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PubMed1996

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.

Animals↗

PubMed1989

High nucleotide substitution error frequencies in clonal pools of vesicular stomatitis virus.

Nucleotide substitution error frequencies were determined for several specific guanine base positions in the genomes of cloned vesicular stomatitis virus populations. Predetermined sites were examined in coding regions for the N, M, and L proteins and at a site in the genome 5'-end regulatory region. Misincorporation frequencies were estimated to be on the order of 10(-3) to 10(-4) at all positions analyzed. Isolates taken from virus populations after disruption of equilibrium conditions displayed replicase fidelity similar to that of cloned wild-type vesicular stomatitis virus. These mutation frequencies apply to all virus genomes present, including viruses rendered nonviable by lethal mutations. At one selected site in the N gene, two of three G----N base substitutions generated lethal nonsense mutations, yet their frequency was also very high. Biological implications for rapid virus evolution are discussed.

Animals↗

PubMed1995

Determination and comparative analysis of the small RNA genomic sequences of California encephalitis, Jamestown Canyon, Jerry Slough, Melao, Keystone and Trivittatus viruses (Bunyaviridae, genus Bunyavirus, California serogroup).

The nucleotide sequences of the small (S) genomic RNAs of six California (CAL) serogroup bunyaviruses (Bunyaviridae: genus Bunyavirus) were determined. The S RNAs of two California encephalitis virus strains, two Jamestown Canyon virus strains, Jerry Slough virus, Melao virus, Keystone virus and Trivittatus virus contained the overlapping nucleocapsid (N) and non-structural (NSs) protein open reading frames (ORFs) as described previously for the S RNAs of other CAL serogroup viruses. All N protein ORFs were 708 nucleotides in length and encoded a putative 235 amino acid gene product. The NSs ORFs were found to be of two lengths, 279 and 294 nucleotides, which potentially encode 92 and 97 amino acid proteins, respectively. The complementary termini and a purine-rich sequence in the 3' non-coding region (genome-complementary sense) were highly conserved amongst CAL serogroup bunyavirus S RNAs. Phylogenetic analyses of N ORF sequences indicate that the CAL serogroup bunyaviruses can be divided into three monophyletic lineages corresponding to three of the complexes previously derived by serological classification. The truncated version of the NSs protein, which is found in five CAL serogroup bunyaviruses, appears to have arisen twice during virus evolution.

Amino Acid Sequence↗

PubMed2006

Screening of the yeast yTHC collection identifies essential host factors affecting tombusvirus RNA recombination.

RNA recombination is a major process in promoting rapid virus evolution in an infected host. A previous genome-wide screen with the yeast single-gene deletion library of 4,848 strains, representing approximately 80% of all genes of yeast, led to the identification of 11 host genes affecting RNA recombination in Tomato bushy stunt virus (TBSV), a small model plant virus (E. Serviene, N. Shapka, C. P. Cheng, T. Panavas, B. Phuangrat, J. Baker, and P. D. Nagy, Proc. Natl. Acad. Sci. USA 102:10545-10550, 2005). To further test the role of host genes in viral RNA recombination, in this paper, we extended the screening to 800 essential yeast genes present in the yeast Tet-promoters Hughes Collection (yTHC). In total, we identified 16 new host genes that either increased or decreased the ratio of TBSV recombinants to the nonrecombined TBSV RNA. The identified essential yeast genes are involved in RNA transcription/metabolism, in protein metabolism/transport, or unknown cellular processes. Detailed analysis of the effect of the identified yeast genes revealed that they might affect RNA recombination by altering (i) the ratio of the two viral replication proteins, (ii) the stability of the viral RNA, and/or (iii) the replicability of the recombinant RNAs. Overall, this and previous works firmly establish that a set of essential and nonessential host genes could affect TBSV recombination and evolution.

Base Sequence↗

PubMed1993

Diversity within natural populations of eastern equine encephalomyelitis virus.

We evaluated genetic and phenotypic diversity within natural populations of the alphavirus, Eastern equine encephalomyelitis (EEE) virus. RNA fingerprinting revealed that most populations within infected hosts (unpassaged isolates) contained a consensus genotype along with minority genotypes differing in one to three T1-resistant oligonucleotides. Mutation frequencies appeared to be similar to those reported for other RNA viruses, suggesting that the slow rate of EEE virus evolution is not limited by fidelity of genome replication. Within a given year, genetic diversity was generally greater among geographically distant isolates than among those from the same transmission focus, suggesting that dispersal among EEE viruses in North America is not complete annually. Two of three bird isolates from Maryland and New York contained relatively distantly related genotypes, differing in 15-19 oligonucleotides. A 1985 mosquito isolate from Maryland contained stable, small plaque variants which comprised the majority of that population. These small plaque variants differed by up to eight T1-resistant oligonucleotides when compared with their large plaque counterparts. Temperature sensitive virus was not detected in six unpassaged mosquito isolates from Maryland and New York.

