Journal of Clinical Virology最新文献

{"title":"Investigation of suspected false positive norovirus results on a syndromic gastrointestinal multiplex molecular panel","authors":"Mélissa Caza ,&nbsp;Kevin Kuchinski ,&nbsp;Kerstin Locher ,&nbsp;Jonathan Gubbay ,&nbsp;Matisse Harms ,&nbsp;David M. Goldfarb ,&nbsp;Rachel Floyd ,&nbsp;Ethan Kenmuir ,&nbsp;Marzieh Kalhor ,&nbsp;Marthe Charles ,&nbsp;Natalie Prystajecky ,&nbsp;Amanda Wilmer","doi":"10.1016/j.jcv.2024.105732","DOIUrl":"10.1016/j.jcv.2024.105732","url":null,"abstract":"<div><h3>Background</h3><div>Suspected false positive norovirus results occurred after introduction of the BioFire® FilmArray® Gastrointestinal panel (BF-GIP) into 6 laboratory sites, in British Columbia, Canada.</div></div><div><h3>Objectives</h3><div>The primary objective was to investigate suspected false positive results by performing additional molecular assays and whole genome sequencing (WGS). The second objective was to determine if melting curve review could predict false positive results.</div></div><div><h3>Study design</h3><div>From February 2023 to May 2024, the proportion of potential false positive norovirus results from the BF-GIP was calculated based on confirmatory testing using alternate molecular method. A subset of 65 norovirus BF-GIP positive specimens, including 35 negatives and 30 positives on additional molecular assays, underwent WGS. Melting curves appearances from 150 specimens were reviewed.</div></div><div><h3>Results</h3><div>Overall, 215/784 (27.4 %) BF-GIP norovirus results were suspected to be false positives. When using WGS, 64/65 results were in agreement with confirmatory testing. Notably, 35 specimens negative on confirmatory testing and suspected to be BF-GIP norovirus false positive results were undetectable by WGS. Melting curves did not accurately predict false positives, since 20/72 (27.8 %) had typical appearances upon review.</div></div><div><h3>Conclusions</h3><div>BF-GIP produces false positive results for norovirus, which cannot be predicted by melting curve review.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"175 ","pages":"Article 105732"},"PeriodicalIF":4.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380967","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}

{"title":"What have we learned from animal studies of immune responses to respiratory syncytial virus infection?","authors":"Simon B Drysdale ,&nbsp;Ryan S Thwaites ,&nbsp;Josephina Price ,&nbsp;Devika Thakur ,&nbsp;Joseph McGinley ,&nbsp;Calum McPherson ,&nbsp;Deniz Öner ,&nbsp;Jeroen Aerssens ,&nbsp;Peter JM Openshaw ,&nbsp;Andrew J Pollard ,&nbsp;On behalf of the RESCEU investigators","doi":"10.1016/j.jcv.2024.105731","DOIUrl":"10.1016/j.jcv.2024.105731","url":null,"abstract":"<div><div>Respiratory syncytial virus (RSV) is a common cause of severe respiratory tract infection at the extremes of age and in vulnerable populations. However, it is difficult to predict the clinical course and most infants who develop severe disease have no pre-existing risk factors. With the recent licencing of RSV vaccines and monoclonal antibodies, it is important to identify high-risk individuals in order to prioritise those who will most benefit from prophylaxis. The immune response to RSV and the mechanisms by which the virus prevents the establishment of immunological memory have been extensively investigated but remain incompletely characterised. In animal models, beneficial and harmful immune responses have both been demonstrated. While only chimpanzees are fully permissive for human RSV replication, most research has been conducted in rodents, or in calves infected with bovine RSV. Based on these studies, components of innate and adaptive immune systems, cytokines, chemokines and metabolites, and specific genetic and transcriptomic signatures are identified as potential predictive indicators of RSV disease severity. These findings may inform the development of future human studies and contribute to the early identification of patients at high risk of severe infection. This narrative review summarises the factors involved in the immune response to RSV infection in these models and highlights the relationship between potential biomarkers and disease severity.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"175 ","pages":"Article 105731"},"PeriodicalIF":4.0,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142377883","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}

