Journal of Clinical Virology最新文献

{"title":"Clinical and sociodemographic correlates of emergent or evolving HIV drug resistance in low viral load specimens in British Columbia, Canada","authors":"Hanwei Sudderuddin ,&nbsp;Charlotte Johanna Beelen ,&nbsp;Jenny Li ,&nbsp;Wendy Zhang ,&nbsp;Melanie C.M. Murray ,&nbsp;Viviane D. Lima ,&nbsp;Julio S.G. Montaner ,&nbsp;Chanson J. Brumme","doi":"10.1016/j.jcv.2025.105807","DOIUrl":"10.1016/j.jcv.2025.105807","url":null,"abstract":"<div><h3>Background/methods</h3><div>Treatment guidelines recommend genotypic HIV drug resistance testing (DRT) at virologic failure, typically for plasma viral loads (pVL) &gt; 1000 HIV RNA c/mL. In some settings, DRT can be performed on low viral load (LVL) samples (pVL of 50–250 c/mL); however, such testing is resource-intensive and its clinical benefit is unclear. Therefore, we investigated the frequency and factors associated with emergent resistance in LVL samples using a comprehensive, provincial database of HIV Protease-Reverse Transcriptase and Integrase sequences.</div></div><div><h3>Results</h3><div>A total of 43,979 Protease-RT DRTs were performed in British Columbia between 1999 and 2022, of which 2970 (6.8 %) were on LVL samples. Testing was successful for 1575 (53.0 %) LVL samples compared to 81.4 % and 94.4 % of samples with pVL 250–999 and pVL ≥ 1000 c/mL, respectively (p &lt; 0.001). Compared to prior genotypes collected from samples with pVL &gt; 250 c/mL, a total of 104 (7.3 %) cases of new or evolving drug resistance were identified from 1423 LVL DRTs. Of these, 49.5 %, 42.9 % and 22.9 % exhibited new Nucleoside Reverse Transcriptase, Non-Nucleoside Reverse Transcriptase and Protease resistance, respectively. Of 9309 Integrase DRTs performed between 2008 and 2022, only 4 (1.2 %) cases of new or evolving integrase resistance were observed. Multivariable analyses identified clinical/sociodemographic factors significantly associated with emergent resistance, including time elapsed between DRTs, historic cumulative resistance and NNRTI-based antiretroviral therapy.</div></div><div><h3>Conclusions</h3><div>Emergent or evolving resistance is identified infrequently in low viral load specimens. Given its resource-intensive nature, resistance testing of low viral load specimens may not be generally warranted.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105807"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189834","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":"Retraction notice to “Evaluating the efficacy and safety of a novel prophylactic nasal spray in the prevention of SARS-CoV-2 infection: A multi-centre, double blind, placebo-controlled, randomised trial” [J. Clin. Virol. 155C (2022) 105248]","authors":"Damian Balmforth ,&nbsp;James A. Swales ,&nbsp;Laurence Silpa ,&nbsp;Alan Dunton ,&nbsp;Kay E. Davies ,&nbsp;Stephen G. Davies ,&nbsp;Archana Kamath ,&nbsp;Jayanti Gupta ,&nbsp;Sandeep Gupta ,&nbsp;M. Abid Masood ,&nbsp;Áine McKnight ,&nbsp;Doug Rees ,&nbsp;Angela J. Russell ,&nbsp;Manu Jaggi ,&nbsp;Rakesh Uppal","doi":"10.1016/j.jcv.2025.105782","DOIUrl":"10.1016/j.jcv.2025.105782","url":null,"abstract":"","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105782"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078130","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":"Coordinated implementation of a conventional PCR assay to detect all Ebola and Marburg virus species in a European laboratory network","authors":"K.C. Heimsch ,&nbsp;T. Bleicker ,&nbsp;T.D. Best ,&nbsp;L.D. Presser ,&nbsp;R. Molenkamp ,&nbsp;A.J. Jääskeläinen ,&nbsp;A. Milewska ,&nbsp;J. Šmahelová ,&nbsp;C. Baronti ,&nbsp;S. Pappa ,&nbsp;I. Tabain ,&nbsp;R. Cordeiro ,&nbsp;G. Marsili ,&nbsp;K. Huik ,&nbsp;V. Pinho dos Reis ,&nbsp;L. Barzon ,&nbsp;P. Maes ,&nbsp;C. Drosten ,&nbsp;V.M. Corman","doi":"10.1016/j.jcv.2025.105808","DOIUrl":"10.1016/j.jcv.2025.105808","url":null,"abstract":"<div><h3>Background</h3><div>Filoviruses, including Ebola and Marburg viruses, cause severe hemorrhagic fever in humans and primates. These viruses pose significant threats to public health, making rapid and sensitive detection critical for controlling outbreaks. We developed and validated a hemi-nested generic PanFilo assay to detect all Ebola virus species, Marburg viruses, and recently discovered bat filoviruses. This assay was deployed to 15 European laboratories and evaluated through testing of eight non-infectious samples.