Search

The aim of this study was to describe the prevalence, characteristics and outcome of critically burn patients with pulmonary HSV reactivation.Retrospective, single-center cohort study in a burn critical care unit in a tertiary center, including all consecutive severely burn patients with bronchoalveolar lavage performed for pneumoniae suspicion and screened for HSV from January 2013 and April 2017. We used logistic regression to identify factors associated with HSV reactivation and outcomes.94 patients were included, mean age was 51 (39-64) years; median total body surface area burned was 36 (25-54)% and ICU mortality 38%. Fifty-five patients (59%) had pulmonary HSV reactivation and 30 (55%) were treated with acyclovir. Patients with HSV reactivation were more severely ill with higher SOFA score at admission compared to patient without HSV reactivation (6 [3-8] vs. 2 [1-4], p0.0001 respectively). In multivariate analysis, sex, SOFA score at admission and smoke inhalation were significantly associated with HSV reactivation. Only septic shock was associated with 90-day mortality when HSV reactivation was not.Pulmonary HSV reactivation is frequent among severely ill burn patients. Initial severity and smoke inhalation are risk factors. Antiviral treatment was not associated with outcome.

Background Unlike other viruses, the pathogenicity of human metapneumovirus (hMPV) in adults remains uncertain. To address this question, a retrospective monocentric cohort including all patients admitted to ICU with hMPV infection between January 1, 2010, and June 30, 2018 was performed. The characteristics of hMPV infected patients were studied and compared to matched influenza infected patients. Consecutively, a systematic review and meta-analyses investigating PUBMED, EMBASE and COCHRANE databases was conducted to explore the hMPV infections in adult patients (PROSPERO number: CRD42018106617). Trials, case series, and cohorts published between January 1, 2008 and August 31, 2019 compiling adults presenting hMPV infections were included. Pediatric studies were excluded. Data were extracted from published reports. Primary endpoint was the rate of low respiratory tract infections (LRTIs) among all hMPV infected patients. Results During the study period, 402 patients were tested positive for hMPV. Among them 26 (6.5%) patients were admitted to the ICU, 19 (4.7%) for acute respiratory failure. Twenty-four (92%) were immunocompromised. Bacterial coinfections were frequent 53.8%. Hospital mortality rate was 30.8%. In the case–control analysis, the clinical and imaging characteristics were not different between hMPV and influenza infected patients. The systematic review identified 156 studies and 69 of them (1849 patients) were eligible for analysis. Although there was heterogeneity between the studies, the rate of hMPV LRTIs was 45% (95% CI 31–60%; I2 = 98%). Intensive care unit (ICU) admission was required for 33% (95% CI 21–45%; I2 = 99%). Hospital mortality rate was 10% (95% CI 7–13%; I2 = 83%) and ICU mortality rate was 23% (95% CI 12–34%; I2 = 65%). Underlying malignancy was independently associated with increased mortality rate. Conclusions This preliminary work suggested that hMPV may be associated with severe infection and high mortality in patients with underlying malignancies. However, regarding the small size of the cohort and the heterogeneity of the review, more cohort studies are warranted.

Characterization of the respiratory tract bacterial microbiome is in its infancy when compared to the gut microbiota. To limit bias mandates a robust methodology. Specific amplification of the hypervariable (V) region of the 16SrRNA gene is a crucial step. Differences in accuracy exist for one V region to another depending on the sampled environment. We aimed to assess the impact of the primer sequences targeting the V4 region currently used for gut microbiota studies in respiratory samples.

The World Health Organization (WHO) reported an outbreak of monkeypox virus (MPXV) in Western countries on May 12We collected air samples using the AerosolSense™ device in a dedicated room where monkeypox suspected patients were examined in our quaternary hospital's outpatient infectious disease clinic. Samples were analyzed with a MPXV PCR to determine the presence of viral DNA in the air.The study took place from July 26This investigation reports the presence of MPXV DNA in air samples collected in a room dedicated to monkeypox-infected patients' examination and testing. Thus, we highlight the importance of personal protective equipment worn by consulting patients and healthcare workers and surface decontamination to avoid infection transmission.

International audience; BackgroundThe outbreak of chilblain-like lesions (CLL) during the COVID-19 pandemic has been reported extensively, potentially related to SARS-CoV-2 infection, yet its underlying pathophysiology is unclear.ObjectivesTo study skin and blood endothelial and immune system activation in CLL in comparison with healthy controls and seasonal chilblains (SC), defined as cold-induced sporadic chilblains occurring during 2015 and 2019 with exclusion of chilblain lupus.MethodsThis observational study was conducted during 9–16 April 2020 at Saint-Louis Hospital, Paris, France. All patients referred with CLL seen during this period of the COVID-19 pandemic were included in this study. We excluded patients with a history of chilblains or chilblain lupus. Fifty patients were included.ResultsHistological patterns were similar and transcriptomic signatures overlapped in both the CLL and SC groups, with type I interferon polarization and a cytotoxic–natural killer gene signature. CLL were characterized by higher IgA tissue deposition and more significant transcriptomic activation of complement and angiogenesis factors compared with SC. We observed in CLL a systemic immune response associated with IgA antineutrophil cytoplasmic antibodies in 73% of patients, and elevated type I interferon blood signature in comparison with healthy controls. Finally, using blood biomarkers related to endothelial dysfunction and activation, and to angiogenesis or endothelial progenitor cell mobilization, we confirmed endothelial dysfunction in CLL.ConclusionsOur findings support an activation loop in the skin in CLL associated with endothelial alteration and immune infiltration of cytotoxic and type I IFN-polarized cells leading to clinical manifestations.

Rapid identification of SARS-CoV-2-infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swabs. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Overall, 117 of the 1718 participants (7%) tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97%, respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration number: NCT04578509.

Haematopoietic stem cell transplantation (HSCT) recipients are at risk for severe respiratory syncytial virus (RSV) infection. Two prognostic scores have been proposed to predict the risk of progression from upper respiratory tract infection (URTI) to lower respiratory tract infection (LRTI) and death. This was a multicentre study of allogeneic HSCT recipients diagnosed with an RSV infection between 2010 and 2019 who were retrospectively stratified by the immunodeficiency scoring index (ISI) and the severe immunodeficiency (SID) score. Endpoints were overall survival, RSV-attributable mortality and progression to LRTI after URTI. Prognostic analyses were performed using Cox regression models. We included 147 consecutive patients, including 94 (63.9%) initially diagnosed with URTI and 53 (36.1%) with LRTI. At 90 days, 14 patients had died (survival rate, 90.5%; 95% CI: 85.9–95.3), and nine deaths were attributable to RSV (attributable mortality rate, 5.4%; 95% CI: 2.5–10.0). The cumulative 90-day incidence of LRTI after URTI was 13.8% (95% CI: 7.8–21.6). Neither score showed prognostic value for mortality, while the ISI allowed the prediction of progression to LRTI (p = 0.0008). Our results do not fully replicate the results previously reported in cohorts of HSCT recipients. This may reflect the recent epidemiology of RSV infections in this HSCT cohort.

