A5003038383- Influenza Virus Research Studies
- Respiratory viral infections research
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- RNA and protein synthesis mechanisms
- Animal Virus Infections Studies
- Viral Infections and Outbreaks Research
- Viral gastroenteritis research and epidemiology
- COVID-19 Clinical Research Studies
- Animal Disease Management and Epidemiology
- vaccines and immunoinformatics approaches
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
- interferon and immune responses
- Cancer Genomics and Diagnostics
- Reproductive Health and Technologies
- Long-Term Effects of COVID-19
- CRISPR and Genetic Engineering
- Mitochondrial Function and Pathology
- Pulmonary Hypertension Research and Treatments
- Reproductive Biology and Fertility
- Genetic Mapping and Diversity in Plants and Animals
- Adipose Tissue and Metabolism
- Cardiovascular Issues in Pregnancy
Centers for Disease Control and Prevention
2016-2024
National Center for Immunization and Respiratory Diseases
2017-2023
UK Health Security Agency
2022
Imperial College London
2022
Murata (United States)
2022
Battelle
2018-2021
Leidos (United States)
2021
The University of Texas Medical Branch at Galveston
2021
Oak Ridge Associated Universities
2021
Oak Ridge Institute for Science and Education
2021
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays detecting severe acute respiratory syndrome 2 (SARS-CoV-2) other viruses their emerging variants. Here, we present cost-effective virus variant detection platform, called microfluidic Combinatorial Arrayed Reactions Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics microfluidics with streamlined workflow clinical use. We...
Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy sensitivity than ever before. Existing platforms can be used multiplex a large number of samples; however, analysis the resulting data is complex involves separating barcoded samples various read manipulation processes ending in final assembly. Many assembly tools were designed larger genomes higher fidelity polymerases mind do not perform well reads derived from highly...
The 2023-24 U.S. influenza season was characterized by a predominance of A(H1N1)pdm09 virus circulation with co-circulation A(H3N2) and B/Victoria viruses. We estimated vaccine effectiveness (VE) in the United States against mild-to-moderate medically attended illness season. enrolled outpatients aged ≥8 months acute respiratory 7 states. Respiratory specimens were tested for type/subtype reverse-transcriptase polymerase chain reaction (RT-PCR). Influenza VE test-negative design comparing...
For the first time, a coding complete genome of an RNA virus has been sequenced in its original form. Previously, was by chemical degradation radiolabeled RNA, difficult method that produced only short sequences. Instead, usually indirectly copying it into cDNA, which is often amplified to dsDNA PCR and subsequently analyzed using variety DNA sequencing methods. We designed adapter highly conserved termini influenza A target (-) sense protein nanopore on Oxford Nanopore MinION platform....
Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into current disease pandemic. SARS-CoV-2 is a virus that causes symptoms similar to those caused by influenza A B viruses. On July 2, 2020, US Food Drug Administration granted emergency use authorization for vitro diagnostic of Influenza Multiplex Assay. This assay detects at 102.0, 102.2, 100.3 50% tissue culture or egg infectious dose, as few 5 RNA copies/reaction....
Abstract To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta–Omicron recombinant genomes from Centers for Disease Control Prevention national genomic surveillance. Laboratory bioinformatic investigations identified validated 9 genetically related viruses with a hybrid spike protein.
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence new variant lineages that have exacerbated COVID-19 pandemic. Some those variants were designated as concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact vaccine-mediated protection from disease. To ascertain and rank risk VOCs VOIs, we analyze ability 14 (614G, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta,...
Abstract During the evolution of SARS-CoV-2 in humans a D614G substitution spike (S) protein emerged and became predominant circulating variant (S-614G) COVID-19 pandemic 1 . However, whether increasing prevalence S-614G represents fitness advantage that improves replication and/or transmission or is merely due to founder effects remains elusive. Here, we generated isogenic variants demonstrate has (i) enhanced binding human ACE2, (ii) increased primary bronchial nasal airway epithelial...
