Master Sequences Research Articles

RNA three-dimensional structure drives the sequence organization of potato spindle tuber viroid quasispecies.

RNA viruses and viroids exist and evolve as quasispecies due to error-prone replication. Quasispecies consist of a few dominant master sequences alongside numerous variants that contribute to genetic diversity. Upon environmental changes, certain variants within quasispecies have the potential to become the dominant sequences, leading to the emergence of novel infectious strains. However, the emergence of new infectious variants remains unpredictable. Using mutant pools prepared by saturation mutagenesis of selected stem and loop regions, our study of potato spindle tuber viroid (PSTVd) demonstrates that mutants forming local three-dimensional (3D) structures similar to the wild type (WT) are more likely to accumulate in PSTVd quasispecies. The selection mechanisms underlying this biased accumulation are likely associated with cell-to-cell movement and long-distance trafficking. Moreover, certain trafficking-defective PSTVd mutants can be spread by functional sister genomes in the quasispecies. Our study reveals that the RNA 3D structure of stems and loops constrains the evolution of viroid quasispecies. Mutants with a structure similar to WT have a higher likelihood of being maintained within the quasispecies and can potentially give rise to novel infectious variants. These findings emphasize the potential of targeting RNA 3D structure as a more robust approach to defend against viroid infections.

Expansion of error thresholds for the Moran model

We study a finite population of individuals evolving through mutation and selection. We generalize the Eigen quasispecies model to a finite population with the Moran model. This model also presents an asymptotic phase transition, and a proper definition of the critical parameter is discussed. We retrieve the same expression for the error threshold appearing in the Eigen model along with a correction term due to the finiteness of the population. To achieve this, we estimate the average lifetime of master sequences and find it grows like an exponential in the size of the population. Our technique consists in bounding from above and below the number of master sequences in the Moran model by two simpler birth and death chains. The expectation of this lifetime is then computed with the help of explicit formulas which are in turn expanded with Laplace method.

Unveiling of Evolution Pattern for HY12 Enterovirus Quasispecies and Pathogenicity Alteration.

Enterovirus, like the majority of RNA viruses, evolves to survive the changeable environments by a variety of strategies. Here, we showed that HY12 virus evolved to alter its characteristics and pathogenicity by employing a non-synonymous mutation. Analyses of 5′UTR, VP1 and VP2 gene sequences revealed the existence of HY12 virus in an array of mutants defined as quasispecies. The determination of diversity and complexity showed that the mutation rate and complexity of HY12 virus quasispecies increased, while the proportion of HY12 VP1 and VP2 consensus (master) sequences decreased with increasing passages. Synonymous mutation and non-synonymous mutation analysis displayed a positive selection for HY12 quasispecies evolution. A comparison of HY12 virus in different passages demonstrated that HY12 virus altered its characteristic, phenotype, and pathogenicity via non-synonymous mutation. These findings revealed the evolution pattern for HY12 virus, and the alteration of HY12 virus characteristics and pathogenicity by mutation.

In vivo evolution of viral virulence: switching of deformed wing virus between hosts results in virulence changes and sequence shifts.

The health of the Western honey bee is threatened by a global epidemic of deformed wing virus (DWV) infections driven by the ectoparasitic mite Varroa destructor acting as mechanical and biological virus vector. Three different variants of DWV, DWV-A, -B and -C exist. Virulence differences between these variants and their relation to V. destructor are still controversially discussed. We performed laboratory experiments to analyze the virulence of DWV directly isolated from crippled bees (DWVP0 ) or after one additional passage in bee pupae (DWVP1 ). We demonstrated that DWVP0 was more virulent than DWVP1 for pupae, when pupal mortality was taken as virulence marker, and for adult bees, when neurotropism and cognitive impairment were taken as virulence markers. Phylogenetic analysis supported that DWV exists as quasispecies and showed that DWVP0 clustered with DWV-B and DWVP1 with DWV-A when the phylogeny was based on the master sequences of the RNA-dependent RNA polymerase but not so when it was based on the VP3 region master sequences. We propose that switching of DWV between the bee and the mite host is accompanied by changes in viral sequence, tissue tropism and virulence and that the RNA-dependent RNA polymerase is involved in determining host range and virulence.

