Genetic characterization of pathogen isolates is increasingly important in healthcare settings, yet the bioinformatic workflows required can be complex and resource-intensive. Here we analyzed 19 environmental Legionella pneumophila isolates using whole genome sequencing (WGS) and compared results from an established multi-step bioinformatic pipeline with several accessible, single-step analysis tools. All approaches produced consistent clustering patterns, resolving the isolates into two major genetic clusters. No clear association between spatial sampling distance and genetic relatedness was observed within this dataset: one cluster was detected in two settlements 50 km apart, while both clusters also co-occurred on a single hospital floor. Across this dataset, all WGS-based approaches provided clustering resolution broadly comparable to MLST/cgMLST. These findings indicate that accessible WGS analysis tools can reproduce the main genomic relationships inferred by more complex workflows while reducing analytical complexity and required bioinformatic expertise. Based on these observations, we discuss how rapid low-complexity WGS workflows may support future same-day bacterial isolate characterization in applied settings.

Virus infections elicit long-term IgG antibody and memory responses. Human cytomegalovirus (HCMV) is widespread in humans and disseminates despite the presence of virus-specific antibodies. Here, we report that the HCMV Fc gamma-binding glycoprotein 34 modulates humoral immunity by binding to IgG(+) memory B cells. gp34-B cell receptor (BCR) interaction initiates activation of the PDK1/AKT/mTOR/S6 pathway and BCR internalization in a SYK-independent manner. Prolonged stimulation also induces B-cell activation via upregulation of CD69 and CD86. In a T-cell-dependent response, however, interaction with gp34 blocks B-cell proliferation, differentiation into plasmablasts, and soluble IgG production, while stimulating TNF-alpha secretion. Through gp34 stimulation on IgG(+) B cells, neighboring IgM(+) and IgA(+) B cells are likewise impaired in proliferation, plasmablast formation, and immunoglobulin secretion. In summary, gp34 specifically interacts with IgG(+) memory B cells, inducing a hyporesponsive state across the B-cell compartment through direct and indirect regulation. This reveals a novel mode of viral evasion from B-cell responses by suppressing secondary immunity.

Immunocompromised patients struggle to adequately clear viral infections, offering the virus the opportunity to adapt to the immune system in the host. Here we present a case study of a patient undergoing allogeneic hematopoietic stem cell transplantation with a 521-day follow-up of a SARS-CoV-2 infection with the BF.7.21 variant. Virus samples from five time points were submitted to whole genome sequencing. Between the first detection of SARS-CoV-2 infection and its clearance, the patient’s virus population acquired 34 amino acid substitutions and 8 deletions in coding regions. With 11 amino acid substitutions in the receptor binding domain of the virus’ spike protein, substitutions were 15 times more abundant than expected for a random distribution in this highly functional region. Amongst them were the substitutions S:K417T, S:N440S, S:K444R, S:V445A, S:G446N, S:L452Q, S:N460K, and S:E484V at positions that are notorious for their resistance-mediating effects. The substitution patterns found indicate ongoing adaptive evolution.

Infection of cells with the human cytomegalovirus (HCMV) triggers the expression of interferon-stimulated genes (ISGs). ISGs encode proteins with antiviral functions, such as inhibiting viral replication, promoting cell death of infected cells and enhancing immune responses. HCMV has evolved mechanisms to evade the antiviral effects of ISGs. The viral proteins encoded by the viral genes US7, US8, and US9 have been shown to interfere with interferon induction. US7 to US9 are embedded in a cluster of HCMV genes, termed US2 to US11. The individual members of this gene family interfere on multiple levels with innate and adaptive immune responses to HCMV infection. Using viral mutants with different deletions in US2 to US11, we addressed the question if genes other than US7 to US9 would also influence the IFN responses. Surprisingly, deletion of the complete US2 to US11 gene region led to reduced levels of selected ISGs. Cells infected with viruses in which individual US2 to US11 genes were deleted showed a less pronounced reduction of the selected ISGs. The experiments including RNA-seq analyses indicate that genes of the US2 to US11 gene family have a complex interaction with the IFN-ISG response which is likely regulated on the level of ISG protein stability. As US2–US11 are dispensable for replication in cell culture, the genomic region was frequently used for the insertion of bacterial artificial chromosome vectors in the process of cloning the complete HCMV genome. The results shown here must be considered when viruses derived from BACs with US2–US11 deletions are used and whether appropriate controls must be applied.