Abstract Recombination between SARS-CoV-2 virus variants can result in different viral properties (e.g., infectiousness or pathogenicity). In this report, we describe viruses with recombinant genomes containing signature mutations from Delta and Omicron variants. These are the first evidence for a Delta-Omicron hybrid Spike protein United States.
While working overnight at a swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, Nanopore sequenced 13 IAV genomes from samples collected, and predicted real time that these viruses posed novel risk to humans due genetic mismatches between the current prepandemic candidate vaccine (CVVs). We developed used portable sequencing analysis platform called
The fifth wave of the H7N9 influenza epidemic in China was distinguished by a sudden increase human infections, an extended geographic distribution, and emergence highly pathogenic avian (HPAI) viruses. Genetically, some viruses from have acquired novel amino acid changes at positions involved mammalian adaptation, antigenicity, hemagglutinin cleavability. Here, several low-pathogenic (LPAI) HPAI virus isolates were assessed for their pathogenicity transmissibility models, as well ability to...
Co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses has been reported. We evaluated cell lines commonly used to isolate diagnose related diseases for their susceptibility SARS-CoV-2. Although multiple kidney from monkeys were susceptible SARS-CoV-2, we found many types derived humans, dogs, minks, cats, mice, chicken not. analyzed MDCK cells, which are most surveillance study of influenza viruses, that they not The low expression level the...
Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe, intermittently cause pandemics. Sequence information from virus genomes is instrumental in determining mechanisms underpinning antigenic evolution antiviral resistance. However, due to sequence diversity dynamics evolution, rapid high-throughput sequencing remains a challenge. We developed single-reaction A/B (FluA/B) multiplex reverse transcription-PCR (RT-PCR) method amplifies most critical...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically globally. Although COVID-19 vaccines are available, new variants the capacity for immune evasion continue to emerge. To understand characterize evolution of circulating SARS-CoV-2 in U.S., Centers Disease Control Prevention (CDC) initiated National Strain Surveillance (NS3) program received thousands clinical specimens from...
Abstract The early Omicron lineage variants evolved and gave rise to diverging lineages that fueled the COVID-19 pandemic in 2022. Bivalent mRNA vaccines, designed broaden protection against circulating future variants, were authorized by U.S. Food Drug Administration (FDA) August 2022 recommended Centers for Disease Control Prevention (CDC) September impact of bivalent vaccination on eliciting neutralizing antibodies homologous BA.4/BA.5 viruses as well emerging heterologous needs be...
Baloxavir, a new antiviral drug targeting cap-dependent endonuclease activity of polymerase acidic (PA) protein influenza viruses, is now approved in multiple countries. Several substitutions at isoleucine 38 PA (e.g., PA-I38T) have been associated with decreased baloxavir susceptibility vitro and vivo. In recent years, next generation sequencing (NGS) analysis pyrosequencing used by CDC U.S. Public Health Laboratories to monitor viruses. Here we described an improved assay for detecting A...
The varying influenza A virus (IAV) exposure and infection status of individual swine facilitates introduction, transmission, dissemination diverse IAVs. Since agricultural fairs bring people into intimate contact with swine, they provide a unique interface for zoonotic transmission IAV. Understanding the dynamics IAV through exhibition is critical to mitigating high incidence variant cases reported in association fairs. We used genomic sequences from our surveillance characterize...
Abstract Background In 2019, the Louisiana Department of Health reported an early influenza B/Victoria (B/VIC) virus outbreak. Method As it was atypically large outbreak, we deployed to investigate using genomics and a triplex real‐time RT‐PCR assay detect three antigenically distinct B/VIC lineage variant viruses. Results The investigation indicated that V1A.3 subclade, containing amino acid deletion in hemagglutinin known be B/Colorado/06/2017 vaccine virus, most prevalent circulating...
Swine harbors a genetically diverse population of swine influenza A viruses (IAV-S), with demonstrated potential to transmit the human population, causing outbreaks and pandemics. Here, we describe development one-step, triplex real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay that detects distinguishes majority antigenically distinct virus hemagglutinin (HA) clades currently circulating in North American swine, including IAV-S H1 1A.1 (α), 1A.2 (β), 1A.3 (γ), 1B.2.2...