Journal of Clinical Virology最新文献

{"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}

{"title":"Characterising the molecular epidemiology of human parechovirus in young infants in the UK and Canada","authors":"Seilesh Kadambari ,&nbsp;Heli Harvala ,&nbsp;Dung Nguyen ,&nbsp;Manish Sadarangani ,&nbsp;Natalie G Martin ,&nbsp;Ghada N. Al-Rawahi ,&nbsp;Inna Sekirov ,&nbsp;Sylviane Defres ,&nbsp;Tom Solomon ,&nbsp;Tanya Golubchik ,&nbsp;Rory Bowden ,&nbsp;Andrew J Pollard ,&nbsp;Peter Simmonds","doi":"10.1016/j.jcv.2024.105715","DOIUrl":"10.1016/j.jcv.2024.105715","url":null,"abstract":"<div><h3>Objectives</h3><p>We evaluated the extent of virus heterogeneity in PeV infected infants in the UK, Canada and Australia.</p></div><div><h3>Methods</h3><p>Samples were collected from PeV infected infants during 2013–16. Next generation sequencing was used to obtain sequencing data and construct phylogenetic trees based on analysis of the VP1 region. Comparison was made with sequencing data available from an outbreak in Australia.</p></div><div><h3>Results</h3><p>We amplified and sequenced 58 samples. All obtained PeV sequences were genotype 3 apart from one UK sample which was PeV-A5. Phylogenetic analysis revealed that all strains clustered together on the same clade and showed no significant genetic variation. We saw no significant evidence of association between sequence and either clinical severity (defined by admission to paediatric intensive care), geographical origin (compared between Canada and U.K) or year of sample collection (samples sequenced during 2013 – 2018).</p></div><div><h3>Conclusions</h3><p>In this small cohort, sequencing data indicate that PeV circulating in the UK and Canada from 2013 to 18 are derived from a common ancestor. No association between disease severity and genetic sequence was seen in the UK or Canadian cohorts. Larger studies are required to support these findings.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105715"},"PeriodicalIF":4.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000775/pdfft?md5=1811610f423921eb8a709a05215011a7&pid=1-s2.0-S1386653224000775-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141784346","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":"Optimising nucleic acid recovery from rapid antigen tests for whole genome sequencing of respiratory viruses","authors":"G Butel-Simoes ,&nbsp;E Steinig ,&nbsp;I Savic ,&nbsp;M Zhanduisenov ,&nbsp;G Papadakis ,&nbsp;T Tran ,&nbsp;J Moselen ,&nbsp;L Caly ,&nbsp;DA Williamson ,&nbsp;CK Lim","doi":"10.1016/j.jcv.2024.105714","DOIUrl":"10.1016/j.jcv.2024.105714","url":null,"abstract":"<div><h3>Background</h3><p>Whole genome sequencing (WGS) of respiratory viruses from rapid antigen tests (RAT-WGS) is a novel approach to expanding genomic surveillance of respiratory infections. To date however, there are limited data on the genomic stability of these viruses on RATs. In this study, we investigated the effect of storage conditions and nucleic acid preservatives on the ability to enhance stability and improve recovery of respiratory virus genomes from RATs.</p></div><div><h3>Methods</h3><p>A mixture of common respiratory viruses was used to inoculate RATs at different environmental temperatures (4°C, 20°C and 36°C), with two preservative reagents (RNALater and DNA/RNA shield) Nucleic acid was extracted from RATs at two different timepoints (72 h and seven days) and subject to real-time multiplex respiratory PCR to detect a range of respiratory viruses. WGS was performed using target-enrichment with the TWIST Comprehensive Viral Research Panel. Defined metrics from an automated in-house bioinformatic pipeline were used to assess and compare viral genome recovery under different conditions.</p></div><div><h3>Results</h3><p>Nucleic acid degradation (indicated by relative change in PCR cycle threshold and WGS-based metrics) was most notable at 20 °C and 36 °C. Storage in either RNALater or DNA / RNA shield improved genome recovery for respiratory viruses across all temperature conditions, although this was most pronounced for RNALater. Subtyping of Influenza viruses demonstrated the applicability of RAT-WGS in downstream genomic epidemiological surveillance.</p></div><div><h3>Conclusions</h3><p>Under simulated conditions, RAT-WGS demonstrated that (i) viral genomes were generally stable at 4°C at 72 h and 1 week, (ii) RNALater has a more significant preservation of nucleic acids compared to DNA/RNA Shield and (iii) genome recovery can be achieved using a sequencing depth of 500,000 reads per sample in RNALater, across all respiratory viruses and conditions.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105714"},"PeriodicalIF":4.0,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000763/pdfft?md5=f50d339c540d3690c352e4d137a662ba&pid=1-s2.0-S1386653224000763-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141705848","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":"Epstein-Barr virus qPCR testing on bronchoalveolar lavage fluid from immunocompromised patients","authors":"Brooke Liang ,&nbsp;Jordan Mah ,&nbsp;Malaya K. Sahoo ,&nbsp;Benjamin A. Pinsky","doi":"10.1016/j.jcv.2024.105705","DOIUrl":"10.1016/j.jcv.2024.105705","url":null,"abstract":"<div><h3>Background</h3><p>Epstein-Barr Virus (EBV) is associated with lung disease in immunocompromised patients, particularly transplant recipients. EBV DNA testing of lower respiratory tract specimens may have diagnostic utility.</p></div><div><h3>Methods</h3><p>This was a retrospective, observational study of all patients with bronchoalveolar lavage (BAL) fluids submitted for EBV qPCR testing from February 2016 to June 2022 at the Stanford Clinical Virology Laboratory.</p></div><div><h3>Results</h3><p>There were 140 patients that underwent 251 EBV qPCR BAL tests (median 1; range 1 – 10). These patients had a mean age of 15.9 years (standard deviation, 15.1 years) and 50 % were female. Transplant recipients accounted for 67.1 % (94/140) of patients, including 67.0 % (63/94) solid organ transplant (SOT) and 33.0 % (31/94) hematopoietic cell transplant. Diagnostic testing was performed more commonly than surveillance testing [57.0 % (143/251) v. 43.0 % (108/251)]; 96.2 % (104/108) of surveillance samples were from lung transplant recipients. Excluding internal control failures, 34.7 % (83/239) of BAL had detectable EBV DNA, encompassing a wide range of viral loads (median=3.03 log₁₀ IU/mL, range 1.44 to 6.06). Overall agreement of EBV DNA in BAL compared to plasma was 74.1 % [117/158; 95 % confidence interval (CI): 66.5 % to 80.7 %], with a kappa coefficient of 0.44 (95 % CI: 0.30 to 0.57). Only 20.1 % (48/239) of results were discussed in a subsequent clinical note, and one result (0.4 %; 1/239) changed clinical management.</p></div><div><h3>Conclusions</h3><p>EBV qPCR testing on BAL offers limited clinical impact. Additional biomarkers are required to improve the diagnosis of EBV-associated lung diseases.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105705"},"PeriodicalIF":4.0,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603727","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}