Inborn errors of immunity (IEI) are a heterogeneous entity with an increasing number of late diagnoses. Besides infections, inflammatory manifestations are a growing part of the clinical landscape of IEI. These complications are of unknown causes and often lead to the prescription of immunosuppressive agents that worsen the underlying immune defect. We here report the case of an adult patient diagnosed with chronic Human Adenovirus C-1 arthritis in the setting of primary agammaglobulinemia. Metagenomic next-generation sequencing led to the correct diagnosis and high-dose intravenous immunoglobulins resulted in complete recovery. This observation gives new insights into adenoviral immunity and underlines the importance of metagenomics in the diagnosis of inflammatory manifestations in immunocompromised patients.

Human parainfluenza virus type 3 (HPIV-3) may cause lower respiratory tract infection disease (LRTI-D) after hematopoietic stem cell transplantation (HSCT). Most previous studies focused on recipients of hematopoietic stem cell transplantation (HSCT) whereas data on characteristics and outcomes in patients with hematological malignancies (HM) compared to non-hematological patients are limited. The prognostic value of viral load in respiratory specimens remains elusive. In a two-year retrospective study, we determined frequencies of LRTI-D in HM, HSCT and in non-hematological patients, and HPIV-3 levels in respiratory tract secretions. Among 98 patients with HPIV-3 infection, including 31 HSCT and 40 HM, 36 had a diagnosis of LRTI-D. LRTI-D was significantly more frequent in patients with HM or HSCT (n=32, 45.1%) than in non-hematological patients (n=4, 14.8%) (p=0.006). The median HPIV-3 loads were high in upper respiratory tract secretions regardless of the presence or absence of LRTI-D (8.3 log10 vs 7.6 log10 TCID50 /106 cells). HPIV-3 loads in respiratory tract samples in HM were not significantly higher than those found in HSCT but significantly higher than in non-hematological patients (p=0.007). In conclusion, LRTI-D was frequent in HM patients who were diagnosed with HPIV-3 infection. This article is protected by copyright. All rights reserved.

Nasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the standard diagnostic test of coronavirus disease 2019. Our objectives were to assess, in real-life conditions, the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambulatory care. This was a prospective cohort study from 19 October through 18 December 2020 in two community COVID-19 screening centers in Paris, France. Two nasopharyngeal swabs and one saliva sample were simultaneously collected. Diagnostic accuracies of nasopharyngeal Ag testing and of three saliva NAAT methods were assessed as compared to nasopharyngeal NAAT. A total of 1452 ambulatory children and adults were included. Overall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was 94%, 23%, 96%, and 94% for the three different protocols of saliva NAAT and for the nasopharyngeal Ag test, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals. Diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT is similar to that of nasopharyngeal NAAT, subject to compliance with specific protocols for saliva. Registration number: NCT04578509 Supplementary Information The online version contains supplementary material available at 10.1007/s10096-021-04327-x.

Human adenoviruses (HAdV) infections are generally mild and resolve spontaneously in immunocompetent individuals. However, HAdV infections can have a major clinical impact in immunocompromised patients. HAdV infections are associated with high morbidity and mortality in recipients of allogeneic stem cell transplants, particularly children. There are currently no drug approved for the treatment of HAdV infections. Nevertheless, some nucleotide analogues are used under temporary authorization for use, such as cidofovir or brincidofovir. Cidofovir inhibits the replication of HAdV but its nephrotoxicity and its low tissue concentrations severely limit its use. Brincidofovir, a cidofovir prodrug, with a better bioavailability and no nephrotoxicity was evaluated in the treatment of HAdV infections, but its development was recently stopped and it is currently no longer available in ATU. Other molecules with anti-HAdV activity are still in early stages of development. Adoptive immunotherapy by adenovirus-specific T-cell transfer is an interesting option but should be anticipated in patients with high risks of disseminated infections. Given the small therapeutic panel available, it is critical to continue the search for new anti-HAdV molecules, which remains mainly conducted by academic laboratories.

Immune checkpoint inhibitors for melanoma improve adaptive T cell immunity during COVID-19 without exacerbating inflammation., The COVID-19 pandemic has spread worldwide, yet the role of antiviral T cell immunity during infection and the contribution of immune checkpoints remain unclear. By prospectively following a cohort of 292 patients with melanoma, half of which treated with immune checkpoint inhibitors (ICIs), we identified 15 patients with acute or convalescent COVID-19 and investigated their transcriptomic, proteomic, and cellular profiles. We found that ICI treatment was not associated with severe COVID-19 and did not alter the induction of inflammatory and type I interferon responses. In-depth phenotyping demonstrated expansion of CD8 effector memory T cells, enhanced T cell activation, and impaired plasmablast induction in ICI-treated COVID-19 patients. The evaluation of specific adaptive immunity in convalescent patients showed higher spike (S), nucleoprotein (N), and membrane (M) antigen-specific T cell responses and similar induction of spike-specific antibody responses. Our findings provide evidence that ICI during COVID-19 enhanced T cell immunity without exacerbating inflammation.

Background Rapid identification of SARS-Cov-2 infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Methods We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV™) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Results Overall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97% respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. Conclusion The detection of SARS-CoV-2 from crude saliva samples with a RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration number : NCT04578509

International audience; No abstract available

BackgroundRapid identification of SARS-Cov-2 infected individuals is a cornerstone in strategies for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis.Objectives and methodsWe conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV™) specifically designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR (reference test), to saliva RT-PCR and to nasopharyngeal antigen testing.ResultsOverall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% (95%CI: 26-44) and 97% (95%CI: 96-98) respectively. The performance was similar in symptomatic and asymptomatic participants. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p=0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%.ConclusionIn the ambulatory setting, the detection of SARS-CoV-2 from crude saliva samples with the RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration numberNCT04578509Funding SourcesFrench Ministry of Health and the Assistance Publique-Hôpitaux de Paris Foundation.

Introduction Le DITRA, déficit de l’antagoniste du récepteur de l’interleukine trente-six (IL36RA), est un syndrome monogénique auto-inflammatoire rare résultant de l’interaction de mutations autosomiques récessives ou double hétérozygotes composites du gène IL36RN codant pour l’IL-36RA, avec des facteurs déclenchants tels que l’infection et la grossesse. Matériel et méthodes Un patient de 16 ans souffrant de DITRA (mutation c.4G > T) à début précoce se présentait pour une poussée de psoriasis pustuleux généralisé (PPG) couvrant 60 % de la surface corporelle (GPPPGA = 3/5 ; GPPASI = 45,2/72), survenant 2 jours après l’apparition des premiers symptômes de COVID-19: céphalalgie fébrile, asthénie, anosmie. Il était en rémission clinique complète depuis des mois après l’arrêt de l’adalimumab, initié suite aux échecs de l’acitrétine et de la ciclosporine. On notait une hyperleucocytose sanguine à neutrophiles (17610/mm3), une CRP normale. La PCR multiplex nasopharyngée confirmait l’atteinte exclusive par un SARS-CoV-2. À j32, la sérologie COVID-19 était fortement positive (indice 5,79) associée à une forte augmentation de la signature transcriptomique sanguine neutrophilique mais pas chez la sœur légèrement atteinte et non infectée. L’expression de l’ARNm des gènes de signature de l’interféron (ISG) était normale dans les 2 cas. La poussée de PPG s’est amendée à 2 mois de la réintroduction de l’adalimumab, sans rechute. Discussion Le DITRA est caractérisé par des poussées aiguës de PPG parfois mortelles, associées à une anomalie d’expression ou fonction de l’IL36RA. Des signatures transcriptomiques neutrophilique et de l’IFN de type 1 ont été décrites, mais inconstantes pour cette dernière. Il s’agit du 1er cas de poussée de DITRA induite par le SARS-CoV-2, confirmant l’impact des déclencheurs infectieux, en particulier des infections respiratoires virales (IRV), sur le profil évolutif de ce syndrome auto-inflammatoire. Les interactions moléculaires et cellulaires reliant l’inflammation bronchique induite par le SARS-CoV-2 et l’inflammation cutanée/systémique dans le PPG, restent inconnues. La forte signature neutrophilique est associée à une augmentation de l’IL-36 et des chimiokines attirant/activant les neutrophiles (CXCL-1, CXCL-2, CXCL-8,…). L’IFN-I joue un rôle déterminant dans une réponse immunitaire efficace contre le SARS-CoV-2 mais n’était pas augmenté contrairement à d’autres PPG, démontrant l’existence de voies d’inflammation alternatives pour le déclenchement des poussées. Le clivage catalytique par l’élastase de la forme immature et inactive de l’IL-36RA pour une fonction optimale de l’antagoniste est obligatoire pour prévenir l’inflammation neutrophilique cutanée aiguë après des événements déclencheurs. Le rôle de la voie IL-36 dans l’inflammation bronchique et ce cas ouvrent la voie à des études mécanistiques visant à déchiffrer les liens moléculaires et cellulaires entre les IRV et les poussées de psoriasis.

