Retrovirus variation and evolution.
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Genes, Viral↗
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Nucleotides in the panhandle structure of the influenza B virus virion RNA are involved in the specificity between influenza A and B viruses.
Influenza A and B viruses share common sequences and potentially similar panhandle structures in the terminal noncoding regions of virion RNA (vRNA). Interesting differences exist, however, in the number of conserved nucleotides at the 5' and 3' ends of the vRNAs, in base pairs constituting the panhandle duplex, and the length of uridine stretch (U stretch) juxtaposed to the RNA duplex. To analyse the contribution of these signals to the specificity between the two viruses, a transient ribonucleoprotein transfection method was used for the expression of the chloramphenicol acetyltransferase (CAT) reporter gene flanked by the noncoding nucleotides derived from influenza B vRNA. While the base pairing in the RNA duplex was primarily important for template activity, mismatch mutations G11 x G12' and C12 x A13' in the terminal RNA duplex region were utilized by influenza B virus, whereas these mutations were detrimental for influenza A virus. Different activity profiles were observed in the length preference of the RNA duplexes: maximum template activity was observed with 11 base pairs for influenza B virus, and 8 base pairs for influenza A virus. When the mutants with various lengths of U stretch were tested, highest CAT activities were observed with 5 to 7 uridine residues in influenza A virus, whereas in influenza B virus the activity was drastically decreased with 7 uridine residues. We suggest that the specific interaction of influenza virus RNA polymerase with these noncoding cis-acting signals in transcription of the RNA genome, along with unique coding strategies adopted by influenza B virus, has contributed to the divergence of these two closely related viruses.
Animals↗
Short- and long-term clinical outcomes in rhesus monkeys inoculated with a highly pathogenic chimeric simian/human immunodeficiency virus.
A highly pathogenic simian/human immunodeficiency virus (SHIV), SHIV(DH12R), isolated from a rhesus macaque that had been treated with anti-human CD8 monoclonal antibody at the time of primary infection with the nonpathogenic, molecularly cloned SHIV(DH12), induced marked and rapid CD4(+) T cell loss in all rhesus macaques intravenously inoculated with 1.0 50% tissue culture infective dose (TCID(50)) to 4.1 x 10(5) TCID(50)s of virus. Animals inoculated with 650 TCID(50)s of SHIV(DH12R) or more experienced irreversible CD4(+) T lymphocyte depletion and developed clinical disease requiring euthanasia between weeks 12 and 23 postinfection. In contrast, the CD4(+) T-cell numbers in four of five monkeys receiving 25 TCID(50)s of SHIV(DH12R) or less stabilized at low levels, and these surviving animals produced antibodies capable of neutralizing SHIV(DH12R). In the fifth monkey, no recovery from the CD4(+) T cell decline occurred, and the animal had to be euthanized. Viral RNA levels, subsequent to the initial peak of infection but not at peak viremia, correlated with the virus inoculum size and the eventual clinical course. Both initial infection rate constants, k, and decay constants, d, were determined, but only the latter were statistically correlated to clinical outcome. The attenuating effects of reduced inoculum size were also observed when virus was inoculated by the mucosal route. Because the uncloned SHIV(DH12R) stock possessed the genetic properties of a lentivirus quasispecies, we were able to assess the evolution of the input virus swarm in animals surviving the acute infection by monitoring the emergence of neutralization escape viral variants.
Amino Acid Substitution↗
Characterization of phi12, a bacteriophage related to phi6: nucleotide sequence of the large double-stranded RNA.
The isolation of additional bacteriophages besides phi6 containing segmented double-stranded RNA genomes (dsRNA) has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the large double-stranded RNA genomic segment of bacteriophage phi12 was copied as cDNA and its nucleotide sequence determined. This genome's organization is similar to that of the large segment of bacteriophages phi6, phi8, and phi13. In the amino acid sequence of the viral RNA-dependent RNA polymerase (P2), similarity was found to the comparable proteins of phi6, phi8, and phi13. Amino acid sequence similarity was also noted in the nucleotide triphosphate phosphorylase (P4) to the comparable proteins of phi8 and phi13.
