A Natural Language Processing Pipeline to Identify COVID-19 Outbreaks from Contact Tracing Interview Forms for Public Health Departments

BACKGROUND

In Wisconsin, COVID-19 case interview forms contain free text fields that need to be mined to identify potential outbreaks for targeted policy making. We developed an automated pipeline to ingest the free text into a pre-trained neural language model to identify businesses and facilities as outbreaks.

OBJECTIVE

We aimed to examine the precision and recall of our natural language processing pipeline against existing outbreaks and potentially new clusters.

METHODS

Data on cases of COVID-19 were extracted from the Wisconsin Electronic Disease Surveillance System (WEDSS) for Dane County between July 1, 2020, and June 30, 2021. Features from the case interview forms were fed into a Bidirectional Encoder Representations from Transformers (BERT) model that was fine-tuned for named entity recognition (NER). We also developed a novel location mapping tool to provide addresses for relevant NERs. Precision and recall were measured against manually verified outbreaks and valid addresses in WEDSS.

RESULTS

There were 46,798 cases of COVID-19 with 4,183,273 total BERT tokens and 15,051 unique tokens. The recall and precision of the NER tool were 0.67 (95 % CI 0.66-0.68) and 0.55 (95 % CI: 0.54-0.57), respectively. For the location mapping tool, the recall and precision were 0.93 (95% CI: 0.92-0.95) and 0.93 (95% CI: 0.92-0.95), respectively. Across monthly intervals, the NER tool identified more potential clusters than were verified in the WEDSS system.

CONCLUSIONS

We developed a novel pipeline of tools that identified existing outbreaks and novel clusters with associated addresses. Our pipeline ingests data from a statewide database and may be deployed to assist local health departments for targeted interventions.

H in α-Zr and in zirconium hydrides: solubility, effect on dimensional changes, and the role of defects

Structural, thermodynamic and elastic properties of the hydrogen-zirconium system including all major hydrides are studied from first principles. Interstitial hydrogen atoms occupy preferentially tetrahedral sites. The calculations show that a single vacancy in α-Zr can trap up to nine hydrogen atoms. Self-interstitial Zr atoms attract hydrogen to a lesser extent. Accumulation of hydrogen atoms near self-interstitials may become a nucleation site for hydrides. By including the temperature-dependent terms of the free energy based on ab initio calculations, hydrogen adsorption isotherms are computed and shown to be in good agreement with experimental data. The solubility of hydrogen decreases in Zr under compressive strain. The volume dependence on hydrogen concentration is similar for hydrogen in solution and in hydrides. The bulk modulus increases with hydrogen concentration from 96 to 132 GPa.

O17. The development of 'time release' nail enamels

In our recent studies on the effects of plasticizers on nail enamel films, we developed a high interest in a phenomenon that we named as 'internal flow'[1]. During the film forming process there is an area that develops beneath the film surface where the film components remain dynamic and mobile. The time frame during which the film maintains this status is directly related to the balance of the resins, plasticizers, polymers and solvents utilized. We found that the longer this 'internal flow' persists, the better the nail enamel wears. At Tevco, we have been able to control the rate at which the solvents and plasticizers flash off the substrate during the film forming process by regulating the interactions and the levels of film constituents. This 'time release' action is the foundation of our study. This study shows that the alkyl adipates are an integral component in controlling the film's internal flow through time release. As plasticizers, these materials, when in proper balance with other components, can create a film surface that is crack-and scuff-resistant. Finally, the substrate in this study is the human nail. The film we developed has to adhere and provide consistent performance over a wide range of temperatures, oil content and the surface abrasion of human nails. We have found that by utilizing adhesion promoters in conjunction with our optimized internal flow time release formula, our film meets all required criteria and generally outperforms conventional quick dry films. In conclusion, we have been able to optimize the film characteristics of conventional quick dry nail enamels. By controlling the internal flow of the film, we can enhance the performance criteria generally expected by consumers in nail enamels.

Summary of workshop 'Theory Meets Industry'-the impact of ab initio solid state calculations on industrial materials research

A workshop, 'Theory Meets Industry', was held on 12-14 June 2007 in Vienna, Austria, attended by a well balanced number of academic and industrial scientists from America, Europe, and Japan. The focus was on advances in ab initio solid state calculations and their practical use in industry. The theoretical papers addressed three dominant themes, namely (i) more accurate total energies and electronic excitations, (ii) more complex systems, and (iii) more diverse and accurate materials properties. Hybrid functionals give some improvements in energies, but encounter difficulties for metallic systems. Quantum Monte Carlo methods are progressing, but no clear breakthrough is on the horizon. Progress in order-N methods is steady, as is the case for efficient methods for exploring complex energy hypersurfaces and large numbers of structural configurations. The industrial applications were dominated by materials issues in energy conversion systems, the quest for hydrogen storage materials, improvements of electronic and optical properties of microelectronic and display materials, and the simulation of reactions on heterogeneous catalysts. The workshop is a clear testimony that ab initio computations have become an industrial practice with increasingly recognized impact.

