Pub Date : 2025-02-17DOI: 10.1016/j.jcv.2025.105774
Anne Thierbach , Veronica Di Cristanziano , Kirsten A. Eberhardt , Martin Pirkl , Gertrud Steger , Eva Heger , Rolf Kaiser , Manuel Koch , Florian Klein , Dominic Rauschning , Jakob J. Malin
Background
Immunocompromised individuals, hemato-oncologic diseases or post-transplantation included, are, due to impaired immune response, at increased risk for severe and prolonged COVID-19. Observational Studies showed that SARS-CoV-2 RNAemia has been associated with poorer prognosis and higher disease severity.
Objective
The aim of this study was to investigate the occurrence of RNAemia and its association with anti-SARS-CoV-2 antibodies in immunocompromised COVID-19 patients. Risk factors for RNAemia were included in the analysis.
Study design
A retrospective study was conducted in 55 immunocompromised patients tested positive for SARS-CoV-2, who received treatment with monoclonal antibodies (mAb) between December 2021 and March 2022. Serological and virological tests were performed before mAb administration and clinical data were collected from electronic health records.
Results
Out of 55 patients, 35 % showed SARS-CoV-2 RNAemia. RNAemia was present in the 2 reported fatal cases. It was associated with negative testing for anti-receptor binding domain (RBD) IgG, anti-S2 domain of spike protein (S2) IgG and a lower leukocyte count. No association was found between previous COVID-19 vaccinations and the risk for RNAemia in immunocompromised patients.
Conclusion
The study underscores the importance of humoral response in controlling SARS-CoV-2 replication. RNAemia can serve as a potential biomarker for disease severity in immunocompromised individuals. Therefore, it should be considered in clinical settings for appropriate therapy decisions. Further research is needed to evaluate the pathophysiology and implications of RNAemia in immunodeficient patients with COVID-19.
{"title":"High rate of RNAemia and impaired immunity in patients with immunodeficiency in the vaccination era","authors":"Anne Thierbach , Veronica Di Cristanziano , Kirsten A. Eberhardt , Martin Pirkl , Gertrud Steger , Eva Heger , Rolf Kaiser , Manuel Koch , Florian Klein , Dominic Rauschning , Jakob J. Malin","doi":"10.1016/j.jcv.2025.105774","DOIUrl":"10.1016/j.jcv.2025.105774","url":null,"abstract":"<div><h3>Background</h3><div>Immunocompromised individuals, hemato-oncologic diseases or post-transplantation included, are, due to impaired immune response, at increased risk for severe and prolonged COVID-19. Observational Studies showed that SARS-CoV-2 RNAemia has been associated with poorer prognosis and higher disease severity.</div></div><div><h3>Objective</h3><div>The aim of this study was to investigate the occurrence of RNAemia and its association with anti-SARS-CoV-2 antibodies in immunocompromised COVID-19 patients. Risk factors for RNAemia were included in the analysis.</div></div><div><h3>Study design</h3><div>A retrospective study was conducted in 55 immunocompromised patients tested positive for SARS-CoV-2, who received treatment with monoclonal antibodies (mAb) between December 2021 and March 2022. Serological and virological tests were performed before mAb administration and clinical data were collected from electronic health records.</div></div><div><h3>Results</h3><div>Out of 55 patients, 35 % showed SARS-CoV-2 RNAemia. RNAemia was present in the 2 reported fatal cases. It was associated with negative testing for anti-receptor binding domain (RBD) IgG, anti-S2 domain of spike protein (S2) IgG and a lower leukocyte count. No association was found between previous COVID-19 vaccinations and the risk for RNAemia in immunocompromised patients.</div></div><div><h3>Conclusion</h3><div>The study underscores the importance of humoral response in controlling SARS-CoV-2 replication. RNAemia can serve as a potential biomarker for disease severity in immunocompromised individuals. Therefore, it should be considered in clinical settings for appropriate therapy decisions. Further research is needed to evaluate the pathophysiology and implications of RNAemia in immunodeficient patients with COVID-19.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"177 ","pages":"Article 105774"},"PeriodicalIF":4.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143454269","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 : 2025-02-07DOI: 10.1016/j.jcv.2025.105771
Mark Anderson , Lara Teodoro , Fiona Harley , Eduardo Almaraz , Ana Vallari , Carolyn Strobel , Barbara Harris , Todd V. Meyer , Nicaise Ndembi , Dora Mbanya , Linda James , Souleymane Mboup , Jean-Christophe Plantier , Gavin Cloherty , Mary Rodgers
Background
HIV displays exceptionally high virus diversity that can impact detection by diagnostic assays, which rely on sequence conservation.
