景应对 HIV 耐药性是结束艾滋病流行的主要挑战之一,但尖端基因组学的高昂费用阻碍了临床护理中 HIV 基因型检测的发展。通过与固定点 Pacbio 测序获得的平行数据进行比较,验证了准确性。我们将完整的多基因测序策略与便携式高通量测序技术相结合,对来自接受抗逆转录病毒疗法治疗的洛杉矶综合医疗中心兰德-施拉德诊所(LARSC)队列(7 人 7 份样本)和接受抗逆转录病毒疗法治疗的艾滋病疫苗免疫学中心(CHAVI)队列(38 人 51 份样本)的 58 份样本进行耐药性突变鉴定。结果 通过便携式 Nanopore 测序技术获得的 140 多万个碱基序列中,共产生了 472 个 HIV 共识序列,每个序列都标有唯一的分子标识符,这些序列与通过 Pacbio 测序技术独立获得的序列相匹配。有了这种理想的准确性,我们首次记录了在第二代 INSTI 方案失败的个体中,整合酶链转移抑制剂(INSTIs)和非核苷逆转录酶抑制剂(NNRTIs)之间的多药交叉耐药性突变联系。通过在一次便携式测序中生成 500 多个全长 HIV pol 基因序列,我们检测到了蛋白酶抑制剂 (PI)、核苷类逆转录酶抑制剂 (NRTI)、NNRTI 和 INSTI 的耐药性突变。通过便携式测序发现的所有耐药性突变都经过了固定点 Pacbio 测序的交叉验证。
{"title":"Portable Nanopore sequencing solution for next-generation HIV drug resistance testing","authors":"Sung Yong Park , Gina Faraci , Kevin Ganesh , Michael P. Dubé , Ha Youn Lee","doi":"10.1016/j.jcv.2024.105639","DOIUrl":"10.1016/j.jcv.2024.105639","url":null,"abstract":"<div><h3>Background</h3><p>Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care.</p></div><div><h3>Methods</h3><p>We developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals).</p></div><div><h3>Results</h3><p>A total of 472 HIV consensus sequences, each tagged with a unique molecular identifier, were produced from over 1.4 million bases acquired through portable Nanopore sequencing, which matched those obtained independently via Pacbio sequencing. With this desirable accuracy, we first documented the linkage of multidrug cross-resistance mutations across Integrase Strand Transfer inhibitors (INSTIs) and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from an individual failing a second-generation INSTI regimen. By producing more than 500 full-length HIV pol gene sequences in a single portable sequencing run, we detected Protease Inhibitor (PI), Nucleoside Reverse Transcriptase Inhibitor (NRTI), NNRTI and INSTI resistance mutations. All drug resistance mutations identified through portable sequencing were cross-validated using fixed-site Pacbio sequencing.</p></div><div><h3>Conclusions</h3><p>Our accurate and affordable HIV drug resistance testing solution is adaptable for both individual patient care and large-scale surveillance initiatives.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"171 ","pages":"Article 105639"},"PeriodicalIF":8.8,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139410355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}