Objectives The relevance of syndromic multiplex-PCR for the etiological diagnosis of meningitis or meningoencephalitis is still a matter of debate. Here, we studied the impact of a 24/7 multiplex-PCR on the management of patients consulting in the emergency department for suspicion of community-acquired meningitis. Methods We conducted a single-center retrospective study at the Emergency department of Lariboisiere University Hospital (Paris, France) including all patients suspected of meningitis. During period 1 (April 2014-March 2017), the molecular assays used for the detection of infectious agents in the cerebrospinal fluid (CSF) were performed during the daytime. During period 2 (April 2017-March 2019), multiplex-PCR (BioFire® Filmarray® Meningitis/Encephalitis Panel [ME], bioMerieux) was performed 24/7. Results During the periods 1 and 2, 4 100 and 3 574 patients were included and 284 (6.9%) and 308 (8.6%) meningitis were diagnosed, respectively. During the periods 1 and 2, the most common causes of meningitis were enterovirus (23.9% and 29.5%), varicella zoster virus (10.2% and 6.8%) and herpes simplex virus-2 (4.2% and 8.1%). For patients with confirmed viral meningitis, a significant decrease was found between period 1 and period 2 respectively for the rate of hospitalization (73.9% vs 42.0%; p Conclusions Multiplex-PCR is an important tool in the diagnosis of infectious meningitis in the emergency department and is relevant in the management of meningitis by screening for patients who do not require hospitalization and antibacterial therapy.

Human adenovirus (HAdV) represents a major cause of mortality and morbidity in pediatric recipients of allogeneic hematopoietic stem cell transplants (HSCT). HAdV species F type 41 (HAdV-F41) infections in HSCT patients are scarce, whereas HAdV-F41 circulates commonly in healthy individuals. Between March and July 2018, HAdV-F41 infections were identified in four children (A, B, C, and E) who received allogeneic HSCT and one child before HSCT (D) at Robert Debré Hospital, Paris, France. We report here the clinical course of HAdV-F41 infection and the phylogenetic investigation to identify interpatient transmission. HAdV DNA was quantified in stool and plasma samples by real-time PCR. HAdV type was determined by sequencing of the fiber and hexon genes. Phylogenetic investigation was done with whole-genome sequences obtained by next-generation sequencing. HAdV loads in stool samples ranged from 6.60 to 10.10 log(10) copies/ml. HAdV-F41 detection in plasma was observed in four patients, but no disseminated disease was reported. Two patients died, but neither death was attributed to HAdV. While sequencing limited to the fiber gene suggested a cluster with four patients, phylogenetic analysis with whole-genome sequencing (WGS) and HVR7 revealed a cluster that included three patients (C, D, and E), suggesting an interpatient transmission in that cluster and two other independent infections. HAdV-F41 levels in stool specimens of pediatric HSCT patients are high and represent a risk of interpatient transmission. WGS helped to identify related cases. Prompt detection of HAdV in stool and control measures are warranted to limit any risk of nosocomial transmission.

We report evaluation of 30 assays’ (17 rapid tests (RDTs) and 13 automated/manual ELISA/CLIA assay (IAs)) clinical performances with 2594 sera collected from symptomatic patients with positive SARS-CoV-2 rRT-PCR on a respiratory sample, and 1996 pre-epidemic serum samples expected to be negative. Only 4 RDT and 3 IAs fitted both specificity (> 98%) and sensitivity (> 90%) criteria according to French recommendations. Serology may offer valuable information during COVID-19 pandemic, but inconsistent performances observed among the 30 commercial assays evaluated, which underlines the importance of independent evaluation before clinical implementation. Supplementary Information The online version contains supplementary material available at 10.1007/s10096-021-04232-3.

BackgroundCharacterization of the respiratory tract bacterial microbiota is in its infancy when compared to the gut microbiota knowledge. As key methodological steps can directly affect the accuracy of the results, it is crucial to determine a robust methodology in order to limit bias.Two different pairs of primers 515F-806R targeting the V4 hypervariable region of the 16SrRNA gene, “S-V4” for “Stringent V4” primer pair and “R-V4” for “Relaxed V4” primer pair, are respectively used in two ongoing international projects “the Human microbiome project” and “the Earth microbiome project”. We compared two methods of sample processing using these two different primer pairs for bacterial microbiota analyses of respiratory samples from critically-ill ventilated patients. For the later, Illumina 250 paired-end sequencing was done on a MiSeq platform after DNA extraction using mechanical lysis (bead-beating) and NucliSENS easyMAG. The concordance with conventional microbiology is the criterion of choice to determine the optimal method.ResultsTwenty samples from seven patients and four controls were sequenced. The two primer pair provided highly different results. Only 54% of the samples had a similar microbial composition with both pairs of primers. “S-V4” gave the best agreement with the conventional microbiology for ETA: 89% as compared to 44% for the “R-V4” primer pair. The main difference related to Enterobacteriaceae, which were concordant between conventional cultures and microbiota analyses using “S-V4”. Enterobacteriaceae detection was poor for “R-V4”. Among patients with VAP, a decrease in alpha diversity in ETA was observed. The mean of pairwise Unifrac distance was higher inside this group of patients at the time of VAP diagnosis as compared to control patients.ConclusionAccuracy of the bacterial lung microbiota composition was highly correlated to the pair of primers used for amplification of the 16s rRNA hypervariable sequence. Comparison of microbiota results obtained by sequencing and conventional microbiology allowed us to select the best option for further studies. This work validates our methodology based on 16SrRNA gene amplification with 515F-806R “S-V4” primer pair associated to Illumina® MiSeq 250 paired-end sequencing.