Methods
We tested the m-PIMA HIV-1/2 Detect point-of-care (POC) assay (Abbott Rapid Diagnostics) against a diverse HIV panel of 340 serum/plasma specimens and diluted cultured virus isolates for which viral load (VL) and classified sequences were known, including HIV-1 groups M, N, O, P, Circulating Recombinant Forms (CRF), and Unique Recombinant Forms (URF), and HIV-2. An in silico inclusivity analysis of 53,503 HIV-1 and 68 HIV-2 sequences from NCBI was performed to predict performance of m-PIMA HIV-1/2 Detect against a broader range of circulating strains.
Results
m-PIMA HIV-1/2 Detect detected HIV in 329/340 (96.8 %) tested samples. The mean VL was 3.80 (2.09–6.14) log copies/mL. Among samples with HIV VL >4000 copies/mL (3.60 log copies/mL; m-PIMA HIV-1/2 Detect design sensitivity), 181/181 (100 %) were detected. Among samples with VL between 3.0 and 3.6 log copies/mL, m-PIMA HIV-1/2 Detect detected 93/96 (96.9 %), and 55/63 (87.3 %) samples with VL below 3.0 log copies/mL were detected. At least one member from each subtype/CRF and all URFs were detected. In silico analysis identified 2/53,503 (0.0037 %) HIV-1 (both group O) and 1/68 (1.47 %) HIV-2 (subtype F) sequences with target region mutations that decreased identity below a 90 % threshold.
Conclusions
The m-PIMA HIV-1/2 Detect assay detected each of the major circulating HIV strains, including rare divergent strains. In silico analysis predicted that m-PIMA HIV-1/2 Detect would detect the majority of HIV-1 and HIV-2 strains indicating that this assay can detect the full range of HIV viral diversity.
{"title":"Detection of diverse HIV strains by the m-PIMATM HIV-1/2 detect point-of-care assay","authors":"Mark Anderson , Lara Teodoro , Fiona Harley , Eduardo Almaraz , Ana Vallari , Carolyn Strobel , Barbara Harris , Todd V. Meyer , Nicaise Ndembi , Dora Mbanya , Linda James , Souleymane Mboup , Jean-Christophe Plantier , Gavin Cloherty , Mary Rodgers","doi":"10.1016/j.jcv.2025.105771","DOIUrl":"10.1016/j.jcv.2025.105771","url":null,"abstract":"<div><h3>Background</h3><div>HIV displays exceptionally high virus diversity that can impact detection by diagnostic assays, which rely on sequence conservation.</div></div><div><h3>Methods</h3><div>We tested the m-PIMA HIV-1/2 Detect point-of-care (POC) assay (Abbott Rapid Diagnostics) against a diverse HIV panel of 340 serum/plasma specimens and diluted cultured virus isolates for which viral load (VL) and classified sequences were known, including HIV-1 groups M, N, O, P, Circulating Recombinant Forms (CRF), and Unique Recombinant Forms (URF), and HIV-2. An <em>in silico</em> inclusivity analysis of 53,503 HIV-1 and 68 HIV-2 sequences from NCBI was performed to predict performance of m-PIMA HIV-1/2 Detect against a broader range of circulating strains.</div></div><div><h3>Results</h3><div>m-PIMA HIV-1/2 Detect detected HIV in 329/340 (96.8 %) tested samples. The mean VL was 3.80 (2.09–6.14) log copies/mL. Among samples with HIV VL >4000 copies/mL (3.60 log copies/mL; m-PIMA HIV-1/2 Detect design sensitivity), 181/181 (100 %) were detected. Among samples with VL between 3.0 and 3.6 log copies/mL, m-PIMA HIV-1/2 Detect detected 93/96 (96.9 %), and 55/63 (87.3 %) samples with VL below 3.0 log copies/mL were detected. At least one member from each subtype/CRF and all URFs were detected. <em>In silico</em> analysis identified 2/53,503 (0.0037 %) HIV-1 (both group O) and 1/68 (1.47 %) HIV-2 (subtype F) sequences with target region mutations that decreased identity below a 90 % threshold.</div></div><div><h3>Conclusions</h3><div>The m-PIMA HIV-1/2 Detect assay detected each of the major circulating HIV strains, including rare divergent strains. In silico analysis predicted that m-PIMA HIV-1/2 Detect would detect the majority of HIV-1 and HIV-2 strains indicating that this assay can detect the full range of HIV viral diversity.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"177 ","pages":"Article 105771"},"PeriodicalIF":4.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421224","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 : 2025-02-01DOI: 10.1016/j.jcv.2024.105756
Tatiana M. Lanzieri , A. Chantal Caviness , Jill J. Williams , Gail Demmler-Harrison , the Houston Congenital Cytomegalovirus Longitudinal Study Group
Background
Cytomegalovirus (CMV) infection in children is associated with prolonged viral excretion in urine and saliva. This study characterizes CMV urinary excretion in children with congenital (cCMV) and postnatally acquired CMV infection.
