Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift

The population dynamics of RNA viruses have an important influence on fitness variation and, in consequence, on the adaptative potential and virulence of this ubiquitous group of pathogens. Earlier work with vesicular stomatitis virus showed that large population transfers were reproducibly associated with fitness increases, whereas repeated transfers from plaque to plaque (genetic bottlenecks) lead to losses in fitness. We demonstrate here that repeated five-plaque to five-plaque passage series yield long-term fitness stability, except for occasional stochastic fitness jumps. Repeated five-plaque passages regularly alternating with two consecutive large population transmissions did not cause fitness losses, but did limit the size of fitness gains that would otherwise have occurred. These results underscore the profound effects of bottleneck transmissions in virus evolution.

Self-expandable endovascular stent for treatment of venous stenoses

The increase in survival among patients undergoing haemodialysis, the non-limitation of patient age regarding the start of renal substitution treatment, and the high incidence of vascular problems--particularly in diabetics--have caused the positioning of percutaneous catheters in central vessels to become a common practice in haemodialysis.

Evolution of a persistent aphthovirus in cytolytic infections: partial reversion of phenotypic traits accompanied by genetic diversification

Foot-and-mouth disease virus (FMDV) shows a dual potential to be cytolytic or to establish persistent infections in cell culture. FMDV R100, a virus rescued after 100 passages of carrier BHK-21 cells persistently infected with FMDV clone C-S8c1, showed multiple genetic and phenotypic alterations relative to the parental clone C-S8c1. Several FMDV R100 populations have been subjected to 100 serial cytolytic infections in BHK-21 cells, and the reversion of phenotypic and genetic alterations has been analyzed. An extreme temperature sensitivity of R100 reverted totally or partially in some passage series but not in others. The small-plaque morphology reverted to normal size in all cases. The hypervirulence for BHK-21 cells did not revert, and even showed an increase, upon cytolytic passage. Most of the mutations that had been fixed in the R100 genome during persistence did not revert in the course of cytolytic passages, but the extended polyribocytidylate tract of R100 (about 460 residues, versus 290 in C-S8c1) decreased dramatically in length, to the range of 220 to 260 residues in all passage series examined. In passages involving very large viral populations, a variant with two amino acid substitutions (L-144-->V and A-145-->P) next to the highly conserved Arg-Gly-Asp (RGD motif; positions 141 to 143) within the G-H loop of capsid protein VP1 became dominant. A clonal analysis allowed isolation of a mutant with the single replacement A-145-->P. Viral production and growth competition experiments showed the two variants to have a fitness very close to that of the parental virus. The results provide evidence that the repertoire of variants that could potentially become dominant in viral quasispecies may be influenced by the population size of the evolving virus. The net results of a series of persistent-infection passages followed by a series of cytolytic passages was progressive genomic diversification despite reversion or stasis of phenotypic traits. Implications for the evolution of RNA viruses are discussed.

Long-term, large-population passage of aphthovirus can generate and amplify defective noninterfering particles deleted in the leader protease gene

During serial undiluted passage of a clonal population of foot-and-mouth disease virus (FMDV C-S8c1) in BHK-21 cells, two species of defective RNA were generated and selected. Sequence analysis revealed that they included deletions within the L-coding region, and retained the correct reading frame for viral protein synthesis. These deleted RNAs directed the synthesis of capsid protein VP1, were packaged in particles sedimenting with standard virus, required homologous infectious helper virus in order to produce viral particles, but did not interfere with the replication of helper virus. While detection of defective particles in FMDV required more than 100 serial passages, once produced, these defective RNAs could be stably maintained upon further passages in the FMDV C-S8c1 quasispecies. Furthermore, a high fitness, monoclonal-antibody-resistant virus was able to replace the standard virus and support the amplification of the deleted particles. This is the first description of naturally occurring, defective particles of FMDV.

