Biology subjects

Henke, D. M.

Publications and source records attributed to Henke, D. M..

6 recordsLinked to original sources

bioRxiv2026

RSV & rhinovirus coinfection order dictates outcome via type III interferon-mediated interference in infant respiratory epithelium

Coinfection with respiratory syncytial virus (RSV) and rhinovirus (RV) is the most frequently detected coinfection in infants, yet mechanisms governing viral interference and disease outcome remain poorly understood. Although infection order is a key determinant of coinfection outcome involving RSV, influenza, rhinovirus, and SARS-CoV-2, its role in RSV/RV coinfections has not been defined. Using infant-derived human nasal organoids at air-liquid interface, we demonstrate that coinfection order fundamentally determines the outcome of RSV/RV interactions. An initial RSV infection almost completely inhibits secondary RV coinfection, whereas primary RV infection only partially impairs a subsequent RSV coinfection. These distinct outcomes are accompanied by divergent temporal antiviral and pro-inflammatory responses. Mechanistically, we identify type III interferons as a sufficient mediator of RSV-induced restriction of RV, establishing a host-driven mechanism of viral interference. In contrast, partial impairment of RSV following RV infection occurs through an interferon-independent mechanism. Despite marked differences, RSV/RV coinfections do not exacerbate epithelial injury or innate immune responses beyond that induced by RSV alone, indicating RSV is the dominant driver of pathology in coinfections. Collectively, our data establishes coinfection order as a critical determinant of RSV/RV outcome and reveals novel and mechanistic insight into critical viral-host interactions in the infant nasal epithelium.

microbiology↗

bioRxiv2025

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

BackgroundRespiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infections in infants and poses significant risks to immuno-compromised individuals and the elderly. The COVID-19 pandemic disrupted typical RSV seasonality, leading to unusual patterns of viral circulation and resurgence. However, the impact of these disruptions on RSV evolutionary dynamics remains incompletely understood. This study aimed to investigate the evolutionary dynamics of RSV in Houston, Texas, across pre-pandemic (November 2015 - March 2020), pandemic (April 2021 - June 2023), and post-pandemic periods (July 2023 - December 2024), focusing on genetic diversity, lineage dynamics, and selective pressures. MethodsIn one of the largest comprehensive RSV genomic evolutionary analyses, we analyzed 1,344 RSV-positive respiratory samples collected from children seeking outpatient care or hospitalized with acute respiratory infections between November 2015 to February 2024, which is one of the largest comprehensive RSV genomic evolutionary analyses. We successfully sequenced the whole genomes for 87.5% of the isolates (606 RSV/A and 570 RSV/B). To assess genetic diversity, lineage dynamics, and selective pressures, we conducted phylogenetic analysis, variant calling, and dN/dS ratio calculations. We clustered variant prevalence patterns using k-means and used Shannon entropy to quantify genetic variability. We performed statistical regression analyses to evaluate the accumulation of variants and their impact on gene expression. ResultsRSV circulation in Houston was markedly disrupted during the pandemic, with an absence of cases in 2020-2021 followed by off-season surges from 2021 to 2023. Phylogenetic analysis revealed distinct lineage dynamics, with RSV/A showing remarkable persistence of specific lineages such as A.D.1 and emergence of new lineages including A.D.3. In contrast, RSV/B underwent a dramatic restructuring, dominated by the B.D.E.1 lineage in the pandemic and post-pandemic period. Bayesian molecular clock analysis estimated nucleotide substitution rates of 9.37 x 10-4 (95% HPD: 7.99 x 10-4 - 1.07 x 10-3) substitutions/site/year for RSV/A and 9.79 x 10-4 (95% HPD: 8.96 x 10-4 - 1.06 x 10-3) for RSV/B. The time to the most recent common ancestor (tMRCA) of the dominant RSV/A clade, A.D.1, is dated to approximately 2010 (95% HPD: 2008-2011), while for RSV/B the dominant clade- B.D.E.1 traces back to 2002 (95% HPD: 1997-2007). Despite reduced lineage diversity, RSV/B accumulated non-synonymous variants at nearly twice the rate of RSV/A, notably in the M2-2 gene, reflecting high within-lineage variability. The significant increase in non-synonymous mutations in M2-2 in RSV/B during the pandemic and post-pandemic time phases strongly correlated with increased transcriptional activity. Additionally, antigenic site mutations in the F protein, particularly in RSV/B, were also observed, with implications for immune evasion and effectiveness of the current monoclonal antibody immunoprophylaxis intervention. ConclusionsThe COVID-19 pandemic significantly impacted RSV evolution, leading to reduced genetic diversity during the pandemic and the emergence of novel lineages post-pandemic. RSV/B exhibited more dynamic evolutionary changes, particularly in the M2-2 gene, suggesting potential adaptive advantages. Ongoing genomic surveillance coupled with functional studies is crucial for monitoring variants and assessing the clinical impact of these mutations on transmission, disease severity, fitness, and long-term effectiveness of RSV prevention and treatment strategies.