Methods
Children with virologically confirmed cCMV (75 symptomatic and 105 asymptomatic at birth) and 51 children without cCMV were followed through median 11, 18 and 17 years of age, respectively. In children with cCMV, duration of CMV excretion was defined as uninterrupted positive results from initial to last positive culture, and recurrent CMV excretion as ≥1 positive following >1 negative result. CMV urinary excretion in children without cCMV was defined as resulting from postnatally acquired CMV infection.
Results
Mean duration of persistent CMV urinary excretion in children with cCMV was 1.9 (maximum 8.7) years for symptomatic and 2.8 (maximum 9.8) years for asymptomatic children (P = 0.011). Mean duration of CMV excretion was not statistically different for 17 symptomatic children treated with ganciclovir (2.4 years) compared with 58 untreated (1.8 years); P = 0.356. Recurrent excretion occurred in 19 (25 %) symptomatic and 21 (20 %) asymptomatic children, at mean age 4.0 and 6.2 years, respectively (P = 0.084). In 16 (31 %) children with postnatally acquired CMV infection, CMV urinary excretion began at mean age 1.8 (range 0.3–7.3) years.
Conclusions
Both symptomatic and asymptomatic cCMV were associated with persistent long-term CMV excretion in urine, which was significantly longer in asymptomatic cCMV and not influenced by ganciclovir treatment in symptomatic cCMV. CMV urinary excretion was common in young children without cCMV, suggesting rapid CMV acquisition in childhood.
{"title":"Cytomegalovirus urinary excretion in children with congenital and postnatally acquired infection","authors":"Tatiana M. Lanzieri , A. Chantal Caviness , Jill J. Williams , Gail Demmler-Harrison , the Houston Congenital Cytomegalovirus Longitudinal Study Group","doi":"10.1016/j.jcv.2024.105756","DOIUrl":"10.1016/j.jcv.2024.105756","url":null,"abstract":"<div><h3>Background</h3><div>Cytomegalovirus (CMV) infection in children is associated with prolonged viral excretion in urine and saliva. This study characterizes CMV urinary excretion in children with congenital (cCMV) and postnatally acquired CMV infection.</div></div><div><h3>Methods</h3><div>Children with virologically confirmed cCMV (75 symptomatic and 105 asymptomatic at birth) and 51 children without cCMV were followed through median 11, 18 and 17 years of age, respectively. In children with cCMV, duration of CMV excretion was defined as uninterrupted positive results from initial to last positive culture, and recurrent CMV excretion as ≥1 positive following >1 negative result. CMV urinary excretion in children without cCMV was defined as resulting from postnatally acquired CMV infection.</div></div><div><h3>Results</h3><div>Mean duration of persistent CMV urinary excretion in children with cCMV was 1.9 (maximum 8.7) years for symptomatic and 2.8 (maximum 9.8) years for asymptomatic children (<em>P</em> = 0.011). Mean duration of CMV excretion was not statistically different for 17 symptomatic children treated with ganciclovir (2.4 years) compared with 58 untreated (1.8 years); <em>P</em> = 0.356. Recurrent excretion occurred in 19 (25 %) symptomatic and 21 (20 %) asymptomatic children, at mean age 4.0 and 6.2 years, respectively (<em>P</em> = 0.084). In 16 (31 %) children with postnatally acquired CMV infection, CMV urinary excretion began at mean age 1.8 (range 0.3–7.3) years.</div></div><div><h3>Conclusions</h3><div>Both symptomatic and asymptomatic cCMV were associated with persistent long-term CMV excretion in urine, which was significantly longer in asymptomatic cCMV and not influenced by ganciclovir treatment in symptomatic cCMV. CMV urinary excretion was common in young children without cCMV, suggesting rapid CMV acquisition in childhood.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105756"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791864","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 : 2025-02-01DOI: 10.1016/j.jcv.2024.105757
Kevin Brown , Sabine Ditrich , John Harris , Miren Iturriza , Cherry Kang , Marion Koopmans , Satu Kurkela , Ben Lopman , Mick Mulders , Sarah O'Brien , Jan Vinjé , Hubert Niesters
{"title":"In memoriam David Brown, December 2024","authors":"Kevin Brown , Sabine Ditrich , John Harris , Miren Iturriza , Cherry Kang , Marion Koopmans , Satu Kurkela , Ben Lopman , Mick Mulders , Sarah O'Brien , Jan Vinjé , Hubert Niesters","doi":"10.1016/j.jcv.2024.105757","DOIUrl":"10.1016/j.jcv.2024.105757","url":null,"abstract":"","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105757"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379219","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 : 2025-02-01DOI: 10.1016/j.jcv.2025.105762
Michael Payne , Gordon Ritchie , Tanya Lawson , Matthew Young , Willson Jang , Aleksandra Stefanovic , Marc G. Romney , Nancy Matic , Christopher F. Lowe
Background
Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time.