Virulence as a positive trait in viral persistence

A population replacement experiment has been devised to test the ability of a challenge virus to replace the resident virus in a persistently infected cell culture. BHK-21 cells persistently infected with foot-and-mouth disease virus of serotype C (clone C-S8c1) were challenged with a large excess of either the parental foot-and-mouth disease virus C-S8c1, genetically marked variants differing in their degree of virulence, or a mutant rescued after prolonged persistence in BHK-21 cells. After challenge, the composition of the resident virus population in the carrier culture was analyzed by reverse transcription-PCR amplification and nucleotide sequencing. The dominance of the initial persisting virus was seen in all cases, except when virulent viruses were used in the challenge. The experiments document that, paradoxically, virulence can be a positive factor in the reestablishment of a virus population in a persistently infected cell culture. A model based on the selection of virus-resistant cell variants during persistence is proposed to interpret these observations. Implications about the persistence of viruses in their host cells and organisms are discussed.

Large-population passages of vesicular stomatitis virus in interferon-treated cells select variants of only limited resistance

Vesicular stomatitis virus (VSV) populations were repeatedly passaged in L-929 cells treated with alpha interferon (IFN-alpha) at levels of 25 U/ml. This IFN-alpha concentration induced a 99.9% inhibition of viral yield in standard infections. Analysis of viral fitness (overall replicative ability measured in direct competition with a reference wild-type VSV) after 21 passages in IFN-treated cells showed only a limited increase or no increase in fitness, compared with the greater increase upon parallel passage in cells not treated with IFN-alpha. However, this limited increase in fitness was more pronounced when competition assays were carried out with IFN-alpha-treated cells, suggesting the selection of VSV populations with a low level of resistance to IFN-alpha. Thus, despite the extensively documented capacity of VSV to adapt to changing environments, the antiviral state induced by IFN-alpha imposes adaptive constraints on VSV which are not readily overcome.

Human immunodeficiency virus type 1 reverse transcriptase: role of Tyr115 in deoxynucleotide binding and misinsertion fidelity of DNA synthesis

Tyr115 is located in the vicinity of the polymerase catalytic site of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase. Site-directed mutagenesis was used to generate variant enzymes having Phe, Trp, Ala, Ser, Asp or Lys instead of Tyr115. The substitution of Tyr115 by Phe renders a fully active polymerase, displaying similar kinetic parameters, processivity and misinsertion fidelity of DNA synthesis as the wild-type enzyme. In contrast, the replacement of Tyr by Asp or Lys produced enzymes with a very low polymerase activity. The activity of the variant enzymes having Trp, Ala or Ser instead of Tyr115 was reduced significantly, particularly when poly(rA)484 was used as template. This effect was caused by a dramatic increase in the Km value for dTTP, and was detected using a DNA template mimicking a proviral HIV-1 gag sequence. Misinsertion fidelity assays revealed that mutants Y115W, Y115A and Y115S had a higher misinsertion efficiency than the wild-type reverse transcriptase. The low fidelity of these mutants appears to be related to nucleotide recognition rather than altered DNA-DNA template-primer interactions. The effects observed on the steady state kinetic constants, processivity and fidelity were mediated by the 66 kDa subunit, as demonstrated using chimeric heterodimers with the Y115A substitution in either p66 or p51.

Point mutant frequencies in the pol gene of human immunodeficiency virus type 1 are two- to threefold lower than those of env