Optimal operations sequence retrieval from master operations sequence for part/product families

This research capitalises on commonalities between members of a product family to increase the speed, consistency and efficiency of constructing a master operations sequence and optimal operations sequences for new variants. Two novel mixed integer programming (MIP) models are developed for generating master operations sequence based on available operations sequences of a family of part/product variants. The use of master operations sequence reduces the time, cost and effort required for developing new operations sequences, hence improving the planning efficiency and productivity. The first MIP model is developed for variants with serial operations sequence while the second is a generalised model for serial, networked operations sequences or a combination of both structures. The developed models generate master operations sequences which have minimum total dissimilarity distance from existing variants. The master operations sequence is then used to construct the operations sequence for new variants falling within or significantly overlapping with the boundary of the considered product family. As the number of operations increases, the efficiency of mathematical models decreases. Therefore, a novel algorithm is proposed to generate master operations sequences for product variants with any type of process sequence structure (i.e. serial, networked, or combination). Computational results demonstrated the capability of developed MIP algorithms to find optimum solutions and optimal operations sequence for new variants in a fraction of a second in most cases of small, medium and large size studied problems. Two assembly and fabrication case studies are provided for demonstration.

Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses.

Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) comprises the first 27 N-terminal amino acid residues of E2. It is classically seen as the most heterogeneous region of the HCV genome. In this study, we assessed HVR1 evolution by using ultradeep pyrosequencing for a cohort of treatment-naive, chronically infected patients over a short, 16-week period. Organization of the sequence set into connected components that represented single nucleotide substitution events revealed a network dominated by highly connected, centrally positioned master sequences. HVR1 phenotypes were observed to be under strong purifying (stationary) and strong positive (antigenic drift) selection pressures, which were coincident with advancing patient age and cirrhosis of the liver. It followed that stationary viromes were dominated by a single HVR1 variant surrounded by minor variants comprised from conservative single amino acid substitution events. We present evidence to suggest that neutralization antibody efficacy was diminished for stationary-virome HVR1 variants. Our results identify the HVR1 network structure during chronic infection as the preferential dominance of a single variant within a narrow sequence space. HCV infection is often asymptomatic, and chronic infection is generally well established in advance of initial diagnosis and subsequent treatment. HVR1 can undergo rapid sequence evolution during acute infection, and the variant pool is typically seen to diverge away from ancestral sequences as infection progresses from the acute to the chronic phase. In this report, we describe HVR1 viromes in chronically infected patients that are defined by a dominant epitope located centrally within a narrow variant pool. Our findings suggest that weakened humoral immune activity, as a consequence of persistent chronic infection, allows for the acquisition and maintenance of host-specific adaptive mutations at HVR1 that reflect virus fitness.