The phosphoprotein 65 (pp65, pUL83) of human cytomegalovirus (HCMV) serves several functions during the viral life cycle. It is one of the most abundant constituents of the virion tegument and the major component of subviral particles termed Dense Bodies. It is also one of several tegument proteins that mediate the subversion of cellular antiviral defence functions like the induction of IFNs. It is also involved in the transcriptional activation of the major immediate early IE1/IE2 gene. Despite its strong nucleophilic nature, pp65 is found in the cytoplasm at late stages of infection. We have previously shown that the nuclear retention phenotype of a mutated pp65 is associated with a distinct deficit in viral productivity. In this study, we generated HCMV mutant viruses in which the nuclear localization signals (nls) of pp65 were mutated, thus preventing nuclear entry and pp65 shuttling. Since the genetic manipulation of UL83 led to the deregulation of the adjacent pp71 gene in initial experiments, we chose to express pp65 with mutated nls from a distant locus within the genome of a TB40/e strain derivative. This virus, termed v65stop-pp65nls, was significantly impaired in its capacity to produce infectious progeny. Using knockout fibroblast cells for the DNA sensors IFI16 or cGAS, no differences were seen when progeny production was compared between v65stop-pp65nls and a strain expressing wt pp65. Thus, differences in the known subversive effect on these DNA sensors could not account for the differences seen in productivity. Surprisingly, the upload of pp65 into virions and the synthesis of subviral Dense Bodies were abrogated by the mutation of its nls. Although an impairment of pp65 interaction with other proteins by the mutations cannot be excluded, the data suggest that the migration of pp65 through the nucleus was important for HCMV progeny production and packaging.

Background During the SARS-CoV-2 pandemic, dominant viral variants were repeatedly replaced by new variants with altered properties, frequently changing the dynamics of the infection event, as well as the effectiveness of vaccines and therapeutics. SARS-CoV-2 variant monitoring by whole genome sequencing was established at the University Medical Center Mainz, Germany to support patient management during the pandemic. Methods SARS-CoV-2 RNA samples from the University Medical Center were analysed weekly with whole genome sequencing. The genome sequences obtained were aligned with sequences from public databases to perform variant assignment. For classification purposes, phylogenetic trees were constructed to map the variant distribution in the clinical settings and the current outbreak events at that time. We describe the surveillance procedures using an example from a geriatric ward. Results For monitoring, a time series was created covering two years of the pandemic. The changes from the Alpha to the Delta and the Omicron variants of SARS-CoV-2 could thus be precisely observed. The increasingly rapid switch of Omicron subvariants in the recent past could be tracked. The elucidation of phylogenetic relationships between circulating strains allowed conclusions about transmission pathways. Using an example from a geriatric ward, we demonstrated how variant monitoring by whole genome sequencing supported the infection prevention and control procedures on a ward and contribute to the control of outbreaks. Conclusions This example of SARS-CoV-2 demonstrates the effectiveness of targeted, local monitoring by molecular variant analysis. The program proved to be instrumental in controlling an outbreak on a geriatric ward.

In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.

(1) Background: Intrinsic defense mechanisms are pivotal host strategies to restrict viruses already at early stages of their infection. Here, we addressed the question of how the autophagy receptor sequestome 1 (SQSTM1/p62, hereafter referred to as p62) interferes with human cytomegalovirus (HCMV) infection. (2) Methods: CRISPR/Cas9-mediated genome editing, mass spectrometry and the expression of p62 phosphovariants from recombinant HCMVs were used to address the role of p62 during infection. (3) Results: The knockout of p62 resulted in an increased release of HCMV progeny. Mass spectrometry revealed an interaction of p62 with cellular proteins required for nucleocytoplasmic transport. Phosphoproteomics further revealed that p62 is hyperphosphorylated at position S272 in HCMV-infected cells. Phosphorylated p62 showed enhanced nuclear retention, which is concordant with enhanced interaction with viral proteins relevant for genome replication and nuclear capsid egress. This modification led to reduced HCMV progeny release compared to a non-phosphorylated version of p62. (4) Conclusions: p62 is a restriction factor for HCMV replication. The activity of the receptor appears to be regulated by phosphorylation at position S272, leading to enhanced nuclear localization, viral protein degradation and impaired progeny production.