{"title":"Circulating serotypes and genotypes of dengue virus during the 2023 outbreak in Eastern Nepal","authors":"Niten Bharati ,&nbsp;Shyam Prakash Dumre ,&nbsp;Yogendra Shah ,&nbsp;Takeshi Nabesima ,&nbsp;Meghnath Dhimal ,&nbsp;Srijana Pandey ,&nbsp;Merveille Kapandji ,&nbsp;Yuki Takamatsu ,&nbsp;Takeshi Urano ,&nbsp;Basu Dev Pandey ,&nbsp;Kouichi Morita ,&nbsp;Mya Myat Ngwe Tun ,&nbsp;Kishor Pandey","doi":"10.1016/j.jcv.2024.105721","DOIUrl":"10.1016/j.jcv.2024.105721","url":null,"abstract":"<div><p>Dengue virus (DENV) is one of the most significant mosquito-borne diseases in Nepal. In 2023, DENV outbreaks began in Eastern Nepal, near the border with India, and rapidly spread nationwide. The study aims to describe the outbreak's epidemiological pattern, laboratory characteristics, DENV serotypes, and genotypes. A hospital-based cross-sectional study was conducted in four hospitals in Jhapa, Eastern Nepal, in 2023. Acute serum samples were obtained from dengue suspected patients within 7 days of illness and subjected to virus isolation, conventional and real-time polymerase chain reaction (RT-PCR), and phylogenetic analysis. Out of 60 samples, 42 (70 %), 11 (18.3 %) and 7 (11.7 %) were primary, secondary and non-dengue infection, respectively. Among 53 dengue confirmed patients, 46 (86.7 %) were positive for NS1 and 12 (22.6 %) were positive for both NS1 and IgM. Out of 42 dengue isolates, a new clade of the cosmopolitan genotype of DENV-2 was the most prevalent (28, 66.7 %), followed by genotype III of DENV-3 (11, 26.2 %) and genotype V of DENV-1 (3, 7.1 %). Genotype III of DENV-3 was first introduced in 2022–2023 in Nepal. Phylogenetic analysis of the E gene revealed the DENV-2 isolates from Nepal had 98 % homologous nucleotide similarity with the strains from India and Bangladesh. To our knowledge, this is the first report of circulating serotypes and genotypes of DENV in Jhapa. Integrating molecular findings into the dengue control plan can enhance surveillance efforts, monitor disease trends, and implement proactive measures to reduce the burden of dengue and prevent fatalities in future outbreaks.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105721"},"PeriodicalIF":4.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142129268","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}

{"title":"Opportunities and challenges for the U.S. laboratory response to highly pathogenic avian influenza A(H5N1)","authors":"Benjamin A. Pinsky ,&nbsp;Benjamin T. Bradley","doi":"10.1016/j.jcv.2024.105723","DOIUrl":"10.1016/j.jcv.2024.105723","url":null,"abstract":"<div><p>On March 25, 2024 an outbreak of highly pathogenic avian influenza (HPAI) A H5N1 was identified in dairy cows across multiple farms in the United States. Zoonotic cases originating in individuals with close contact to infected herds and poultry flocks have been subsequently identified. Spillover events such as this raise the specter of recent pandemics including COVID-19 and Mpox and may lead clinical laboratories to assess their capacity for diagnosis of HPAI H5N1. In this review, we detail the origins of the H5N1 clade 2.3.4.4b outbreak as well as the existing capacity to identify HPAI H5N1 as influenza A virus by commercially available assays. Furthermore, we highlight the absence of commercially available influenza A H5 subtyping assays and limitations associated with the current 510(k)-cleared assay. This outbreak also serves as an early opportunity to assess the new and unknown regulatory challenges faced by laboratory-developed tests in light of the FDA's final rule on <em>in vitro</em> diagnostic devices. National agencies along with public health and clinical laboratories all serve an essential role in the response to HPAI H5N1. To most effectively utilize each group's strength requires open communication and willingness to embrace novel approaches.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105723"},"PeriodicalIF":4.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142087909","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}