Understanding short-timescale neuronal firing sequences via bias matrices

The brain generates persistent neuronal firing sequences across varying timescales. The short-timescale (~100ms) sequences are believed to be crucial in the formation and transfer of memories. Large-amplitude local field potentials known as sharp-wave ripples (SWRs) occur irregularly in hippocampus when an animal has minimal interaction with its environment, such as during resting, immobility, or slow-wave sleep. SWRs have been long hypothesized to play a critical role in transferring memories from the hippocampus to the neocortex [1]. While sequential firing during SWRs is known to be biased by the previous experiences of the animal, the exact relationship of the short-timescale sequences during SWRs and longer-timescale sequences during spatial and non-spatial behaviors is still poorly understood. One hypothesis is that the sequences during SWRs are replays or preplays of which are sequences that closely mimic the order of place fields on a linear track [2,3]. Rather than particular hard-coded master sequences, an alternative explanation of the observed correlations is that similar sequences arise naturally from the intrinsic biases of firing between pairs of cells. To distinguish these and other possibilities, one needs mathematical tools beyond the center-of-mass sequences and Spearman's rank-correlation coefficient that are currently used. We introduce a new mathematical tool that captures the intrinsic properties of neuronal firing sequences. The bias matrix of a given sequence (Figure ​(Figure1)1) contains more detailed information than the center-of-mass average and captures more complex relationships among different neuronal sequences. This tool enabled us to directly investigate the relationships among firing sequences across different conditions: short-timescale sequences (during SWRs) and long-timescale behavioral sequences (during spatial navigation and wheel running). We also performed a pharmacological manipulation that resulted in elimination of theta oscillation (as previously reported in [4]) and increased the frequency of SWRs. We have found that the pairwise biases of sequences during SWRs are highly correlated with sequences during most of the conditions. Moreover, while sequences of neuronal activations are uncorrelated across different behaviors, the bias matrices of SWR sequences are highly correlated with those of various behavior sequences. Our findings provide a new tool for understanding the structure of short-timescale neuronal sequences and suggest that intrinsic pairwise biases are likely the underlying mechanism for the replay/preplay of longer-timescale sequences observed in the hippocampus [2,3]. Figure 1 Neuronal spike trains (top) are converted to bias matrices (middle) by computing the probability of pairs of neurons spiking in a particular order. The correlation between bias matrices (bottom) is then computed via the angle between the bias matrices. ...

Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses.

Bracoviruses represent the most complex endogenous viral elements (EVEs) described to date. Nudiviral genes have been hosted within parasitoid wasp genomes since approximately 100 Ma. They play a crucial role in the wasp life cycle as they produce bracovirus particles, which are injected into parasitized lepidopteran hosts during wasp oviposition. Bracovirus particles encapsidate multiple dsDNA circles encoding virulence genes. Their expression in parasitized caterpillars is essential for wasp parasitism success. Here, we report on the genomic organization of the proviral segments (i.e. master sequences used to produce the encapsidated dsDNA circles) present in the Cotesia congregata parasitoid wasp genome. The provirus is composed of a macrolocus, comprising two-thirds of the proviral segments and of seven dispersed loci, each containing one to three segments. Comparative genomic analyses with closely related species gave insights into the evolutionary dynamics of bracovirus genomes. Conserved synteny in the different wasp genomes showed the orthology of the proviral macrolocus across different species. The nudiviral gene odv-e66-like1 is conserved within the macrolocus, suggesting an ancient co-localization of the nudiviral genome and bracovirus proviral segments. By contrast, the evolution of proviral segments within the macrolocus has involved a series of lineage-specific duplications.

VARIABILITY OF POTATO SPINDLE TUBER VIROID ISOLATES FROM ORNAMENTAL HOSTS IN SLOVENIA

A survey of Potato spindle tuber viroid (PSTVd) was initiated in Slovenia in December 2006. Out of 398 samples collected between the beginning of the survey and the end of 2010, a quarter tested positive for PSTVd, in particular Brugmansia cordata (1), Solanum jasminoides (88), S. rantonnetii (5), Petunia spp (3), and S. muricatum (3). Analysis of 96 complete master sequences of Slovene positive samples revealed new variants, although the majority of master sequences were identical to the sequence variant of PSTVd found in S. rantonnetii in Italy (EF459700). A substitution of G to U at position 65 was found in several sequence variants otherwise identical to EF459700. The variability of this site was confirmed by cloning three samples that showed ambiguity at position 65 when the PCR products were sequenced directly. Phylogenetic analyses of Slovene sequence variants and sequence variants from GenBank showed two clearly separated clusters. High variability was observed within each cluster. Although most of the sequence variants from the same ornamental host tended to group together, sequence variants from the same hosts also showed high variability. On the other hand different hosts were found to be infected by the same sequence variant.

Secondary structures of Potato spindle tuber viroid variants detected in Slovenia

A survey of Potato spindle tuber viroid was initiated in Slovenia in 2006. Until the end of 2010, 100 samples of ornamental plants were found to be infected. Analysis of 96 complete master sequences of Slovene samples revealed new genetic variants. Our sequence variants showed considerable variation in their predicted secondary structure. The variability was observed in the pathogenic, central and variable domains. In several cases even single mutations were sufficient for the change in predicted secondary structure.