Nucleotide sequences have been determined for the HIV-1 genomic regions encoding codons 41-108 and 181-219 of reverse transcriptase (RT) (pol gene), and codons 198-331 of gp120 (the C2V3 domains; env gene). Eighty-one HIV-1 samples from patients treated or untreated with RT inhibitors were used to sequence pol and 28 HIV-1 samples were used to sequence env. Several individual quasispecies have also been analyzed. All HIV-1 isolates belonged to subtype B. Point mutant frequencies and nucleotide diversities for pol were at most two- to threefold lower than env, with the proportion of nonsynonymous mutations ranging from 33 to 67%. A new variability index that takes into account the type of amino acid substitution as well as genetic distances between the compared sequences is introduced, and its main features for sequence comparisons emphasized. Extension of the calculations to gag, pol, and env sequences contained in the current HIV-1 database confirmed the high mutant frequencies for all HIV-1 genomic regions. The results indicate that although env is more tolerant to insertions and deletions than pol, point mutant frequencies for HIV-1 regions encoding nonstructural proteins are only two- to threefold lower than for regions encoding structural proteins. This implies the occurrence of frequent changes in HIV-1 phenotypes that are dependent on amino acid substitutions in viral enzymes.

Schistosomiasis japonica in the Philippines: the long-term impact of population-based chemotherapy on infection, transmission, and morbidity

The long-term impact of annual case-finding and chemotherapy with praziquantel on schistosomiasis japonica was examined in an 8-year longitudinal study in the Philippines. The prevalence, incidence, and intensity of infection and schistosome-induced hepatomegaly significantly decreased within 3-4 years of treatment and then stabilized despite continual population-based chemotherapy. Hepatomegaly rapidly developed in acutely infected persons, with 82% of subjects developing hepatic enlargement within 2 years of reinfection. These data suggest that abrupt discontinuation of current control measures in the Philippines may result in a rapid rebound in morbidity. Age-dependent acquired resistance to reinfection also developed in subjects chronically exposed to schistosomiasis japonica, suggesting that a vaccine may represent an alternative approach for control of this parasitic infection.

Basic concepts in RNA virus evolution

A hallmark of RNA genomes is the error-prone nature of their replication and retrotranscription. The major biochemical basis of the limited replication fidelity is the absence of proofreading/repair and postreplicative error correction mechanisms that normally operate during replication of cellular DNA. In spite of this unique feature of RNA replicons, the dynamics of viral populations seems to follow the same basic principles that classical population genetics has established for higher organisms. Here we review recent evidence of the profound effects that genetic bottlenecks have in enhancing the deleterious effects of Muller's ratchet during RNA virus evolution. The validity of the Red Queen hypothesis and of the competitive exclusion principle for RNA viruses are viewed as the expected result of the highly variable and adaptable nature of viral quasispecies. Viral fitness, or ability to replicate infectious progeny, can vary a million-fold within short time intervals. Paradoxically, functional and structural studies suggest extreme limitations to virus variation. Adaptability of RNA viruses appears to be based on the occupation of very narrow portions of sequence space at any given time.

Systematic replacement of amino acid residues within an Arg-Gly-Asp-containing loop of foot-and-mouth disease virus and effect on cell recognition

The conserved Arg-Gly-Asp (RGD) motif found in a hypervariable, mobile antigenic loop of foot-and-mouth disease virus (FMDV) is critically involved in virus attachment to cells by binding to an integrin, probably related to alphavbeta3. Here we describe (i) the synthesis of 241 15-mer peptides, which represent this loop of FMDV (isolate C-S8c1) and single variants in which each amino acid residue was replaced by 16 others and (ii) the inhibitory activity of these peptides on the ability of FMDV C-S8c1 to recognize and infect susceptible cells. This approach has allowed a first detailed evaluation of the specificity of each residue within a RGD-containing protein loop on cell recognition. The results indicate that, in addition to the exquisitely specific RGD triplet, two highly conserved Leu residues located at positions +1 and +4 downstream of the RGD and, to a lesser extent, the residue at position +2 are the only critical and specific determinants within the loop in promoting cell recognition of a viral ligand. The results support the proposal that, in spite of their involvement in antibody recognition, RGD and other FMDV loop residues are remarkably conserved because of their essential role in cell recognition.

Evolution of fitness in experimental populations of vesicular stomatitis virus

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait "fitness" in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of Muller's ratchet and genetic drift as opposed to the appearance of beneficial mutations.