Methods
We performed amplicon sequencing of the HBV polymerase gene from patient plasma and external quality assessment (EQA) samples on the MiSeq Reagent Nano Kit v2 and GridION ONT with R10.4.1 flowcells. Mutational analysis and genotyping were performed by DeepChek®Assay-HBV (version 2.0).
Results
A total of 49 patient samples and 15 EQA samples were tested on both the MiSeq and ONT. There was high agreement for both patient and EQA samples between the MiSeq and ONT systems, with regards to total drug resistance mutations detected and total patient sample agreement, 68/70 (97 %) and 47/49 (96 %), respectively.
Conclusion
The ONT NGS platform provided accurate HBV AVR results, with improved turn-around times. Sequencing error rates at AVR codons were below 1 %.
{"title":"Evaluation of a next generation sequencing assay for Hepatitis B antiviral drug resistance on the oxford nanopore system","authors":"Michael Payne , Gordon Ritchie , Tanya Lawson , Matthew Young , Willson Jang , Aleksandra Stefanovic , Marc G. Romney , Nancy Matic , Christopher F. Lowe","doi":"10.1016/j.jcv.2025.105762","DOIUrl":"10.1016/j.jcv.2025.105762","url":null,"abstract":"<div><h3>Background</h3><div>Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time.</div></div><div><h3>Methods</h3><div>We performed amplicon sequencing of the HBV polymerase gene from patient plasma and external quality assessment (EQA) samples on the MiSeq Reagent Nano Kit v2 and GridION ONT with R10.4.1 flowcells. Mutational analysis and genotyping were performed by DeepChek®Assay-HBV (version 2.0).</div></div><div><h3>Results</h3><div>A total of 49 patient samples and 15 EQA samples were tested on both the MiSeq and ONT. There was high agreement for both patient and EQA samples between the MiSeq and ONT systems, with regards to total drug resistance mutations detected and total patient sample agreement, 68/70 (97 %) and 47/49 (96 %), respectively.</div></div><div><h3>Conclusion</h3><div>The ONT NGS platform provided accurate HBV AVR results, with improved turn-around times. Sequencing error rates at AVR codons were below 1 %.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105762"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006206","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 : 2025-02-01DOI: 10.1016/j.jcv.2025.105763
Lívia Sacchetto , Victória Bernardi , Marini L. Brancini , Beatriz de C. Marques , Andreia Negri , Nikos Vasilakis , Cassia F. Estofolete , Maurício L. Nogueira
Background
In dengue hyperendemic regions, the evolution of the virus is marked by frequent virus introduction/reintroduction and clade replacement events, occasionally linked to an epidemic outbreak. From 2023 onwards, an increase in the detection of DENV-3 cases has been reported in different regions of Brazil. Thus, molecular and genomic surveillance of circulating DENV strains is crucial for public health preparedness and response efforts for the disease.
Objectives
This work aimed to characterize and provide preliminary insights into dengue virus serotype 3 (DENV-3) re-emergence in São Paulo state, Brazil.
Study design
We conducted active arbovirus molecular surveillance on samples from patients with acute febrile illness combined with next-generation sequencing and phylogenetic analyses.
Results
We detected and characterized DENV-3 circulation in São Paulo, Brazil, since late 2023. The genomes clustered within genomes recently (2022–2024) identified in Florida, the Caribbean region, and Brazil.
Conclusions
Our results demonstrate the resurgence of DENV-3 in the region since 2009, raising concerns about a potential outbreak in regions with a high epidemic history.
