Reliability of QuantiFERON®-CMV in predicting CMV recurrence in heart transplant recipients: A single-center retrospective study.

BACKGROUND: Recurrence after Cytomegalovirus (CMV) infection in heart transplant recipients is difficult to predict, in spite of its high incidence. Secondary prophylaxis could reduce this burden; however, its duration remains unestablished. We evaluated the QuantiFERON®-CMV test to see if it could predict CMV recurrence and help optimize the duration of secondary prophylaxis. METHODS: This observational retrospective single center study included all heart transplant recipients who developed CMV infection between 2019 and 2021, with the CD8+ T-cell-mediated CMV immunity QuantiFERON®-CMV test assessed at the time of (val)ganciclovir curative treatment completion. The main outcomes were CMV recurrence and duration of secondary prophylaxis. Secondary outcomes included immunosuppressive regimen, rejection, lymphocyte count, CMV viral load, infection type, and duration as possible confounding factors for recurrence. RESULTS: Among the 15 patients included, five (33%) experienced recurrence, of whom three (60%) had a positive QuantiFERON®-CMV test. The duration of secondary prophylaxis was similar regardless of QF-CMV positivity. No confounding factor was significantly associated with CMV recurrence; however, it occurred in only 1/7 (14%) of the patients receiving an everolimus-containing immunosuppressive regimen. CONCLUSION: In the population of heart transplant recipients, most of whom received ATG-based induction, the QuantiFERON®-CMV assay may not accurately predict CMV recurrence and would have not helped refining the duration of secondary prophylaxis in our patients. Other cell-mediated immunity tests and strategies in this specific population, including everolimus-containing regimens, may help predict and manage CMV recurrence.

Genotypic and Phenotypic Study of Antiviral Resistance Mutations in Refractory Cytomegalovirus Infection.

BACKGROUND: This study describes the genotypic and phenotypic characterization of novel human cytomegalovirus (HCMV) genetic variants of a cohort of 94 clinically resistant HCMV patients. METHODS AND RESULTS: Antiviral-resistant mutations were detected in the UL97, UL54, and UL56 target genes of 25 of 94 (26.6%) patients. The genotype-phenotype correlation study resolved the status of 5 uncharacterized UL54 deoxyribonucleic acid polymerase (G441S, A543V, F460S, R512C, A928T) and 2 UL56 terminase (F345L, P800L) mutations found in clinical isolates. A928T conferred high, triple resistance to ganciclovir, foscarnet, and cidofovir, and A543V had 10-fold reduced susceptibility to cidofovir. Viral growth assays showed G441S, A543V, F345L, and P800L impaired viral growth capacities compared with wild-type AD169 HCMV. Three-dimensional modeling predicted A543V and A928T phenotypes but not R512C, reinforcing the need for individual characterization of mutations by recombinant phenotyping. CONCLUSIONS: Extending mutation databases is crucial to optimize treatments and to improve the assessment of patients with resistant/refractory HCMV infection.

[Monkeypox to Mpox or the re-emergence of an old zoonosis]. / De la variole du singe à la Mpox ou la réémergence d'une ancienne zoonose.

Monkeypox is a zoonotic disease caused by the Monkeypox virus (MPXV) of the Orthopoxvirus genus. The first human cases occurred in Africa in the 1970s and remained confined to the African continent for a long time until 2003, when several dozen cases occurred in the United States, following contamination by prairie dogs. Unprecedented transmission events have led to more than 80,000 reported cases worldwide between May 2022 and February 2023, primarily affecting men who have sex with men. The changing epidemiology of Mpox has raised concerns about its ability to become endemic beyond its traditional geographic areas. Confirmatory diagnosis is based on direct detection by molecular biology. Pre- or post-exposure smallpox vaccination was widely deployed in early summer 2022 to limit the spread of the disease. In case of severe forms, the use of antivirals can be considered, only tecovirimat being recommended in this indication. The current epidemic has had the merit of showing that a disease that was previously confined to regions of initial virus circulation can spread very rapidly in Western countries and of the need to reinforce the implementation of tools for the surveillance and control of communicable diseases.