We are grateful to the inhabitants and authorities in southeastern Cameroon for their warm welcome and their support of this study. We also acknowledge the invaluable assistance of the European zoo and its employees where we conducted the investigation. We also greatly appreciate the contributions of Olivia Cheny of the Center for Translational Science at the Institut Pasteur.; International audience; Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations. Over the last decade, numerous studies have demonstrated the importance of environmental changes on the mammalian gut microbiome, which is strongly associated with host metabolic, immune, and neurological functions 1. Broad-ranging influences, including host genetics, living conditions, diet, stress, and antibiotic use can affect gut microbial diversity 2-5. Among these influences, diet and living conditions have been evaluated for human and animal populations, entailing significant effects on gut microbiota and consequences for human and animal health. Adverse microbial profile shifts, for instance, have been associated with dysbiosis and wide-ranging diseases among human beings, from obesity to pediatric environmental enteropathy, and from autism to asthma 2,6,7. Outside of laboratory conditions, disentangling the effects of living and dietary conditions on gut microbial composition from other influences remains a complex question. In humans, such questions have catalyzed multiple studies comparing environmental and gut microbiota between "westernized" and "rural" peoples 8-10. Among other mammalian populations, degradation in habitat quality affects the diversity of available flora and fauna for consumption, and in some cases, is associated with declines in microbial gut composition 11-14. Microbiome OPEN

Objectives Human adenovirus (HAdV) infections are associated with a high morbidity and mortality in transplant patients requiring the use of antiviral treatments. Brincidofovir (BCV), a cytidine analog, inhibits HAdV replication through viral DNA elongation termination and likely through other mechanisms. To elucidate if BCV regulates cellular antiviral pathways, we analyzed its impact on HAdV-infected and non-HAdV-infected lung epithelial cells. Methods We assessed the cellular and viral transcriptome of A549 cells infected and non-infected with HAdV C5 and treated or non-treated with BCV by RNAseq after 72 h. Results BCV treatment of HAdV infected cells resulted in a profound decrease of viral transcription associated with a relative overexpression of the early genes E1A and E4 and of the late gene L1. BCV had also a profound impact on A549 cells’ transcriptome. Ontologic analysis revealed an effect of BCV on several pathways known to interact with adenovirus replication as mTor signalling and Wnt pathways. A549 cells treated with BCV demonstrated a significant inhibition of the biological function of “viral replication” including 25 dysregulated genes involved in inflammation pathways. Conclusion We demonstrated that BCV alters viral gene expression and promotes the expression of antiviral cellular pathways in A549 cells. These results provide new insights how to interfere with cellular pathways to control HAdV infections.

BackgroundRT-PCR testing is crucial in the diagnostic of SARS-CoV-2 infection. The use of reliable and comparable PCR assays is a cornerstone to allow use of different PCR assays depending on the local equipment. In this work, we provide a comparison of the Cobas® (Roche) and the RealStar® assay (Altona).MethodsAssessment of the two assays was performed prospectively in three reference Parisians hospitals, using 170 clinical samples. They were tested with the Cobas® assay, selected to obtain a distribution of cycle threshold (Ct) as large as possible, and tested with the RealStar assay with three largely available extraction platforms: QIAsymphony (Qiagen), MagNAPure (Roche) and NucliSENS-easyMag (BioMérieux).ResultsOverall, the agreement (positive for at least one gene) was 76%. This rate differed considerably depending on the Cobas Ct values for gene E: below 35 (n = 91), the concordance was 99%. Regarding the positive Ct values, linear regression analysis showed a determination correlation (R2) of 0.88 and the Deming regression line revealed a strong correlation with a slope of 1.023 and an intercept of -3.9. Bland-Altman analysis showed that the mean difference (Cobas® minus RealStar®) was + 3.3 Ct, with a SD of + 2.3 Ct.ConclusionsIn this comparison, both RealStar® and Cobas® assays provided comparable qualitative results and a high correlation when both tests were positive. Discrepancies exist after 35 Ct and varied depending on the extraction system used for the RealStar® assay, probably due to a low viral load close to the detection limit of both assays.

Prior to transplantation of hematopoietic stem cells or solid organ, donor and recipient EBV serostatus has to be determined to assess risks of post-transplant lymphoproliferative disorders. Sensitivity of EBV Viral capsid antigens (VCA) IgG and EBV nuclear antigen-1 (EBNA-1) is critical to define past infection and a good specificity of VCA IgM is required to avoid any disqualification of cord blood (CB) units. Architect™ EBV antibody panel (Architect assay) providing a high throughput was compared to a semi-automated ELISA (Etimax assays Diasorin) to assess sensitivities and specificities of VCA and EBNA-1 IgG and VCA IgM on 419 sera collected from immunocompromised patients (n=184) and from pregnant women who agreed to give CB cells (n=235). Intra and inter-assay coefficient of variations ranged from 1.63 to 4.8 % for VCA IgM, VCA IgG and EBNA-1 IgG. Index of VCA IgG and IgM and EBNA IgG of the two assays were highly correlated. The concordance in the interpretation between the two assays was moderate for VCA IgM (kappa=0.5), substantial for VCA IgG (kappa =0.60) and good for EBNA-1 IgG (kappa=0.75). Using serial dilutions of positive controls and in accordance with clinical results VCA IgG and EBNA IgG were detected at lower dilutions with Architect than Etimax. Conversely, 96.1% (74/77) of samples negative with Architect and positive with Etimax for VCA IgM did not have any heterophile antibodies and had VCA IgG and EBNA IgG antibodies supporting past infections. Architect™ EBV serology panel provided good sensitivities and specificities for EBV serostatus determination prior to transplantation. This article is protected by copyright. All rights reserved

Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46-4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.

The virome has been recently studied in hematology and mostly in the setting of allogeneic hematopoietic stem cell transplantation. However, in hematology (as in the setting of nonhematological disorders) the study of the microbiome (that indeed includes the virome) is a growing field. The overall field is moving beyond species catalogue to the understanding of the complex ecological relationship that microbes have with each other and with their host. Here we review the existing literature on the virome in transplant recipients and in other settings, and discuss potential applications of the virome study in hematology.

Background Standardized and sensitive assays for Epstein Barr Virus (EBV) are needed to define universal cutoff for treatment initiation in allogeneic hematopoietic stem cells transplant recipients. In a context of accreditation and the availability of EBV international standard, we evaluated the Abbott RealTime EBV (RT) assay for EBV quantification in whole blood. Methods The RT assay was compared on 282 prospective clinical samples with the Artus EBV PCR Kit V1 assay (V1) and we analyzed the kinetics of EBV load in 11 patients receiving rituximab treatment. Results The estimated limit of detection was 88 IU/mL. The assay was linear (r2 = 0.9974) in the range of all samples tested (100 to 1,000,000 IU/mL). Intra-assay coefficients of variation (CV) ranged between 0.35 and 1.35%, and inter-assay CV between 3.40 and 4.5%. On samples above the limit of quantification, the two assays were strongly correlated. EBV RT values were on average 0.30 log10 IU/mL lower than those measured with the V1 assay. In patients treated with rituximab, the RT assay remained positive in 5 patients at the time it dropped below undetectable levels with the V1 assay. Conclusions In conclusion, the RT assay is a reliable assay for EBV load in whole blood. Its sensitivity will enable to estimate the kinetics of EBV load and the impact of treatments to control EBV reactivations.