</div></div><div><h3>Objectives</h3><div>Laboratories were asked to determine the detection limit of positive controls and test all samples using the assay provided. The deployed assay enables direct Nanopore sequencing of PCR products, by using tagged primers during the second round of PCR. Sequencing of the samples was carried out on a voluntary basis.</div></div><div><h3>Results</h3><div>Multicenter validation revealed a 95 % limit of detection of 5309 RNA copies/µL for Ebola, 10,273 copies/µL for Marburg, and 2145 copies/µL for Mengla virus. In an implementation quality assessment, 93.3 % (84/90) of samples containing filovirus RNA were correctly identified and 100 % (30/30) of filovirus-negative samples were correctly identified. Thirteen laboratories sequenced PCR products, with nine identifying all positive samples correctly.</div></div><div><h3>Conclusion</h3><div>The assay enables rapid and reliable detection of filoviruses, with sequencing capabilities for identifying both known and novel variants. This assay might be used for detection during the initial phase of an emerging filovirus outbreak, before a specific assay has been developed. However, our distribution across 15 laboratories revealed variability challenges due to reagents, human performance, and sequencing capacity, emphasizing the need for more training and standardization.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105808"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144185662","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":"Human cytomegalovirus (HCMV) glycoprotein M occurs in three distinct genotypes in laboratory strains and clinical isolates","authors":"Alia Al-Alfard ,&nbsp;Zahrah Buhamad ,&nbsp;Julia Duffey ,&nbsp;Simon Lovell ,&nbsp;Paul Klapper ,&nbsp;Pamela Vallely","doi":"10.1016/j.jcv.2025.105799","DOIUrl":"10.1016/j.jcv.2025.105799","url":null,"abstract":"<div><h3>Background</h3><div>HCMV carries virus-encoded envelope glycoproteins important for viral attachment, entry into host cells and replication. These glycoproteins have polymorphic features resulting in distinct genotypes some of which have been associated with disease outcome. Glycoprotein complex II comprises glycoproteins M (gM) and N (gN) and is essential for viral replication. Glycoprotein N is highly polymorphic while gM is highly conserved. The existence of distinct gM genotypes has not previously been reported.</div></div><div><h3>Study design</h3><div>PCR amplification of the entire gM gene (1298 bp) was carried out on five HCMV laboratory strains (AD169, Towne, Davis, Toledo, Merlin) and ten clinical isolates. PCR product was sequenced and nucleotide and aminoacid phylogenetic trees constructed for these samples and for an additional 287 HCMV gM sequences obtained from NCBI database. The hydrophobicity of the predicted protein sequences was compared.</div></div><div><h3>Results</h3><div>Three distinct genotypes were identified (gM1, gM2 and gM3) with every sequence aligning with one genotype, suggesting they are stable polymorphisms rather than random nucleotide substitutions. Aminoacid translation of the nucleotide sequences merged gM1 and gM2, but gM3 remained as a distinct and separate type. The aminoacid substitutions led to changes in the hydrophobicity of the 3 glycoprotein types particularly between gM3 and the other two types.</div></div><div><h3>Conclusions</h3><div>Glycoprotein M is highly conserved, but we have identified three distinct genotypes, arising from variability in a small region of the genome. These changes altered the predicted hydrophobicity of the glycoprotein potentially altering the conformational structure of the glycoprotein and affecting its function <em>in vivo</em>.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105799"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873579","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":"Insights into the clinical and molecular epidemiology of an infections outbreak of human parvovirus B19 in France, 2023–2024","authors":"Elisa Creuzet ,&nbsp;Wendy Pulby ,&nbsp;Christine Archimbaud ,&nbsp;Amélie Brebion ,&nbsp;Hélène Chabrolles ,&nbsp;Audrey Mirand ,&nbsp;Ophélie Perruche ,&nbsp;Mathilde Picard ,&nbsp;Christel Regagnon ,&nbsp;Céline Lambert ,&nbsp;Siméon Bakyono ,&nbsp;Jean-Luc Bailly ,&nbsp;Maxime Bisseux ,&nbsp;Cécile Henquell","doi":"10.1016/j.jcv.2025.105798","DOIUrl":"10.1016/j.jcv.2025.105798","url":null,"abstract":"<div><h3>Background</h3><div>The human parvovirus B19 (B19V) infections cycle occurs in 3- to 4-year periods and is responsible for benign childhood erythema infectiosum. It is also associated with transient aplastic crisis in patients with underlying hemolytic diseases and with severe fetal sometimes fatal infection. This study investigated the epidemiological, clinical and molecular characteristics of an unusually large 2023–2024 outbreak of B19V.