Biology subjects

Lauber, C.

Publications and source records attributed to Lauber, C..

9 recordsLinked to original sources

bioRxiv2026

The actin motor protein MYO10 facilitates post-entry spread of respiratory syncytial virus

Human respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infections in infants. However, host factors that influence disease severity remain incompletely defined. While clinical risk factors are known, identifying genetic susceptibility has been challenging. In this study, we combined human genetics with functional virology to identify host factors that modulate RSV infection and spread. Starting from a cohort of infants hospitalized with severe RSV disease, we prioritized rare coding variants present in homozygous form and predicted to cause strong functional impairment, and selected candidate genes for mechanistic follow-up. Functional interrogation of 23 candidates by CRISPR/Cas9 knockout screening in human lung epithelial cells identified unconventional myosin-X (MYO10), encoding the actin-based motor protein myosin-X, as a critical host factor for RSV. Genetic disruption or siRNA-mediated depletion of MYO10 significantly reduced RSV infectivity, with the strongest effects at post-entry stages of the viral life cycle. Loss of MYO10 impaired filopodia formation, cell migration, and wound healing, leading to altered cell-cell connectivity and restricted viral dissemination. MYO10 depletion reduced both short-range cell-to-cell transmission and longer-distance extracellular spread, resulting in fewer infected cells and diminished accumulation of progeny virus in culture supernatants. In contrast, RSV entry, early gene expression, and interferon responses were unaffected. Finally, a rare homozygous MYO10 motor-domain variant (rs7737765; H148Y), enriched in severe cases, also reduced RSV replication in cell culture--opposite to expectations for a risk allele--yet underscoring biological relevance and suggesting that MYO10 variation may influence disease in vivo through additional effects on epithelial function. ImportanceRespiratory syncytial virus (RSV) is a major cause of severe respiratory illness in infants, yet it remains unclear why some children develop more serious disease than others. In this study, we combined patient genetic data with laboratory experiments to identify host factors that influence how RSV spreads in the lung. We found that the human protein MYO10, which mediates the formation of small cell protrusions, plays a key role in enabling the virus to spread from cell to cell. When MYO10 was disrupted, viral spread was strongly reduced, even though early steps of infection were unaffected. Interestingly, a rare genetic variant in MYO10 found in patients also altered viral replication, highlighting potential clinical relevance. These findings provide new insight into how host cell architecture contributes to RSV infection and suggest that targeting host pathways involved in viral spread could complement existing antiviral strategies.

microbiology↗

bioRxiv2026

Data-Driven Virus Discovery with Virushunter and Virusgatherer

We present Virushunter and Virusgatherer, a bipartite computational workflow for discovering viral genomes from unprocessed next-generation sequencing data. Virushunter conducts a profile Hidden Markov Model-based sequence homology search for viral hallmark protein-coding sequence reads to construct microcontigs, which are used as seeds for targeted viral genome assembly by Virusgatherer. We showcase the application of Virushunter and Virusgatherer through an RNA virus-wide screen in 3348 bat transcriptome sequencing experiments from the Sequence Read Archive. Many of the discovered viruses are likely prototypes of new putative virus species, including a novel alphacoronavirus identified in a South American velvety free-tailed bat and a novel rhabdovirus in a European barbastelle bat. The tools are implemented as a reproducible Snakemake pipeline, which is available at https://github.com/lauberlab/VirusHunterGatherer.

bioinformatics↗

bioRxiv2026

A large replicase of nidovirus-like complexity in a putative RNA virus order "Quisvirales" expands the known diversity of helicase superfamilies

Helicases are essential ATPases that unwind nucleic acids and are classified into six recognized superfamilies (SF1-SF6). All positive-stranded RNA viruses (ssRNA+) with genomes larger than [~]7 kb encode SF1-SF3 helicases, linking them to RNA genome expansion. In the phylum Pisuviricota that includes many pathogens, helicases of SF1-SF3 are integrated into multi-enzyme replicases including 3C(-like) proteases (3CLpro) and RNA-dependent RNA polymerases (RdRp). Here, large-scale mining of invertebrate metastranscriptomes uncovered six related spider-associated ssRNA+ viruses that, based on their conserved 3CLpro-RdRp module, genome size (20-22 kb), and phylogeny, form a putative new order, "Quisvirales". Quisviruses have similar genome and replicase architectures to enveloped coronaviruses and other nidoviruses. However, the nidovirus SF1 helicase is replaced in quisviruses by a novel superfamily helicase that, like the Picornavirales SF3 helicase, comprises an AAA+ (ATPase-like) domain. Thus, viruses with large replicases of nidovirus-like complexity may have evolved repeatedly from an 3CLpro-RdRp-encoding ancestor.