Background Accurate quantification of Epstein-Barr virus (EBV) load in blood is essential for the management of post-transplant lymphoproliferative disorders. The automation of DNA extraction and amplification may improve accuracy and reproducibility. We evaluated the EBV PCR Kit V1 with fully automated DNA extraction and amplification on the m 2000 system ( Abbott assay ). Methodology Conversion factor between copies and international units (IU), lower limit of quantification, imprecision and linearity were determined in a whole blood (WB) matrix. Results from 339 clinical WB specimens were compared with a home-brew real-time PCR assay used in our laboratory ( in-house assay ). Results The conversion factor between copies and IU was 3.22 copies/IU. The lower limit of quantification (LLQ) was 1000 copies/mL. Intra- and inter-assay coefficients of variation were 3.1% and 7.9% respectively for samples with EBV load higher than the LLQ. The comparison between Abbott assay and in-house assay showed a good concordance (kappa = 0.77). Loads were higher with the Abbott assay (mean difference=0.62 log 10 copies/mL). Significance The EBV PCR Kit V1 assay on the m 2000 system provides a reliable and easy-to-use method for quantification of EBV DNA in WB.

Sensitive molecular assays have greatly improved the diagnosis of viral gastroenteritis. However, the proper preparation of stool samples for clinical testing remains an issue. bioMérieux has developed a stool preprocessing device (SPD) that includes a spoon for calibrated sampling and a vial containing buffer, glass beads, and two filters. The resulting stool filtrate is used for nucleic acid extraction. The purpose of this study was to evaluate the performance of the SPD for the quantification of human adenovirus (HAdV) DNA in stool samples collected from hematopoietic stem cell transplant (HSCT) recipients. HAdV DNA was quantified with the Adenovirus R-gene kit. The suitability of the device to reproducibly quantify HAdV DNA in stools using different extraction platforms (easyMAG and QIAsymphony) was determined using archived HAdV-positive stool samples. Coefficients of variation of HAdV DNA quantifications ranged from 1.79% to 1.83%, and no difference in quantification was observed between the two extraction systems. The HAdV DNA limit of quantification using the SPD was 3.75 log 10 copies/g of stool. HAdV DNA quantification using the SPD was then compared to that of the routine preprocessing technique on 75 fresh stool samples collected prospectively from pediatric HSCT recipients at risk for HAdV infections. Thirty-eight samples were HAdV DNA positive with both the SPD and routine preprocessing methods. HAdV DNA loads were on average 1.14-log 10 copies/g of stool higher with the SPD ( P < 0.0001) than with routine methods. This new device enabled a standardized preparation of stool samples in

Rationale: Noninvasive diagnostic multiplex molecular tests may enable the early identification and treatment of viral infections in critically ill immunocompromised patients. Objectives: To assess the association between viral detection in nasopharyngeal swabs and ICU mortality in critically ill hematology patients. Methods: This was a post hoc analysis of a prospective cohort of critically ill hematology patients admitted to 17 ICUs. Nasal swabs sampled and frozen at ICU admission were tested using a multiplex PCR assay. Predictors of ICU mortality and assay positivity were identified. Measurements and Main Results: Of the 747 patients (447 with acute respiratory failure [ARF]), 21.3% had a virus detected (56.4% rhinovirus/enterovirus and 30.7% influenza/ parainfluenza/respiratory syncytial viruses). Overall ICU and hospital mortality rates were 26% and 37%, respectively. Assay positivity was associated with lymphoproliferative disorders, hematopoietic stem cell transplantation, treatment with steroids or other immunosuppressants, ARF (25.5% vs. 16.3%; P = 0.004), and death in the ICU (28.9% vs. 19.3%; P = 0.008). The association with ICU mortality was significant for all viruses and was strongest for influenza/parainfluenza/respiratory syncytial viruses. In patients with ARF, detection of any respiratory virus was independently associated with ICU mortality (odds ratio, 2.07; 95% confidence interval, 1.22–3.50). Conclusions: Respiratory virus detection in the upper airway by multiplex PCR assay is common in critically ill hematology patients. In patients with ARF, respiratory virus detection was independently associated with ICU mortality. Multiplex PCR assay may prove helpful for the risk stratification of hematology patients with ARF. Studies to understand whether respiratory tract viruses play a causal role in outcomes are warranted., SCOPUS: ar.j, info:eu-repo/semantics/published

Background Viruses have been considered potential triggers for the development of diabetes. This study assessed insulin secretion and insulin sensitivity in human herpesvirus 8 (HHV8)-infected and uninfected sub-Saharan African people with diabetes. Methods In all, 173 people with non-autoimmune diabetes were enrolled consecutively: 124 with type 2 diabetes mellitus (T2DM) and 49 with ketosis-prone diabetes (KPD) admitted in hyperglycemic crisis. Those with KPD were further subdivided into those with new-onset ketotic-phase KPD (n = 34) or non-ketotic phase KPD (n = 15). All participants were screened for HHV8-specific antibodies and genomic DNA. Blood samples were collected for analysis of fasting glucose, HbA1c, lipid profile, and C-peptide, with insulin resistance and secretion estimated by homeostasis model assessment. Results Among the 173 diabetic participants, 88 (50.9%) were positive for HHV8 antibodies (Ac-HHV8+), including 15 (8.7%) positive for HHV8 DNA (DNA-HHV8+). The seroprevalence of HHV8 was similar between T2DM (55.6%) and KPD (61.2%) subjects. Of those with and without ketotic-phase KPD, 35.3% and 46.7% were Ac-HHV8+, respectively. Body mass index was significantly in lower DNA-HHV8+ than DNA-HHV8- subjects. Low-density lipoprotein and total cholesterol were significantly higher, but C-peptide and homeostatic model assessment of β-cell function (HOMA-β) were significantly lower in DNA-HHV8+ than DNA-HHV8- participants. After excluding DNA-HHV8+ participants, triglyceride concentrations were significantly higher in Ac-HHV8+ (n = 73) than Ac-HHV8- (n = 85) subjects. In contrast, HOMA-β was significantly higher among Ac-HHV8+ than Ac-HHV8- participants. Conclusions In the present study, HHV8 DNA positivity was associated with low insulin secretion in this sub-Saharan African diabetes population.

Introduction The worldwide use of yellow fever (YF) live attenuated vaccines came recently under close scrutiny as rare but serious adverse events have been reported. The population identified at major risk for these safety issues were extreme ages and immunocompromised subjects. Study NCT01426243 conducted by the French National Agency for AIDS research is an ongoing interventional study to evaluate the safety of the vaccine and the specific immune responses in HIV-infected patients following 17D-204 vaccination. As a preliminary study, we characterized the molecular diversity from E gene of the single 17D-204 vaccine batch used in this clinical study. Materials and methods Eight vials of lyophilized 17D-204 vaccine (Stamaril®, Sanofi-Pasteur, Lyon, France) of the E5499 batch were reconstituted for viral quantification, cloning and sequencing of C/prM/E region. Results The average rate of virions per vial was 8.68 ± 0.07 log10 genome equivalents with a low coefficient of variation (0.81%). 246 sequences of the C/prM/E region (29–33 per vials) were generated and analyzed for the eight vials, 25 (10%) being defective and excluded from analyses. 95% of sequences had at least one nucleotide mutation. The mutations were observed on 662 variant sites distributed through all over the 1995 nucleotides sequence and were mainly non-synonymous (66%). Genome variability between vaccine vials was highly homogeneous with a nucleotide distance ranging from 0.29% to 0.41%. Average p-distances observed for each vial were also homogeneous, ranging from 0.15% to 0.31%. Conclusion This study showed a homogenous YF virus RNA quantity in vaccine vials within a single lot and a low clonal diversity inter and intra vaccine vials. These results are consistent with a recent study showing that the main mechanism of attenuation resulted in the loss of diversity in the YF virus quasi-species.