Influence of cardiopulmonary resuscitation on levels of tumour markers

Tumour markers (TM), including alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA), cancer antigen (CA) 15-3 and prostate-specific antigen (PSA), are serum markers for malignant diseases. Previous studies investigating the effect of acute and chronic inflammation, cardiopulmonary bypass surgery and cardiopulmonary resuscitation (CPR) on levels of TM showed conflicting results. Cardiopulmonary resuscitation (CPR) may result in a profound inflammatory response, and is frequently associated with severe tissue hypoperfusion. The present study investigated whether AFP, CEA, CA 15-3 and PSA are influenced by CPR. Alpha-fetoprotein (AFP), CEA, CA 15-3 and PSA (only in male patients) were assessed immediately after hospital admission, 6 h, 12 h and 2 days after prolonged CPR in eight male and 12 female patients. Serum levels of AFP, CEA, CA 15-3 did not change significantly after CPR. Prostate-specific antigen (PSA) levels increased significantly with a highest level in the study period 48 h after CPR (3.3 +/- 3.1 and 28.3 +/- 30.5 ng/mL for baseline and 48 h levels, respectively; P < 0.001). Alpha-fetoprotein (AFP), CEA, CA 15-3 and PSA (in men) values above the normal range were observed in 0%, 13.8%, 3.8% and 46.9% of all measurements respectively. At least one value above the normal range were observed in 0%, 20%, 5% and 75% of all patients for AFP, CEA, CA 15-3 and PSA (in men) respectively. Baseline values of AFP, CEA, CA 15-3 and PSA (in men) were above the normal range in 0%, 15%, 5% and 10% of all patients respectively. Levels for all markers did not differ significantly between survivors and non-survivors. In conclusion, prolonged CPR does not influence AFP, CEA, CA 15-3 serum levels, but is frequently associated with increases of PSA. Thus, in contrast to PSA, interpretation of AFP, CEA, CA 15-3 serum levels is not influenced by recent CPR.

Biochemical and genetic studies of the VPg uridylylation reaction catalyzed by the RNA polymerase of poliovirus

The first step in poliovirus (PV) RNA synthesis is the covalent linkage of UMP to the terminal protein VPg. This reaction can be studied in vitro with two different assays. The simpler assay is based on a poly(A) template and requires synthetic VPg, purified RNA polymerase 3D(pol), UTP, and a divalent cation. The other assay uses specific viral sequences [cre(2C)] as a template for VPg uridylylation and requires the addition of proteinase 3CD(pro). Using one or both of these assays, we analyzed the VPg specificities and metal requirements of the uridylylation reactions. We determined the effects of single and double amino acid substitutions in VPg on the abilities of the peptides to serve as substrates for 3D(pol). Mutations in VPg, which interfered with uridylylation in vitro, were found to abolish viral growth. A chimeric PV containing the VPg of human rhinovirus 14 (HRV14) was viable, but substitutions of HRV2 and HRV89 VPgs for PV VPg were lethal. Of the three rhinoviral VPgs tested, only the HRV14 peptide was found to function as a substrate for PV1(M) 3D(pol) in vitro. We also examined the metal specificity of the VPg uridylylation reaction on a poly(A) template. Our results show a strong preference of the RNA polymerase for Mn(2+) as a cofactor compared to Mg(2+) or other divalent cations.

Will the polio niche remain vacant?

C-Cluster enteroviruses (C-CEVs), consisting of Coxsackie A viruses (C-CAV1, 11, 13, 15, 17, 18, 19, 20, 21, 22, 24, 24v) and polioviruses (PV1, 2, 3), have been grouped together in relation to their genomic sequences. On the basis of disease syndromes caused in humans, however, C-CAVs and PVs are vastly different: the former cause respiratory disease, just like the major receptor group rhinoviruses (magHRV), whereas PVs, on invasion of the CNS, can cause poliomyelitis. It is assumed that the difference in pathogenesis of C-CEVs is governed predominantly by cellular receptor specificity. C-CAVs use ICAM-1, just like magHRV, whereas PVs uniquely use CD155. Both ICAM-1 and CD155 are Ig-like molecules. Remarkably, based on a phylogenetic analysis of non-structural proteins, CAV 11, 13, 17 and 18 are interleaved with, rather than separated from, the three PV serotypes, e.g. PV1 is more closely related to CAV18 that to PV2. This observation suggests that PVs may have emerged from a pool of C-CAVs by evolving a unique receptor specificity. We have been studying virion structure, virion/receptor interactions, genetics, and the molecular biology of C-CEVs with the objective of identifying the molecular basis of phenotypic diversity of these viruses. Of particular interest is the prospect that C-CEVs can be genetically manipulated to switch their receptor affinity: from CD155 to ICAM-1 for PVs, or from ICAM-1 to CD155 for C-CAVs. We propose a hypothesis that in a world free of poliovirus and anti-poliovirus neutralizing antibodies C-CAVs would be given a greater chance to switch receptor specificity from ICAM-1 to CD155 and thus, to evolve gradually into a new polio-like virus.

The viral protein 3CD induces an equilibrium between the viral protein and RNA synthesis in a cell-free system for poliovirus replication

In a cell-free system derived from uninfected HeLa cells and programmed with poliovirus RNA, an unbalance between the different replication steps is observed. After programming, the vRNA is exclusively used as a template for viral translation. It takes hours before there is a switch from protein synthesis to RNA replication. This is probably the reason for the inefficient production of infectious virus (compared to the synthesis in infected cells). If, however, the cell-free system is programmed with vRNA and with a mRNA coding for the viral protein 3CD, an increase in vRNA synthesis is found early post-programming, resulting in a better balance of protein synthesis and RNA synthesis and an increased virus yield of at least 2 log10. These data show that a balance between translation, RNA replication and packaging is required to allow efficient viral proliferation. The virus yield could be increased by a further log10 by the addition of pirodavir (a capsid stabiliser) and 10% of rabbit reticulocyte lysate to the cell-free system.

Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: purification and enzymatic analysis of the RNA-dependent RNA polymerase 3D(pol)

The replication of human rhinovirus 2 (HRV2), a positive-stranded RNA virus belonging to the Picornaviridae, requires a virus-encoded RNA polymerase. We have expressed in Escherichia coli and purified both a glutathione S-transferase fusion polypeptide and an untagged form of the HRV2 RNA polymerase 3D(pol). Using in vitro assay systems previously described for poliovirus RNA polymerase 3D(pol) (J. B. Flanegan and D. Baltimore, Proc. Natl. Acad. Sci. USA 74:3677-3680, 1977; A. V. Paul, J. H. van Boom, D. Filippov, and E. Wimmer, Nature 393:280-284, 1998), we have analyzed the biochemical properties of the two different enzyme preparations. HRV2 3D(pol) is both template and primer dependent, and it catalyzes two types of synthetic reactions in the presence of UTP, Mn(2+), and a poly(A) template. The first consists of an elongation reaction of an oligo(dT)(15) primer into poly(U). The second is a protein-priming reaction in which the enzyme covalently links UMP to the hydroxyl group of tyrosine in the terminal protein VPg, yielding VPgpU. This precursor is elongated first into VPgpUpU and then into VPg-linked poly(U), which is identical to the 5' end of picornavirus minus strands. The two forms of the enzyme are about equally active both in the oligonucleotide elongation and in the VPg-primed reaction. Various synthetic mutant VPgs were tested as substrates in the VPg uridylylation reaction.

Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: identification of a cis-replicating element in the coding sequence of 2A(pro)

We have previously shown that the RNA polymerase 3D(pol) of human rhinovirus 2 (HRV2) catalyzes the covalent linkage of UMP to the terminal protein (VPg) using poly(A) as a template (K. Gerber, E. Wimmer, and A. V. Paul, J. Virol. 75:10969-10978, 2001). The products of this in vitro reaction are VPgpU, VPgpUpU, and VPg-poly(U), the 5' end of minus-strand RNA. In the present study we used an assay system developed for poliovirus 3D(pol) (A. V. Paul, E. Rieder, D. W. Kim, J. H. van Boom, and E. Wimmer, J. Virol. 74: 10359-10370, 2000) to search for a viral sequence or structure in HRV2 RNA that would provide specificity to this reaction. We now show that a small hairpin in HRV2 RNA [cre(2A)], located in the coding sequence of 2A(pro), serves as the primary template for HRV2 3D(pol) in the uridylylation of HRV2 VPg, yielding VPgpU and VPgpUpU. The in vitro reaction is strongly stimulated by the addition of purified HRV2 3CD(pro). Our analyses suggest that HRV2 3D(pol) uses a "slide-back" mechanism during synthesis of the VPg-linked precursors. The corresponding cis- replicating RNA elements in the 2C(ATPase) coding region of poliovirus type 1 Mahoney (I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590-4600, 2000) and VP1 of HRV14 (K. L. McKnight and S. M. Lemon, RNA 4:1569-1584, 1998) can be functionally exchanged in the assay with cre(2A) of HRV2. Mutations of either the first or the second A in the conserved A(1)A(2)A(3)CA sequence in the loop of HRV2 cre(2A) abolished both viral growth and the RNA's ability to serve as a template in the in vitro VPg uridylylation reaction.

Viruses for the treatment of malignant glioma

Viruses have been considered for use as therapeutic agents against cancer, and malignant glioma in particular. Oncolytic viruses were designed to target malignant cells supporting efficient virus replication, or rendered vulnerable to viral destruction due to tumor-specific defects in their defense against virus infection. Other than conventional cancer chemotherapy, viral antineoplastic agents require complex interactions with the host organism to reach their target and to unleash their oncolytic activity. Recent progress in the design and therapeutic application of oncolytic viruses carries the promise to make these agents available for treatment of malignant glioma.

The poliovirus receptor CD155 mediates cell-to-matrix contacts by specifically binding to vitronectin

The human receptor for poliovirus (CD155) is an immunoglobulin-like molecule with unknown normal function(s). Here we provide evidence that CD155 binds specifically to vitronectin with a dissociation constant (K(d)) of 72 nM as determined by surface plasmon resonance. Based on sequence homology to the CD155 gene, three poliovirus receptor-related genes (PRR1, PRR2, and PRR3) were cloned recently. PRR proteins were reported by others to mediate homophilic cell adhesion. Neither PRR1 nor PRR2 binds poliovirus and it is assumed that their physiological functions differ from that of CD155. Indeed, mPRR2 was found to bind to vitronectin only weakly, while its self-adhesion activity is characterized by a K(d) of 310 nM. Moreover, there is no evidence for CD155 self-adhesion. Both CD155 and vitronectin colocalize to follicular dendritic cells and B cells inside the germinal centers of secondary lymphoid tissue (tonsils)-an observation suggesting that the CD155/vitronectin interaction is required for the establishment of a proper immune response in this particular context.

Genetic analysis of a poliovirus/hepatitis C virus chimera: new structure for domain II of the internal ribosomal entry site of hepatitis C virus

Internal ribosomal entry sites (IRESs) of certain plus-strand RNA viruses direct cap-independent initiation of protein synthesis both in vitro and in vivo, as can be shown with artificial dicistronic mRNAs or with chimeric viral genomes in which IRES elements were exchanged from one virus to another. Whereas IRESs of picornaviruses can be readily analyzed in the context of their cognate genome by genetics, the IRES of hepatitis C virus (HCV), a Hepacivirus belonging to Flaviviridae, cannot as yet be subjected to such analyses because of difficulties in propagating HCV in tissue culture or in experimental animals. This enigma has been overcome by constructing a poliovirus (PV) whose translation is controled by the HCV IRES. Within the PV/HCV chimera, the HCV IRES has been subjected to systematic 5' deletion analyses to yield a virus (P/H710-d40) whose replication kinetics match that of the parental poliovirus type 1 (Mahoney). Genetic analyses of the HCV IRES in P/H710-d40 have confirmed that the 5' border maps to domain II, thereby supporting the validity of the experimental approach applied here. Additional genetic experiments have provided evidence for a novel structural region within domain II. Arguments that the phenotypes observed with the mutant chimera relate solely to impaired genome replication rather than deficiencies in translation have been dispelled by constructing novel dicistronic poliovirus replicons with the gene order [PV]cloverleaf-[HCV]IRES-Deltacore-R-Luc-[PV]IRES-F-Luc-P2,3-3'NTR, which have allowed the measurement of HCV IRES-dependent translation independently from the replication of the replicon RNA.

Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1

Coxsackievirus A21 (CAV21), like human rhinoviruses (HRVs), is a causative agent of the common cold. It uses the same cellular receptor, intercellular adhesion molecule 1 (ICAM-1), as does the major group of HRVs; unlike HRVs, however, it is stable at acid pH. The cryoelectron microscopy (cryoEM) image reconstruction of CAV21 is consistent with the highly homologous crystal structure of poliovirus 1; like other enteroviruses and HRVs, CAV21 has a canyon-like depression around each of the 12 fivefold vertices. A cryoEM reconstruction of CAV21 complexed with ICAM-1 shows all five domains of the extracellular component of ICAM-1. The known atomic structure of the ICAM-1 amino-terminal domains D1 and D2 has been fitted into the cryoEM density of the complex. The site of ICAM-1 binding within the canyon of CAV21 overlaps the site of receptor recognition utilized by rhinoviruses and polioviruses. Interactions within this common region may be essential for triggering viral destabilization after attachment to susceptible cells.

Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase

Southampton virus (SHV) is a member of the Norwalk-like viruses (NLVs), one of four genera of the family Caliciviridae. The genome of SHV contains three open reading frames (ORFs). ORF 1 encodes a polyprotein that is autocatalytically processed into six proteins, one of which is p41. p41 shares sequence motifs with protein 2C of picornaviruses and superfamily 3 helicases. We have expressed p41 of SHV in bacteria. Purified p41 exhibited nucleoside triphosphate (NTP)-binding and NTP hydrolysis activities. The NTPase activity was not stimulated by single-stranded nucleic acids. SHV p41 had no detectable helicase activity. Protein sequence comparison between the consensus sequences of NLV p41 and enterovirus protein 2C revealed regions of high similarity. According to secondary structure prediction, the conserved regions were located within a putative central domain of alpha helices and beta strands. This study reveals for the first time an NTPase activity associated with a calicivirus-encoded protein. Based on enzymatic properties and sequence information, a functional relationship between NLV p41 and enterovirus 2C is discussed in regard to the role of 2C-like proteins in virus replication.

Genetic and biochemical studies of poliovirus cis-acting replication element cre in relation to VPg uridylylation

In addition to highly conserved stem-loop structures located in the 5'- and 3'-nontranslated regions, genome replication of picornaviruses requires cis-acting RNA elements located in the coding region (termed cre) (K. L. McKnight and S. M. Lemon, J. Virol. 70:1941-1952, 1996; P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560-11565, 1999; I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590-4600, 2000). cre elements appear to be essential for minus-strand RNA synthesis by an as-yet-unknown mechanism. We have discovered that the cre element of poliovirus (mapping to the 2C coding region of poliovirus type 1; nucleotides 4444 to 4505 in 2C), which is homologous to the cre element of poliovirus type 3, is preferentially used as a template for the in vitro uridylylation of VPg catalyzed by 3D(pol) in a reaction that is greatly stimulated by 3CD(pro) (A. V. Paul, E. Rieder, D. W. Kim, J. H. van Boom, and E. Wimmer, J. Virol. 74:10359-10370, 2000). Here we report a direct correlation between mutations that eliminate, or severely reduce, the in vitro VPg-uridylylation reaction and produce replication phenotypes in vivo. None of the genetic changes significantly influenced translation or polyprotein processing. A substitution mapping to the first A (A4472C) of a conserved AAACA sequence in the loop of PV-cre(2C) eliminated the ability of the cre RNA to serve as template for VPg uridylylation and abolished RNA infectivity. Mutagenesis of the second A (A4473C; AAACA) severely reduced the yield of VPgpUpU and RNA infectivity was restored only after reversion to the wild-type sequence. The effect of substitution of the third A (A4474G; AAACA) was less severe but reduced both VPg uridylylation and virus yield. Disruption of base pairing within the upper stem region of PV-cre(2C) also affected uridylylation of VPg. Virus derived from transcripts containing mutations in the stem was either viable or quasi-infectious.

Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg

The first step in the replication of the plus-stranded poliovirus RNA is the synthesis of a complementary minus strand. This process is initiated by the covalent attachment of UMP to the terminal protein VPg, yielding VPgpU and VPgpUpU. We have previously shown that these products can be made in vitro in a reaction that requires only synthetic VPg, UTP, poly(A), purified poliovirus RNA polymerase 3D(pol), and Mg(2+) (A. V. Paul, J. H. van Boom, D. Filippov, and E. Wimmer, Nature 393:280-284, 1998). Since such a poly(A)-dependent process cannot confer sufficient specificity to poliovirus RNA replication, we have developed a new assay to search for a viral RNA template in conjunction with viral or cellular factors that could provide this function. We have now discovered a small RNA hairpin in the coding region of protein 2C as the site in PV1(M) RNA that is used as the primary template for the in vitro uridylylation of VPg. This hairpin has recently been described in poliovirus RNA as being an essential structure for the initiation of minus strand RNA synthesis (I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590-4600, 2000). The uridylylation reaction either with transcripts of cre(2C) RNA or with full-length PV1(M) RNA as the template is strongly stimulated by the addition of purified viral protein 3CD(pro). Deletion of the cre(2C) RNA sequences from minigenomes eliminates their ability to serve as template in the reaction. A similar signal in the coding region of VP1 in HRV14 RNA (K. L. McKnight and S. M. Lemon, RNA 4:1569-1584, 1998) and the poliovirus cre(2C) can be functionally exchanged in the assay. The mechanism by which the VPgpUpU precursor, made specifically on the cre(2C) template, might be transferred to the site where it serves as primer for poliovirus RNA synthesis, remains to be determined.