(1) Background: Infection with human cytomegalovirus (HCMV) leads to the production and release of subviral particles, termed Dense Bodies (DB). They are enclosed by a membrane resembling the viral envelope. This membrane mediates the entrance of DBs into cells in a way that is comparable to virus infection. HCMV attachment and entry trigger the induction of interferon synthesis and secretion, and the subsequent expression of interferon-regulated genes (IRGs) that might inhibit replication of the virus. Recently, we demonstrated that DBs induce a robust interferon response in the absence of infection. Little is known thus far, including how DBs influence HCMV infection and virus–host interaction. (2) Methods: Purified DBs were used to study the impact on virus replication and on the innate defense mechanisms of the cell. (3) Results: The incubation of cells with DBs at the time of infection had little effect on viral genome replication. Preincubation of DBs, however, led to a marked reduction in viral release from infected cells. These cells showed an enhancement of the cytopathic effect, associated with a moderate increase in early apoptosis. Despite virus-induced mechanisms to limit the interferon response, the induction of interferon-regulated genes (IRGs) was upregulated by DB treatment. (4) Conclusions: DBs sensitize cells against viral infection, comparable to the effects of interferons. The activities of these particles need to be considered when studying viral–host interaction.

Human cytomegalovirus (HCMV) is a pathogen of high medical relevance. Subviral Dense Bodies (DB) were developed as a vaccine candidate to ameliorate the severe consequences of HCMV infection. Development of such a candidate vaccine for human application requires detailed knowledge of its interaction with the host. A comprehensive mass spectrometry (MS)- based analysis was performed regarding the changes in the proteome of cell culture cells, exposed to DB.

(1) Background: Cells infected with the human cytomegalovirus (HCMV) produce subviral particles, termed dense bodies (DBs), both in-vitro and in-vivo. They are released from cells, comparable to infectious virions, and are enclosed by a membrane that resembles the viral envelope and mediates the entry into cells. To date, little is known about how the DB uptake influences the gene expression in target cells. The purpose of this study was to investigate the impact of DBs on cells, in the absence of a viral infection. (2) Methods: Mass spectrometry, immunoblot analyses, siRNA knockdown, and a CRISPR-CAS9 knockout, were used to investigate the changes in cellular gene expression following a DB exposure; (3) Results: A number of interferon-regulated genes (IRGs) were upregulated after the fibroblasts and endothelial cells were exposed to DBs. This upregulation was dependent on the DB entry and mediated by the type I interferon signaling through the JAK-STAT pathway. The induction of IRGs was mediated by the sensing of the DB-introduced DNA by the pattern recognition receptor cGAS. (4) Conclusions: The induction of a strong type I IFN response by DBs is a unique feature of the HCMV infection. The release of DBs may serve as a danger signal and concomitantly contribute to the induction of a strong, antiviral immune response.

Human cytomegalovirus (HCMV) infection is associated with severe disease conditions either following congenital transmission of the virus or viral reactivation in immunosuppressed individuals. Consequently, the establishment of a protective vaccine is of high medical need. Several candidates have been tested in preclinical and clinical studies, yet no vaccine has been licensed. Subviral dense bodies (DB) are a promising vaccine candidate. We have recently provided a GMP-compliant protocol for the production of DB, based on a genetically modified version of the HCMV laboratory strain Towne, expressing the pentameric complex of envelope protein gH-gL-pUL128-131 (Towne-UL130rep). In this work, we genetically attenuated Towne-UL130rep by abrogating the expression of the tegument protein pUL25 and by fusing the destabilizing domain ddFKBP to the N-terminus of the IE1- and IE2-proteins of HCMV. The resulting strain, termed TR-VAC, produced high amounts of DB under IE1/IE2 repressive conditions and concomitant supplementation of the viral terminase inhibitor letermovir to the producer cell culture. TR-VAC DB retained the capacity to induce neutralizing antibodies. A complex pattern of host protein induction was observed by mass spectrometry following exposure of primary human monocytes with TR-VAC DB. Human monocyte-derived dendritic cells (DC) moderately increased the expression of activation markers and MHC molecules upon stimulation with TR-VAC DB. In a co-culture with autologous T cells, the TR-VAC DB-stimulated DC induced a robust HCMV-specific T cell-activation and –proliferation. Exposure of donor-derived monocytic cells to DB led to the activation of a rapid innate immune response. This comprehensive data set thus shows that TR-VAC is an optimal attenuated seed virus strain for the production of a DB vaccine to be tested in clinical studies.