Viruses have been considered potential triggers for the development of diabetes. This study assessed insulin secretion and insulin sensitivity in human herpesvirus 8 (HHV8)-infected and uninfected sub-Saharan African people with diabetes.In all, 173 people with non-autoimmune diabetes were enrolled consecutively: 124 with type 2 diabetes mellitus (T2DM) and 49 with ketosis-prone diabetes (KPD) admitted in hyperglycemic crisis. Those with KPD were further subdivided into those with new-onset ketotic-phase KPD (n = 34) or non-ketotic phase KPD (n = 15). All participants were screened for HHV8-specific antibodies and genomic DNA. Blood samples were collected for analysis of fasting glucose, HbA1c, lipid profile, and C-peptide, with insulin resistance and secretion estimated by homeostasis model assessment.Among the 173 diabetic participants, 88 (50.9%) were positive for HHV8 antibodies (Ac-HHV8+), including 15 (8.7%) positive for HHV8 DNA (DNA-HHV8+). The seroprevalence of HHV8 was similar between T2DM (55.6%) and KPD (61.2%) subjects. Of those with and without ketotic-phase KPD, 35.3% and 46.7% were Ac-HHV8+, respectively. Body mass index was significantly in lower DNA-HHV8+ than DNA-HHV8- subjects. Low-density lipoprotein and total cholesterol were significantly higher, but C-peptide and homeostatic model assessment of β-cell function (HOMA-β) were significantly lower in DNA-HHV8+ than DNA-HHV8- participants. After excluding DNA-HHV8+ participants, triglyceride concentrations were significantly higher in Ac-HHV8+ (n = 73) than Ac-HHV8- (n = 85) subjects. In contrast, HOMA-β was significantly higher among Ac-HHV8+ than Ac-HHV8- participants.In the present study, HHV8 DNA positivity was associated with low insulin secretion in this sub-Saharan African diabetes population.

International audience; Background: Human Adenovirus (HAdV) are responsible for severe infections in hematopoietic stem cells transplant (HSCT) recipient, species C viruses being the most commonly observed in this population. There is no approved antiviral treatment yet. Cidofovir (CDV), a cytidine analog, is the most frequently used and its lipophilic conjugate, brincidofovir (BCV), is under clinical development. These drugs target the viral DNA polymerase (DNA pol). Little is known about the natural polymorphism of HAdV DNA pol in clinical strains. Methods: We assessed the inter- and intra-species variability of the whole gene coding for HAdV DNA pol of HAdV clinical strains of species C. The study included 60 species C HAdV (21 C1, 27 C2 and 12 C5) strains isolated from patients with symptomatic infections who had never experienced CDV or BCV treatments and 20 reference strains. We also evaluated the emergence of mutations in thrirteen patients with persistent HAdV infection despite antiviral treatment. Results: We identified 356 polymorphic nucleotide positions (9.9% of the whole gene), including 102 positions with nonsynonymous mutations (28.0%) representing 8.7% of all amino acids. The mean numbers of nucleotide and amino acid mutations per strain were 23.1 (+/- 6.2) and 5.2 (+/- 2.4) respectively. Most of amino acid substitutions (60.6%) were observed in one instance only. A minority (13.8%) were observed in more than 10% of all strains. The most variable region was the NH2 terminal domain (44.2% of amino acid mutations). Mutations in the exonuclease domain accounted for 27.8%. The binding domains for the terminal protein (TPR), TPR1 and TPR2, presented a limited number of mutations, which were nonetheless frequently observed (62.5% and 58.8% of strains for TPR1 and TPR2, respectively). None of the mutations associated with CDV or BCV resistance were detected. In patients receieving antiviral drugs with persistent HAdV replication, we identified a new mutation in the NH2 terminal region. Conclusions: Our study shows a high diversity in HAdV DNA pol sequences in clinical species C HAdV and provides a comprehensive mapping of its natural polymorphism. These data will contribute to the interpretation of HAdV DNA pol mutations selected in patients receiving antiviral treatments.

Viral respiratory infections (VRIs) are frequent after hematopoietic stem cell transplantation and constitute a potential cause of mortality. We analyzed the incidence, risk factors, and prognosis of VRIs in a cohort of transplanted patients. More frequent viruses were human coronavirus and human rhinovirus followed by flu-like viruses and adenovirus. Risk factors for death were lymphocytopenia and high steroid dosage.

Background In patients with human immunodeficiency virus (HIV) infection, genital herpetic lesions may be extensive and tend to persist for longer periods; in addition, atypical hypertrophic, ulcerative, or pseudotumor forms have been reported, frequently showing resistance to acyclovir (ACV) treatment. Methods Between 2003 and 2011, 10 HIV-1-infected patients presenting with chronic pseudotumoral anogenital herpes simplex type 2 (HSV-2) infections were studied. Results All patients developed chronic, hypertrophic HSV-2 anogenital lesions with multilesional presentation in 7 cases and involvement of 2 anatomical sites in 6 of them. At the time of diagnosis, the median CD3(+)CD4(+) absolute blood count was 480.5 cells/µL (range, 165-632 cells/µL), whereas the plasma HIV load was undetectable in all cases. Histopathologic analysis of lesion biopsies showed a moderately dense dermal polytypic plasma cell infiltrate. Detection of HSV-2 by culture and/or polymerase chain reaction was positive for all patients, with evidence for ACV-resistant strains in 6 of 8 cases. In addition, viral resistance to ACV was found only in HSV-2 isolated from ulcerative lesions, whereas purely pseudotumoral ones harbored sensitive strains. Durable control was observed with HSV DNA polymerase inhibitors in only 2 cases, and the immunomodulators imiquimod and thalidomide allowed 5 patients to reach sustained complete response. Conclusions HSV-2-related pseudolymphoma in HIV-infected patients is characterized by a predominant polyclonal lymphoplasmacytic infiltration, and is frequently refractory to antiherpetic drugs. Immunomodulatory therapeutic strategies using thalidomide showed consistent efficacy, and should be considered early during the course of disease.

Respiratory viruses (RVs) are ubiquitous pathogens that represent a major cause of community-acquired pneumonia and chronic pulmonary diseases exacerbations. However, their contribution to acute respiratory failure events requiring intensive care unit admission in the era of rapid multiplex molecular assay deserves further evaluation. This study investigated the burden of viral infections in non immunocompromised patients admitted to the intensive care unit for acute respiratory failure using a multiplex molecular assay. Patients were investigated for RVs using immunofluoresence testing and a commercial multiplex molecular assay, and for bacteria using conventional culture. Half the patients (34/70, 49%) had a documented RVs infection. No other pathogen was found in 24 (71%) patients. Viral infection was detected more frequently in patients with obstructive respiratory diseases (64% vs. 29%; P = 0.0075). Multiplex molecular assay should be considered as an usefull diagnostic tool in patients admitted to the intensive care unit with acute respiratory failure, especially those with acute exacerbations of chronic obstructive pulmonary disease and asthma. J. Med. Virol. 86:1198–1202, 2014. © 2013 Wiley Periodicals, Inc.