{"title":"Performance evaluation of the quantitative assay Adenovirus ELITe MGB® Kit on EDTA-plasma, using the ELITe BeGenius® system","authors":"Edwin Fries,&nbsp;Tessa Kalmeijer,&nbsp;Lara Spaans,&nbsp;Martin Rakké,&nbsp;Rob Schuurman,&nbsp;Jolanda D F De Groot-Mijnes","doi":"10.1016/j.jcv.2024.105722","DOIUrl":"10.1016/j.jcv.2024.105722","url":null,"abstract":"<div><h3>Background</h3><p>Adenovirus infections constitute an important cause of morbidity and mortality after hematopoietic stem cell transplantation. Detection and monitoring of adenovirus in EDTA-plasma by real-time quantitative PCR is a sensitive tool for identification and management of patients at risk of a potentially fatal infection.</p></div><div><h3>Objectives</h3><p>The aim of this study was to evaluate the analytical and clinical performance of the quantitative Adenovirus ELITe MGB® Kit (ELITechGroup S.p.A.) using the ELITe BeGenius® (ELITechGroup S.p.A.) system and compare the assay to a laboratory-developed quantitative real-time PCR assay.</p></div><div><h3>Study design</h3><p>Analytical sensitivity of the Adenovirus ELITe MGB® Kit was determined by testing serial dilutions of the WHO standard. Detection of adenovirus serotypes was assessed using a panel of 51 serotypes. Clinical sensitivity and specificity were determined by comparing the Adenovirus ELITe MGB® Kit results with the laboratory-developed assay results of 155 retrospective and prospective EDTA-plasma samples from transplant recipients.</p></div><div><h3>Results</h3><p>The analytical sensitivity of the Adenovirus ELITe MGB® Kit was at least 54 (1.7 Log) IU/mL and the quantitative results showed a high correlation with the WHO standard (R² = 0.9978; Pearson) within the range of 1.7 to 6.6 Log IU/mL. All 51 adenovirus serotypes were detected. The clinical specificity and sensitivity for EDTA plasma of the Adenovirus ELITe MGB® Kit were 97.4 % and 99.1 % respectively.</p></div><div><h3>Conclusion</h3><p>The Adenovirus ELITe MGB® Kit performed on the ELITe BeGenius® system is a highly sensitive and specific assay for the detection of adenovirus in EDTA-plasma from transplantation patients.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105722"},"PeriodicalIF":4.0,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000842/pdfft?md5=88fd9eb10ab5d2d1b647b5baa173f74d&pid=1-s2.0-S1386653224000842-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142087910","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}

{"title":"Influenza C virus in U.S. children with acute respiratory infection 2016–2019","authors":"Bethany K. Sederdahl ,&nbsp;Geoffrey A. Weinberg ,&nbsp;Angela P. Campbell ,&nbsp;Rangaraj Selvarangan ,&nbsp;Jennifer E. Schuster ,&nbsp;Joana Y. Lively ,&nbsp;Samantha M. Olson ,&nbsp;Julie A. Boom ,&nbsp;Pedro A. Piedra ,&nbsp;Natasha B. Halasa ,&nbsp;Laura Stewart ,&nbsp;Peter G. Szilagyi ,&nbsp;G.K. Balasubramani ,&nbsp;Theresa Sax ,&nbsp;Judith M. Martin ,&nbsp;Robert W. Hickey ,&nbsp;Marian G. Michaels ,&nbsp;John V. Williams ,&nbsp;New Vaccine Surveillance Network","doi":"10.1016/j.jcv.2024.105720","DOIUrl":"10.1016/j.jcv.2024.105720","url":null,"abstract":"<div><p>Influenza C virus (ICV) is an orthomyxovirus related to influenza A and B, yet due to few commercial assays, epidemiologic studies may underestimate incidence of ICV infection and disease. We describe the epidemiology and characteristics of ICV within the New Vaccine Surveillance Network (NVSN), a Centers for Disease Control and Prevention (CDC)-led network that conducts population-based surveillance for pediatric acute respiratory illness (ARI). Nasal or/combined throat swabs were collected from emergency department (ED) or inpatient ARI cases, or healthy controls, between 12/05/2016–10/31/2019 and tested by molecular assays for ICV and other respiratory viruses. Parent surveys and chart review were used to analyze demographic and clinical characteristics of ICV+ children. Among 19,321 children tested for ICV, 115/17,668 (0.7 %) ARI cases and 8/1653 (0.5 %) healthy controls tested ICV+. Median age of ICV+ patients was 18 months and 88 (71.5 %) were ≤36 months. Among ICV+ ARI patients, 40 % (46/115) were enrolled in the ED, 60 % (69/115) were inpatients, with 15 admitted to intensive care. Most ICV+ ARI patients had fever (67.8 %), cough (94.8 %), or wheezing (60.9 %). Most (60.9 %) ARI cases had ≥1 co-detected viruses including rhinovirus, RSV, and adenovirus. In summary, ICV detection was rarely associated with ARI in children, and most ICV+ patients were ≤3 years old with co-detected respiratory viruses.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105720"},"PeriodicalIF":4.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000829/pdfft?md5=1daa5b3386730e21ae46a680c9eb47af&pid=1-s2.0-S1386653224000829-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978363","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}