Humoral Response after SARS-CoV-2 mRNA Vaccination in a Cohort of Hemodialysis Patients and Kidney Transplant Recipients.

BACKGROUND: Kidney transplant recipients and patients receiving hemodialysis are immunocompromised populations that are prioritized for COVID-19 vaccination but were excluded from clinical trials of SARS-CoV-2 mRNA vaccines. Antibody titers and rates of seroconversion after vaccination are lower among patients with CKD and those taking immunosuppressants compared with controls. Data are lacking regarding their humoral response to vaccination to prevent COVID-19. METHODS: This investigation of early serological response after COVID-19 vaccination with the Pfizer/BioNTech (BNT162b2) mRNA vaccine included 78 patients undergoing hemodialysis, 74 kidney transplant recipients, and seven healthy controls. We recorded data from the medical file for various clinical parameters, including response to hepatitis B vaccination, and measured antibody titers against SARS-CoV-2 at 0, 14, 28, 36, and 58 days after the first injection. RESULTS: In controls, we detected antibodies at a positive level (>13 arbitrary units per ml; AU/ml) at day 14 postinjection, which increased progressively to peak at day 36 (1082 AU/ml; interquartile range [IQR], 735.0-1662.0). Patients undergoing hemodialysis had lower titers that peaked at day 58 (276 AU/ml; IQR, 83.4-526.0). We detected a positive antibody level in only three transplant recipients at day 36. In patients on hemodialysis, those aged <75 years had a higher antibody response versus those aged >75 years, and serum albumin and Kt/V were positively correlated with serological response (P<0.04 and P<0.0, respectively); nonresponders to HBV vaccine had the lowest anti-SARS-CoV-2 antibody titers. CONCLUSIONS: Our results suggest that the postvaccination humoral response is strongly inhibited by immunosuppressant therapy in kidney transplant recipients, and is reduced by the uremic condition in patients undergoing hemodialysis.

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020.

BackgroundThe COVID-19 pandemic has led to an unprecedented daily use of RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of quantification cycles (Cq), is debated because of strong potential biases.AimWe explored the possibility to use Cq values from SARS-CoV-2 screening tests to better understand the spread of an epidemic and to better understand the biology of the infection.MethodsWe used linear regression models to analyse a large database of 793,479 Cq values from tests performed on more than 2 million samples between 21 January and 30 November 2020, i.e. the first two pandemic waves. We performed time series analysis using autoregressive integrated moving average (ARIMA) models to estimate whether Cq data information improves short-term predictions of epidemiological dynamics.ResultsAlthough we found that the Cq values varied depending on the testing laboratory or the assay used, we detected strong significant trends associated with patient age, number of days after symptoms onset or the state of the epidemic (the temporal reproduction number) at the time of the test. Furthermore, knowing the quartiles of the Cq distribution greatly reduced the error in predicting the temporal reproduction number of the COVID-19 epidemic.ConclusionOur results suggest that Cq values of screening tests performed in the general population generate testable hypotheses and help improve short-term predictions for epidemic surveillance.

Viral metagenomics analysis of kidney donors and recipients: Torque teno virus genotyping and prevalence.

The viral load of the ubiquitous and nonpathogenic torque teno virus (TTV) is associated with the grade of immunosuppression of its host. The development of next-generation sequencing (NGS) allowed to describe the human virome of the blood compartment in transplanted patients, and showed that TTV is the most important part of the virome. This study is a descriptive retrospective pilot study of sequencing plasma samples from 15 matched donors and recipients. After sample processing, nucleic acids were amplified by rolling circle amplification and submitted to NGS by ion proton sequencing technology. Results were analyzed after mapping of reads on the 29 TTV reference genomes and de novo assembling of the reads with MIRA software. The number of TTV species present in donors and recipients was, on average, 12 in donors and 33 in recipients. TTV species predominantly present in donors were TTV-13 and TTV-18; and in recipients were TTV-P15-2, TTV-27, TTV-HD14a, and TTV-22. We highlighted a significant variability in abundance and composition in sequential samples from recipients. Temporal evolution of TTV populations was clearly observed in recipients, but no preferential transmission of a species from donor to recipient was evidenced. Diversity and population expansion were observed in kidney recipients. Further study of TTV species could help assess the potential impact of each species of this virus.