{"title":"Early insights of dengue virus serotype 3 (DENV-3) re-emergence in São Paulo, Brazil","authors":"Lívia Sacchetto , Victória Bernardi , Marini L. Brancini , Beatriz de C. Marques , Andreia Negri , Nikos Vasilakis , Cassia F. Estofolete , Maurício L. Nogueira","doi":"10.1016/j.jcv.2025.105763","DOIUrl":"10.1016/j.jcv.2025.105763","url":null,"abstract":"<div><h3>Background</h3><div>In dengue hyperendemic regions, the evolution of the virus is marked by frequent virus introduction/reintroduction and clade replacement events, occasionally linked to an epidemic outbreak. From 2023 onwards, an increase in the detection of DENV-3 cases has been reported in different regions of Brazil. Thus, molecular and genomic surveillance of circulating DENV strains is crucial for public health preparedness and response efforts for the disease.</div></div><div><h3>Objectives</h3><div>This work aimed to characterize and provide preliminary insights into dengue virus serotype 3 (DENV-3) re-emergence in São Paulo state, Brazil.</div></div><div><h3>Study design</h3><div>We conducted active arbovirus molecular surveillance on samples from patients with acute febrile illness combined with next-generation sequencing and phylogenetic analyses.</div></div><div><h3>Results</h3><div>We detected and characterized DENV-3 circulation in São Paulo, Brazil, since late 2023. The genomes clustered within genomes recently (2022–2024) identified in Florida, the Caribbean region, and Brazil.</div></div><div><h3>Conclusions</h3><div>Our results demonstrate the resurgence of DENV-3 in the region since 2009, raising concerns about a potential outbreak in regions with a high epidemic history.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105763"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028930","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}
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis, responsible for large outbreaks in resource limited countries. The virus belongs to the genus Orthohepevirus which is subdivided into eight distinct genotypes (HEV-1 to HEV-8). Human disease transmission is mostly through the faecal-oral route. However, zoonotic transmission could also occur. In the Niger Republic, the first documented HEV outbreak was recorded in 2017 around displaced persons camps in the Diffa region across the Lake Chad basin, resulting in 736 confirmed cases and 38 (1.9%) deaths. Since then, sporadic cases were annually reported despite the lack of specific surveillance. Overall, from 2017 to 2023, a total of 2820 HEV suspected cases were sampled, out of which 906 (32.12%) were confirmed positive by either qRT-PCR and/or IgM ELISA. Out of the 21 characterized isolates, we identified 15 sequences belonging to the genotype 1e and 6 sequences to the genotype 2b. The newly characterized sequences from Niger clustered with those circulating in neighbouring countries, suggesting a cross-border virus circulation. The co-circulation of HEV genotypes 1 and 2 is an indicator of the probable virus transmission through contaminated water sources. Thus, there is a crucial need to improve the preparedness and implement an active and integrated community-based surveillance. This should include field testing for rapid detection and characterization of HEV as well as actions for disease containment, strengthening of hygiene measures and community-based sensitization for behavioural changes.
{"title":"Molecular epidemiology of Hepatitis E virus among humans in the Niger Republic, 2017–2023","authors":"Adamou Lagare , Issifi Kollo Abdoulkader , Gamou Fall , Hadiza Ousmane , Wilfried Hounkanrin , Balki Aoula , Bacary Djilocalisse Sadio , Bassira Issaka , Zaneidou Maman , Ousmane Faye , Sabo Haoua Seini , Martin Faye","doi":"10.1016/j.jcv.2025.105761","DOIUrl":"10.1016/j.jcv.2025.105761","url":null,"abstract":"<div><div>Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis, responsible for large outbreaks in resource limited countries. The virus belongs to the genus <em>Orthohepevirus</em> which is subdivided into eight distinct genotypes (HEV-1 to HEV-8). Human disease transmission is mostly through the faecal-oral route. However, zoonotic transmission could also occur. In the Niger Republic, the first documented HEV outbreak was recorded in 2017 around displaced persons camps in the Diffa region across the Lake Chad basin, resulting in 736 confirmed cases and 38 (1.9%) deaths. Since then, sporadic cases were annually reported despite the lack of specific surveillance. Overall, from 2017 to 2023, a total of 2820 HEV suspected cases were sampled, out of which 906 (32.12%) were confirmed positive by either qRT-PCR and/or IgM ELISA. Out of the 21 characterized isolates, we identified 15 sequences belonging to the genotype 1e and 6 sequences to the genotype 2b. The newly characterized sequences from Niger clustered with those circulating in neighbouring countries, suggesting a cross-border virus circulation. The co-circulation of HEV genotypes 1 and 2 is an indicator of the probable virus transmission through contaminated water sources. Thus, there is a crucial need to improve the preparedness and implement an active and integrated community-based surveillance. This should include field testing for rapid detection and characterization of HEV as well as actions for disease containment, strengthening of hygiene measures and community-based sensitization for behavioural changes.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105761"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006208","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 : 2025-02-01DOI: 10.1016/j.jcv.2025.105760
Payton Clark , Natalya Karasik , Shauna R. Campbell , Neil M. Woody , Jamie A. Ku , Natalie Silver , Danielle Bottalico , Brandon L. Prendes , Eric D. Lamarre , Joseph Scharpf , Tamara A. Sussman , Jessica L. Geiger , Hannah Wang , Timothy A. Chan , Shlomo A. Koyfman , Jacob A. Miller
Background
Plasma cell-free Human Papillomavirus DNA (cfHPVDNA) is a biomarker for oropharyngeal carcinoma. Existing diagnostics may be limited by inadequate sensitivity or high cost/complexity for longitudinal monitoring.
