A5088190634- Influenza Virus Research Studies
- Viral Infections and Immunology Research
- Respiratory viral infections research
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- Viral Infectious Diseases and Gene Expression in Insects
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- Mosquito-borne diseases and control
- Viral Infections and Vectors
- Viral gastroenteritis research and epidemiology
- Viral Infections and Outbreaks Research
- Insect symbiosis and bacterial influences
- Biosensors and Analytical Detection
- Evolution and Genetic Dynamics
University of Illinois Urbana-Champaign
2018-2024
Agency for Science, Technology and Research
2024
Abstract Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard protocols are invasive and rely on numerous items that can subject supply chain bottlenecks, as such not suitable frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, associated viral transport media (VTM), kits RNA isolation purification have all been in short at various times...
ABSTRACT The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize within-host acute infection, we sequenced saliva and nasal samples collected daily from vaccinated unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection reveals missed by less-frequent strategies. Within-host both appeared largely stochastic;...
The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. development next-generation sequencing (NGS) technologies has made it possible to identify large numbers DIP-associated sequences, providing a powerful tool better understand their biological relevance. However, NGS approaches pose numerous technical challenges, including the precise identification mapping deletion junctions in presence frequent...
Abstract In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health the university and surrounding communities, viability in-person instruction. Here we report a case study at University Illinois Urbana-Champaign, where multimodal “SHIELD: Target, Test, Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms laboratories open. The program included epidemiological modeling surveillance, fast/frequent...
Abstract Productive infections by RNA viruses require faithful replication of the entire genome. Yet many also produce deletion-containing viral genomes (DelVGs), aberrant products with large internal deletions. DelVGs interfere wild-type virus and their presence in patients is associated better clinical outcomes. The DelVG itself hypothesized to confer this interfering activity. antagonize out-competing full-length genome triggering innate immune responses. Here, we identify an additionally...
Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that have an internal deletion in one their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon coinfection with infectious standard (STV), DIPs interfere STV replication through competitive inhibition. Thus, proposed as potent antivirals for treatment the disease. To select corresponding candidates, we studied
Defective interfering particles (DIPs) are commonly produced by RNA viruses and have been implicated in modulating clinical infection outcomes; hence, there is increasing interest the potential of DIPs as antiviral therapeutics. For influenza viruses, formed packaging genomic RNAs harboring internal deletions.
Abstract The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize within-host acute infection, we deep sequenced saliva and nasal samples collected daily from unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection reveals missed by less-frequent strategies. Within-host both naïve appeared largely stochastic;...
Recombination is a common feature of many positive-strand RNA viruses, playing an important role in virus evolution. However, to date, there limited understanding the mechanisms behind process. Utilising vitro assays, we have previously shown that template-switching event recombination random and ubiquitous process often leads recombinant viruses with imprecise genomes containing sequence duplications. Subsequently, termed resolution, has yet be mechanistically studied, removes these...
In the Fall of 2020, many universities saw extensive transmission SARS-CoV-2 among their populations, threatening health students, faculty and staff, viability in-person instruction, surrounding communities. 1, 2 Here we report that a multimodal “SHIELD: Target, Test, Tell” program mitigated spread at large public university, prevented community transmission, allowed continuation classes amidst pandemic. The combines epidemiological modelling surveillance (Target); fast frequent testing...
Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation, and compromises vaccine efficacy. Both the molecular mechanism initial products of are relatively poorly understood. We used established poliovirus-based vitro assay investigate roles sequence identity structure, implicated or inferred from analysis circulating recombinant viruses, process. In addition, we next-generation sequencing early after cellular...
Abstract Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation and compromises vaccine efficacy. Both the molecular mechanism initial products of are relatively poorly understood. We used established poliovirus-based vitro assay investigate roles sequence identity structure, both implicated or inferred from analysis circulating recombinant viruses, process. In addition, we next generation sequencing early...
Abstract Recombination is a common feature of many positive-strand RNA viruses, playing an important role in virus evolution. However, to date, there limited understanding the mechanisms behind process. Utilising vitro assays, we have previously shown that template-switching event recombination random and ubiquitous process often leads recombinant viruses with imprecise genomes containing sequence duplications. Subsequently, termed resolution, has yet be mechanistically studied, removes...
Abstract The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. development next generation sequencing (NGS) technologies has made it possible to identify large numbers DIP-associated sequences, providing a powerful tool better understand their biological relevance. However, NGS approaches pose numerous technical challenges including the precise identification mapping deletion junctions in presence frequent...
Abstract Japanese encephalitis virus (JEV) is a zoonotic mosquito-transmitted Flavivirus circulating in birds and pigs. In humans, JEV can cause severe viral with high mortality. Considering that vector-free direct transmission was observed pigs, introduction into an immunologically naïve pig population could result series of transmissions disrupting the alternating host cycling between vertebrates mosquitoes. To assess potential consequences such realistic scenario, we passaged ten times...
Japanese encephalitis virus (JEV) is a zoonotic mosquito-transmitted Flavivirus circulating in birds and pigs. In humans, JEV can cause severe viral with high mortality. Considering that vector-free direct transmission was observed experimentally infected pigs, introduction into an immunologically naïve pig population could result series of transmissions disrupting the alternating host cycling between vertebrates mosquitoes. To assess potential consequences such realistic scenario, we...
Abstract Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection and have been implicated in influencing clinical outcomes. Despite their ubiquity, the specific molecular mechanisms that govern DelVG formation packaging into defective interfering particles (DIPs) remain poorly understood. Here, we utilized next-generation sequencing to analyze DelVGs form de novo early infection, prior packaging. Analysis of these revealed deletion occurs clearly...
Productive infections by RNA viruses require faithful replication of the entire genome. Yet many also produce deletion-containing viral genomes (DelVGs), aberrant products with large internal deletions. DelVGs interfere wild-type virus and their presence in patients is associated better clinical outcomes as they. The DelVG itself hypothesized to confer this interfering activity. antagonize out-competing full-length genome triggering innate immune responses. Here, we identify an additionally...
Abstract Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that comprise an internal deletion in one their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon co-infection with infectious standard (STV), DIPs interfere STV replication through competitive inhibition. Thus, proposed as potent antivirals for treatment the disease. To select corresponding candidates, we studied de novo generation and propagation...