Objectives Interleukin-2 (IL-2) therapy increased CD4 cell counts and delayed antiretroviral therapy (ART) initiation in HIV-infected patients in the Agence Nationale de Recherche sur le SIDA et les Hepatites Virales (ANRS) 119 trial. However, four cases of lymphoma were reported. Epstein−Barr virus (EBV) replication is associated with an increased risk of lymphoma in immunocompromised patients. We assessed whether IL-2 had an impact on EBV replication and the development of lymphoma. Methods A total of 130 ART-naive patients were randomized to receive IL-2 therapy (n = 66) or no treatment (n = 64). Clinical data for patients with lymphomas were reviewed and tumours assessed for evidence of EBV infection and CD25 (the IL-2 receptor) expression. EBV DNA levels were measured in whole blood and plasma in both arms using real-time polymerase chain reaction (PCR), up to 48 weeks after baseline (BL). Results Four lymphomas occurred, a median of 61 weeks [range 40−94 weeks] after randomization at a median CD4 cell count of 396 cells/μL (IQR 234–536 cells/μL). In the IL-2 arm, two patients developed EBV-positive Hodgkin's lymphoma, and one developed EBV-negative Burkitt-type lymphoma. One patient in the control group developed EBV-positive non-Hodgkin's lymphoma. CD25 was negative in all cases. Among the 41 of 55 (control arm) and 44 of 58 (IL-2 arm) patients with detectable EBV DNA in whole blood at both BL and week 48, the median change in EBV DNA between BL and week 48 was +0.04 log10 copies/ml in both arms (P = 0.7). In plasma, EBV was detected at least once in 22 of 52 controls and 21 of 54 IL-2-treated patients (P = 0.8). Conclusions IL-2 therapy had no significant effect on EBV replication over 48 weeks in these ART-naive patients. The occurrence of lymphomas did not seem to be associated with IL-2 therapy.

Summary Objectives We report the biological and clinical impacts possibly associated with HHV-6 reactivation in autologous hematopoietic stem cell transplant (AHSCT) recipients after intensive chemotherapy regimen for lymphoma. Methods We retrospectively reviewed clinical, biological, radiological, treatment and outcomes of patients with positive HHV-6 DNA in whole blood following autologous hematopoietic stem cell transplantation. Results Blood HHV-6 reactivation was reported in 27 (8.5%) patients among 316 AHSCT recipients after high dose therapy for lymphoma. Thirteen (4.1%) patients were symptomatic with fever (100%), diarrhea (61.5%), skin rash (46.1%), and pneumonia (23.1%). Antiviral treatment was administered in 9 (69%) patients and outcome was favorable in all cases. Conclusion Our study suggests a possible pathogenic role of HHV-6 in AHSCT recipients and suggests an impact of antiviral treatments on viral replication and clinical signs resolution.

We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2.

Skin rash are common in immunocompromised patients, particularly after bone marrow transplantation. Human herpes virus 6 (HHV6) reactivation is often suspected, but its clinical presentation and the routine laboratory tests may be unspecific, thus leading to late diagnosis. In this case, we report specific intralymphocytic cytopathic inclusions on skin biopsy as a sign of systemic HHV6 reactivation. A 56-year-old patient presented progressive erythroderma and fever occurring after autologous hematopoietic stem-cell transplantation for mantle cell lymphoma. The skin biopsy showed a perivascular infiltrate of medium-to-large lymphocytes with irregular nuclei containing a large central basophilic inclusion surrounded by a clear halo. High levels of HHV-6 genomic in skin biopsy confirm HHV-6-induced cytopathic effect. The clinical course improved with intravenous foscavir. The specific histopathological findings encountered in this case are exceptional but recognizable, and along with HHV-6 DNA detection allow a prompt recognition of HHV6 skin rash.

OBJECTIVES: Few studies have examined the frequency and duration of genital herpes simplex virus (HSV) shedding in sub-Saharan Africa. This study describes HSV shedding patterns among a sample of HSV-2-seropositive women enrolled in a placebo-controlled trial of HSV suppressive therapy (acyclovir 400 mg twice a day) in Tanzania. METHODS: Trial participants were invited to participate in a substudy involving 12 clinic visits over 4 weeks. At each visit, cervical, vaginal and external skin swabs were taken and analysed for HSV DNA using inhouse real-time PCR. RESULTS: HSV shedding was mainly subclinical (90%; 57/63 shedding days in the placebo arm). The most frequent shedding site was the external skin, but HSV DNA was detected from all three sites on 42% (27/63) of shedding days. In HIV-negative women, HSV DNA was detected on 3% (9/275) of days in the acyclovir versus 11% (33/309) in the placebo arm, while in HIV-positive women, detection was on 14% (23/160) versus 19% (30/155) of days, respectively. CONCLUSIONS: HSV shedding was common, varying greatly by individual. Shedding rates were similar to studies in African and non-African settings. Among HIV-negative women, shedding rates were lower in the acyclovir arm; however, acyclovir did not substantially impact on HSV shedding in HIV-positive women.

Herpes simplex virus (HSV) suppressive therapy reduces genital and plasma human immunodeficiency virus type 1 (HIV-1) RNA over periods up to 3 months, but the long-term effect is unknown.A total of 484 HIV-1 and HSV type 2 seropositive Tanzanian women aged 16-35 years were enrolled in a randomized placebo-controlled trial of acyclovir administered at a dosage of 400 mg twice daily. Cervico-vaginal lavage and blood samples were collected at 6 months, 12 months, and 24 months for quantification of genital and plasma HIV-1 RNA and genital HSV DNA. Primary outcomes were detection and quantity of cervico-vaginal HIV-1 RNA at 6 months.At 6 months, there was little difference between the acyclovir and placebo arms for cervico-vaginal HIV-1 RNA detection (88 [ 41 .3%] of 213 vs 84 [ 44 .0%] of 191; odds ratio [OR], 0.90; 95% confidence interval [CI], 0.60-1.33), HSV DNA detection (20 [ 9 .4%] of 213 vs 22 [ 11 .5%] of 191; OR, 0.80; 95% CI, 0.42-1.51), genital HIV or HSV loads, or plasma HIV-1 RNA load. Estimated median adherence was 91%. There was a suggestion of an impact on cervico-vaginal HIV-1 RNA detection among women with estimated adherence 90% (OR, 0.74; 95% CI, 0.50-1.09) when data from all 3 visits were included.Acyclovir administered at a dosage of 400 mg twice daily is unlikely to be a useful long-term intervention to reduce HIV transmission. The lack of effect on HIV may be attributable to suboptimal adherence or treatment regimen.