Induced pocket to accommodate the cell attachment Arg-Gly-Asp motif in a neutralizing antibody against foot-and-mouth-disease virus

The three-dimensional structure of the Fab fragment of a neutralizing monoclonal antibody (SD6) elicited against foot-and-mouth disease virus (FMDV) has been determined at 2.5 A resolution and refined to a crystallography agreement R-factor of 0.186. The structure has been compared with that of the same Fab molecule complexes with a 15 amino acid peptide (A15) representing a major antigenic site of FMDV, and determined at 2.8 A resolution. The Fab quaternary structure, defined both by the elbow angle between modules and by the relative disposition of the light and heavy domains inside the modules, remains essentially unchanged. However, the comparison shows important conformational variations in the paratope, especially in the hypervariable loops of the heavy chain. The CDR-H3 loop has a peculiar amino acid sequence (RREDGGDEGF) with a high content of charged residues. Some of these Fab residues were fully reoriented upon complex formation. The reorientation resulted not only in an alteration of shape but also in an important redistribution of charges, providing multiple points of interaction with the A15 antigen and in particular with the cell attachment Arg-Gly-Asp motif in the peptide. Thus the recognition of A15 by SD6 represents an extreme example of the induced fit mechanism in antibody interactions. The electron density maps provide evidence that in the uncomplexed Fab structure some CDR residues show, with lower occupancy, the conformations found in the complex, suggesting that the rearrangements observed can have only minor energetic requirements.

Antibody and host cell recognition of foot-and-mouth disease virus (serotype C) cleaved at the Arg-Gly-Asp (RGD) motif: a structural interpretation

Foot-and-mouth disease virus (FMDV) of serotype C (isolate C-S8c1) was cleaved in situ by trypsin at the Arg-Gly-Asp (RGD) motif, which is involved both in attachment of FMDV to cells and in recognition of a major antigenic site (site A) by antibodies. Though 99.4% of the RGD moieties were cleaved, the virus remained infectious. A synthetic peptide which represented the sequence of the VP1 G-H loop of C-S8c1, including the RGD motif, greatly inhibited FMDV attachment to cells. The same peptide inhibited, very effectively and to the same extent (50% inhibition at about 1 microM), the infectivity of both intact and trypsin-treated virus. Replacement of Asp with Glu at the RGD motif abolished the inhibitory effects of the peptide. Thus, the RGD motif is involved in the infectivity of both intact and RGD-cleaved serotype C FMDV. Trypsin treatment did not affect the reactivity of the virus with some monoclonal antibodies (MAbs) directed to site A whose epitopes involve mainly residues contiguous to the cleaved bond, but diminished the reactivity with site A MAbs whose epitopes include the RGD sequence and flanking residues. However, high concentrations of any site A MAb tested neutralized close to 100% of the infectious trypsin-treated virus. We propose that, in spite of covalent cleavage, the high number of intramolecular non-covalent interactions observed within the G-H loop of FMDV C-S8c1 (complexed to antibody) may hold the RGD in a nearly correct conformation and allow--albeit with reduced affinity--antibody and cell receptor recognition of RGD-cleaved FMDV.

Emerging foot-and-mouth disease virus variants with antigenically critical amino acid substitutions predicted by model studies using reference viruses

One of the major obstacles to the design of effective antiviral vaccines is the frequent generation of antigenic viral variants in the field. The types of variants that will become dominant during disease outbreaks is often unpredictable. However, here we report the genetic and antigenic characterization of emerging foot-and-mouth disease virus (FMDV) variants with antigenically critical amino acid substitutions predicted by model studies using reference viruses and monoclonal antibodies. The new variants belong to serotype C and have caused a number of recent disease outbreaks in Argentina. The variants harbor antigenically drastic amino acid substitutions in each of the antigenic sites identified in FMDV. In particular, a substitution found at a major antigenic site (site A, the G-H loop of VP1) had been repeatedly selected in viruses resistant to neutralization by monoclonal and polyclonal antibodies. The association of critical amino acid replacements at predicted positions with new FMD outbreaks has a number of implications for FMD epidemiology and for the design of vaccines intended to control diseases caused by highly variable RNA viruses.