Amino Acid Sequence↗

PubMed2025

Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution.

Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the rapid emergence of new variants, (2) human interactions within a heterogeneous population, and (3) public health responses which constrain individual actions to control the disease transmission. We then present a pandemic modelling framework satisfying these requirements and capable of simulating feedback loops between dynamics unfolding at these different scales. The developed framework comprises a stochastic agent-based model of pandemic spread, coupled with a phylodynamic model that incorporates within-host pathogen evolution. It is validated with a case study, modelling the punctuated evolution of SARS-CoV-2, based on global and contemporary genomic surveillance data, which captures a large heterogeneous population. We demonstrate that the model replicates the essential features of the COVID-19 pandemic and virus evolution, while retaining computational tractability and scalability.

SARS-CoV-2↗

PubMed1987

Molecular pathogenesis of virus infections.

Although a very wide range of viral diseases exists in vertebrates, certain generalizations can be made regarding pathogenetic pathways on the molecular level. The presentation will focus on interactions of virions and their components with target cells. Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organ- or animal species-spectrum) can dramatically change. Receptor molecules are essential for the early interactions during infection and some of these have been identified. Events in the target cell and the host organism are discussed, and wherever possible, aspects of virus evolution and cooperation between infectious agents are highlighted.

Adsorption↗

PubMed1996

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.

Adaptation, Physiological↗

PubMed1997

The antiretrovirus drug 3'-azido-3'-deoxythymidine increases the retrovirus mutation rate.

It was previously observed that the nucleoside analog 5-azacytidine increased the spleen necrosis virus (SNV) mutation rate 13-fold in one cycle of retrovirus replication (V. K. Pathak and H. M. Temin, J. Virol. 66:3093-3100, 1992). Based on this observation, we hypothesized that nucleoside analogs used as antiviral drugs may also increase retrovirus mutation rates. We sought to determine if 3'-azido-3'-deoxythymidine (AZT), the primary treatment for human immunodeficiency virus type 1 (HIV-1) infection, increases the retrovirus mutation rate. Two assays were used to determine the effects of AZT on retrovirus mutation rates. The strategy of the first assay involved measuring the in vivo rate of inactivation of the lacZ gene in one replication cycle of SNV- and murine leukemia virus-based retroviral vectors. We observed 7- and 10-fold increases in the SNV mutant frequency following treatment of target cells with 0.1 and 0.5 microM AZT, respectively. The murine leukemia virus mutant frequency increased two- and threefold following treatment of target cells with 0.5 and 1.0 microM AZT, respectively. The second assay used an SNV-based shuttle vector containing the lacZ alpha gene. Proviruses were recovered as plasmids in Escherichia coli, and the rate of inactivation of lacZ alpha was measured. The results indicated that treatment of target cells increased the overall mutation rate two- to threefold. DNA sequence analysis of mutant proviruses indicated that AZT increased both the deletion and substitution rates. These results suggest that AZT treatment of HIV-1 infection may increase the degree of viral variation and alter virus evolution or pathogenesis.

Antiviral Agents↗

PubMed2004

Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution.

Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was approximately 0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.

Base Pairing↗

PubMed2003

Molecular epidemiology of infectious hematopoietic necrosis virus reveals complex virus traffic and evolution within southern Idaho aquaculture.

Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus which infects salmon and trout and may cause disease with up to 90% mortality. In the Hagerman Valley of Idaho, IHNV is endemic or epidemic among numerous fish farms and resource mitigation hatcheries. A previous study characterizing the genetic diversity among 84 IHNV isolates at 4 virus-endemic rainbow trout farms indicated that multiple lineages of relatively high diversity co-circulated at these facilities (Troyer et al. 2000 J Gen Virol. 81:2823-2832). We tested the hypothesis that high IHNV genetic diversity and co-circulating lineages are present in aquaculture facilities throughout this region. In this study, 73 virus isolates from 14 rainbow trout farms and 3 state hatcheries in the Hagerman Valley, isolated between 1978 and 1999, were genetically characterized by sequence analysis of a 303 nucleotide region of the glycoprotein gene. Phylogenetic and epidemiological analyses showed that multiple IHNV lineages co-circulate in a complex pattern throughout private trout farms and state hatcheries in the valley. IHNV maintained within the valley appears to have evolved significantly over the 22 yr study period.

