Effect of steroid pulses in severe BK virus allograft nephropathy with extensive interstitial inflammation.

INTRODUCTION: As there is no specific antiviral treatment currently available for BK polyomavirus associated nephropathy (BKVAN), its management relies on immunosuppression reduction in kidney transplant patients. Data on efficacy of steroid pulses in this indication are lacking. METHODS: We performed a retrospective monocenter study on 64 patients diagnosed with biopsy-proven BKVAN. Patients within the "pulse group" (n = 37) received IV methylprednisolone 10 mg/kg 3 days consecutively. In the "low dose" steroid group (n = 27), patients were continued oral prednisone 5 mg daily. RESULTS: Mean follow up was 78 months in the steroid pulse group and 56 months in the low dose group (p = 0.15). Mean eGFR values at diagnosis were comparable, as well as other demographic characteristics. Mean BK plasma viral load was higher in "pulse" than in "low dose" steroid group. Pulse group had higher inflammation and tubulitis (p < 0.05). Graft loss reached 57% in the "pulse" group versus 41% in the "low dose" group, p = 0.20. Rejection events were similar. No major adverse event was statistically associated with steroid pulse, including infections, cancer, and de novo diabetes. CONCLUSION: No significant differences were found in the evolution of both groups of patients, despite patients receiving "pulse" steroids were identified as the most severe sharing higher BK viral load and more frequent active lesions on histology.

Influence of Nasopharyngeal Viral Load on the Spread of the Omicron BA.2 Variant.

We used variant typing polymerase chain reaction to describe the evolution of severe acute respiratory syndrome coronavirus 2 Omicron sublineages between December 2021 and mid-March 2022. The selective advantage of the BA.2 variant over BA.1 is not due to greater nasopharyngeal viral loads.

Effects of Acute Dengue Infection on Sperm and Virus Clearance in Body Fluids of Men.

We investigated the effects of dengue virus (DENV) on semen using samples collected 7, 15, 30, 60, and 90 days after symptom onset from 10 infected volunteers on Réunion Island. We assessed characteristics of semen and reproductive hormones and isolated motile spermatozoa from semen. We assayed semen for DENV using reverse transcription PCR and searched for DENV RNA by virus isolation in Vero E6 cell cultures. Four volunteers had >1 DENV RNA-positive semen samples; 2 volunteers had DENV RNA-positive semen at day 15 and 1 at day 30. No motile sperm were DENV positive. After exposure to positive semen, few Vero E6 cells stained positive for DENV antigens, indicating low levels of replicative virus. We found DENV had shorter duration in semen than in blood. These findings support the possibilities that DENV is sexually transmissible for a short period after acute dengue illness and that acute dengue induces reversible alterations in sperm.

Estimating the impact of public health strategies on the spread of SARS-CoV-2: Epidemiological modelling for Toulouse, France.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting disease COVID-19 has killed over 2 million people as of 22 January 2021. We have used a modified susceptible, infected, recovered epidemiological model to predict how the spread of the virus in France will vary depending on the public health strategies adopted, including anti-COVID-19 vaccination. Our prediction model indicates that the French authorities' adoption of a gradual release from lockdown could lead in March 2021 to a virus prevalence similar to that before lockdown. However, a massive vaccination campaign initiated in January 2021 and the continuation of public health measures over several months could curb the spread of virus and thus relieve the load on hospitals.

Hydroxychloroquine in Coronavirus Disease 2019 Patients: What Still Needs to Be Known About the Kinetics.

Different dosage regimens of hydroxychloroquine are used to manage coronavirus disease 2019 (COVID-19) patients, without information on the pharmacokinetics in this population. Blood samples (n = 101) were collected from 57 COVID-19 patients for 7 days, and concentrations were compared with simulated kinetic profiles. Hydroxychloroquine exposure is low and cannot be predicted by other populations.

Peripheral Plasma and Semen Cytokine Response to Zika Virus in Humans.

We assessed Zika virus RNA and select cytokine levels in semen, blood, and plasma samples from an infected patient in South America. Viral RNA was detected in semen >2 months after viremia clearance; cytokine profiles differed in semen and plasma. After viremia, Zika virus appears to become compartmentalized in the male reproductive tract.

