Institut de Virologie

TTick-borne encephalitis (TBE), caused by the tick-borne encephalitis virus (TBEV), is primarily transmitted to humans through Ixodes tick bites. TBEV comprises three main subtypes describing distinct severity and clinical course: European (TBEV-Eu), Siberian (TBEV-Sib), and Far Eastern (TBEV-Fe). Over the past decade, TBE epidemiology significantly changed in Europe, with an increasing incidence in endemic countries and the discovery of new human case foci and areas of virus circulation. This emergence involves many factors whose impact is not easily determined. While most TBEV-Eu infections are asymptomatic, some patients develop meningitis, or meningoencephalitis, associated with post-infectious sequelae. Several studies recently evaluated the burdens of these sequelae and their associated medical costs. During the complex TBE neuropathogenesis, the antagonism between viral and immunological factors is not clearly identified, nor are the predictive factors of clinical severity. New diagnostic tools are being developed. While TBE treatment is currently only symptomatic, several antiviral treatments are under study.

BackgroundAlthough the annual number of newly reported human immunodeficiency virus (HIV) infections in Beijing has shown a continuous decline since 2016, the population of people living with HIV (PLWH) has maintained a persistent upward trend. This retrospective study aimed to analyse data from newly diagnosed PLWH from 2015 to 2023 in Beijing to develop precision interventions.MethodsAll newly diagnosed PLWH were subjected to sequence splicing, quality control, information matching, and analysis for pretreatment drug resistance (PDR) and molecular transmission network. The Stanford Drug Resistance Database was used to analyse drug resistance, and Hyphy and Cytoscape software were used to construct a molecular transmission network with the gene distance threshold of 0.015.ResultsA total of 3,569 newly diagnosed PLWH were included in this study. A total of 42 HIV-1 subtypes were identified, with CRF01_AE being the most common subtype, followed by the CRF07_BC and B subtypes. However, for the first time, the dominant strain shifted from CRF01_AE to CRF07_BC in 2023. A total of 340 drug-resistant sequences were obtained, and the overall prevalence of PDR was 9.53% from 2015 to 2023. The most common mutations were distributed among V179, K103, M184, S68 and M46, which presented diverse distributions and combined mutation features. A total of 64 transmission clusters were identified in the network, among which CRF07_BC was dominated by large spreading clusters, whereas CRF01_AE was dominated by small- and medium-sized spreading clusters. The largest cluster for CRF07_BC expanded rapidly from 8 cases in 2015 to 161 cases in 2023.ConclusionsThis study revealed the prevalence of HIV-1 drug resistance and molecular transmission network in Beijing. The change in the dominant HIV strain of participants should be emphasized. Subtype CRF07_BC is prone to forming fast-spreading clusters, and targeted interventions should be designed to prevent high-risk transmission sources and reduce new HIV infections.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12985-025-02985-3.

Severe acute respiratory syndrome coronavirus 2, the virus responsible for coronavirus disease 2019, affects multiple organs. The virus enters cells through angiotensin-converting enzyme-2 and host factors present in genital organs, leading to concern over virus shedding in semen and reproductive function. To investigate severe acute respiratory syndrome coronavirus 2 in semen from patients with a mild infection, identify the seminal infected cells, and explore the effect of the infection on sex hormones and semen parameters. Prospective study of 54 men with mild severe acute respiratory syndrome coronavirus 2 infection. Semen was collected at 7, 15, 30, 60, 90, 180, and 365 days after symptom onset, and severe acute respiratory syndrome coronavirus 2 RNA was measured in serum, saliva, urine, and semen. The presence of infectious severe acute respiratory syndrome coronavirus 2 in semen was assessed using Vero cell culture. Infected semen cells were identified using immunofluorescence against severe acute respiratory syndrome coronavirus 2 nucleoprotein antigen and cell markers. Semen characteristics as well as testosterone, inhibin B, luteinizing hormone, and follicle-stimulating hormone levels were determined. 11% of patients had at least one severe acute respiratory syndrome coronavirus 2 RNA-positive semen. One patient had viral semen shedding up to day 90 after infection onset, with replication-competent virus isolated from semen and 40% cell fraction at day 7. After sperm preparation, 90% fraction was severe acute respiratory syndrome coronavirus 2 RNA-positive at days 7 and 15. The swim-up fraction was positive only on day 7. In semen, nucleoprotein antigen was detected mainly in exfoliated epithelial cells and less frequently in Sertoli cells. Sperm count and motile sperm count were lower at day 30 than at day 7. Round cells in semen were increased during the acute phase. At days 7 and 15, sperm count and motile sperm count were lower in severe acute respiratory syndrome coronavirus 2 RNA-positive semen compared with negative semen, while semen volume and follicle-stimulating hormone levels were increased. Long-term follow-up shows no evidence of a detrimental effect on hormonal or semen characteristics. 11% of patients with mild coronavirus disease 2019 who were not hospitalized had severe acute respiratory syndrome coronavirus 2 excretions in semen, which persisted for up to 90 days in one patient. No germ cells appeared infected by the virus, but the detection of nucleoprotein antigen-positive epithelial semen cells and Sertoli cells suggests genital tract infection. Albeit infrequent, semen may contain the replication-competent virus during the acute phase with potential risk of severe acute respiratory syndrome coronavirus 2 transmissions during sexual contact and assisted reproduction procedures. The effect of mild coronavirus disease 2019 on spermatogenesis and reproductive hormones was moderate and reversible.