</div></div><div><h3>Methods</h3><div>Laboratory-confirmed cases were retrospectively and prospectively recorded at the Clermont-Ferrand University Hospital, France, between January, 2018 and November, 2023 and between December 2023 and May 2024 (2023/2024), respectively. Demographical and clinical data were investigated for the 2023/2024 period. Subgenome sequences (2690 nt) were obtained by next generation sequencing for virus genotyping and temporal molecular analysis.</div></div><div><h3>Results</h3><div>The positive rate of B19V positive laboratory-confirmed cases was seven times higher between December 2023 and May 2024 than in the previous 5-year period (14.6 % vs 2.1 %, p &lt; 0.001). No atypical clinical presentation or increased pathogenicity were observed, but this large outbreak resulted in a higher number of severe infections in pregnant women (8/16, 50.0 % of fetal complications) and those with chronic anemia. Phylogenetic analysis revealed that the 2023/2024 outbreak in France and Europe was mainly driven by a pre-existing lineage of B19V 1a subgenotype that emerged in 2017 (95 % highest posterior density interval: 2000–2018).</div></div><div><h3>Conclusions</h3><div>The recent epidemic of B19V infections re-illustrates the immunity gap of the post-pandemic COVID-19 pandemic. This highlight the impact of any outbreak on at-risk population and the need for a more global and genomic surveillance.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105798"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143864515","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":"Post-mortem study of endemic human coronaviruses (HCoV-NL63, OC43, 229E and HKU-1) in deaths of children under five in low- and middle-income countries: Findings from the Child Health and Mortality Prevention Surveillance (CHAMPS) study","authors":"Vicky Baillie ,&nbsp;Ziyaad Dangor ,&nbsp;Dianna M. Blau ,&nbsp;Sana Mahtab ,&nbsp;Jeanie du Toit ,&nbsp;Nega Assefa ,&nbsp;Joseph Oundo ,&nbsp;Zelalem Teklemariam Kidanemariam ,&nbsp;J. Anthony G. Scott ,&nbsp;Soter Ameh ,&nbsp;Ikechukwu Udo Ogbuanu ,&nbsp;Julius Ojulong ,&nbsp;James Bunn ,&nbsp;Karen L. Kotloff ,&nbsp;Samba O. Sow ,&nbsp;Milagritos D. Tapia ,&nbsp;Adama Mamby Keita ,&nbsp;Marcelino Garrine ,&nbsp;Inacio Mandomando ,&nbsp;Rosauro Varo ,&nbsp;Shabir A. Madhi","doi":"10.1016/j.jcv.2025.105804","DOIUrl":"10.1016/j.jcv.2025.105804","url":null,"abstract":"<div><h3>Background</h3><div>Endemic human coronaviruses (HCoV-229E, HKU1, NL63, and OC43) are common causes of mild or asymptomatic respiratory infections in children but are considered rare causes of death.</div></div><div><h3>Methods</h3><div>We evaluated pediatric deaths from January 2017 through December 2022. A panel of experts determined the cause of death (CoD) by reviewing available data, including pathological and molecular findings from minimally invasive tissue sampling (lung tissues, blood, CSF, and nasopharyngeal swabs), clinical records, and verbal autopsies.</div></div><div><h3>Results</h3><div>Endemic HCoV were detected in the respiratory samples of 3 % (n = 86/3357) of enrolled decedents: 1 % (n = 12/2043) of neonates, 5 % (n = 35/681) of infants and 6 % (n = 39/633) of children deaths. However, HCoVs were attributed as the CoD in only two cases — both involving young infants with underlying birth defects and severe wasting, who succumbed to polymicrobial hospital-acquired infections involving <em>HCoV-OC43</em>, <em>Klebsiella pneumoniae</em>, and <em>Acinetobacter baumannii</em>. Amongst the remaining 84 decedents in whom an HCoV was detected, 82 % (n = 69/84; median Ct of 25.34; range: 15.28–36.17) were deaths attributed to other infections, including 54 % (n = 32/69; median Ct of 23.86; range: 15.28–35.2) with lower respiratory infections determined to be the CoD. The bulk of these deaths (96 %, n = 66/69) were attributed to other pathogens – <em>Plasmodium falciparum</em> (27 %, n = 19/69), <em>K. pneumoniae</em> (23 %, n = 16/69), <em>Streptococcus pneumoniae</em> (20 %, n = 14/69), <em>Escherichia coli</em> (16 %, n = 11/69) and Cytomegalovirus (10 %, n = 7/69).