{"title":"What the pox? Review of poxviruses affecting humans","authors":"D.Jane Hata ,&nbsp;Eleanor A. Powell ,&nbsp;Meghan W. Starolis ,&nbsp;Susan E. Realegeno","doi":"10.1016/j.jcv.2024.105719","DOIUrl":"10.1016/j.jcv.2024.105719","url":null,"abstract":"<div><p>The re-emergence of human mpox with the multi-country outbreak and a recent report of borealpox (previously Alaskapox) resulting in one death has heightened awareness of the significance of the <em>Poxviridae</em> family and their zoonotic potential. This review examines various poxviruses affecting humans, with discussion of less commonly encountered <em>Poxviridae</em> members, including pathogenesis, epidemiology, and diagnostic methods. Poxvirus treatment is beyond the intended scope of this review and will not be discussed.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105719"},"PeriodicalIF":4.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141985267","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}

{"title":"Corrigendum to A systematic review and meta-analysis of the risk of hepatitis B virus (HBV) resistance in people treated with entecavir or tenofovir.","authors":"Sheila F. Lumley ,&nbsp;Marion Delphin ,&nbsp;Jolynne Mokaya ,&nbsp;Cedric C.S. Tan ,&nbsp;Emily Martyn ,&nbsp;Motswedi Anderson ,&nbsp;Ka Chun Li ,&nbsp;Elizabeth Waddilove ,&nbsp;Gloria Sukali ,&nbsp;Louise O. Downs ,&nbsp;Khadija Said ,&nbsp;Dorcas Okanda ,&nbsp;Cori Campbell ,&nbsp;Eli Harriss ,&nbsp;Yusuke Shimakawa ,&nbsp;Philippa C. Matthews","doi":"10.1016/j.jcv.2024.105716","DOIUrl":"10.1016/j.jcv.2024.105716","url":null,"abstract":"","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105716"},"PeriodicalIF":4.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000787/pdfft?md5=6b4bb575710a50c791994288890ff806&pid=1-s2.0-S1386653224000787-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141784344","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}