Multirecombinant Enterovirus A71 Subgenogroup C1 Isolates Associated with Neurologic Disease, France, 2016-2017.

In 2016, an upsurge of neurologic disease associated with infection with multirecombinant enterovirus A71 subgenogroup C1 lineage viruses was reported in France. These viruses emerged in the 2000s; 1 recombinant is widespread. This virus lineage has the potential to be associated with a long-term risk for severe disease among children.

Zika Virus Infection and Prolonged Viremia in Whole-Blood Specimens.

We tested whole-blood and plasma samples from immunocompetent patients who had had benign Zika virus infections and found that Zika virus RNA persisted in whole blood substantially longer than in plasma. This finding may have implications for diagnosis of acute symptomatic and asymptomatic infections and for testing of blood donations.

A nationwide survey of hepatitis E viral infection in French blood donors.

UNLABELLED: Most cases of hepatitis E viral (HEV) infection in developed countries are autochthonous. Nevertheless, the reported seroprevalence of HEV varies greatly depending on the geographical area and the performance of the immunoassay used. We used validated assays to determine the prevalence of anti-HEV immunoglobulin G (IgG) and IgM among 10,569 French blood donors living in mainland France and three overseas areas. Epidemiological information was collected using a specific questionnaire. We found an overall IgG seroprevalence of 22.4% (8%-86.4%) depending on the geographical area (P < 0.001). The presence of anti-HEV IgG was associated with increasing age (P < 0.001) and eating pork meat (P = 0.03), pork liver sausages (P < 0.001), game meat (P < 0.01), offal (P < 0.001), and oysters (P = 0.02). Conversely, drinking bottled water was associated with a lower rate of anti-HEV IgG (P = 0.02). Overall IgM seroprevalence was 1% (0%-4.6%). The frequency of anti-HEV IgM was higher in donors living in a high anti-HEV IgG seroprevalence area (1.9% versus 0.7%, P < 0.001) and in those eating pork liver sausage (1.4% versus 0.7%, P < 0.01), pâté (1% versus 0.4, P = 0.04), and wild boar (1.3% versus 0.7%, P < 0.01). CONCLUSION: HEV is endemic in France and hyperendemic in some areas; eating habits alone cannot totally explain the exposure to HEV, and contaminated water could contribute to the epidemiology of HEV infection in France.

Epidemiological and clinical characteristics of patients infected with enterovirus D68, France, July to December 2014.

In 2014, the United States (US) experienced a nationwide outbreak of enterovirus D68 (EV-D68) infection with 1,152 cases reported mainly in hospitalised children with severe asthma or bronchiolitis. Following the US alert, 11 laboratories of the French enterovirus (EV) surveillance network participated in an EV-D68 survey. A total of 6,229 respiratory samples, collected from 1 July to 31 December 2014, were screened for EV-D68 resulting in 212 EV-D68-positive samples. These 212 samples corresponded to 200 EV-D68 cases. The overall EV-D68 positivity rates among respiratory samples were of 5% (184/3,645) and 1.1% (28/2,584) in hospitalised children and adults respectively. The maximum weekly EV-D68 positivity rates were of 16.1% for children (n = 24/149; week 43) and 2.6% for adults (n = 3/115; week 42). Of 173 children with EV-D68 infection alone, the main symptoms were asthma (n = 83; 48.0%) and bronchiolitis (n = 37; 21.4%). One child developed acute flaccid paralysis (AFP) following EV-D68-associated pneumonia. Although there was no significant increase in severe respiratory tract infections reported to the French public health authorities, 10.7% (19/177) of the EV-D68 infected children and 14.3% (3/21) of the EV-D68 infected adults were hospitalised in intensive care units. Phylogenetic analysis of the viral protein 1 (VP1) sequences of 179 EV-D68 cases, revealed that 117 sequences (65.4%), including that of the case of AFP, belonged to the B2 variant of clade B viruses. Continuous surveillance of EV-D68 infections is warranted and could benefit from existing influenza-like illness and EV surveillance networks.

Characterization of the polyproline region of the hepatitis E virus in immunocompromised patients.