The antiviral compound 5-(3,4-dichlorophenyl) methylhydantoin inhibits the post-synthetic cleavages and the assembly of poliovirus in a cell-free system

The mode of action of the antiviral drug 5-(3,4-dichlorophenyl) methylhydantoin (hydantoin) was studied in a cell-free system allowing de novo synthesis of poliovirus. This cell-free system, which is programmed with viral RNA, is suitable for the study of the late stages of poliovirus replication and, thus, for a study of antiviral compounds acting on these late stages. It was shown that, apart from the known inhibition of the assembly of poliovirus, hydantoin also blocks post-synthetic cleavages of poliovirus proteins. Our data demonstrate that the cell-free system is a sensitive tool to study the mode of action of antiviral compounds.

Expression of the human poliovirus receptor/CD155 gene during development of the central nervous system: implications for the pathogenesis of poliomyelitis

The gene for the human poliovirus receptor (hPVR/CD155) is the founding member of a new family of genes encoding proteins belonging to the immunoglobulin superfamily. To determine whether CD155 is expressed during mammalian development, we have made use of the previously characterized promoter of the CD155 gene and generated mice transgenic for a CD155 promoter-driven beta-galactosidase reporter gene. Expression of the reporter gene in transgenic embryos was observed during midgestation in anterior midline structures of the developing central nervous system and in the neuroretina. During that period, reporter gene expression appeared within the notochord and floor plate along the entire spinal cord reaching into the caudal diencephalon. In addition, transgene expression was observed in axonal projections emanating from retinal ganglion cells forming the optic nerve to reach the future region of the optic chiasm. Analysis of expression of CD155 during human embryonic development confirmed the distribution of reporter gene expression specified by CD155 promoter activity. The anatomical distribution of CD155 promoter activity during embryogenesis matches that of transacting factors previously identified to regulate transcription of the CD155 gene. Expression of CD155 within embryonic structures giving rise to spinal cord anterior horn motor neurons may explain the restrictive host cell tropism of poliovirus for this cellular compartment of the CNS.

Genetic analysis of a poliovirus/hepatitis C virus (HCV) chimera: interaction between the poliovirus cloverleaf and a sequence in the HCV 5' nontranslated region results in a replication phenotype

Internal ribosomal entry sites (IRESs) can function in foreign viral genomes or in artificial dicistronic mRNAs. We describe an interaction between the wild-type hepatitis C virus (HCV)-specific sequence and the poliovirus (PV) 5'-terminal cloverleaf in a PV/HCV chimeric virus (containing the HCV IRES), resulting in a replication phenotype. Either a point mutation at nucleotide (nt) 29 or a deletion up to nt 40 in the HCV 5' nontranslated region relieved the replication block, yielding PV/HCV variants replicating to high titers. Fortuitous yet crippling interactions between an IRES and surrounding heterologous RNA must be considered when IRES-based dicistronic expression vectors are being constructed.

Poliovirus and its cellular receptor: a molecular genetic dissection of a virus/receptor affinity interaction

The ability of a virus to attach to a susceptible host cell is of utmost importance for the initiation of viral life cycle. Cell surface proteins called viral receptors mediate the initial steps of virus attachment and uptake. Poliovirus (PV) is one of the most studied animal viruses and its interaction with its cellular receptor, the human poliovirus receptor (hPVR) has been well characterized. This review will present our current understanding of the PV/hPVR interaction at the genetic and biochemical level. In addition, we will also discuss the implications of the PV/hPVR interaction on PV tissue tropism and the evolution of the three PV serotypes.

Studies on the attenuation phenotype of polio vaccines: poliovirus RNA polymerase derived from Sabin type 1 sequence is temperature sensitive in the uridylylation of VPg

Determinants of temperature sensitivity and/or attenuation in Sabin type 1 poliovirus reside in the 5' NTR and coding sequences of the capsid proteins and viral RNA polymerase, 3D(pol). Previous studies have implicated at least two mutations in 3D(pol) of Sabin 1 vaccine strain [PV1(S)], including a Y73H change, as contributing to these phenotypes. We have used an in vitro assay to test the first step in RNA synthesis, the uridylylation of the terminal protein VPg with 3D(pol) isolated from PV1(S). Wt and two mutant 3D(pol) proteins (Y73H, D53N/Y73H) were expressed in Escherichia coli and were purified, and their activities were measured in the synthesis of VPgpU(pU) and of VPg-linked poly(U) at 30 and 39.5 degrees C. Our results show that at 39.5 degrees C the Y73H mutation leads to a defect in the synthesis of VPgpUp(U) and of VPg-poly(U) but not in the elongation of a (dT)(15) primer. The double mutant protein had the same activities as Y73H 3D(pol). Using the yeast two-hybrid assay, we detected a reduced interaction between 3D(pol) molecules carrying either the single or double mutations. Tyrosine-73 maps to the finger domain in the three-dimensional structure of 3D(pol). A model will be presented in which a change of Y73 to H73 may interfere with an interaction between two polymerase molecules that, in turn, may interfere with VPg uridylylation. Alternative explanations, however, cannot be excluded at the present time.