{"title":"Genomic evolution of influenza during the 2023–2024 season, the johns hopkins health system","authors":"Madeline Yunker ,&nbsp;David A. Villafuerte ,&nbsp;Amary Fall ,&nbsp;Julie M. Norton ,&nbsp;Omar Abdullah ,&nbsp;Richard E. Rothman ,&nbsp;Katherine Z.J. Fenstermacher ,&nbsp;C.Paul Morris ,&nbsp;Andrew Pekosz ,&nbsp;Eili Klein ,&nbsp;Heba H. Mostafa","doi":"10.1016/j.jcv.2024.105718","DOIUrl":"10.1016/j.jcv.2024.105718","url":null,"abstract":"<div><p>Influenza, a human disease caused by viruses in the Orthomyxoviridae family, is estimated to infect 5% –10 % of adults and 20% –30 % of children annually. Influenza A (IAV) and Influenza B (IBV) viruses accumulate amino acid substitutions (AAS) in the hemagglutinin (HA) and neuraminidase (NA) proteins seasonally. These changes, as well as the dominating viral subtypes, vary depending on geographical location, which may impact disease prevalence and the severity of the season. Genomic surveillance is crucial for capturing circulation patterns and characterizing AAS that may affect disease outcomes, vaccine efficacy, or antiviral drug activities. In this study, whole-genome sequencing of IAV and IBV was attempted on positive remnant clinical samples (587) collected from 580 patients between June 2023 and February 2024 in the Johns Hopkins Health System (JHHS). Full-length HA segments were obtained from 424 (72.2 %) samples. H1N1pdm09 (71.7 %) was the predominant IAV subtype, followed by H3N2 (16.7 %) and IBV-Victoria clade V1A.3a.2 (11.6 %). Within H1N1pdm09 HA sequences, the 6B1A.5a.2a.1 (60.5 %) clade was the most represented. Full-length NA segments were obtained from 421 (71.7 %) samples. Within H1N1pdm09 and IBV, AAS previously proposed to change susceptibility to NA inhibitors were infrequently detected. Phylogeny of HA and NA demonstrated heterogeneous HA and NA H1N1pdm09 and IBV subclades. No significant differences were observed in admission rates or use of supplemental oxygen between different subtypes or clades. Influenza virus genomic surveillance is essential for understanding the seasonal evolution of influenza viruses and their association with disease prevalence and outcomes.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105718"},"PeriodicalIF":4.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000805/pdfft?md5=0e18b1b03770eeb2fe159be7a3766aee&pid=1-s2.0-S1386653224000805-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141850580","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}

{"title":"HIV-1 genotypic resistance testing using single molecule real-time sequencing","authors":"Stéphanie Raymond ,&nbsp;Nicolas Jeanne ,&nbsp;Camille Vellas ,&nbsp;Florence Nicot ,&nbsp;Karine Saune ,&nbsp;Noémie Ranger ,&nbsp;Justine Latour ,&nbsp;Romain Carcenac ,&nbsp;Agnès Harter ,&nbsp;Pierre Delobel ,&nbsp;Jacques Izopet","doi":"10.1016/j.jcv.2024.105717","DOIUrl":"10.1016/j.jcv.2024.105717","url":null,"abstract":"<div><h3>Background</h3><p>HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories.</p></div><div><h3>Objectives</h3><p>To evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping.</p></div><div><h3>Study design</h3><p>111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing. We developed a SMRT sequencing protocol and a bio-informatics pipeline to infer antiretroviral resistance on both haplotype and variant calling approaches.</p></div><div><h3>Results</h3><p>The polymerase was successfully sequenced by the three platforms in 98 % of plasma RNA samples for viral loads above 4 log copies/mL. The success rate decreased to 83 % using Sanger or Vela sequencing and to 67 % using SMRT sequencing for viral loads of 3 to 4 log copies/mL. Sensitivities of 50 %, 54 % and 61 % were obtained using SMRT, Vela, and Sanger sequencing, respectively, in cellular DNA from patients with prolonged undetectable plasma HIV-1 RNA. Ninety-eight percent of resistance-associated mutations (RAMs) identified with Sanger sequencing were detected using SMRT sequencing. Furthermore, 91 % of RAMs (&gt; 5 % threshold) identified with Vela NGS were detected using SMRT sequencing. RAM quantification using Vela and SMRT sequencing was well correlated (Spearman correlation ρ = 0.82; P &lt; 0.0001).</p></div><div><h3>Conclusions</h3><p>SMRT sequencing of the full-length HIV-1 polymerase appeared performant for characterizing HIV-1 genotypic resistance on both RNA and DNA clinical samples. Long-read sequencing is a new tool for mutation haplotyping and resistance analysis.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105717"},"PeriodicalIF":4.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141784345","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}