microbiology↗

bioRxiv2025

RNA virus genomes from centuries- to millennia-old Adelie penguin mummies

Direct studies of long-term RNA virus evolution are largely limited to chemically-fixed specimens from museums collected over the past two centuries. Detecting genomic traces of RNA viruses in older, buried remains is considered highly unlikely. The cold, dry conditions of Antarctica may represent an exception. Here, natural mummification of penguins and seals--animals that form large colonies where RNA viruses circulate--is common, potentially facilitating RNA virus genome recovery. Here, we show that Adelie penguin (Pygoscelis adeliae) mummies, ranging in age from recent to nearly two millennia, indeed contain ancient viral genome fragments. Metatranscriptomic analyses yielded near-complete genome sequences of a picornavirus (Megrivirus epengu) and a rotavirus D (Rotavirus deltagastroenteritidis) from relatively recent specimens. We further retrieved rotavirus D sequences from a 280-year-old individual and a near-complete rotavirus G (Rotavirus gammagastroenteritidis) genome from a 2000-year-old one. These findings pave the way to direct studies of RNA virus evolution across millennia.

molecular biology↗

bioRxiv2024

Porphyromonas gingivalis outer membrane vesicles alter neuronal architecture and Tau phosphorylation in the embryonic mouse brain

Porphyromonas gingivalis (Pg) is an oral bacterial pathogen that has been associated with systemic inflammation and adverse pregnancy outcomes such as low birth weight and preterm birth. Pg drives these sequelae through virulence factors decorating the outer membrane that are present on non-replicative outer membrane vesicles (OMV) that are suspected to be transmitted systemically. Given that Pg abundance can increase during pregnancy, it is not well known whether Pg-OMV can have deleterious effects on the brain of the developing fetus. We tested this possibility by treating pregnant C57/Bl6 mice with PBS (control) and OMV from ATCC 33277 by tail vein injection every other day from gestational age 3 to 17. At gestational age 18.5, we measured dam and pup weights and collected pup brains to quantify changes in inflammation, cortical neuron density, and Tau phosphorylated at Thr231. Dam and pup weights were not altered by Pg-OMV exposure, but pup brain weight was significantly decreased in the Pg-OMV treatment group. We found a significant increase of Iba-1, indicative of microglia activation, although the overall levels of IL-1{beta}, IL-6, TNF, IL-4, IL-10, and TGF{beta} mRNA transcripts were not different between the treatment groups. Differences in IL-1{beta}, IL-6, and TNF concentrations by ELISA showed IL-6 was significantly lower in Pg-OMV brains. Cortical neuron density was modified by treatment with Pg-OMV as immunofluorescence showed significant decreases in Cux1 and SatB2. Overall Thr231 was increased in pups exposed to Pg-OMV with the appearance of a secondary band of 60 kD. Together these results demonstrate that Pg-OMV can significantly modify the embryonic brain and suggests that Pg may impact offspring development via multiple mechanisms.

neuroscience↗

bioRxiv2024

RNA genome expansion up to 64 kb in nidoviruses is host constrained and associated with new modes of replicase expression

Positive-strand RNA viruses of the order Nidovirales with genomes larger than [~]20 kb, including the largest known 36.7 kb RNA genome in vertebrate viruses, encode a proofreading exoribonuclease (ExoN). Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. We classify multi-cistronic ExoN-encoding nidoviruses into five groups, according to canonical and non-canonical modes of viral polymerase expression by ribosomes and genome segmentation. The largest group employing the canonical mode comprises invertebrate and vertebrate nidoviruses, including coronaviruses, with genomes ranging from 20-to-36 kb. Four groups with non-canonical expression modes include giant invertebrate nidoviruses with 31-to-64 kb genomes, some of which utilize dual ribosomal frameshifting that we validate experimentally. Thus, expansion of giant RNA virus genomes, the vertebrate/invertebrate host division, and the control of viral replicase expression are interconnected.

microbiology↗

bioRxiv2022

Comprehensive profiling of wastewater viromes by genomic sequencing

Genomic material in wastewater provides a rich source of data for detection and surveillance of microbes. Used for decades to monitor poliovirus and other pathogens, the SARS-CoV-2 pandemic and the falling costs of high-throughput sequencing have substantially boosted the interest in and the usage of wastewater monitoring. We have longitudinally collected over 100 samples from a wastewater treatment plant in Berlin/Germany, from March 2021 to July 2022, in order to investigate three aspects. First, we conducted a full metagenomic analysis and exemplified the depth of the data by temporal tracking strains and to a certain extent also variants of human astroviruses and enteroviruses. Second, targeting respiratory pathogens, a broad enrichment panel enabled us to detect waves of RSV, influenza, or common cold coronaviruses in high agreement with clinical data. Third, by applying a profile Hidden Markov Model-based search for novel viruses, we identified more than 100 thousand novel transcript assemblies likely not belonging to known virus species, thus substantially expanding our knowledge of virus diversity. Taken together, we present a longitudinal and deep investigation of the viral genomic information in wastewater that underlines the value of sewage surveillance for both public health purposes and planetary virome research.