First report of Iresine viroid 1 in Portulaca sp. in Slovenia.

In October 2011, during a survey for pospiviroids in ornamental plants, leaf samples were collected from two symptomless Portulaca sp. plants of two different varieties grown in a flower bed. Total RNA of each sample was extracted twice from 15 mg of leaf tissue using the MagMaxTM-96 total RNA isolation kit (Ambion, USA). The samples were tested by RT-PCR using semiuniversal pospiviroid primers [Pospi1-RE/FW and Vid-RE/FW (Verhoeven et al., 2004)]. A product was amplified with primer pair Pospi1-RE/FW but not with primer pair Vid-RE/FW. The amplicon from each total RNA extract was custom sequenced (Macrogen, The Netherlands). Blast sequence analysis showed high identity with Iresine viroid 1 (IrVd-1). Primer pair IrVdFW1/IrVd-RE1 (Verhoeven et al., 2010) was used to amplify the full-length viroidal genomes. Amplicons were successfully cloned into pGEM-T easy vector (Promega, USA) and transformed into E. coli JM109 competent cells (Promega, USA). At least eight clones per sample were sequenced. Master sequences of each sample were deposited in GenBank under accession Nos. JQ889689 and JQ889690. They showed 99.7% identity between each other and 96.7-98.6% identity with other IrVd-1 sequences (GU911350, DQ094294, NC_003613 and DQ94293). This is the first report of IrVd-1 in Slovenia and the second report of IrVd-1 in Portulaca sp. worldwide. Portulaca sp. was first reported as a host of IrVd-1 in 2010 (Verhoeven, 2010). Unlike other pospiviroids IrVd-1 does not seem to present a threat to potato and tomato (Verhoeven et al., 2010).

TREE-RING DATE LISTS 2012

Dates of outermost measured complete rings and sapwood ring number are given in brackets. Complete sapwood is indicated by ‘C’ and where the character of the fi nal ring has been identifi ed, some laboratories signify seasonal felling dates as winter (C), spring (1⁄4C), and summer (1⁄2C), referring approximately to October to February, March to May and June to September respectively; ‘c’ indicates the presence of complete sapwood but not on the sample; ‘h/s’ indicates the presence of the heartwood-sapwood boundary; ‘NM’ indicates rings counted but not measured. Superscript numbers, e.g. ‘2’, denote two or more samples with the same end date and sapwood complement. Felling date ranges for which the sapwood estimate has been refi ned using the Dendro function of OxCal (D. H. Miles, ‘Refi nements in the interpretation of tree-ring dates for oak building timbers in England and Wales’, VA 37 (2006), 84–96) are given in italics to indicate that they are ‘interpretative’, with the unrefi ned date in brackets. Site Master gives the years spanned and three highest or representative t-values. All timbers dated are of oak, Quercus spp. unless otherwise stated. References to the master sequences are not printed but are available from the editor on request. RDRS [English Heritage Research Department Report Series] reports may be obtained from English Heritage; their address and the list of available reports published in 2011 are printed below, pp. 107–8. Corrigendum: The grid reference (NU 2469 0618) for Northumberland, Warkworth, Church of St Lawrence (List 236, no. 13, VA 42 (2011), 102) was omitted from the list.

Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.

Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and infect cells that are rarely in suspension but spatially organized. Surprisingly, most quasispecies models of virus replication have ignored these two phenomena. In order to study these two viral characteristics, we have developed stochastic cellular automata models that simulate two different modes of replication (geometric vs stamping machine) for quasispecies replicating and spreading on a two-dimensional space. Furthermore, we explored these two replication models considering epistatic fitness landscapes (antagonistic vs synergistic) and different scenarios for cell-to-cell spread, one with free superinfection and another with superinfection inhibition. We found that the master sequences for populations replicating geometrically and with antagonistic fitness effects vanished at low critical mutation rates. By contrast, the highest critical mutation rate was observed for populations replicating geometrically but with a synergistic fitness landscape. Our simulations also showed that for stamping machine replication and antagonistic epistasis, a combination that appears to be common among plant viruses, populations further increased their robustness by inhibiting superinfection. We have also shown that the mode of replication strongly influenced the linkage between viral loci, which rapidly reached linkage equilibrium at increasing mutations for geometric replication. We also found that the strategy that minimized the time required to spread over the whole space was the stamping machine with antagonistic epistasis among mutations. Finally, our simulations revealed that the multiplicity of infection fluctuated but generically increased along time.