Abstract Following a pacemaker implantation, a 75-years-old patient suffered from five successive bacteremia episodes between in 1999 and 2013 despite long-term antibiotic treatment, with intermittent vegetation apparition on the device atrial lead. Four blood isolates, identified asYersinia enterocoliticabioserotype 4/O:3, were further genetically and phenotypically characterized. Phylogenetic reconstruction showed that the patient was chronically infected by the same strain, which evolved within the host for 14 years. Single-nucleotide polymorphism (SNP) analysis indicates that the last two isolates evolved in parallel and formed two independent lineages within the host. Pan-genome analysis and genome comparison showed that their common evolution was characterized by 41 small insertion/deletion events, loss of three large DNA fragments and mutations in 140 genes. A phylogenetic analysis by maximum likelihood identified two genes presenting a positive selection signal, suggesting that these mutations provided a survival advantage to bacteria during chronic infection. Quinolone resistance in the last two isolates was acquired through a so far undescribed deletion in thegyrAgene.Mass-spectrometry analysis revealed a strong proteome remodeling in the last two isolates which was correlated with a truncation in the stringent response regulator DksA. A reduced carbon, energy and purine metabolism supports their severe growth defectsin vitro. 3rd-generation cephalosporin resistance of the last isolate was correlated with a truncation of OmpF, the main porin translocating antibiotics through the outer-membrane, as well as an increased production of BlaA and AmpC β-lactamases.This is the first report of genetic and phenotypic changes associated to within-host adaptation of a pathogenicYersiniaspecies under antibiotic pressure.

Polyomaviruses BK (BKPyV) and JC (JCPyV), belonging to the Polyomaviridae, are responsible for human pathologies. In kidney transplant recipients, BKPyV replication can lead to irreversible nephron damage whereas JCPyV replication remains asymptomatic. Concomitant replication is rare and potential competition between the infections has been described. The aim of this retrospective case-control study was to describe the molecular epidemiology and risk factors associated with BKPyV and JCPyV replication in a cohort of kidney transplant recipients. In total, 655 urine samples from 460 patients were tested for BKPyV and JCPyV DNA. Positive samples were submitted to strain genotyping. Demographic and clinical characteristics were also compared. Isolated JCPyV and BKPyV was found in 16.5% and 23.3% of patients, respectively; co-replication was rare (3.9%). BKPyV strains Ib-2, Ib-1, and IVc-2 were the most prevalent. JCPyV strains mostly belonged to genotypes 4 and 1B. During follow-up, JCPyV shedding significantly reduced the risk of BKPyV DNAuria, with an odds ratio of 0.57 (95% confidence interval: 0.35-0.99), and was associated with better prognosis than BKPyV replication, based on the estimated glomerular filtration rate. Molecular epidemiology of BKPyV and JCPyV strains in our region was similar to previous studies. This study suggests that JCPyV is benign and appears to limit damaging BKPyV replication. JCPyV DNAuria screening could thus be a useful strategy to predict BKPyV-related outcomes.

In their study "Pancreatic Enucleation Patients Share the Same Quality of Life as the General Population at Long-Term Follow-Up", Giuliani et al. (1) assess short-and longterm outcomes including quality of life after pancreatic enucleation (PE). PE aims to preserve endocrine and exocrine function while ensuring surgical ablation of a presumed benign pancreatic tumor (neuroendocrine tumors, mucinous cystadenoma, serous cystadenoma, branch duct intraductal papillary mucinous neoplasms and solid pseudopapillary tumors). However, the rate of postoperative pancreatic fistula is up to 70%, particularly when the tumor is localized at the head and is close to the main duct (2-6). To assess if this advantage is perceived by patients, quality of life was considered knowing that there is no literature data concerning the quality of life following PE unlike the other pancreatic resections (7-11). Data collected were from consecutive patients who underwent PE from

The study enrolled 284 patients with chronic hepatitis B virus infection. Participants included people with mild fibrotic lesions (32.5%), moderate to severe fibrotic lesions (27.5%), cirrhotic lesions (22%), hepatocellular carcinoma (HCC) in 5%, and people with no fibrotic lesions in 13%. Eleven SNPs within DIO2, PPARG, ATF3, AKT, GADD45A, and TBX21 were genotyped by mass spectrometry. The rs225014 TT (DIO2) and rs10865710 CC (PPARG) genotypes were independently associated with susceptibility to advanced liver fibrosis. However, cirrhosis was more prevalent in individuals with the GADD45A rs532446 TT and ATF3 rs11119982 TT genotypes. In addition, the rs225014 CC variant of DIO2 was more frequently found in patients with a diagnosis of HCC. These findings suggest that the above SNPs may play a role in HBV-induced liver damage in a Caucasian population.