genomics↗

bioRxiv2021

Deep mining of the Sequence Read Archive reveals bipartite coronavirus genomes and inter-family Spike glycoprotein recombination

Genetic variation in RNA viruses is generated by point mutation and recombination as well as reassortment in the case of viruses with segmented genomes. While point mutation concerns only few sites per genome copy, recombination and reassortment can affect large genome regions, possibly facilitating the sudden emergence of novel traits. The contribution of recombination and reassortment to genomic plasticity and their rates remain poorly understood and might be underappreciated because of the lack of a comprehensive description of the virosphere. Here we employed a computational approach that directly queries primary sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy. By screening more than 213,000 data sets from the Sequence Read Archive repository and using two metrics that quantitatively assess assembly quality we discovered 25 novel nidoviruses from a wide range of vertebrate hosts. These include eight fish coronaviruses with bipartite genomes, a giant 36.1 kilobase coronavirus genome with a duplicated Spike glycoprotein (S) gene, and 16 additional so far undescribed vertebrate nidoviruses. Some of these novel virus genomes encode protein domains that have not been described for nidoviruses. We provide evidence for a possible inter-family homologous recombination event involving S between ancestral bipartite coronaviruses and unsegmented tobaniviruses and report a case example of an individual fish simultaneously infected with members from both virus families. Our results shed light on the evolution and genomic plasticity of coronaviruses and identify recombinants with a possibly improved ability to cross species barriers, which might elevate their pandemic potential.

microbiology↗

bioRxiv2021

Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements

Transcriptional profiling provides global snapshots of virus-mediated cellular reprogramming, which can simultaneously encompass pro- and antiviral components. To determine early transcriptional signatures associated with HCV infection of authentic target cells, we performed ex vivo infections of adult primary human hepatocytes (PHHs) from seven donors. Longitudinal sampling identified minimal gene dysregulation at six hours post infection (hpi). In contrast, at 72 hpi, massive increases in the breadth and magnitude of HCV-induced gene dysregulation were apparent, affecting gene classes associated with diverse biological processes. Comparison with HCV-induced transcriptional dysregulation in Huh-7.5 cells identified limited overlap between the two systems. Of note, in PHHs, HCV infection initiated broad upregulation of canonical interferon (IFN)-mediated defense programs, limiting viral RNA replication and abrogating virion release. We further find that constitutive expression of IRF1 in PHHs maintains a steady-state antiviral program in the absence of infection, which can additionally reduce HCV RNA translation and replication. We also detected infection-induced downregulation of [~]90 genes encoding components of the EIF2 translation initiation complex and ribosomal subunits in PHHs, consistent with a signature of translational shutoff. As HCV polyprotein translation occurs independently of the EIF2 complex, this process is likely pro-viral: only translation initiation of host transcripts is arrested. The combination of antiviral intrinsic and inducible immunity, balanced against pro-viral programs, including translational arrest, maintains HCV replication at a low-level in PHHs. This may ultimately keep HCV under the radar of extra-hepatocyte immune surveillance while initial infection is established, promoting tolerance, preventing clearance and facilitating progression to chronicity. IMPORTANCEAcute HCV infections are often asymptomatic and therefore frequently undiagnosed. We endeavored to recreate this understudied phase of HCV infection using explanted PHHs and monitored host responses to initial infection. We detected temporally distinct virus-induced perturbations in the transcriptional landscape, which were initially narrow but massively amplified in breadth and magnitude over time. At 72 hpi, we detected dysregulation of diverse gene programs, concurrently promoting both virus clearance and virus persistence. On the one hand, baseline expression of IRF1 combined with infection-induced upregulation of IFN-mediated effector genes suppresses virus propagation. On the other, we detect transcriptional signatures of host translational inhibition, which likely reduces processing of IFN-regulated gene transcripts and facilitates virus survival. Together, our data provide important insights into constitutive and virus-induced transcriptional programs in PHHs, and identifies simultaneous antagonistic dysregulation of pro-and anti-viral programs which may facilitate host tolerance and promote viral persistence.

immunology↗