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera.

BackgroundTnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum.ResultsTnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions.ConclusionThe results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.

Genetic analysis of dog rabies viruses circulating in Bangkok

The genetic diversity of the rabies virus glycoprotein (G) gene isolated from individual rabid dogs (inter-hosts) and within a single infected dog (intra-host) has been analyzed in an effort to better understand selective pressures and population shifts among rabies viruses circulating in Bangkok. Comparison of individual master sequences among inter-hosts revealed that the dog virus isolates circulating in Bangkok were phylogenetically closely related. The ectodomain of the glycoprotein was highly conserved among the virus isolates. Furthermore, the genetic diversity of the G gene within an intra-host was assessed by comparing the cloned sequences in the virus population. The comparisons revealed that rabies virus circulating in an intra-host consisted of closely related heterogenous populations with minor substitutions at nucleotide (0.19%) and amino acid levels.

Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model.

This paper develops a two-gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by sigma(via), yields a viable organism with first-order growth rate constant k>1 if it is equal to some target "master" sequence sigma(via,0). The second gene, denoted by sigma(rep), yields an organism capable of genetic repair if it is equal to some target "master" sequence sigma(rep,0). This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on micro identical with Lepsilon, the product of sequence length and per base pair replication error probability, and epsilon(r), the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of the three possible "phases." In the first phase, the population is localized about the viability and repairing master sequences. As epsilon(r) exceeds the fraction of deleterious mutations, the population undergoes a "repair" catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when micro exceeds ln k/epsilon(r), while above the repair catastrophe, the distribution undergoes the error catastrophe when micro exceeds ln k/f(del), where f(del) denotes the fraction of deleterious mutations.

RNA replication kinetics, genetic polymorphism and selection in the case of the hepatitis C virus.

We show in a simple theoretical quasispecies model that the replication dynamics of hepatitis C virus and a related model-system, the bovine viral diarrhoea virus, result in an effective reduction of RNA templates in infected cells. Viral fitness does not translate directly into RNA sequence replication efficiency, and hence the abundance of the viral master sequences diminishes over time. Our results suggest that genes not involved in RNA replication accumulate mutations over time because they do not undergo selection during this phase. The selection of viral RNA occurs not only during replication but also during the ensuing stages of the viral life cycle: (i) envelopment of viral RNA and (ii) successful infection of other cells, which also requires functionality of non-replicative genes. In particular, viral fitness requires the ability of the genome to encode structural proteins which do not encounter selective pressure during RNA replication. We conclude by discussing the potential value of antiviral drugs which inhibit selection on parts of the viral genome.