Intergeneric poliovirus recombinants for the treatment of malignant glioma

Poliovirus neuropathogenicity depends on sequences within the 5' nontranslated region of the virus. Exchange of the poliovirus internal ribosomal entry site with its counterpart from human rhinovirus type 2 resulted in attenuation of neurovirulence in primates. Despite deficient virus propagation in cells of neuronal origin, nonpathogenic polio recombinants retain excellent growth characteristics in cell lines derived from glial neoplasms. Susceptibility of malignant glioma cells to poliovirus may be mediated by expression of a poliovirus receptor, CD155, in glial neoplasms. Intergeneric polio recombinants with heterologous internal ribosomal entry site elements unfolded strong oncolytic potential against experimentally induced gliomas in athymic mice. Our observations suggest that highly attenuated poliovirus recombinants may have applicability as biotherapeutic antineoplastic agents.

Phenotypic suppression of empty spiracles is prevented by buttonhead

Unlike the trunk segments, the anterior head segments of Drosophila are formed in the absence of pair-rule and HOX-cluster gene expression, by the activities of the gap-like genes orthodenticle (otd), empty spiracles (ems) and buttonhead (btd). The products of these genes are transcription factors, but only EMS has a HOX-like homeodomain. Indeed, ems can confer identity to trunk segments when other HOX-cluster gene activities are absent. In trunk segments of wild-type embryos, however, ems activity is prevented by phenotypic suppression, in which more posterior HOX-cluster genes inactivate the more anterior without affecting transcription or translation. ems is suppressed by all other Hox-cluster genes and so is placed at the bottom of their hierarchy. Here we show that misexpression of EMS in the head transforms segment identity in a btd-dependent manner, that misexpression of BTD in the trunk causes ems-dependent structures to develop, and that EMS and BTD interact in vitro. The data indicate that this interaction may allow ems to escape from the bottom of the HOX-cluster gene hierarchy and cause a dominant switch of homeotic prevalence in the anterior-posterior direction.

Identification of a nuclear respiratory factor-1 binding site within the core promoter of the human polio virus receptor/CD155 gene

In this report we describe a cis-acting element within the core promoter of the CD155 gene specifying the polio virus receptor that is bound by the nuclear respiratory factor-1 (NRF-1) transcription factor. DNase I footprint analysis identified a nuclear protein binding site from -282 to -264 nucleotides upstream of the translation initiation codon of the CD155 gene, which we have called foot print IV (FPIV). Linker scanning mutagenesis revealed that a tandem repeat motif, GCGCAGGCGCAG, located within FPIV was essential for the basal activity of the CD155 core promoter. The results of the electrophoretic mobility shift assay experiments suggested that identical FPIV binding activities were present in a variety of nuclear extracts and that the tandem repeat was essential for binding. A one-hybrid screen was then carried out using FPIV as bait to clone the cDNA of the FPIV binding factor. The sequences of the cDNAs that were cloned from the screen were identical to NRF-1, a result that was confirmed by further electrophoretic mobility shift assay experiments. Overexpression of full-length NRF-1 and a dominant-negative form of NRF-1 modulated reporter gene expression driven by the core promoter. Remarkably, CD155 is the first gene shown to be regulated by NRF-1 that possesses an expression profile during embryogenesis correlating with this factor's proposed role in the development of the vertebrate optic system. We propose that NRF-1, which has been shown by others to be expressed during embryogenesis in animal systems, may be involved in regulating the expression of CD155 at specific stages of central nervous system development.

Interaction of the poliovirus receptor with poliovirus

The structure of the extracellular, three-domain poliovirus receptor (CD155) complexed with poliovirus (serotype 1) has been determined to 22-A resolution by means of cryo-electron microscopy and three-dimensional image-reconstruction techniques. Density corresponding to the receptor was isolated in a difference electron density map and fitted with known structures, homologous to those of the three individual CD155 Ig-like domains. The fit was confirmed by the location of carbohydrate moieties in the CD155 glycoprotein, the conserved properties of elbow angles in the structures of cell surface molecules with Ig-like folds, and the concordance with prior results of CD155 and poliovirus mutagenesis. CD155 binds in the poliovirus "canyon" and has a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. However, the orientation of the long, slender CD155 molecule relative to the poliovirus surface is quite different from the orientation of intercellular adhesion molecule-1 on rhinoviruses. In addition, the residues that provide specificity of recognition differ for the two receptors. The principal feature of receptor binding common to these two picornaviruses is the site in the canyon at which binding occurs. This site may be a trigger for initiation of the subsequent uncoating step required for viral infection.

A cysteine-rich motif in poliovirus protein 2C(ATPase) is involved in RNA replication and binds zinc in vitro

Protein 2C(ATPase) of picornaviruses is involved in the rearrangement of host cell organelles, viral RNA replication, and encapsidation. However, the biochemical and molecular mechanisms by which 2C(ATPase) engages in these processes are not known. To characterize functional domains of 2C(ATPase), we have focused on a cysteine-rich motif near the carboxy terminus of poliovirus 2C(ATPase). This region, which is well conserved among enteroviruses and rhinoviruses displaying an amino acid arrangement resembling zinc finger motifs, was studied by genetic and biochemical analyses. A mutation that replaced the first cysteine residue of the motif with a serine was lethal. A mutant virus which lacked the second of four potential coordination sites for zinc was temperature sensitive. At the restrictive temperature, RNA replication was inhibited whereas translation and polyprotein processing, assayed in vitro and in vivo, appeared to be normal. An intragenomic second-site revertant which reinserted the missing coordination site for zinc and recovered RNA replication at the restrictive temperature was isolated. The cysteine-rich motif was sufficient to bind zinc in vitro, as assessed in the presence of 4-(2-pyridylazo)resorcinol by a colorimetric assay. Zinc binding, however, was not required for hydrolysis of ATP. 2C(ATPase) as well as its precursors 2BC and P2 were found to exist in a reduced form in poliovirus-infected cells.