The regulation of the nucleocytoplasmic release of herpesviral capsids is defined by the process of nuclear egress. Due to their large size, nuclear capsids are unable to traverse via nuclear pores, so that herpesviruses evolved to develop a vesicular transport pathway mediating their transition through both leaflets of the nuclear membrane. This process involves regulatory proteins, which support the local distortion of the nuclear envelope. For human cytomegalovirus (HCMV), the nuclear egress complex (NEC) is determined by the pUL50-pUL53 core that initiates multicomponent assembly with NEC-associated proteins and capsids. Hereby, pUL50 serves as a multi-interacting determinant that recruits several viral and cellular factors by direct and indirect contacts. Recently, we generated an ORF-UL50-deleted recombinant HCMV in pUL50-complementing cells and obtained first indications of putative additional functions of pUL50. In this study, we produced purified ΔUL50 particles under both complementing (ΔUL50C) and non-complementing (ΔUL50N) conditions and performed a phenotypical characterization. Findings were as follows: (i) ΔUL50N particle preparations exhibited a clear replicative defect in qPCR-based infection kinetics compared to ΔUL50C particles; (ii) immuno-EM analysis of ΔUL50C did not reveal major changes in nuclear distribution of pUL53 and lamin A/C; (iii) mass spectrometry-based quantitative proteomics showed a large concordance of protein contents in the NIEP fractions of ΔUL50C and ΔUL50N particles, but virion fraction was close to the detection limit for ΔUL50N; (iv) confocal imaging of viral marker proteins of immediate early (IE) and later phases of ΔUL50N infection indicated a very low number of cells showing an onset of viral lytic protein expression; and, finally (v) quantitative measurements of encapsidated genomes provided evidence for a substantial reduction in the DNA contents in ΔUL50N compared to ΔUL50C particles. In summary, the results point to a complex and important regulatory role of the HCMV nuclear egress protein pUL50 in the maturation of infectious virus.

Reactivation of latent cytomegalovirus (CMV) endangers the therapeutic success of hematopoietic cell transplantation (HCT) in tumor patients due to cytopathogenic virus spread that leads to organ manifestations of CMV disease, to interstitial pneumonia in particular. In cases of virus variants that are refractory to standard antiviral pharmacotherapy, immunotherapy by adoptive cell transfer (ACT) of virus-specific CD8 + T cells is the last resort to bridge the “protection gap” between hematoablative conditioning for HCT and endogenous reconstitution of antiviral immunity. We have used the well-established mouse model of CD8 + T-cell immunotherapy by ACT in a setting of experimental HCT and murine CMV (mCMV) infection to pursue the concept of improving the efficacy of ACT by therapeutic vaccination (TherVac) post-HCT. TherVac aims at restimulation and expansion of limited numbers of transferred antiviral CD8 + T cells within the recipient. Syngeneic HCT was performed with C57BL/6 mice as donors and recipients. Recipients were infected with recombinant mCMV (mCMV-SIINFEKL) that expresses antigenic peptide SIINFEKL presented to CD8 + T cells by the MHC class-I molecule K b . ACT was performed with transgenic OT-I CD8 + T cells expressing a T-cell receptor specific for SIINFEKL-K b . Recombinant human CMV dense bodies (DB-SIINFEKL), engineered to contain SIINFEKL within tegument protein pUL83/pp65, served for vaccination. DBs were chosen as they represent non-infectious, enveloped, and thus fusion-competent subviral particles capable of activating dendritic cells and delivering antigens directly into the cytosol for processing and presentation in the MHC class-I pathway. One set of our experiments documents the power of vaccination with DBs in protecting the immunocompetent host against a challenge infection. A further set of experiments revealed a significant improvement of antiviral control in HCT recipients by combining ACT with TherVac. In both settings, the benefit from vaccination with DBs proved to be strictly epitope-specific. The capacity to protect was lost when DBs included the peptide sequence SIINFEKA lacking immunogenicity and antigenicity due to C-terminal residue point mutation L8A, which prevents efficient proteasomal peptide processing and binding to K b . Our preclinical research data thus provide an argument for using pre-emptive TherVac to enhance antiviral protection by ACT in HCT recipients with diagnosed CMV reactivation.