Little is known about virus adaptation in immunocompromised patients with chronic genotype 3 hepatitis E virus (HEV3) infections. Virus-host recombinant strains have been isolated recently from chronically infected patients. The nature and incidence of such recombinant events occurring during infections of solid-organ transplant (SOT) recipients are essentially unknown. The polyproline region (PPR) of strains isolated from SOT patients was sequenced during the acute-infection phase (n = 59) and during follow-up of patients whose infections became chronic (n = 27). These 27 HEV strains included 3 (11%) that showed recombinant events 12, 34, 48, or 88 months after infection. In one strain, parts of the PPR and the RNA-dependent RNA polymerase were concomitantly inserted. In the second, a fragment of a human tyrosine aminotransferase (TAT) gene was inserted first, followed by a fragment of PPR. A fragment of the human inter-α-trypsin inhibitor (ITI) gene was inserted in the third. All the inserted sequences were rich in aliphatic and basic amino acids. In vitro growth experiments suggest that the ITI insertion promoted more vigorous virus growth. In silico studies showed that the inserted sequences could provide potential acetylation, ubiquitination, and phosphorylation sites. We found that recombinant events had occurred in the HEV PPR in approximately 11% of the strains isolated from chronically infected transplant patients followed up in Toulouse University Hospital. These inserted fragments came from the HEV genome or a human gene and could enhance virus replication. Importance: Hepatitis E virus (HEV) can cause chronic infections in immunocompromised patients, including solid-organ transplant (SOT) recipients. Two strains that had undergone recombination with human ribosomal genes were described recently. The strains with inserted sequences replicated better in vitro. Little is known about the frequency of such recombinant events or how such an insertion enhances replication. We therefore investigated 59 SOT patients infected with HEV and found 3 strains with 4 recombinant events in 27 of these patients whose infection became chronic. The 4 inserted sequences were of different origins (human gene or HEV genome), but all were enriched in aliphatic and basic amino acids and provided potential regulation sites. Our data indicate that recombinant events occur in approximately 11% of strains isolated from chronically infected patients. The structures of the inserted sequences provide new clues as to how the inserted sequences could foster virus replication.

Influence of polyproline region and macro domain genetic heterogeneity on HEV persistence in immunocompromised patients.

Hepatitis E virus (HEV) can chronically infect immunocompromised patients. The polyproline region (PPR) and the macro domain of ORF1 protein may modulate virus production and/or the host immune response. We investigated the association between the genetic heterogeneity of HEV quasispecies in ORF1 and the outcome of infection in solid-organ transplant patients. Both sequence entropy and genetic distances during the hepatitis E acute phase were higher in patients whose infection became chronic than in those who cleared the virus. Hence, great quasispecies heterogeneity in the regions encoding the PPR and the macro domain may facilitate HEV persistence.

Hepatitis E virus reinfections in solid-organ-transplant recipients can evolve into chronic infections.

BACKGROUND: Hepatitis E virus (HEV) infections are a major cause of acute hepatitis in developing and industrialized countries. Little is known about anti-HEV immunity in solid-organ recipients. METHODS: We screened 263 solid-organ recipients for anti-HEV immunoglobulin G (IgG) at transplantation. They were followed up for 1 year and tested for HEV RNA and anti-HEV antibodies 1 year after transplantation and if their liver enzyme activities increased. RESULTS: A total of 38.4% had anti-HEV IgG at transplantation. The mean concentrations (±SD) of anti-HEV IgG at transplantation (8 ± 17.5 U/mL) and 1 year later (6.4 ± 12.0 U/mL, P = .4) were similar. There were 3 de novo HEV infections during the 1-year follow-up among patients who were HEV seronegative before transplantation, giving an annual incidence of 2.1%. We also identified 3 HEV reinfections among patients who were seropositive before transplantation through detection of HEV RNA, for an annual incidence of 3.3%. Their anti-HEV IgG concentrations were 0.3, 2.1, and 6.2 World Health Organization (WHO) units/mL before transplantation. Reinfection of the patient with the lowest IgG concentration at transplantation had evolved to a chronic infection. CONCLUSIONS: Low anti-HEV antibodies (<7 WHO units/mL) seemed not to protect solid-organ recipients. HEV reinfection in immunocompromised patients can lead to chronic infection, as in primary infections.