Objectives
We hypothesized that sensitive and specific plasma cfHPVDNA detection may be achieved via a highly-multiplex qPCR method.
Study Design
We designed and validated a single-tube one-step genotype-specific qPCR assay for detection of cfHPV16DNA in human plasma using >8,000 genomes spanning 18 genotypes. Amplicons were optimized for cfHPVDNA fragment size.
Results
The cfHPV16DNA qPCR amplicons spanned 16 % of the HPV16 genome. Amplicons were conserved in a median of 99.0 % of 3,944 genomes in silico. The 95 % lower limit of detection was 0.35 genome copies/reaction and the limit of blank was 0. Multiplexing achieved a tenfold improvement in sensitivity compared with single amplicons using in silico simulations of cfHPVDNA fragmentation, which was in close agreement with experimental observations. An assay was replicated for HPV18 with similar observations.
Among 36 patients with head/neck mucosal carcinomas (26 HPV-positive, 12 HPV-negative), there was 100 % concordance with tissue HPV status and with NavDx digital PCR. Pre-treatment specimens with sub-genomic cfHPVDNA concentration were detected. False negatives were observed with single amplicons but not with this multiplexed method. Among 17 patients with post-treatment landmark specimens, there was 100 % PPV and 100 % NPV for recurrence.
Conclusions
This assay is specific for plasma cfHPVDNA detection and prognostic for recurrence. Sub-genomic sensitivity was in close agreement with in silico simulations. The format might be more accessible than dPCR or NGS for longitudinal testing.
{"title":"Highly-multiplex detection of plasma cell-free human papillomavirus-16 DNA in oropharyngeal carcinoma","authors":"Payton Clark , Natalya Karasik , Shauna R. Campbell , Neil M. Woody , Jamie A. Ku , Natalie Silver , Danielle Bottalico , Brandon L. Prendes , Eric D. Lamarre , Joseph Scharpf , Tamara A. Sussman , Jessica L. Geiger , Hannah Wang , Timothy A. Chan , Shlomo A. Koyfman , Jacob A. Miller","doi":"10.1016/j.jcv.2025.105760","DOIUrl":"10.1016/j.jcv.2025.105760","url":null,"abstract":"<div><h3>Background</h3><div>Plasma cell-free Human Papillomavirus DNA (cfHPVDNA) is a biomarker for oropharyngeal carcinoma. Existing diagnostics may be limited by inadequate sensitivity or high cost/complexity for longitudinal monitoring.</div></div><div><h3>Objectives</h3><div>We hypothesized that sensitive and specific plasma cfHPVDNA detection may be achieved via a highly-multiplex qPCR method.</div></div><div><h3>Study Design</h3><div>We designed and validated a single-tube one-step genotype-specific qPCR assay for detection of cfHPV16DNA in human plasma using >8,000 genomes spanning 18 genotypes. Amplicons were optimized for cfHPVDNA fragment size.</div></div><div><h3>Results</h3><div>The cfHPV16DNA qPCR amplicons spanned 16 % of the HPV16 genome. Amplicons were conserved in a median of 99.0 % of 3,944 genomes <em>in silico</em>. The 95 % lower limit of detection was 0.35 genome copies/reaction and the limit of blank was 0. Multiplexing achieved a tenfold improvement in sensitivity compared with single amplicons using <em>in silico</em> simulations of cfHPVDNA fragmentation, which was in close agreement with experimental observations. An assay was replicated for HPV18 with similar observations.</div><div>Among 36 patients with head/neck mucosal carcinomas (26 HPV-positive, 12 HPV-negative), there was 100 % concordance with tissue HPV status and with NavDx digital PCR. Pre-treatment specimens with sub-genomic cfHPVDNA concentration were detected. False negatives were observed with single amplicons but not with this multiplexed method. Among 17 patients with post-treatment landmark specimens, there was 100 % PPV and 100 % NPV for recurrence.</div></div><div><h3>Conclusions</h3><div>This assay is specific for plasma cfHPVDNA detection and prognostic for recurrence. Sub-genomic sensitivity was in close agreement with <em>in silico</em> simulations. The format might be more accessible than dPCR or NGS for longitudinal testing.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105760"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142965161","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 : 2025-02-01DOI: 10.1016/j.jcv.2024.105758
Jordan K. Mah , Patrick C.K. Tam , Yeh-Chung Chang , Jennifer H. Saullo , Arthur W. Baker , Eileen K. Maziarz , Julia A. Messina , Beatrice Sim , Lana Abusalem , Sandrine Hanna , Matthew R. Pipeling , Laurie D. Snyder , John M. Reynolds , Cameron R. Wolfe , Mark J. Lee , Barbara D. Alexander , Madeleine R. Heldman
Background
EBV DNAemia surveillance, with reduction of immunosuppression at certain viral load (VL) thresholds, is a common practice for mitigating progression from EBV DNAemia to post-transplant lymphoproliferative disorder (PTLD) in lung transplant recipients (LTRs). The utility of EBV surveillance in adult EBV seropositive LTRs is unknown.