Paradoxes of the replication of picornaviral genomes

A wealth of experimental data on the mechanism of the picornavirus genome replication has accumulated. Not infrequently, however, conclusions derived from these data appear to contradict each other. On the one hand, initiation of a complementary RNA strand can be demonstrated to occur in a solution containing only the poliovirus RNA polymerase, VPg, uridine triphosphate, poly(A) template and appropriate ions. On the other hand, convincing experiments suggest that efficient initiation of a viral complementary RNA strand requires complex cis-acting signals on the viral RNA template, additional viral and possibly cellular proteins as well as a membrane-containing environment. On the one hand, there is evidence that the viral RNA, in order to be replicated, should first be translated, but on the other hand, the viral RNA polymerase appears to be unable to overcome the ribosome barrier. Possible solutions for these and several other similar paradoxes are discussed, along with less contradictory results on the properties of the picornaviral replicative proteins. Recent results suggesting that recombination and other rearrangements of the viral RNA genomes may be accomplished not only by the replicative template switching but also by nonreplicative mechanisms are also briefly reviewed.

Genetic recombination of poliovirus in vitro and in vivo: temperature-dependent alteration of crossover sites

Genetic recombination that occurs with high frequency during poliovirus genome replication is a process whose molecular mechanism is poorly understood. Studies of genetic recombination in a cell-free system in vitro and in infected tissue culture cells in vivo have led to the unexpected observation that temperature strongly influences the loci at which cross-over between the two recombining RNA strands occurs. Specifically, cross-over between two genetically marked RNA strands in vitro and in vivo at 34 degrees C occurred over a wide range of the genome. In contrast, recombination in vivo at 37 and 40 degrees C yielded cross-over patterns that had shifted dramatically to a region encoding nonstructural proteins. Preferential selection of recombinants at 37 and 40 degrees C was ruled out by analyses of the growth kinetics of the recombinants. During the studies of recombination in the cell-free system we found that there is a direct correlation between the ability of a poliovirus RNA molecule to replicate in the cell-free system and its capacity to complement de novo virus synthesis programmed by another viral RNA.

Characterization of the nucleoside triphosphatase activity of poliovirus protein 2C reveals a mechanism by which guanidine inhibits poliovirus replication

The highly conserved non-structural protein 2C of picornaviruses is involved in viral genome replication and encapsidation and in the rearrangement of intracellular structures. 2C binds RNA, has nucleoside triphosphatase activity, and shares three motifs with superfamily III helicases. Motifs "A" and "B" are involved in nucleotide triphosphate (NTP) binding and hydrolysis, whereas a function for motif "C" has not yet been demonstrated. Poliovirus RNA replication is inhibited by millimolar concentrations of guanidine hydrochloride (GdnHCl). Resistance and dependence to GdnHCl map to 2C. To characterize the nucleoside triphosphatase activity of 2C, we purified poliovirus recombinant 2C fused to glutathione S-transferase (GST-2C) from Escherichia coli. GST-2C hydrolyzed ATP with a Km of 0.7 mM. Other NTPs, including GTP, competed with ATP for binding to 2C but were poor substrates for hydrolysis. Mutation of conserved residues in motif A and B abolished ATPase activity, as did mutation of the conserved asparagine residue in motif C, an observation indicating the involvement of this motif in ATP hydrolysis. GdnHCl at millimolar concentrations inhibited ATP hydrolysis. Mutations in 2C that confer poliovirus resistant to or dependent on GdnHCl increased the tolerance to GdnHCl up to 100-fold.

Poliovirus/Hepatitis C virus (internal ribosomal entry site-core) chimeric viruses: improved growth properties through modification of a proteolytic cleavage site and requirement for core RNA sequences but not for core-related polypeptides

H.-H. Lu and E. Wimmer (Proc. Natl. Acad. Sci. USA 93:1412-1417, 1996) have demonstrated that the internal ribosomal entry site (IRES) of poliovirus (PV) can be functionally replaced by the related genetic element from hepatitis C virus (HCV). One important finding of this study was that open reading frame sequences 3' of the initiating AUG, corresponding to the open reading frame of the HCV core polypeptide, are required to create a viable chimeric virus. This made necessary the inclusion of a PV 3C protease (3Cpro) cleavage site for proper polyprotein processing to create the authentic N terminus of the PV capsid precursor. Chimeric PV/HCV (P/H) viruses, however, grew poorly relative to PV. The goal of this study was to determine the molecular basis of impaired replication and enhance the growth properties of this chimeric virus. Genetic modifications leading to a different proteinase (PV 2Apro) cleavage site between the HCV core sequence and the PV polyprotein (P/H701-2A) proved far superior with respect to viral protein expression, core-PV fusion polyprotein processing, plaque phenotype, and viral titer than the original prototype PV/HCV chimera containing the PV 3Cpro-specific cleavage site (P/H701). We have used this new virus model to answer two questions concerning the role of the HCV core protein in P/H chimeric viral proliferation. First, a derivative of P/H701-2A with frameshifts in the core-encoding sequence was used to demonstrate that production of the core protein was not necessary for the translation and replication of the P/H chimera. Second, a viral construct with a C-terminal truncation of 23 amino acids of the core gene was used to show that a signal sequence for signal peptidase processing, when present in the viral construct, is detrimental to P/H virus growth. The novel P/H chimera described here are suitable models for analyzing the function(s) of the HCV elements by genetic analyses in vivo and for antiviral drug discovery.