Neurological involvement related to the influenza virus in children: A 5-year single-centre retrospective study.

INTRODUCTION: Inflammation related to influenza virus infection can lead to multiple neurological presentations. Encephalitis is one of them, mostly accompanied by seizures, with different profiles depending on the epidemics and previous medical conditions. MATERIALS AND METHODS: All children presenting neurological symptoms and positive for influenza virus RNA detection in a respiratory sample between November 2018 and April 2023, hospitalized in the Department of Paediatric Neurology of Toulouse Children's Hospital, were retrospectively analysed. RESULTS: Among the 1,277 children diagnosed with influenza in our centre, 131 (10.3 %) were hospitalized for neurological features. The year 2020-2021 was marked by zero incidence of positive influenza tests, associated with the COVID-19 pandemic. Among the 131 patients included, 71.6 % were under 5 years old. Most of them (80.9 %) were infected by influenza A virus. The first neurological symptoms were mainly seizures in 73.3 % of patients. Possible or confirmed encephalitis was observed in 29 % of cases, including one acute necrotizing encephalopathy. Few children (6.1 %) presented with acute myositis. Twenty-seven patients (20.6 %) had a personal history of significant previous neurological disorders. Most patients (88.5 %) displayed a rapid favourable outcome, marked by the disappearance of their neurological symptoms within the first 2 days. Anti-epileptic drugs were introduced in 1.5 % of cases, and adapted in 16.8 %, mainly in patients with febrile status epilepticus and an abnormal EEG. CONCLUSION: Neurological features were frequently associated with influenza infection in children; most were transient. Effects on long-term neurodevelopmental outcomes need to be clarified as our follow-up was limited, especially in children with pre-existing neurological conditions.

Necrotizing pneumonia in children: Report of 25 cases between 2008 and 2018 at a French tertiary care center.

BACKGROUND: Necrotizing pneumonia (NP) is a serious and rare disease in children. Pediatric data on NP are limited and the impact of the 13-valent pneumococcal conjugate vaccine has been very poorly evaluated. PATIENTS AND METHODS: We conducted a retrospective study at Toulouse University Hospital between 2008 and 2018. Children who presented with thin-walled cavities in the areas of parenchymal consolidation on imaging were included in the study. RESULTS: The incidence of NP did not decrease during this period. Bacterial identification occurred in 56% of cases (14/25) and included six cases of Streptococcus pneumoniae, five of Staphylococcus aureus, two of Streptococcus pyogenes, and one of Streptococcus viridans. Streptococcus pneumoniae NP are more frequently associated with empyema/parapneumonic effusion compared to S. aureus NP (p = 0.02). Patients with S. pyogenes NP more often required volume expansion than did S. pneumoniae cases (p = 0.03). When comparing children born before and after implementation of the 13-valent pneumococcal conjugate vaccine, we identified a relative modification of the bacterial epidemiology, with an increase in the proportion of S. pyogenes NP and S. aureus NP and a decrease in the proportion of NP caused by S. pneumoniae. CONCLUSION: Future studies are needed to assess the epidemiology of NP in children. Continued surveillance of identified pneumococcal serotypes is essential to document epidemiological changes in the coming years.

Genotype 3 diversity and quantification of hepatitis E virus RNA.

Genotype 3 hepatitis E viruses (HEVs) are distributed across the world and are now considered to be an emerging public health concern in industrialized countries. At least 10 genotype 3 subtypes have been identified in humans and animals worldwide. It was recently reported that the sensitivities of HEV RNA assays differ greatly. We have assessed the influence of genotype 3 diversity on the performances of two HEV RNA assays: one targeting the ORF3 gene and the other targeting the ORF2 gene. We tested a panel of 5 HEV-positive reference samples of genotypes 3a, 3b, 3c, 3e, and 3f at 10-fold serial dilutions. The HEV RNA concentrations obtained with both reverse transcription (RT)-PCRs were correlated, but the RT-PCR based on ORF2 underestimated the HEV RNA concentrations. The mean [ORF3 - ORF2] difference was 1.41 log copies/ml. We also tested 34 clinical specimens of genotypes 3c (n = 15), 3e (n = 4), and 3f (n = 15), representing the most prevalent subtypes in Europe. The mean [ORF3 - ORF2] differences were 1.41 log copies/ml for genotype 3c, 0.96 log copies/ml for genotype 3e, and 0.70 log copies/ml for genotype 3f. The bias between the 2 RT-PCR assays was significantly greater for genotype 3c than for genotype 3f (P = 0.007). We therefore recommend the use of an RT-PCR protocol based on ORF3 to quantify HEV RNA of genotype 3 strains.