Methods
We performed a retrospective cohort study of EBV seropositive adult LTRs who underwent lung transplant between 1/1/19 and 12/31/20 and received whole blood (WB) EBV PCR surveillance. We compared peak WB EBV VLs among 3 groups: 1) asymptomatic LTRs who developed PTLD, before PTLD was clinically suspected, 2) LTRs who developed PTLD, after PTLD was clinically suspected, and 3) LTRs who did not develop PTLD. We calculated the positive predictive value (PPV) of moderate-grade DNAemia (2840 to 11,360 IU/mL) and high-grade DNAemia (≥ 11,360 IU/mL) for identifying active or future PTLD.
Results
Six (2.6 %) of 229 LTRs developed PTLD. Among LTRs who developed PTLD, median peak EBV VL was significantly higher after PTLD was suspected than before clinical signs of PTLD were present (16,004 IU/mL vs. ≤568 IU/mL, p = 0.016). Median peak EBV VLs were similar between asymptomatic LTRs who later developed PTLD and LTRs who did not develop PTLD (median peak EBV VL ≤568 IU/mL vs. ≤568 IU/mL, p = 0.62). The PPVs for moderate- and high-grade DNAemia were 14.7 % and 33.3 %, respectively.
Conclusions
EBV surveillance did not accurately identify EBV seropositive LTRs at risk for progressing to PTLD. EBV PCR testing in asymptomatic EBV seropositive transplant recipients may represent an opportunity for diagnostic stewardship.
{"title":"Limited utility of Epstein–Barr virus (EBV) surveillance for predicting post-transplant lymphoproliferative disorders in adult EBV seropositive lung transplant recipients","authors":"Jordan K. Mah , Patrick C.K. Tam , Yeh-Chung Chang , Jennifer H. Saullo , Arthur W. Baker , Eileen K. Maziarz , Julia A. Messina , Beatrice Sim , Lana Abusalem , Sandrine Hanna , Matthew R. Pipeling , Laurie D. Snyder , John M. Reynolds , Cameron R. Wolfe , Mark J. Lee , Barbara D. Alexander , Madeleine R. Heldman","doi":"10.1016/j.jcv.2024.105758","DOIUrl":"10.1016/j.jcv.2024.105758","url":null,"abstract":"<div><h3>Background</h3><div>EBV DNAemia surveillance, with reduction of immunosuppression at certain viral load (VL) thresholds, is a common practice for mitigating progression from EBV DNAemia to post-transplant lymphoproliferative disorder (PTLD) in lung transplant recipients (LTRs). The utility of EBV surveillance in adult EBV seropositive LTRs is unknown.</div></div><div><h3>Methods</h3><div>We performed a retrospective cohort study of EBV seropositive adult LTRs who underwent lung transplant between 1/1/19 and 12/31/20 and received whole blood (WB) EBV PCR surveillance. We compared peak WB EBV VLs among 3 groups: 1) asymptomatic LTRs who developed PTLD, before PTLD was clinically suspected, 2) LTRs who developed PTLD, after PTLD was clinically suspected, and 3) LTRs who did not develop PTLD. We calculated the positive predictive value (PPV) of moderate-grade DNAemia (2840 to 11,360 IU/mL) and high-grade DNAemia (≥ 11,360 IU/mL) for identifying active or future PTLD.</div></div><div><h3>Results</h3><div>Six (2.6 %) of 229 LTRs developed PTLD. Among LTRs who developed PTLD, median peak EBV VL was significantly higher after PTLD was suspected than before clinical signs of PTLD were present (16,004 IU/mL vs. ≤568 IU/mL, <em>p</em> = 0.016). Median peak EBV VLs were similar between asymptomatic LTRs who later developed PTLD and LTRs who did not develop PTLD (median peak EBV VL ≤568 IU/mL vs. ≤568 IU/mL, <em>p</em> = 0.62). The PPVs for moderate- and high-grade DNAemia were 14.7 % and 33.3 %, respectively.</div></div><div><h3>Conclusions</h3><div>EBV surveillance did not accurately identify EBV seropositive LTRs at risk for progressing to PTLD. EBV PCR testing in asymptomatic EBV seropositive transplant recipients may represent an opportunity for diagnostic stewardship.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105758"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864531","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 : 2025-02-01DOI: 10.1016/j.jcv.2024.105759
Henry Wong , Calvin P. Sjaarda , Brittany Rand , Drew Roberts , Kyla Tozer , Ramzi Fattouh , Robert Kozak , Prameet M. Sheth