Animals↗

PubMed1997

Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo.

To investigate the process of human immunodeficiency virus type 1 (HIV-1) evolution in vivo, a total of 179 HIV-1 V3 sequences derived from cell-free plasma were determined from serial samples in three epidemiologically linked individuals (one infected blood donor and two transfusion recipients) over a maximum period of 8 years. A systematic analysis of pairwise comparisons of intrapatient sequences, both within and between each sample time point, revealed a preponderance and accumulation of nonsynonymous rather than synonymous substitutions in the V3 loop and flanking regions as they diverged over time. This strongly argues for the dominant role that positive selection for amino acid change plays in governing the pattern and process of HIV-1 env V3 evolution in vivo and nullifies hypotheses of purely neutral or mutation-driven evolution or completely chance events. In addition, different rates of evolution of HIV-1 were observed in these three different individuals infected with the same viral strain, suggesting that the degree of positive pressure for HIV-1 amino acid change is host dependent. Finally, the observed similar rate of accumulation in divergence within and between infected individuals suggests that the process of genetic divergence in the HIV epidemic proceeds regardless of host-to-host transmission events, i.e., that transmission does not reset the evolutionary clock.

Amino Acid Sequence↗

PubMed2006

An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants.

Recombination in RNA viruses is considered to play a major role as a driving force in virus variability to counterbalance loss in fitness that can be due to the accumulation of detrimental mutations. Studies on mixed infections are pertinent for understanding the role of recombination in virus evolution. They also provide important baseline information for studying the biosafety of plants expressing viral sequences. To investigate the possibility of RNA recombination occurrence between two sobemoviruses under little or no selection pressure, we co-infected test plants with Cocksfoot mottle virus (CfMV) and Ryegrass mottle virus (RGMoV). CfMV and RGMoV were selected because of their overlapping host range and geographical distribution. First, symptom development of both viruses in barley (Hordeum vulgare) and oat (Avena sativa) was examined. Both viruses generated quite strong infection symptoms in oat, but synergism was not detected. RGMoV was lethal for barley, whereas CfMV infection in barley was nearly symptomless. RT-PCR analysis revealed 100% infection with both viruses in oat but not in barley. Therefore, an RNA recombination study of CfMV and RGMoV was performed in oat. 105 plants were co-inoculated with both viruses and putative recombinational hot spot regions were screened for recombination events by RT-PCR analysis at a sensitivity level down to 0.1-100 pg of viral genomic RNA. No recombination events between the two sobemoviruses were detected.

Avena↗

PubMed2005

Restoration of virulence of escape mutants of H5 and H9 influenza viruses by their readaptation to mice.

Antigenic mapping of the haemagglutinin (HA) molecule of H5 and H9 influenza viruses by selecting escape mutants with monoclonal anti-HA antibodies and subjecting the selected viruses to immunological analysis and sequencing has previously been performed. The viruses used as wild-type strains were mouse-adapted variants of the original H5 and H9 isolates. Phenotypic characterization of the escape mutants revealed that the amino acid change in HA that conferred resistance to a monoclonal antibody was sometimes associated with additional effects, including decreased virulence for mice. In the present study, the low-virulence H5 and H9 escape mutants were readapted to mice. Analysis of the readapted variants revealed that the reacquisition of virulence was not necessarily achieved by reacquisition of the wild-type HA gene sequence, but was also associated either with the removal of a glycosylation site (the one acquired previously by the escape mutant) without the exact restoration of the initial wild-type amino acid sequence, or, for an H5 escape mutant that had no newly acquired glycosylation sites, with an additional amino acid change in a remote part of the HA molecule. The data suggest that such 'compensating' mutations, removing the damaging effects of antibody-selected amino acid changes, may be important in the course of influenza virus evolution.

Adaptation, Physiological↗

PubMed1986

[HB virus infection and delta surinfection in Sahelian Africa].