Dual stem loops within the poliovirus internal ribosomal entry site control neurovirulence

In the human central nervous system, susceptibility to poliovirus (PV) infection is largely confined to a specific subpopulation of neuronal cells. PV tropism is likely to be determined by cell-external components such as the PV receptor CD155, as well as cell-internal constraints such as the availability of a suitable microenvironment for virus propagation. We reported previously that the exchange of the cognate internal ribosomal entry site (IRES) within the 5' nontranslated region of PV with its counterpart from human rhinovirus type 2 (HRV2) can eliminate the neuropathogenic phenotype in a transgenic mouse model for poliomyelitis without diminishing the growth properties in HeLa cells. We now show that attenuation of neurovirulence of PV/HRV2 chimeras is not confined to CD155 transgenic mice but is evident also after intraspinal inoculation into Cynomolgus monkeys. We have dissected the PV and HRV2 IRES elements to determine those structures responsible for neurovirulence (or attenuation) of these chimeric viruses. We report that two adjacent stem loop structures within the IRES cooperatively determine neuropathogenicity.

Identification and characterization of the cis-acting elements of the human CD155 gene core promoter

The CD155 protein is the founding member of a new group of related molecules within the immunoglobulin superfamily sharing a V-C2-C2 domain structure and significant amino acid identity. We have recently isolated the promoter of the CD155 gene so that we may determine the transcription factors that regulate its expression and possibly gain insight into the cell biology of this gene. Here we report the mapping of three cis-elements within the CD155 core promoter, designated FPI, II, and III. The results of linker scanning mutagenesis suggest that all three of these cis-elements are required in varying degrees for the promoter activity of the core promoter fragment. The relative contribution of each region ranked in the following order: III > II > I. Interestingly, footprint and electrophoretic mobility shift assays show that FPIII binding activity is much reduced in a human cell line that does not express CD155. Additionally, protein binding to FPI and FPII was also investigated. DNase I footprinting using recombinant hAP-2alpha indicated that this transcription factor bound to both the FPI and FPII regions of the CD155 core promoter fragment. Electrophoretic mobility shift assays and supershift analysis confirmed the binding of AP-2 from crude nuclear extracts to FPI and to FPII. Lastly, cotransfection of the CD155 promoter with an AP-2alpha expression vector indicates that overexpression of AP-2alpha modulated the promoter activity of a CD155 promoter construct.

Formation of 4,4-dialkoxycyclohexa-2,5-dienone N-(thiol-S-yl)imine during reaction of 4-alkoxynitrosobenzenes with thiols in alcoholic solvents

During the interaction of nitrosoarenes with glutathione in aqueous media, intermediate generation of a highly resonance-stabilized sulfenamide cation has been repeatedly suggested. Most intermediates and end products could be explained by reactions of this sulfenamide cation with different nucleophiles such as excess thiol, solvent water, and metabolically produced arylamine. The present paper presents evidence for adduct formation of the sulfenamide cation with solvent alcohol at neutral pH. Sulfenamide cations generated from 4-nitrosophenetole and 4-nitrosoanisole, respectively, are strongly suggested to form the metastable ketals 4-ethoxy-4-methoxycyclohexa-2,5-dienone N-(glutathion-S-yl)imine and 4,4-dimethoxycyclohexa-2,5-dienone N-(glutathion-S-yl)imine, respectively, during reaction with solvent methanol. Reaction of the two sulfenamide cations in ethanol yielded 4,4-diethoxycyclohexa-2, 5-dienone N-(glutathion-S-yl)imine and 4-ethoxy-4-methoxycyclohexa-2, 5-dienone N-(glutathion-S-yl)imine, respectively. Although the metastability of the ketals did not allow isolation of pure solid material, chromatographic and chemical behavior as well as tandem MS fragmentation substantiate a ketal structure of these intermediates. To confirm the proposed structure, new compounds, 2, 6-dimethyl-4-nitrosophenetole, 2,6-dimethyl-4-nitrophenetole, 2, 6-dimethyl-4-phenetidine, and N-(glutathion-S-yl)-N-hydroxy-4-aminoacetophenone, were synthesized and included in supportive experiments. In summary, the detection of ketals corroborates once more the occurrence of a sulfenamide cation which obviously not only reacts with soft nucleophiles such as GSH but, to a limited extent, also reacts with hard nucleophiles. The toxicological significance of this result is discussed.

Internal ribosomal entry site scanning of the poliovirus polyprotein: implications for proteolytic processing

Based on previous studies of dicistronic polioviruses carrying two internal ribosomal entry sites (IRESes), we performed a novel experiment of IRES scanning through a polypeptide by inserting sequentially the IRES of encephalomyocarditis virus into the open reading frame (ORF) of the poliovirus polyprotein at selected 3Cpro-specific Q*G cleavage sites. No cytopathic effects were observed after transfection of HeLa cells with any of the dicistronic constructs, and no virus was recovered. In vitro translation of the dicistronic RNA transcripts in HeLa cell-free extracts revealed that multiple defects in the processing of the P2-P3 domain of the polyprotein is the primary reason for the lethal phenotypes. Surprisingly, the interruption of 3Cpro-catalyzed cleavages downstream of 2C interfered with the 2Apro-catalyzed, primary cleavage between P1 and P2. In contrast, insertion of a foreign coding sequence (V3 loop of human immunodeficiency virus type 1 gp120) into the ORF of the polyprotein at the 2C-3A junction yielded a viable virus that appeared to be genetically stable over several passages. The results of these experiments, which are generally applicable to analyses of viral polyproteins or multidomain polypeptides, suggest that processing of the P2-P3 domain by 3C-3CDpro is rapid and accurate only in the context of the unperturbed P2-P3 precursor; this is consistent with cleavages occurring in cis. Moreover, an intact 2C-3A precursor is not required for viral proliferation.