Background
Respiratory Syncytial Virus (RSV) infections are a cause of significant morbidity and mortality in children and the elderly. Despite the clinical burden of disease, very little is known about the inter- and intra-seasonal genomic variability of RSV. Furthermore, the recent approval of vaccines and monoclonal antibody therapies will likely lead to higher selective pressure on RSV. Genomic surveillance will be essential to monitor viral changes and inform future therapeutic developments and public health responses. Here, we describe the development of an amplicon-based whole-genome sequencing assay for RSV to enable genomic surveillance.
Methods
A 750-bp overlapping amplicon design was developed to co-amplify RSV-A/-B directly from patient samples collected during two respiratory illness seasons (2022/23, 2023/24) for whole-genome sequencing. RSV subtype, clade, and F-protein antigenic site sequences were determined with a custom analytical pipeline.
Results
Of the 429 specimens included in the study 410 (95.6 %) samples met acceptability. Our data demonstrated co-circulation of both RSV subtypes, with increasing predominance of RSV-A since 2022. There were seven genomic clades of RSV-A, while >95 % of RSV-B belonged to a single clade. 1.5 % of samples had amino acid changes within the binding sites of the current RSV therapeutics Palivizumab or Nirsevimab.
Conclusions
Continuous monitoring of RSV genotypes and mutations will be critical for understanding the impact of new therapeutics and vaccines on RSV epidemiology and detecting emergence of vaccine-escape and/or antiviral resistant mutations.
{"title":"The molecular epidemiology of respiratory syncytial virus in Ontario, Canada from 2022–2024 using a custom whole genome sequencing assay and analytics package","authors":"Henry Wong , Calvin P. Sjaarda , Brittany Rand , Drew Roberts , Kyla Tozer , Ramzi Fattouh , Robert Kozak , Prameet M. Sheth","doi":"10.1016/j.jcv.2024.105759","DOIUrl":"10.1016/j.jcv.2024.105759","url":null,"abstract":"<div><h3>Background</h3><div>Respiratory Syncytial Virus (RSV) infections are a cause of significant morbidity and mortality in children and the elderly. Despite the clinical burden of disease, very little is known about the inter- and intra-seasonal genomic variability of RSV. Furthermore, the recent approval of vaccines and monoclonal antibody therapies will likely lead to higher selective pressure on RSV. Genomic surveillance will be essential to monitor viral changes and inform future therapeutic developments and public health responses. Here, we describe the development of an amplicon-based whole-genome sequencing assay for RSV to enable genomic surveillance.</div></div><div><h3>Methods</h3><div>A 750-bp overlapping amplicon design was developed to co-amplify RSV-A/-B directly from patient samples collected during two respiratory illness seasons (2022/23, 2023/24) for whole-genome sequencing. RSV subtype, clade, and F-protein antigenic site sequences were determined with a custom analytical pipeline.</div></div><div><h3>Results</h3><div>Of the 429 specimens included in the study 410 (95.6 %) samples met acceptability. Our data demonstrated co-circulation of both RSV subtypes, with increasing predominance of RSV-A since 2022. There were seven genomic clades of RSV-A, while >95 % of RSV-B belonged to a single clade. 1.5 % of samples had amino acid changes within the binding sites of the current RSV therapeutics Palivizumab or Nirsevimab.</div></div><div><h3>Conclusions</h3><div>Continuous monitoring of RSV genotypes and mutations will be critical for understanding the impact of new therapeutics and vaccines on RSV epidemiology and detecting emergence of vaccine-escape and/or antiviral resistant mutations.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"176 ","pages":"Article 105759"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894852","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}
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