Compartmentalization of a Multidrug-Resistant Cytomegalovirus UL54 Mutant in a Stem Cell Transplant Recipient with Encephalitis.

We report a case of cytomegalovirus encephalitis in a hematopoietic stem cell transplant recipient. A previously uncharacterized V787E mutation in UL54 was identified in cerebrospinal fluid but not plasma specimens. For the V787E recombinant virus, the half maximal effective concentrations for ganciclovir, foscarnet, and cidofovir were 8.6-, 3.4- and 2.9-fold higher than for wild-type virus, and the replicative capacity was lower. The introduction of a bulkier and negatively charged glutamate residue at position 787 could destabilize the finger domain of UL54 DNA polymerase. Viral genotyping of cerebrospinal fluid is warranted in subjects with cytomegalovirus encephalitis, owing to the low penetration of antivirals in this compartment.

[Biological diagnosis of Sars-CoV-2 infection: strategies and interpretation of results]. / Diagnostic biologique de l'infection à Sars-CoV-2 : stratégies et interprétation des résultats.

In response to the emergence of Sars-CoV-2 responsible for a global pandemic, a large number of diagnostic tests have been developed and brought to market in a very short period of time. RT-PCR on nasopharyngeal swab samples is the reference method for the diagnosis and screening of Sars-CoV-2 infection, but the tests developed are highly variable in terms of sensitivity and turnaround time. Antigenic tests generally have lower sensitivity but have the advantage of simpler and faster implementation. In front of Covid-19 symptoms with negative RT-PCR results, serology can be recommended with IgM and IgG assays. Serology is also a relevant tool for epidemiological studies. However, it is important to remember that the level of anti-Sars-Cov-2 antibodies decreases over time and can therefore impact the results of sero-epidemiological studies. Despite the need to respond rapidly to an urgent diagnostic need, it remains essential to validate the methods chosen on a well-characterized panel of samples, as the performance of certain tests is sometimes unsatisfactory to ensure a reliable diagnosis.

[Cytomegalovirus infections]. / Infections à cytomégalovirus.

Cytomegalovirus infections. Cytomegalovirus (CMV) infections, which are common in children and adolescents, are often asymptomatic or with little specific signs. When they occur in adults, clinical forms may be more severe even in the immunocompetent. CMV is responsible for significant morbidity and mortality in transplant patients. In pregnant women, congenital CMV infection can lead to neurosensory damages requiring diagnosis and early management. The diagnosis of primary infection is based on serology, whereas the monitoring of infection in immunocompromised patients requires the use of polymerase chain reaction. As screening for congenital infection by serology is not recommended so far, it will be realized in an evocative context. Therapeutic options are still limited and expose to haematological or renal toxicity, but new antivirals (maribavir, letermovir) should be available soon to optimize therapeutic management.

Infections à cytomégalovirus. Les infections à cytomégalovirus, fréquentes chez l'enfant et l'adolescent, sont souvent asymptomatiques ou accompagnées de signes peu spécifiques. Lorsqu'elles surviennent chez l'adulte, les formes cliniques peuvent être plus sévères, y compris chez l'immunocompétent. Le cytomégalovirus est responsable d'une morbi-mortalité importante chez les patients greffés. Chez la femme enceinte, l'infection congénitale à cytomégalovirus peut conduire à des atteintes neurosensorielles nécessitant un diagnostic et une prise en charge précoce. Le diagnostic de la primo-infection repose sur la sérologie alors que le suivi de l'infection chez l'immunodéprimé nécessite le recours à la polymerase chain reaction. Le dépistage de l'infection congénitale par sérologie n'étant pas recommandé à ce jour, il n'est réalisé que dans un contexte évocateur. Les options thérapeutiques sont peu nombreuses et peuvent exposer à une toxicité hématologique ou rénale, mais de nouveaux antiviraux (maribavir, letermovir) devraient être disponibles prochainement pour optimiser la prise en charge thérapeutique.