</div></div><div><h3>Conclusion</h3><div>Although endemic HCoV was identified in children who died of respiratory infections, it was rarely attributed to being in the CoD. Nevertheless, further research is warranted to explore the potential role of HCoVs in LRTI pathogenesis and their impact on facilitating more pathogenic infections.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105804"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189833","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":"Highly specific serological diagnosis of Borna disease virus 1 (BoDV-1) and variegated squirrel bornavirus 1 (VSBV-1) encephalitis by novel antibody isotype assay with multiple viral antigens","authors":"Mathias Schlegel ,&nbsp;Petra Allartz ,&nbsp;Ariane Wenzel ,&nbsp;Thomas Faupel ,&nbsp;Klemens Loester ,&nbsp;Dennis Tappe","doi":"10.1016/j.jcv.2025.105803","DOIUrl":"10.1016/j.jcv.2025.105803","url":null,"abstract":"<div><h3>Background</h3><div>Human bornavirus encephalitis is an emerging, severe and nearly uniformly fatal zoonotic disease in Germany. The etiological pathogens so far encompass the Borna disease virus 1 (BoDV-1) and the variegated squirrel bornavirus 1 (VSBV-1). While BoDV-1 is at least harbored by the white-toothed shrew (<em>Crocidura leucodon</em>) as a natural reservoir and autochthonous in Germany, VSBV-1 has been detected in captive exotic squirrels with an unknown geographical origin. Clinically, a rapid progression is typical for both forms of bornavirus encephalitis, however, medical awareness is low, and therefore treatment attempts are notably delayed. Diagnosis relies on symptomatology, epidemiology, imaging, and virologic testing. One cornerstone of laboratory diagnosis is serology with limitations in sensitivity and specificity.</div></div><div><h3>Objectives</h3><div>Here, we describe a newly developed spot immunoassay using recombinant BoDV-1 nucleoprotein (N), phosphoprotein (P), accessory protein X (X), and glycoprotein (GP) to detect bornavirus-reactive IgG, IgM and IgA antibodies.</div></div><div><h3>Study design</h3><div>A comparatively large cohort encompassing 14 patients with BoDV-1 encephalitis and one individual with VSBV-1 encephalitis were tested. In addition, 241 patients with encephalitis of unknown etiology, 58 interference samples, as well as 40 blood donor samples were analyzed.</div></div><div><h3>Results</h3><div>The combined use of different antibody isotype-specific conjugates with four different BoDV-1-specific proteins (N/P/X/GP) while employing a newly developed evaluation scheme enabled a highly specific (97–100 %) diagnosis in patients with either form of bornavirus encephalitis, with a sensitivity of up to 92 %.</div></div><div><h3>Conclusions</h3><div>The novel spot immunoassay is an easy-to-use approach for the specific and sensitive serological diagnosis of human bornavirus encephalitis.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105803"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144099235","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":"Emergence of influenza A(H1N1)pdm09 6B.1A.5a.2a and 6B.1A.5a.2a.1 subclades leading to subtyping failure in a commercial molecular assay","authors":"Bosung Park,&nbsp;Eun Jeong Won,&nbsp;Heungsup Sung,&nbsp;Mi-Na Kim","doi":"10.1016/j.jcv.2025.105797","DOIUrl":"10.1016/j.jcv.2025.105797","url":null,"abstract":"<div><h3>Background</h3><div>During the 2023–2024 and early 2024–2025 influenza seasons, several influenza A-positive specimens in our laboratory failed subtyping for H1, H1pdm09, and H3 using the Allplex Respiratory Panel 1 (Allplex RP1) (Seegene Inc.). This study aimed to identify the cause of these subtyping failures.</div></div><div><h3>Materials and methods</h3><div>Between August 2023 and December 2024, 23 nasopharyngeal specimens tested positive for influenza A but were unsubtypeable for H1, H1pdm09, and H3. Confirmatory testing by the manufacturer included target-specific PCR for the M and HA genes, followed by sequencing to determine subclades.