Genome, Viral

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  Subject Areas on Research

  • 17^th Century Variola Virus Reveals the Recent History of Smallpox. 
  • 2004 ASM Conference on the New Phage Biology: the 'Phage Summit'. 
  • A cluster of HIV type 1 subtype C sequences from Ethiopia, observed in full genome analysis, is not sustained in subgenomic regions. 
  • A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations. 
  • A feline immunodeficiency virus vif-deletion mutant remains attenuated upon infection of newborn kittens. 
  • A functional antigenomic promoter for the paramyxovirus simian virus 5 requires proper spacing between an essential internal segment and the 3' terminus. 
  • A large U3 deletion causes increased in vivo expression from a nonintegrating lentiviral vector. 
  • A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand. 
  • A strongly selected mutation in the HIV-1 genome is independent of T cell responses and neutralizing antibodies. 
  • A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. 
  • Adaptation of an ICAM-1-tropic enterovirus to the mouse respiratory tract. 
  • Age distribution of latent herpes simplex virus 1 and varicella-zoster virus genome in human nervous tissue. 
  • Amplification and cloning of near full-length HIV-2 genomes. 
  • Amplification of a complete simian immunodeficiency virus genome from fecal RNA of a wild chimpanzee. 
  • An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). 
  • Antiretroviral drug resistance among treatment-naïve HIV-1-infected persons in Washington, D.C. 
  • Application and accuracy of molecular phylogenies. 
  • Association of preexisting drug-resistance mutations and treatment failure in hepatitis B patients. 
  • Bacteriophages that infect Gram-negative bacteria as source of signal-arrest-release motif lysins. 
  • Centralized immunogens as a vaccine strategy to overcome HIV-1 diversity. 
  • Characterization of the Transmitted Virus in an Ongoing HIV-1 Epidemic Driven by Injecting Drug Use. 
  • Chemical Modulation of Endocytic Sorting Augments Adeno-associated Viral Transduction. 
  • Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme. 
  • Comparative analysis of the genome sequences and replication profiles of chikungunya virus isolates within the East, Central and South African (ECSA) lineage. 
  • Comparison of the genomes of the wild-type French viscerotropic strain of yellow fever virus with its vaccine derivative French neurotropic vaccine. 
  • Complete genome analysis of one of the earliest SIVcpzPtt strains from Gabon (SIVcpzGAB2). 
  • Complete genome sequencing and analysis of six enterovirus 71 strains with different clinical phenotypes. 
  • Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans. 
  • Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. 
  • Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. 
  • Cowpox virus genome encodes a second soluble homologue of cellular TNF receptors, distinct from CrmB, that binds TNF but not LT alpha. 
  • Cre/LoxP-HBV plasmids generating recombinant covalently closed circular DNA genome upon transfection. 
  • Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification. 
  • Derivation of a biologically contained replication system for human immunodeficiency virus type 1. 
  • Detection of minor drug-resistant populations by parallel allele-specific sequencing. 
  • Determination of neutralization activities by a new versatile assay using an HIV-1 genome carrying the Gaussia luciferase gene. 
  • Differential expression of alternatively spliced pX mRNAs in HTLV-I-infected cell lines. 
  • Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. 
  • Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. 
  • Diversity considerations in HIV-1 vaccine selection. 
  • Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. 
  • Emergence of SARS-CoV-2 through recombination and strong purifying selection. 
  • Engineering and Selection of Shuffled AAV Genomes: A New Strategy for Producing Targeted Biological Nanoparticles. 
  • Epigenetic Silencing of Recombinant Adeno-associated Virus Genomes by NP220 and the HUSH Complex. 
  • Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection. 
  • Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma. 
  • Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. 
  • Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. 
  • Evolution and diversity in human herpes simplex virus genomes. 
  • Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. 
  • Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. 
  • Extensive Epitranscriptomic Methylation of A and C Residues on Murine Leukemia Virus Transcripts Enhances Viral Gene Expression. 
  • Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan. 
  • Filaggrin deficiency promotes the dissemination of cutaneously inoculated vaccinia virus. 
  • Flavivirus RNA transactions from viral entry to genome replication. 
  • Gangliosides are essential endosomal receptors for quasi-enveloped and naked hepatitis A virus. 
  • Generation of reovirus core-like particles in cells infected with hybrid vaccinia viruses that express genome segments L1, L2, L3, and S2. 
  • Generation of transmitted/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages. 
  • Genetic adaptation to untranslated region-mediated enterovirus growth deficits by mutations in the nonstructural proteins 3AB and 3CD. 
  • Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. 
  • Genetic variation in yellow fever virus: duplication in the 3' noncoding region of strains from Africa. 
  • Genome nucleotide lengths that are divisible by six are not essential but enhance replication of defective interfering RNAs of the paramyxovirus simian virus 5. 
  • Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. 
  • Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. 
  • Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. 
  • Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. 
  • Growth phenotypes and biosafety profiles in poliovirus-receptor transgenic mice of recombinant oncolytic polio/human rhinoviruses. 
  • HBV whole-genome mutation profile in HIV-1/HBV coinfected patients in a long-term follow-up study. 
  • HDV ribozyme activity in monovalent cations. 
  • HIV-1 did not contribute to the 2019-nCoV genome. 
  • HIV-1 nomenclature proposal. 
  • Hepatic arterial infusion of a replication-selective oncolytic adenovirus (dl1520): phase II viral, immunologic, and clinical endpoints. 
  • Herpesviruses carrying a Brainbow cassette reveal replication and expression of limited numbers of incoming genomes. 
  • Heterogeneity in codon usages of sobemovirus genes. 
  • High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. 
  • High-Frequency Illegitimate Strand Transfers of Nascent DNA Fragments During Reverse Transcription Result in Defective Retrovirus Genomes. 
  • Human FcRn expression and Type I Interferon signaling control Echovirus 11 pathogenesis in mice. 
  • Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. 
  • Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome. 
  • Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines. 
  • Influenza viruses that require 10 genomic segments as antiviral therapeutics. 
  • Integration of plasmids into the bacteriophage T4 genome. 
  • Intra-arterial administration of a replication-selective adenovirus (dl1520) in patients with colorectal carcinoma metastatic to the liver: a phase I trial. 
  • Megaphages infect Prevotella and variants are widespread in gut microbiomes. 
  • Molecular characterization of a highly divergent HIV type 1 isolate obtained early in the AIDS epidemic from the Democratic Republic of Congo. 
  • Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. 
  • Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. 
  • Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. 
  • New simian immunodeficiency virus infecting De Brazza's monkeys (Cercopithecus neglectus): evidence for a cercopithecus monkey virus clade. 
  • Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. 
  • Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. 
  • Pervasive tertiary structure in the dengue virus RNA genome. 
  • Picornavirus genome replication. Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV 3C2-3Dpol complex. 
  • Plasmid models for bacteriophage T4 DNA replication: requirements for fork proteins. 
  • Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013. 
  • Posttranscriptional m(6)A Editing of HIV-1 mRNAs Enhances Viral Gene Expression. 
  • Poxvirus genomes encode a secreted, soluble protein that preferentially inhibits beta chemokine activity yet lacks sequence homology to known chemokine receptors. 
  • Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. 
  • Preexisting infection with human T-cell lymphotropic virus type 2 neither exacerbates nor attenuates simian immunodeficiency virus SIVmac251 infection in macaques. 
  • Preparing an oncolytic poliovirus recombinant for clinical application against glioblastoma multiforme. 
  • Prevalence and genetic diversity of coronaviruses in bats from China. 
  • RNA replication from the simian virus 5 antigenomic promoter requires three sequence-dependent elements separated by sequence-independent spacer regions. 
  • Rationally Designed Influenza Virus Vaccines That Are Antigenically Stable during Growth in Eggs. 
  • Recombination-dependent DNA replication stimulated by double-strand breaks in bacteriophage T4. 
  • Reversion and T cell escape mutations compensate the fitness loss of a CD8+ T cell escape mutant in their cognate transmitted/founder virus. 
  • Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus. 
  • Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription. 
  • Rotavirus RNA polymerase requires the core shell protein to synthesize the double-stranded RNA genome. 
  • Simulating the growth of viruses. 
  • Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. 
  • Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. 
  • Structural biology: Aerial view of the HIV genome. 
  • Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication. 
  • Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015. 
  • The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense. 
  • The complete genome sequence, organization and affinities of carrot red leaf virus. 
  • The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. 
  • The origins and genomic diversity of American Civil War Era smallpox vaccine strains. 
  • Thousands of small, novel genes predicted in global phage genomes. 
  • Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. 
  • Transcriptional Circuit Fragility Influences HIV Proviral Fate. 
  • Transfer of photosynthesis genes to and from Prochlorococcus viruses. 
  • Transmission of Multiple HIV-1 Subtype C Transmitted/founder Viruses into the Same Recipients Was not Determined by Modest Phenotypic Differences. 
  • Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. 
  • Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. 
  • Use of recombinant adenovirus for metabolic engineering of mammalian cells. 
  • Virology, Epidemiology, Pathogenesis, and Control of COVID-19. 
  • Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses. 
  • Wide variation in the multiplicity of HIV-1 infection among injection drug users. 
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  Keywords of People

  • Ferrari, Guido, Professor in Surgery, Molecular Genetics and Microbiology
  • Weinhold, Kent James, Joseph W. and Dorothy W. Beard Distinguished Professor of Experimental Surgery, Integrative Immunobiology