Q fever and pregnancy: experience from the Limoges Regional University Hospital.

INTRODUCTION: Q fever is an ubiquitous zoonosis caused by Coxiella burnetii. Its tropism for the uterus is a potential source of obstetric complications. MATERIALS AND METHODS: We describe the obstetric consequences of Q fever diagnosed during pregnancy from a series of cases. When an antenatal diagnosis was made, antibiotic therapy with roxithromycin (Rulid(®)) was started until delivery. RESULTS: Between 2007 and 2012, 30 patients were treated for Q fever diagnosed during pregnancy, i.e. 1.9 cases per 1000 people. The most common reasons for performing serology was intrauterine growth retardation, preterm labor and oligoamnios. Q fever was diagnosed as acute and chronic in 26 and 4 cases, respectively. Progression to chronic disease occurred in 8 % of acute forms of the diseases. The prevalence of obstetric complications was 66 %, including 10 % foetal deaths, 31 % preterm delivery and 27 % low birthweight <10th percentile. The obstetric complication rate amongst the 22 patients treated with ante partum macrolides was 60, 30 % of which involved prematurity and 33 % involved low growth. No cases of foetal death were found on treatment and no congenital malformation and placental or neonatal injury was found. No case of disease reactivation was diagnosed in the eight patients who became pregnant again. CONCLUSION: Q fever during pregnancy is responsible for severe obstetric complications. It must be diagnosed early and its clinical forms known in order to start appropriate antibiotic therapy.

Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin.

The pretherapeutic presence of protease inhibitor (PI) resistance-associated variants (RAVs) has not been shown to be predictive of triple-therapy outcomes in treatment-naive patients. However, they may influence the outcome in patients with less effective pegylated interferon (pegIFN)-ribavirin (RBV) backbones. Using hepatitis C virus (HCV) population sequence analysis, we retrospectively investigated the prevalence of baseline nonstructural 3 (NS3) RAVs in a multicenter cohort of poor IFN-RBV responders (i.e., prior null responders or patients with a viral load decrease of <1 log IU/ml during the pegIFN-RBV lead-in phase). The impact of the presence of these RAVs on the outcome of triple therapy was studied. Among 282 patients, the prevalances (95% confidence intervals) of baseline RAVs ranged from 5.7% (3.3% to 9.0%) to 22.0% (17.3% to 27.3%), depending to the algorithm used. Among mutations conferring a >3-fold shift in 50% inhibitory concentration (IC50) for telaprevir or boceprevir, T54S was the most frequently detected mutation (3.9%), followed by A156T, R155K (0.7%), V36M, and V55A (0.35%). Mutations were more frequently found in patients infected with genotype 1a (7.5 to 23.6%) than 1b (3.3 to 19.8%) (P = 0.03). No other sociodemographic or viroclinical characteristic was significantly associated with a higher prevalence of RAVs. No obvious effect of baseline RAVs on viral load was observed. In this cohort of poor responders to IFN-RBV, no link was found with a sustained virological response to triple therapy, regardless of the algorithm used for the detection of mutations. Based on a cross-study comparison, baseline RAVs are not more frequent in poor IFN-RBV responders than in treatment-naive patients and, even in these difficult-to-treat patients, this study demonstrates no impact on treatment outcome, arguing against resistance analysis prior to treatment.

[Implementation of screening for cytomegalovirus congenital infection in a French type 3 maternity]. / Mise en place du dépistage de l'infection congénitale à cytomégalovirus dans une maternité française de type 3.