Fluorescently labeled model DNA sequences for exonucleolytic sequencing

We describe here the enzyme-catalyzed, low-density labeling of DNAs with fluorescent dyes. Firstly, for ‘natural’ template DNAs, dNTPs were partially substituted in the labeling reactions by the respective fluorophore-bearing analogs. The DNAs were labeled by PCR using Taq DNA polymerase. The covalent incorporation of dye-dNTPs decreased in the following order: rhodamine-green-5-dUTP (Molecular Probes, the Netherlands), tetramethylrhodamine-4-dUTP (FluoroRed, Amersham Pharmacia Biotech), Cy5-dCTP (Amersham Pharmacia Biotech). Exonucleolytic degradation by the 3′→5′ exonuclease activity of T7 DNA polymerase (wild type) in the presence of excess reduced thioredoxin proceeded to complete breakdown of the labeled DNAs. The catalytic cleavage constants determined by fluorescence correlation spectroscopy were between 0.5 and 1.5 s −1 at 16°C, normalized for the covalently incorporated dye-nucleotides. Secondly, rhodamine-green-X-dUTP (Roche Diagnostics), tetramethylrhodamine-6-dUTP (Roche Diagnostics), and Cy5-dCTP were covalently incorporated into the antisense strand of ‘synthetic’ 218-b DNA template constructs (master sequences) at well defined positions, starting from the primer binding site, by total substitution for the naturally occuring dNTPs. The 218-b DNA constructs were labeled by PCR with a thermostable 3′→5′ exonuclease deficient mutant of the Tgo DNA polymerase which we have selected. The advantage of the special, synthetic DNA constructs as compared to natural DNAs lies in the possibility of obtaining tailor-made nucleic acids, optimized for testing the performance of exonucleolytic sequencing. The number of incorporated fluorescent nucleotides determined by complete exonucleolytic degradation and fluorescence correlation spectroscopy were six out of six possible incorporations for rhodamine-green-X-dUTP and tetramethylrhodamine-6-dUTP, respectively. Their covalent and base-specific incorporations were confirmed by the novel analysis methodology of re-sequencing (i.e. mobility-shift gel electrophoresis, reversion-PCR and re-sequencing) first developed in the paper Földes-Papp et al. (2001) and in this paper. This methodology was then used by other groups within the whole sequencing project.

Variability of Citrus Exocortis Viroid (CEVd)

Single-strand conformation polymorphism (SSCP) has been adopted as a tool for viroid characterization. Nucleic acid extracts from a viroid field isolate containing CEVd was sub- jected to retrotranscription and PCR amplification using a set of contiguous CEVd-specific prim- ers. The analysis of cloned DNAs recovered from this isolate illustrates the extent of variability within a single CEVd isolate. The relationship between the SSCP profiles observed among clones and the variation in their nucleotide sequences was confirmed by sequence analysis of selected clones. The results indicate that field isolates are complex populations or quasispecies. Two highly conserved sequences (master sequences) as well as several less abundant variants were consis- tently identified. The sequence variants presented a base pairing arrangement in the P domain characteristic of severe strains of CEVd. A branched secondary structure rather than the rod-like structure was predicted to occur at 37 ° C. Index words. Variants, SSCP, quasispecies. Citrus exocortis viroid (CEVd), the causal agent of the exocortis dis- ease, was discovered in 1972 (12). Determination of its primary struc- ture (4, 14), showed that the CEVd molecule is a covalently closed circu- lar RNA with a highly base paired rod-like structure which conforms the model of five structural domains (T L , P, C, V, T R ) (7). Viroid replication which occurs in the absence of proof-reading mecha- nisms accounts for a high rate of variability generation. Although there are numerous structural con- straints, which impair infectivity

Prospective study of mother-to-infant transmission of hepatitis C virus (HCV) infection

Seventy-five women with anti-hepatitis C virus (HCV) antibody were enrolled prospectively during pregnancy or at delivery for study of mother-to-child transmission of HCV. Twenty-three women were coinfected with the human immunodeficiency virus (HIV). Seventy babies were monitored for at least 6 months. HCV infection was diagnosed in six infants (8.6%), four of whom were born to anti-HIV-positive mothers. HCV RNA was first detected between 2 and 6 months, and the genotypes of infected babies matched those of their mothers (type 1: n = 4; type 3: n = 2). Identical master sequences of the hypervariable region (HVR1) were detected in a mother-infant pair. In three babies coinfected with HCV and HIV, anti-HCV disappeared between 2 and 7 months, being persistently negative in two cases monitored for 11 and 26 months. Transmitting mothers did not differ significantly from those who did not transmit the infection with anti-HIV, HCV genotypes, and viral load at delivery, but had lower rate of reactivity to C100 by the recombinant immunoblot assay (RIBA) (P < .01). This prospective study confirms transmission of HCV from anti-HIV-negative mothers (4.4% in this series). Absence of anti-C100 antibodies at delivery is apparently related to increased risk of vertical transmission. Seronegative HCV infection can be observed in children coinfected with HIV.