evolutionary biology↗

bioRxiv2024

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples--a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants. IMPORTANCERespiratory syncytial virus (RSV) and human noroviruses (HuNoV) are NIAID category C and category B priority pathogens, respectively, that inflict significant health consequences on children, adults, immunocompromised patients, and the elderly. Due to the high strain diversity of RSV and HuNoV genomes, obtaining complete genomes to monitor viral evolution and pathogenesis is challenging. In this paper, we present the design, optimization, and benchmarking of a comprehensive oligonucleotide target capture method for these pathogens. All 85 RSV samples and 49/55 HuNoV samples were patient-derived with six human intestinal enteroids. The methodology described here results has a higher success rate in obtaining full-length RSV and HuNoV genomes, enhancing the efficiency of studying these viruses and mutations directly from patient-derived samples.

molecular biology↗

bioRxiv2023

Examining intra-host genetic variation of RSV by short read high-throughput sequencing

Every viral infection entails an evolving population of viral genomes. High-throughput sequencing technologies can be used to characterize such populations, but to date there are few published examples of such work. In addition, mixed sequencing data are sometimes used to infer properties of infecting genomes without discriminating between genome-derived reads and reads from the much more abundant, in the case of a typical active viral infection, transcripts. Here we apply capture probe-based short read high-throughput sequencing to nasal wash samples taken from a previously described group of adult hematopoietic cell transplant (HCT) recipients naturally infected with respiratory syncytial virus (RSV). We separately analyzed reads from genomes and transcripts for the levels and distribution of genetic variation by calculating per position Shannon entropies. Our analysis reveals a low level of genetic variation within the RSV infections analyzed here, but with interesting differences between genomes and transcripts in 1) average per sample Shannon entropies; 2) the genomic distribution of variation hotspots; and 3) the genomic distribution of hotspots encoding alternative amino acids. In all, our results suggest the importance of separately analyzing reads from genomes and transcripts when interpreting high-throughput sequencing data for insight into intra-host viral genome replication, expression, and evolution.

genomics↗

bioRxiv2023

Microbial fingerprints reveal interaction between museum objects, curators and visitors

Microbiomes populate the border between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To answer this question, museum objects varying in material and size from two museums, the Museum fur Naturkunde and the Pergamonmuseum in Berlin, Germany, which forms part of UNESCO World Heritage since 1999, were defined. In total 126 samples of natural and cultural heritage objects were taken with sterile nylon flocked swabs and subsequently subjected to 16S rRNA amplicon sequencing. By comparing the microbial composition of touched and untouched mollusc and fossil natural heritage objects we derived a robust microbial touch signature characterized by increased abundance of microbes known to be present in human skin. Application of this touch signature to cultural heritage objects from the Pergamonmuseum revealed areas of differential exposure to human contact on the Ishtar gate and Samal gate lions. Moreover, we were able to distinguish museum objects and personal office items touched by two different individuals with high sensitivity. Our results demonstrate that the microbial composition of museum objects gives insight into the degree of exposure to human contact, which is an important parameter for conservation and heritage science, and possibly provenance research.

microbiology↗

bioRxiv2021

Multiple RSV strains infecting HEp-2 and A549 cells reveal cell line-dependent differences in resistance to RSV infection.

Respiratory syncytial virus (RSV) is a leading cause of pediatric acute respiratory infection worldwide. There are currently no approved vaccines or antivirals to combat RSV disease. A few transformed cell lines and two historic strains have been extensively used to study RSV. Here we report a thorough molecular and cell biological characterization of HEp-2 and A549 cells infected with four strains of RSV representing both major subgroups as well as historic and more contemporaneous genotypes -- [RSV/A/Tracy (GA1), RSV/A/Ontario (ON), RSV/B/18537 (GB1), RSV/B/Buenos Aires (BA)] -- via measurements of viral replication kinetics and viral gene expression, immunofluorescence-based imaging of gross cellular morphology and cell-associated RSV, and measurements of host response including transcriptional changes and levels of secreted cytokines and growth factors. Our findings strongly suggest 1) the existence of a conserved difference in gene expression between RSV subgroups A and B; 2) the A549 cell line is a more stringent and natural host of replicating RSV than the HEp-2 cell line; and 3) consistent with previous studies, determining the full effects of viral genetic variation in RSV pathogenesis requires model systems as tractable as transformed cell lines but better representative of the human host. IMPORTANCEInfection with respiratory syncytial virus (RSV) early in life is essentially guaranteed and can lead to severe disease. In vitro data from two historic RSV/A strains and two cell lines, HEp-2 and A549, constitute most of our knowledge; but RSV contains ample variation from two evolving subgroups (A and B) showing recent convergent evolution. Here we measure viral action and host response in HEp-2 and A549 cells infected with four RSV strains from both subgroups and representing both historic and more contemporaneous strains. We discover a subgroup-dependent difference in viral gene expression and find A549 cells are more potently antiviral and more sensitive, albeit subtly, to viral variation. Our findings reveal important differences between RSV subgroups and two widely used cell lines and provide baseline data for experiments with model systems better representative of natural RSV infection.

microbiology↗