</div></div><div><h3>Results</h3><div>Among the 23 unsubtypeable specimens, 22 yielded PCR products for sequencing. Of these, 21 belonged to subclade 6B.1A.5a.2a.1 and one to 6B.1A.5a.2a. Sequence analysis revealed mismatches in the H1pdm09 primer/probe-binding regions of Allplex RP1, explaining the subtyping failures. Despite testing negative for H1pdm09 in Allplex RP1, sequencing confirmed their classification as H1N1pdm09 subclades with HA gene mutations.</div></div><div><h3>Conclusions</h3><div>Subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a harbour mutations that contributed to subtyping failures in some specimens tested with a commercial assay. While unsubtypeable influenza A results often raise concerns about emerging strains, sequencing confirmed that all unsubtypeable specimens tested with Allplex RP1 belonged to H1N1pdm09 within recognised subclades. Thus, such subtyping failures in this assay do not necessarily indicate a novel or zoonotic virus, though genomic surveillance remains essential.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105797"},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815565","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":"Sustained circulation of enterovirus D68 in Europe in 2023 and the continued evolution of enterovirus D68 B3-lineages associated with distinct amino acid substitutions in VP1 protein","authors":"Aurora Hirvonen ,&nbsp;Caroline Klint Johannesen ,&nbsp;Peter Simmonds ,&nbsp;Thea K Fischer ,&nbsp;Heli Harvala ,&nbsp;Kimberley S.M. Benschop ,&nbsp;on behalf of ENPEN study collaborators","doi":"10.1016/j.jcv.2025.105785","DOIUrl":"10.1016/j.jcv.2025.105785","url":null,"abstract":"<div><h3>Background</h3><div>Enterovirus D68 (EV-D68) causes respiratory disease ranging from mild to severe and in rare cases a paralytic syndrome, called acute flaccid myelitis (AFM). Since the global EV-D68 outbreak in 2014, the virus has mainly circulated in biennial epidemic cycles with peaks detected during even years. However, following the COVID-19 pandemic, the seasonal pattern of EV-D68 has been characterized by large yearly upsurges. Here, we describe the circulation of EV-D68 in Europe in 2023 and track its genetic evolution.</div></div><div><h3>Study design</h3><div>Data was compiled from members of the European Non-Polio Network (ENPEN). This included monthly data on the total number of EV samples tested, EV positive samples, EV-D68 positive samples and cases, and other EV positive samples detected in 2023. Information on sample types and surveillance system was recorded. Sequence data from the VP1 gene was used for phylogenetic and amino acid sequence analysis.</div></div><div><h3>Results</h3><div>EV was detected in 13585 out of 203622 diagnostic samples tested (6.7%), of which 402 (3.0%) were determined as EV-D68, representing 386 cases. EV-D68 infections peaked in October 2023 (136/386; 35.2%). 267/386 (69.2%) of EV-D68 cases were captured through clinical EV surveillance, almost all of which (202/204 of positive samples with sample type information) were detected in respiratory specimens. Phylogenetic analysis performed on 99 VP1 sequences revealed a distinct B3-derived lineage with a previously undescribed residue change, D554E, in Europe.</div></div><div><h3>Conclusions</h3><div>The study documents sustained circulation of EV-D68 in Europe in 2023, the evolution of B3-derived lineages, and appearance of previously undescribed amino acid substitutions in Europe. This stresses the need for continuous EV-D68 surveillance and harmonization of EV-D68 detection practices towards better data comparability across countries.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"178 ","pages":"Article 105785"},"PeriodicalIF":4.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815564","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":"Detection of diverse HIV strains by the m-PIMATM HIV-1/2 detect point-of-care assay","authors":"Mark Anderson ,&nbsp;Lara Teodoro ,&nbsp;Fiona Harley ,&nbsp;Eduardo Almaraz ,&nbsp;Ana Vallari ,&nbsp;Carolyn Strobel ,&nbsp;Barbara Harris ,&nbsp;Todd V. Meyer ,&nbsp;Nicaise Ndembi ,&nbsp;Dora Mbanya ,&nbsp;Linda James ,&nbsp;Souleymane Mboup ,&nbsp;Jean-Christophe Plantier ,&nbsp;Gavin Cloherty ,&nbsp;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 &gt;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":"2025-04-01","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}