OBJECTIVES: Congenital cytomegalovirus (CMV) infection is the most common congenital infection and the leading cause of infectious neurosensorial disability in newborns. We wanted to organize the management of women from the beginning of pregnancy allowing access to antenatal treatment with valaciclovir, recognized since 2020 as limiting materno-fetal transmission. To this end, we set up and evaluated the interest of systematic screening for CMV infection in our maternity. We wanted to organize care for women from the very start of pregnancy. METHODS: Retrospective and comparative descriptive study carried out at the CHRU de Limoges from July 2017 to December 2019 (targeted screening), then from January 2020 to June 2022, during which period we implemented systematized screening by iterative serologies at the 3rd, 6th, 8th months and before delivery. Our main evaluation criteria were the seroprevalence of CMV infection and the rate of congenital infection. We then described our cases of infection (primary or secondary) during pregnancy. RESULTS: CMV seroprevalence in our pregnant women increased significantly from 52.7% (779/1478 women screened) to 58.4% (3852/6599 women screened) between the 2 study periods (P=0.04). We diagnosed 11 infections during the first part of the study vs. 27 during the second, with a significant increase in primary infections from 0.14% (9/6524 births) to 0.37% (24/6426 births) (P=0.008). Only 3 secondary infections were diagnosed during the second study period. The rate of congenital infections remained stable between the 2 study periods (6 children/6524=0.09% vs. 8 children/6426=0.12%; P=0.57). CONCLUSION: Our results confirmed the interest of screening for CMV infection, while modifying the screening strategy we had initiated.

Cytomegalovirus detected by qPCR in iris and ciliary body of immunocompetent corneal donors.

BACKGROUND: Cytomegalovirus (CMV) can cause a wide panel of ocular infections. The involvement of CMV as a cause of anterior uveitis in the immunocompetent patient is recent and remains poorly understood. OBJECTIVE: To investigate the presence of CMV in anterior uveal tissues of immunocompetent corneal donors. STUDY DESIGN: We collected aqueous humor, iris, and ciliary body from both eyes of 25 donors died at the Limoges University Hospital between January 2020 and July 2021. CMV serology was determined for all patients from post-mortem blood sample. Ocular tissues were split in 2 fragments for qPCR and 2 for histological analysis. CMV genomes copies were quantified by Multiplex qPCR after DNA extraction. RESULTS: 16 of 25 patients (64%) displayed positive CMV serology, with a median age of 67 years. Viremia was positive in 3 of 16 (19%) CMV-positive patients. No CMV DNA copies were found from the aqueous humor samples. CMV DNA was detected in iris and ciliary body of 28 of 32 eyes of seropositive donors, and 5 of 18 eyes of seronegative donors. The median viral copy number [IQR] was 2.41 × 102 [8.91 × 101 - 1.01 × 103] copies/1 × 106 cells in the CMV-positive group and 0.00 [0.00 - 3.54 × 102] copies/1 × 106 cells in the CMV-negative group (p<0.001). Histology and immunohistochemistry did not reveal any CMV lesions from any sample. CONCLUSION: CMV DNA was found in iris and ciliary body of immunocompetent seropositive patients, but also, although less frequently, from seronegative donors. These results highlight mechanisms of infection, latency and reactivation of CMV in ocular tissues.

Comprehensive Herpesviruses Antiviral drug Resistance Mutation Database (CHARMD).

A comprehensive and accessible Herpesvirus drug resistance database was designed to serve as an international reference for diagnosis and clinical studies. This database available at https://www.unilim.fr/cnr-herpesvirus/outils/codexmv/includes both resistance-related mutations and natural polymorphisms. Initially designed for human cytomegalovirus, it will be expanded to include herpes simplex and varicella-zoster viruses. Newly published mutations and new mutations reported by users or collaborating expert laboratories will be reviewed by an international committee of reference laboratories before inclusion in the database. Coupled with the Herpesvirus Sequence Analysis tool (HSA) mutation reports from NGS or Sanger sequences, it will be an open source for researchers in the field of Herpesviruses. We hope to fill this unmet need for the development and standardization of resistance genotyping.

Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron sublineage JN.1 in critically ill COVID-19 patients: a prospective, multicenter cohort study in France, November 2022 to January 2024.