Identification of an essential region for internal initiation of translation in the aphthovirus internal ribosome entry site and implications for viral evolution

Translation of aphthovirus RNA is initiated at an internal ribosome entry site (IRES) element, preceding the first functional AUG initiation codon. The effect of mutations at the base of domain 3 of the aphthovirus IRES on translation activity has been analyzed by site-directed mutagenesis and expression of bicistronic RNAs in transfected cells. The results have shown that the enhanced IRES activity associated with a single pyrimidine transition fixed in a persistent aphthovirus variant (E. Martínez-Salas, J. C. Sáiz, M. Dávila, G. J. Belsham, and E. Domingo, J. Virol. 67:3748-3755, 1993) is base specific. Mutations predicted to destabilize the base of domain 3 were detrimental to IRES function, but subsequent restoration of the RNA structure gave rise to fully competent IRES. In contrast, single or multiple mutations that did not affect predicted helical structures modified the relative efficiency of translation by at most 10-fold, suggesting that primary sequence also plays a role in IRES activity. A correlation between the energy of stabilization of the IRES structure and the efficiency of translation has been noted. None of the 15 mutations studied reached a level of initiation of translation comparable to that of the IRES from the persistent variant. The results indicate a critical participation of the base of domain 3 in the activity of the aphthovirus IRES, with a strong effect of secondary or higher-order structures and minor effects of primary structure.

Evaluation of the use of three different devices for nocturnal oxygen therapy in COPD patients

OBJECTIVE

To determine whether transtracheal catheter and reservoir nasal cannula contribute to maintaining adequate oxygen saturation during sleep, and to calculate the oxygen saving they allow compared to nasal prongs.

DESIGN

A prospective study in which patients were randomly assigned to either nasal prongs or oxymizer device prior to transtracheal oxygen delivery. Arterial oxygen saturation was then monitored by a finger pulse oximeter during 8 h of sleep.

SETTING

Pulmonary ward of 'The Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona/Spain)'.

PATIENTS

Fourteen stable hypoxemic (PaO2 50 +/- 6.9 mm Hg; PaCO2 51.5 +/- 9.3 mm Hg) COPD patients (FVC 44 +/- 19%; FEV1 26.5 +/- 11.5%; FEV1/FVC 44.9 +/- 9.7%) already receiving oxygen therapy at home.

MEASUREMENTS

Pulmonary function test was performed. The lowest flow required to obtain an SaO2 at or above 88% for over 95% of the sleep time was determined for each type of oxygen delivery. Patients were not switched to the next type of oxygen delivery device until 3 reliable pulse oximetries had been obtained. The percentage of oxygen savings was calculated. Awake PaO2 was measured in patients using nasal prongs and transtracheal catheter while continuing to inspire oxygen at the same flow rate as when asleep.

RESULTS

As expected, no differences were found in SaO2 measurements for the three types of oxygen delivery. Oxygen savings were 48.65% for the oxymizer device and 52.87% for the transtracheal catheter. Awake PaO2 was significantly higher (p < 0.04) in patients with nasal prongs than in those with transtracheal catheter at the flow rate required when asleep.

CONCLUSIONS

The oxymizer device and transtracheal oxygen delivery benefit hypoxemic COPD patients reducing oxygen use during sleep by around 50%. Higher PaO2 levels were necessary to prevent nocturnal SaO2 decreases in patients with nasal prongs than in patients with transtracheal oxygen delivery. Oxygen-conserving devices are reliable and advisable methods for nocturnal oxygenation.

Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells

Continuous, persistent replication of a wild-type strain of vesicular stomatitis virus in cultured sandfly cells for 10 months profoundly decreased virus replicative fitness in mammalian cells and greatly increased fitness in sandfly cells. After persistent infection of sandfly cells, fitness was over 2,000,000-fold greater than that in mammalian cells, indicating extreme selective differences in the environmental conditions provided by insect and mammalian cells. The sandfly-adapted virus also showed extremely low fitness in mouse brain cells (comparable to that in mammalian cell cultures). It also showed an attenuated phenotype, requiring a nearly millionfold higher intracranial dose than that of its parent clone to kill mice. A single passage of this adapted virus in BHK-21 cells at 37 degrees C restored fitness to near neutrality and also restored mouse neurovirulence. These results clearly illustrate the enormous capacity of RNA viruses to adapt to changing selective environments.

Effect of expression of the aphthovirus protease 3C on viral infection and gene expression

Cells transformed with specific regions of the foot-and-mouth disease virus (FMDV) genome have been constructed and analyzed with respect to viability and susceptibility to FMDV infection. Constitutive expression of an active protease 3C under the control of the tk promoter has been documented by the ability of transformed cells to catalyze the processing of a P1 capsid precursor. High-level, transient expression but not low-level, constitutive expression, of 3C caused a 10-fold reduction in the yield of FMDV and was detrimental to the expression of the cotransfected reporter luciferase gene. No such effect was observed in assays involving cells transfected with a deleted, inactive form of 3C. The negative effect of 3C was not observed when the same reporter gene was integrated and expressed in a constitutive fashion nor when its translation was directed by the internal ribosome entry site element of FMDV in transient expression assays. The results show that cells with a low level of expression of the aphthoviral 3C can be stably maintained and can provide a useful tool to study polyprotein processing.

Antibodies raised in a natural host and monoclonal antibodies recognize similar antigenic features of foot-and-mouth disease virus

Swine polyclonal antibodies directed against a major antigenic site (site A) of foot-and-mouth disease virus (FMDV) of serotype C, and monoclonal antibodies (MAbs) which recognize different epitopes within this site, have been compared with regard to reactivity with a panel of synthetic peptides. The peptides used represent different segments or variant sequences of site A, and their reactivities reflect differences in antigenic specificity. The results indicate a remarkable immunochemical similarity between the site A epitopes defined by murine MAbs and those recognized by antibodies elicited in a natural host of FMDV. This similarity further validates previous conclusions, based on analyses with MAbs, on the relevance of amino acid substitutions at a few critical positions on the intratypic antigenic variation of FMDV in the field. They also give further support to a dual function of the Arg-Gly-Asp motif of the G-H loop in cell attachment and in the recognition by host antibodies, as recently documented with the elucidation of the three-dimensional structure of an antigen-antibody complex of FMDV. In addition, the results encourage the use of extended panels of well-characterized MAbs for a precise molecular analysis of the antigenic variation of FMDV, and of other viruses, in the field.

Exponential increases of RNA virus fitness during large population transmissions

The great adaptability shown by RNA viruses is a consequence of their high mutation rates. Here we investigate the kinetics of virus fitness gains during repeated transfers of large virus populations in cell culture. Results always show that fitness increases exponentially. Low fitness clones exhibit regular increases observed as biphasic periods of exponential evolutionary improvement, while neutral clones show monophasic kinetics. These results are significant for RNA virus epidemiology, optimal handling of attenuated live virus vaccines, and routine laboratory procedures.

Molecular evolution of aphthoviruses

Aphthoviruses are an important group of animal pathogens. A combination of genetic and structural studies has revealed one of the main principles governing their evolution: severe limitations to variation imposed by functional and structural constraints, in conjunction with high mutation and recombination rates operating during genome replication. Evolution occurs by positive selection and random drift acting on complex quasispecies distributions. The mutant composition of a quasi-species (or mutant spectrum) is largely dictated by tolerance to nucleotide and amino acid substitutions in viral RNAs and proteins, which must remain functionally competent. We review recent evidence to support this proposal, and we suggest that similar concepts may apply to other RNA viruses as well.