A5069618568- Influenza Virus Research Studies
- RNA and protein synthesis mechanisms
- Animal Disease Management and Epidemiology
- Respiratory viral infections research
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Animal Virus Infections Studies
- Bacteriophages and microbial interactions
- Viral Infections and Vectors
- RNA Research and Splicing
- Viral gastroenteritis research and epidemiology
- Machine Learning in Bioinformatics
- COVID-19 epidemiological studies
- Internet Traffic Analysis and Secure E-voting
- Virology and Viral Diseases
- Cancer-related molecular mechanisms research
- vaccines and immunoinformatics approaches
- Viral Infections and Outbreaks Research
- Cryptography and Data Security
- interferon and immune responses
- COVID-19 and Mental Health
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
Centers for Disease Control and Prevention
2013-2024
National Center for Immunization and Respiratory Diseases
2018-2023
UK Health Security Agency
2022
Imperial College London
2022
Murata (United States)
2022
Centers for Disease Control and Prevention
2014
University of Toledo
2008-2012
Bowling Green State University
2007
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...
CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including Omicron variant. This report summarizes U.S. trends in variant proportions from during January 2022-May 2023. During this period, remained predominant, with various descendant lineages reaching predominance (>50% prevalence). first half of 2022, BA.1.1 reached by week ending 8, followed BA.2 (March 26), BA.2.12.1 (May 14), and BA.5 (July...
It has been widely acknowledged that non-coding RNAs are master-regulators of genomic functions. However, the significance presence ncRNA within introns not received proper attention. commonly produced through post-splicing process and specific signals gene transcription events, impacting many other genes modulating their expression. This study, along with following discussion, details association thousands ncRNAs—snoRNA, miRNA, siRNA, piRNA long ncRNA—within human introns. We propose such...
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 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 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.
In mammals a considerable 92% of genes contain introns, with hundreds and these introns reaching the incredible size over 50,000 nucleotides. These "large introns" must be spliced out pre-mRNA in timely fashion, which involves bringing together distant 5′ 3′ acceptor donor splice sites. invertebrates, especially Drosophila, it has been shown that larger can efficiently through process known as recursive splicing—a consecutive splicing from 5′-end at series combined donor-acceptor sites...
Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As virus genome sequencing becomes cheaper, faster, and more readily available, ability to predict potential from sequence data could transform assessment capabilities. However, complexities of relationships between genotype phenotype make such predictions extremely difficult. The integration experimental work, computational tool development, analysis evolutionary...
Few studies have prospectively assessed SARS-CoV-2 community infection in children aged 0 to 4 years. Information about incidence and clinical virological features young could help guide prevention mitigation strategies.To assess incidence, features, symptoms a prospective household cohort compare viral load by age group, symptoms, lineage children, older adults.This study enrolled 690 participants from 175 Maryland households with 1 or more years between November 24, 2020, October 15, 2021....
The ongoing panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses is the largest in history, with unprecedented transmission to multiple mammalian species. Avian A H5 subtype circulate globally among birds and are classified into distinct clades based on their hemagglutinin (HA) genetic sequences. Thus, ability accurately rapidly assign newly sequenced isolates key surveillance outbreak response. Co-circulation endemic, low (LPAI) lineages North American European wild...
Following cessation of continuous Ebola virus (EBOV) transmission within Western Africa, sporadic EBOV disease (EVD) cases continued to re-emerge beyond the viral incubation period. Epidemiological and genomic evidence strongly suggests that this represented from EVD survivors. To investigate whether persistent infections are characterized by ongoing replication, we sequenced semen nine survivors a subset corresponding acute specimens. evolutionary rates during persistence were either...
The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation control measures. We introduce novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number without need time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles support...
ABSTRACT Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples poultry outbreaks and active market surveillance collected January 2012 to August 2015. Six hemagglutinin gene clades characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2013 but gradually disappeared not detected after April 2014. 2.3.2.1c spread rapidly during the south center country. A number clade interclade...
Abstract Background Human respiratory syncytial virus (RSV) is one of the leading causes infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial G gene (200–300 nucleotides) for genotype characterization or diagnostics. However, assignment with has not recapitulated phylogenetic signal other genes, there no consensus definition. Methods We conducted maximum likelihood analysis 10 individual genes whole‐genome sequence (WGS) that...
Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution last three pandemic IAVs. Observed patterns within coinfected are likely to be shaped by several factors, including load, extent mixing stringency selection. These factors turn expected vary diverse species that IAV infects. To investigate differences reassortment, here we examined...
Biosemiotic entropy involves the deterioration of biological sign systems. The genome is a coded system that connected to phenotypic outputs through interpretive functions tRNA/ribosome machinery. This symbolic (semiosis) at core all biology has been termed “biosemiosis”. Layers biosemiosis and cellular information management are analogous in varying degrees semiotics computer programming, spoken, written human languages. — an error or deviation from healthy state results errors copying...
Antigenic variation among circulating H5N1 highly pathogenic avian influenza A viruses mandates the continuous production of strain-specific pre-pandemic vaccine candidates and represents a significant challenge for pandemic preparedness. Here we assessed structural, antigenic receptor-binding properties three HPAI virus hemagglutinins, which were recently selected by WHO as [A/Egypt/N03072/2010 (Egypt10, clade 2.2.1), A/Hubei/1/2010 (Hubei10, 2.3.2.1) A/Anhui/1/2005 (Anhui05, 2.3.4)]. These...
To assess the household secondary infection risk (SIR) of B.1.1.7 (Alpha) and non-Alpha lineages severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children.During January to April 2021, we prospectively followed households with a SARS-CoV-2 infection. We collected questionnaires, serial nasopharyngeal swabs for reverse transcription polymerase chain reaction testing whole genome sequencing, blood samples serology testing. calculated SIRs by primary case age (pediatric vs...
Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized non-human hosts. Elucidating dynamics is important to better understand IAV biology the evolutionary processes that govern spillover into humans. Here, we sampled an outbreak pigs during a week-long county fair characterize viral this reservoir host. Nasal wipes were collected on daily basis from all present at fair, yielding...
Abstract Background Genomes possess different levels of non-randomness, in particular, an inhomogeneity their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence choice base at a site, to long-range, commonly known as isochores, particular composition can span millions nucleotides. A separate genomic issue that has yet be thoroughly elucidated role RNA secondary structure (SS) plays gene expression. Results We present novel data and...
Preexisting antibodies to influenza, shaped by early infection and subsequent exposures, may impact responses influenza vaccination.
Background. Several patients with Ebola virus disease (EVD) managed in the United States have received ZMapp monoclonal antibodies, TKM-Ebola small interfering RNA, brincidofovir, and/or convalescent plasma as investigational therapeutics. Methods. To investigate whether treatment selected for (EBOV) mutations conferring resistance, viral sequencing was performed on RNA extracted from clinical blood specimens EVD following treatment, and putative targets were analyzed. Results. We observed...
Highly pathogenic avian influenza (HPAI) A(H5N1) viruses pose a significant economic burden to the poultry industry worldwide and have pandemic potential. Poultry vaccination against HPAI has been an important component of control measures performed in Vietnam since 2005. To systematically assess antigenic matching current vaccines circulating field variants, we produced panel chicken ferret antisera raised historical contemporary Vietnamese reference representing clade variants that were...