78 hospitalized patients were selected when presenting with at least one of these signs: hepatomegaly, jaundice, ascites, oesophageal varices, abdominal venous pattern, splenomegaly. All had radioimmunoassays for hepatitis B surface antigen (HBsAg) and antidelta antibody (78/78). Acute or chronic hepatic disease was diagnosed in 56 patients: 7 acute viral hepatitis, 13 chronic hepatitis, 23 non alcoholic hepatic cirrhosis, and 13 hepatocellular carcinoma. Twenty-two patients with other diagnoses served as controls. Serum antidelta was present in each group: acute viral hepatitis (2/7), chronic hepatitis (2/13), non alcoholic hepatic cirrhosis (9/23), hepatocellular carcinoma (3/13), controls (2/22). Every patient with acute or chronic hepatic disease and positive serum anti-delta was positive for serum HBsAg. Amony controls, 2 patients with positive serum antidelta were negative for serum HBsAg but positive for antiHBs. Delta superinfection is present in the sahelian region; Patients with acute viral hepatitis, chronic hepatitis, non alcoholic hepatic cirrhosis, and hepatocellular carcinoma are electively infected. Patients with acute or chronic hepatitis and positive serum antidelta have hepatitis B virus evolutive infection (positive serum HBsAg).

Antibodies, Viral↗

PubMed1999

Development of the hot spot-combined PCR assay for detection of retroviral insertions into Marek's disease virus.

A two-step PCR, the Hot Spot-combined PCR assay, was developed for the identification and characterization of recombinant viruses in Marek's disease (herpes) and retrovirus co-infections. In the first PCR the herpesvirus genomic fragment, that was recognized in previous studies as a hot spot site for retroviral integration was amplified [reviewed in Bronovskis, P., Kung, H.-J., 1996. Retrotransposition and herpesvirus evolution. Virus Genes 11, 259-270]. The products served for a second amplification step, performed in six PCR sets, using the six possible combinations of the two herpes and the retrovirus primer sets. Development of the assay employed DNA of the recombinant virus, RM1, which was created by in vitro co-cultivation of Marek's disease and reticuloendotheliosis viruses [Isfort et al., 1992. Proc. Natl. Acad. Sci. 89, 991-995; Witter et al., 1997. Avian Dis. 41, 407-421]. As the retroviral insertion site and junction sequences were determined previously [Jones et al., 1996. J. Virol. 70, 2460-2467], RMI served in the present study as a test virus for the development of the new assay. It is shown now that the Hot Spot-combined PCR can detect the retroviral insert in RM1. the MDV integration site and the insert orientation. For confirmation the herpes and retrovirus chimeric PCR products were sequenced and the results were similar to those published previously [Jones et al., 1996. J. Virol. 70, 2460-2467]. This assay might be adopted in additional systems to detect foreign inserts at suspected genomic sites.

Animals↗

PubMed1995

The larger genomic RNA of Helicoverpa armigera stunt tetravirus encodes the viral RNA polymerase and has a novel 3'-terminal tRNA-like structure.

In this paper we report the complete nucleotide sequence of the larger segment (5312 nucleotides) of the bipartite RNA genome of Helicoverpa armigera stunt tetravirus (HaSV). HaSV therefore becomes the first member of the Tetraviridae, a virus family with a host range restricted to lepidopteran insects, whose genome has been completely sequenced. HaSV RNA 1 encodes a 187K protein which includes three domains conserved in RNA-dependent RNA polymerases of RNA viruses in the alpha-like superfamily. Analysis of the replicase sequence confirms the status of the Tetraviridae as a distinct family within this superfamily, which includes animal, plant, and insect viruses, and shows the least-distantly related replicase for all three domains to be that of the hepatitis E virus. Another feature of the nonpolyadenylated HaSV genomic RNAs is a well-conserved 3'-terminal tRNA-like structure, the first such structure discerned in an animal virus. However, in contrast to the tRNA-like structures on some plant virus RNAs, the HaSV structure, which has a valine anticodon (CAU), appears to form without a pseudoknot and therefore resembles authentic tRNA(Val) more closely than do the plant viral structures. The implications of these observations for our understanding of RNA virus evolution are discussed.

3' Untranslated Regions↗

PubMedDate not supplied

[A mechanism for limiting reproduction influenza A virus reassortants with incomplete functional compatibility of hemagglutinin and neuraminidase gene products].

The mechanism of decrease in the level of virus accumulation in reassortants with hemagglutinin (HA) and neuraminidase (NA) genes from different parents is studied. The reassortant viruses and their passage variants do not differ by the rate of virus protein production or their stability in infected cells. Electron microscopy and titration of infectious virus in culture fluid and cell-associated virus showed that the variants selected by serial passages accumulated mainly in the culture fluid, whereas the initial reassortant virions were predominantly cell-associated. These data suggest that incomplete removal of sialic acid residues by viral neuraminidase N1 in some reassortants results in re-attachment of virions to the infected cells and thus impairs the virus dissemination, which may be regarded as a reassortant-limiting factor probably significant for virus evolution.

Animals↗