A high vaccination rate of older and particularly chronically ill people against coronavirus disease-2019 (COVID-19) is likely one of the most important factors in containing the pandemic. When Germany's vaccination campaign started on December 2020, vaccination prioritization was initially carried out starting with older population groups. Side effect rates in 1065 individuals who had received the first dose of the messenger ribonucleic acid (mRNA) vaccine BNT162b2 Tozinameran from BioNTech/Pfizer three weeks earlier were examined retrospectively. An age- and gender-graded data analysis showed clear age and gender differences with regard to vaccine-related adverse effects. In 77% of all individuals over 80 years of age, no local or systemic side effects were reported after the first vaccination, whereas in the age group up to 80 years, only 37% showed no side effects. In the whole study population, 64% of females and 73% of males reported no adverse effects. The initial vaccination with mRNA vaccine BNT162b2 shows an overall low profile of side effects. Particularly in those over 80 years, an extraordinarily good tolerance with equally good effectiveness is evident. The sex comparison showed that women suffer more often from adverse vaccination reactions. In order to achieve sufficient herd immunity, both age- and gender-dependent vaccination reactions and any difference in the maintenance of immunity should be considered in future vaccination strategies.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has forced the implementation of unprecedented public health measures strategies which might also have a significant impact on the spreading of other viral pathogens such as influenza and Respiratory Syncytial Virus (RSV) . The present study compares the incidences of the most relevant respiratory viruses before and during the SARS-CoV-2 pandemic in emergency room patients. We analyzed the results of in total 14,946 polymerase chain reaction point-of-care tests (POCT-PCR) for Influenza A, Influenza B, RSV and SARS-CoV-2 in an adult and a pediatric emergency room between December 1, 2018 and March 31, 2021. Despite a fivefold increase in the number of tests performed, the positivity rate for Influenza A dropped from 19.32% (165 positives of 854 tests in 2018/19), 14.57% (149 positives of 1023 in 2019–20) to 0% (0 positives of 4915 tests) in 2020/21. In analogy, the positivity rate for Influenza B and RSV dropped from 0.35 to 1.47%, respectively, 10.65–21.08% to 0% for both in 2020/21. The positivity rate for SARS-CoV2 reached 9.74% (110 of 1129 tests performed) during the so-called second wave in December 2020. Compared to the two previous years, seasonal influenza and RSV incidence was eliminated during the COVID-19 pandemic. Corona-related measures and human behavior patterns could lead to a significant decline or even complete suppression of other respiratory viruses such as influenza and RSV.

While establishing a regional SARS-Cov-2 variant surveillance by genome sequencing, we have identified three infected individuals in a clinical setting (two long-term hospitalized patients and a nurse) that shared the spike N501Y mutation within a genotype background distinct from the current viral variants of concern. We suggest that the adaptive N501Y mutation, known to increase SARS-CoV-2 transmissibility, arose by convergent evolution around December in Mainz, Germany. Hospitalized patients with a compromised immune system may be a potential source of novel viral variants, which calls for monitoring viral evolution by genome sequencing in clinical settings.

Zusammenfassung Die Autoren erklären den bisherigen Verlauf von Covid-19 in Deutschland durch Regressionsanalysen und epidemiologische Modelle. Sie beschreiben und quantifizieren den Effekt der gesundheitspolitischen Maßnahmen (GPM), die bis zum 19. April in Kraft waren. Sie berechnen den erwarteten Verlauf der Covid-19-Epidemie in Deutschland, wenn es diese Maßnahmen nicht gegeben hätte, und zeigen, dass die GPM einen erheblichen Beitrag zur Reduktion der Infektionszahlen geleistet haben. Die seit 20. April gelockerten GPM sind zwischen den Bundesländern relativ heterogen, was ein Glücksfall für die Wissenschaft ist. Mittels einer Analyse dieser Heterogenität kann aufgedeckt werden, welche Maßnahmen für eine Bekämpfung einer eventuellen zweiten Infektionswelle besonders hilfreich und besonders schädlich sind.

The assembly of human cytomegalovirus (HCMV) virions is an orchestrated process that requires, as an essential prerequisite, the complex crosstalk between viral structural proteins. Currently, however, the mechanisms governing the successive steps in the constitution of virion protein complexes remain elusive. Protein phosphorylation is a key regulator determining the sequential changes in the conformation, binding, dynamics, and stability of proteins in the course of multiprotein assembly. In this review, we present a comprehensive map of the HCMV virion proteome, including a refined view on the virion phosphoproteome, based on previous publications supplemented by new results. Thus, a novel dataset of viral and cellular proteins contained in HCMV virions is generated, providing a basis for future analyses of individual phosphorylation steps and sites involved in the orchestrated assembly of HCMV virion-specific multiprotein complexes. Finally, we present the current knowledge on the activity of pUL97, the HCMV-encoded and virion-associated kinase, in phosphorylating viral and host proteins.

We model the evolution of the number of individuals that are reported to be sick with COVID-19 in Germany. Our theoretical framework builds on a continuous time Markov chain with four states: healthy without infection, sick, healthy after recovery or after infection but without symptoms and dead. Our quantitative solution matches the number of sick individuals up to the most recent observation and ends with a share of sick individuals following from infection rates and sickness probabilities. We employ this framework to study inter alia the expected peak of the number of sick individuals in a scenario without public regulation of social contacts. We also study the effects of public regulations. For all scenarios we report the expected end of the CoV-2 epidemic.