Performance of a rapid molecular multiplex assay for the detection of influenza and picornaviruses.

BACKGROUND: Multiplex assays are a new strategy for diagnosing respiratory infections. These assays are better than those based on cultures or antigen detection, but few data are available for comparing them to monoplex polymerase chain reactions (PCRs). This study evaluated the performance of the Luminex xTAG Respiratory Viral Panel (RVP) Fast assay with reference to 2 real-time PCR assays for detecting type A influenza H1 viruses and human enteroviruses and rhinoviruses. METHODS: This was an analysis of nasal swab specimens obtained from 590 outpatients suffering from acute respiratory tract disease between September 2009 and February 2010. RESULTS: The RVP Fast assay performed well in less than 4 h for detecting type A influenza H1 viruses, particularly (H1N1)pdm09, and human entero/rhinoviruses, with 95.2% and 90.05% agreement, respectively, when compared to monoplex real-time PCR assays. This multiplex assay also detected at least 1 virus in 69.3% of the specimens and detected multiple infections in 40 samples. CONCLUSIONS: The multiplex assay detected clinically important viruses in a single genomic test. It will thus be useful for detecting several viruses causing respiratory tract disorders.

Will the latest wave of the COVID-19 pandemic be an ecological disaster? There is an urgent need to replace plastic by ecologically virtuous materials.

Background and Aims: Direct virological diagnosis of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infectionis based on either viral antigen or viral genome detection. These methods, in addition to the dedicated reagents and transport packaging, require the use of quantities of plastic that may individually appear negligible but which, in the context of a pandemic, are very high. The aim was to estimate the amount of plastic involved in a diagnostic assay whether molecular or antigenic. Methods: We weighed the plastics used to obtain a diagnostic assay result for SARS-CoV-2 infection in our hospital. Results: Each ready-to-use antigen assay requires about 20 g of plastic whereas the PCR assay implies the use of 30 g. This unit mass, when compared to our laboratory's SARS-CoV-2 genomic screening activity,represents more than 10 tons of plastic for 2021. At our region level (#6.10 inhabitants), more than 350 tons of plastic were used to carry out more than 7 million declared PCR assays and as many antigenic assays. Conclusions: The virologic diagnostic activityl inked to the SARS-CoV-2 pandemic has highlighted once more our dependance for plastic use. We must already think about a more environmentally virtuous diagnostic activity by integrating a reasonned use of diagnostic tools and a higher use of ecological friendly material. Parallel the notion of waste management must also be addressed in order to limit their environmental impact.

Contribution of COVID Antigenic RDT to the Management Strategy of COVID-19 Pandemic in a Senegalese Company.

OBJECTIVE: To describe the contribution of the rapid antigen diagnostic testing (RDT) to the management strategy of the COVID-19 pandemic. METHODOLOGIES: The protein chain reaction (PCR) and the RDT have been performed on each COVID-19 suspected workers from December 2020 to September 2021. RESULTS: A total of 286 people tested. A positivity rate of 38.1% was recorded. The average time to obtain PCR results was 8.3 days. 54.8% (n = 142) of the RDT were followed by a PCR for confirmation or invalidation and 100% of positive cases with Ag-RDT were confirmed by the PCR. We have noticed a 58.3% reduction of lost work days due to COVID-19, since the use of the Ag-RDT. CONCLUSION: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapid diagnostic tests are efficient. They have enabled early treatment of COVID-19 patients, helped hold back the spread of the disease in a high-risk professional environment, and reduced the impact of the pandemic on a vital sector in developing countries.