BACKGROUND: A notable increase in severe cases of COVID-19, with significant hospitalizations due to the emergence and spread of JN.1 was observed worldwide in late 2023 and early 2024. However, no clinical data are available regarding critically-ill JN.1 COVID-19 infected patients. METHODS: The current study is a substudy of the SEVARVIR prospective multicenter observational cohort study. Patients admitted to any of the 40 participating ICUs between November 17, 2022, and January 22, 2024, were eligible for inclusion in the SEVARVIR cohort study (NCT05162508) if they met the following inclusion criteria: age ≥ 18 years, SARS-CoV-2 infection confirmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR) in nasopharyngeal swab samples, ICU admission for acute respiratory failure. The primary clinical endpoint of the study was day-28 mortality. Evaluation of the association between day-28 mortality and sublineage group was conducted by performing an exploratory multivariable logistic regression model, after systematically adjusting for predefined prognostic factors previously shown to be important confounders (i.e. obesity, immunosuppression, age and SOFA score) computing odds ratios (OR) along with their corresponding 95% confidence intervals (95% CI). RESULTS: During the study period (November 2022-January 2024) 56 JN.1- and 126 XBB-infected patients were prospectively enrolled in 40 French intensive care units. JN.1-infected patients were more likely to be obese (35.7% vs 20.8%; p = 0.033) and less frequently immunosuppressed than others (20.4% vs 41.4%; p = 0.010). JN.1-infected patients required invasive mechanical ventilation support in 29.1%, 87.5% of them received dexamethasone, 14.5% tocilizumab and none received monoclonal antibodies. Only one JN-1 infected patient (1.8%) required extracorporeal membrane oxygenation support during ICU stay (vs 0/126 in the XBB group; p = 0.30). Day-28 mortality of JN.1-infected patients was 14.6%, not significantly different from that of XBB-infected patients (22.0%; p = 0.28). In univariable logistic regression analysis and in multivariable analysis adjusting for confounders defined a priori, we found no statistically significant association between JN.1 infection and day-28 mortality (adjusted OR 1.06 95% CI (0.17;1.42); p = 0.19). There was no significant between group difference regarding duration of stay in the ICU (6.0 [3.5;11.0] vs 7.0 [4.0;14.0] days; p = 0.21). CONCLUSIONS: Critically-ill patients with Omicron JN.1 infection showed a different clinical phenotype than patients infected with the earlier XBB sublineage, including more frequent obesity and less immunosuppression. Compared with XBB, JN.1 infection was not associated with higher day-28 mortality.

COVID-19 associated pulmonary aspergillosis in critically-ill patients: a prospective multicenter study in the era of Delta and Omicron variants.

BACKGROUND: During the first COVID-19 pandemic wave, COVID-19-associated pulmonary aspergillosis (CAPA) has been reported in up to 11-28% of critically ill COVID-19 patients and associated with increased mortality. As new SARS-CoV-2 variants emerged, the characteristics of critically ill COVID-19 patients have evolved, particularly in the era of Omicron. The purpose of this study is to investigate the characteristics of CAPA in the era of new variants. METHODS: This is a prospective multicenter observational cohort study conducted in France in 36 participating intensive care units (ICU), between December 7th, 2021 and April 26th 2023. Diagnosis criteria of CAPA relied on European Confederation of Medical Mycology (ECMM)/International Society for Human & Animal Mycology (ISHAM) consensus criteria. RESULTS: 566 patients were included over the study period. The prevalence of CAPA was 5.1% [95% CI 3.4-7.3], and rose to 9.1% among patients who required invasive mechanical ventilation (IMV). Univariable analysis showed that CAPA patients were more frequently immunosuppressed and required more frequently IMV support, vasopressors and renal replacement therapy during ICU stay than non-CAPA patients. SAPS II score at ICU admission, immunosuppression, and a SARS-CoV-2 Delta variant were independently associated with CAPA in multivariable logistic regression analysis. Although CAPA was not significantly associated with day-28 mortality, patients with CAPA experienced a longer duration of mechanical ventilation and ICU stay. CONCLUSION: This study contributes valuable insights into the prevalence, characteristics, and outcomes of CAPA in the era of Delta and Omicron variants. We report a lower prevalence of CAPA (5.1%) among critically-ill COVID-19 patients than previously reported, mainly affecting intubated-patients. Duration of mechanical ventilation and ICU stay were significantly longer in CAPA patients.