Resume Myxovirus influenza est un virus a ARN enveloppe ubiquitaire, agent d’infections respiratoires hautes, voire basses chez les patients les plus fragiles. Malgre l’inquietude croissante concernant la survenue d’une nouvelle pandemie grippale, la grippe saisonniere reste responsable de lourdes morbidite et mortalite ainsi que d’un cout socioeconomique eleve. Les complications de la grippe peuvent etre extrarespiratoires, respiratoires ou liees a la decompensation d’une pathologie cardiaque ou respiratoire sous-jacente, ces dernieres etant responsables de la majorite des deces lies a la grippe. Longtemps sous-estimee chez les patients immunodeprimes, la grippe est maintenant reconnue comme un veritable pathogene respiratoire opportuniste chez ces patients. Sa reelle incidence chez l’immunodeprime est mal connue, mais probablement elevee car superposable a celle de la communaute, veritable reservoir de virus pour les patients immunodeprimes. La grippe se caracterise chez ces patients par une frequence accrue d’atteintes respiratoires basses compliquant l’evolution de pres d’un tiers des patients d’oncohematologie et transplantes pulmonaires. Ces pneumonies liees a la grippe peuvent etre virales, mais aussi secondaires a une surinfection bacterienne ou fongique dont la recherche doit etre systematique. Elles peuvent evoluer vers l’insuffisance respiratoire aigue avec en consequence une mortalite elevee. Aucun traitement antiviral de la grippe n’a ete evalue chez le patient immunodeprime. En l’absence de traitement valide, la prevention de la grippe de l’immunodeprime est capitale. La necessite d’isolement des patients hospitalises atteints de grippe a ete illustree par la survenue d’epidemies nosocomiales dans des services prenant en charge des immunodeprimes. La vaccination reste cependant l’element cle de la prevention. La probable reduction d’efficacite et l’absence d’evaluation clinique du vaccin dans cette population soulignent l’importance de la vaccination de l’entourage et du personnel soignant pour reduire les risques de transmission. Malgre l’incidence elevee de la grippe dans le monde, la physiopathologie des atteintes respiratoires basses grippales reste mal connue. Des etudes evaluant la pathogenicite directe du virus sur l’epithelium alveolaire ou la susceptibilite a la surinfection induite par la lesion virale de l’epithelium bronchique permettraient de definir la place du traitement antiviral preemptif ou curatif.

Methods: We compared the performance of 3 collection methods for cervicovaginal secretions [cervicovaginal lavage (CVL), CVL enriched with a cervical swab (eCVL), and vaginal tampon (VT)] to identify the most reliable method for detection of cervicovaginal HIV-1 and herpes simplex virus type 2 (HSV-2). HIV-1 RNA (Nuclisens EasyQ; BioMerieux, Marcy-l'Etoile, France), HSV-2 DNA (real-time polymerase chain reaction), and microscopic blood and semen traces were detected in samples from 19 HIV-1-HSV-2-coinfected women seen at 4 weekly visits. Results: HIV-1 RNA was detected in 49 (79%) of 62 eCVLs, 41 (61%) of 67 CVLs, and 27 (57%) of 47 VTs. Detection of HIV-1 RNA was higher in eCVL compared with CVL [45/58 (78%) vs. 32/58 (55%); risk ratio 1.41, 95% confidence interval 1.05 to 1.88]. Conclusions: Although more eCVLs were contaminated with microscopic blood (29%) than CVLs (22%) or VTs (7%), detection of HIV-1 RNA remained higher using eCVL compared with CVL (risk ratio 1.43, 95% confidence interval 1.02 to 2.02) in uncontaminated samples. HSV-2 DNA was detected in less than 10% of samples by each method but in 7 (37%) of 19 women overall by 1 or more methods.

Resume Differents outils sont disponibles pour etablir le diagnostic d’une infection herpetique a HSV-1 ou HSV-2. Le diagnostic direct est generalement privilegie. Le diagnostic indirect s’avere dans de nombreuses situations utile voire necessaire. Il comprend la serologie non specifique de type qui revele la presence d’anticorps IgG ou IgM diriges contre l’un ou l’autre des deux virus sans les distinguer et la serologie specifique de type qui revele la presence soit des anticorps anti-HSV-1 soit des anticorps anti-HSV-2. Seule la serologie non specifique de type est inscrite a la nomenclature des actes de biologie medicale. Son interet diagnostique est toutefois limite. Les performances actuelles des serologies specifiques de type permettent de reconsiderer leur place dans les strategies diagnostiques. Plusieurs trousses marquees CE sont disponibles sur le marche. Une attention particuliere doit cependant etre portee sur le choix de la technique, celles utilisant des antigenes recombinants et validees par la communaute scientifique sur differentes populations doivent etre privilegiees. L’interpretation des resultats doit tenir compte de la population evaluee et du contexte clinique.

Points essentiels L’epidemiologie de l’herpes genital evolue La seroprevalence des infections a HSV-2 augmente et HSV-1 est une etiologie des ulcerations genitales herpetiques de plus en plus frequente. L’examen diagnostique de reference est le diagnostic direct par isolement viral en culture cellulaire ou amplification du genome viral. La serologie herpetique est principalement indiquee si l’examen direct est negatif et en l’absence de lesions. La serologie non specifique de type detecte les anticorps communs a HSV-1 et HSV-2. Elle presente d’excellentes specificite et sensibilite. Elle est inscrite a la nomenclature des actes de biologie medicale. Elle ne permet pas de specifier le type de virus en cause. La serologie specifique de type permet de distinguer les anticorps anti-HSV-1 et anti-HSV-2. Les trousses commercialisees presentent, selon la population etudiee, une sensibilite et une specificite d’environ 90 a 100 %. Elle n’est pas inscrite a la nomenclature des actes de biologie medicale. La serologie specifique de HSV-1 ne permet pas d’etablir un diagnostic d’infection genitale ancienne a HSV-1. En revanche, une seropositivite pour HSV-2 permet generalement d’etablir le diagnostic d’herpes genital a HSV-2. L’indication de la serologie specifique de type se discute en fonction du contexte clinique. L’interet de la serologie non specifique de type est restreint.

The performances of commercial enzyme-linked immunosorbent assays (ELISAs) in detecting herpes simplex virus type 2 (HSV-2) antibodies have been inconsistent for African and human immunodeficiency virus (HIV)-positive populations. We compared the performances of the HerpeSelect and Kalon glycoprotein G2 ELISAs for patients with genital ulcer disease in Ghana and the Central African Republic. Sera from 434 women were tested with the HerpeSelect assay, and a subsample ( n = 199) was tested by the Kalon assay. Ulcer swabs and cervicovaginal lavage samples were tested for HSV-2 DNA by PCR. HSV-2-seronegative women with detectable genital HSV-2 DNA were retested for HSV-2 antibodies 14 and 28 days later by the two ELISAs. A total of 346 (80%) women were positive by HerpeSelect at baseline, and 225 (54%) had detectable genital (lesional or cervicovaginal) HSV-2 DNA. Sixty-six (19%) HerpeSelect-positive samples had low-positive index values (1.1 to 3.5), and 58% of these samples had detectable genital HSV-2 DNA. Global agreement between the two serological assays was 86%. Concordance was high (99%) for sera that were negative by HerpeSelect or had high index values (>3.5). Defining infection detected by HSV-2 DNA PCR and/or Kalon assay as true infection, 71% of sera with low-positive index values were associated with true HSV-2 infection. Twenty-five women were identified as having nonprimary first-episode genital HSV-2 infection. Rates of HSV-2 seroconversion at day 14 were 77% (10/13 patients) by HerpeSelect assay and 23% (3/13 patients) by Kalon assay, with four additional seroconversions detected by Kalon assay at day 28. HIV serostatus did not influence assay performance. Low index values obtained with the HerpeSelect assay may correspond to true HSV-2 infection, in particular to nonprimary first episodes of genital HSV-2 infection, and need to be interpreted in the context of clinical history.