Amino Acid Sequence↗
Characterization of phi 12, a bacteriophage related to phi 6: nucleotide sequence of the small and middle double-stranded RNA.
The isolation of additional bacteriophages containing segmented double-stranded RNA genomes has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the small and middle double-stranded RNA genomic segments of bacteriophage phi 12 were copied as cDNA and their nucleotide sequences determined. This genome's organization is similar to that of the small and middle segments of bacteriophages phi 6, phi 8, and phi 13. Although there is little similarity in the nucleotide sequences, similarity exists in the amino acid sequence of the lysis cassette proteins to those of phi 6. The host cell attachment proteins are found to have marked similarity to the phi 13 attachment proteins.
Bacteriophage phi 6↗
Molecular characterization of the Japanese encephalitis virus representative immunotype strain JaGAr 01.
We determined the full genomic sequence of the Japanese encephalitis virus JaGAr 01 strain and its predicted amino acid sequence. Nucleotide sequence comparison with ten fully sequenced JE strains shows a homology range from 89.62 to 99.49%. Amino acid sequence homologies range from 96.85 to 99.74%. Comparison of amino acid sequences shows a unique amino acid, arginine, for JaGAr 01 at position 123 of the E-protein, while the eight other strains contained serine. Secondary structure prediction by free energy minimization shows a unique structure for JaGAr 01 that includes an RNA segment that is conserved for all flaviviruses. Speculation is made about the role these results may play in the replication and antigenic characteristics of JaGAr 01. Phylogenetic analyses of the E-protein of JaGAr 01 together with 35 other JE strains showed diversity in amino acid characteristics between the prototype strains Nakayama, JaGAr 01 and Beijing-1. Phylogenetic trees computed by neighbor joining and Fitch Margoliash analysis of nucleic acid and protein sequences showed Nakayama and Beijing in one cluster different from JaGAr 01.
Amino Acid Sequence↗
In vitro evolution suggests multiple origins for the hammerhead ribozyme.
The hammerhead ribozyme was originally discovered in a group of RNAs associated with plant viruses, and has subsequently been identified in the genome of the newt (Notophthalamus viridescens), in schistosomes and in cave crickets (Dolichopoda species). The sporadic occurrence of this self-cleaving RNA motif in highly divergent organisms could be a consequence of the very early evolution of the hammerhead ribozyme, with all extant examples being descended from a single ancestral progenitor. Alternatively, the hammerhead ribozyme may have evolved independently many times. To better understand the observed distribution of hammerhead ribozymes, we used in vitro selection to search an unbiased sample of random sequences for comparably active self-cleaving motifs. Here we show that, under near-physiological conditions, the hammerhead ribozyme motif is the most common (and thus the simplest) RNA structure capable of self-cleavage at biologically observed rates. Our results suggest that the evolutionary process may have been channelled, in nature as in the laboratory, towards repeated selection of the simplest solution to a biochemical problem.
Base Sequence↗
Isolation and complete nucleotide sequence of a Chinese Sindbis-like virus.
Infection with alphaviruses is common in the Chinese population. Here we report the isolation of a Sindbis-like virus from a pool of Anopheles mosquitoes collected in Xinjiang, China during an arbovirus survey. This virus, designated XJ-160, rapidly produced cytopathic effects on mosquito and hamster cells. In addition, it was lethal to neonatal mice if inoculated intracerebrally. Serologically, XJ-160 reacted with and was neutralized by an anti-Sindbis antibody. Anti-XJ-160 antibodies were found in several cohorts of Chinese subjects. The complete 11626-base nucleotide sequence of XJ-160 was determined. XJ-160 has diverged significantly from the prototype Sindbis virus, with an 18% difference in nucleotide sequence and an 8.6% difference in amino acids; there are 11 deletions and 2 insertions, involving 99 nucleotides in total. XJ-160 is most closely linked to Kyzylagach virus isolated in Azerbaijan. Both belong to the African/European genetic lineage of Sindbis virus, albeit more distantly related to other members.
Alphavirus Infections↗
Fatal hepatitis C virus infection in a heart transplant recipient detectable by polymerase chain reaction only.
Rapidly progressive and ultimately fatal liver failure with evolution to cirrhosis developed in a heart transplant recipient following infection by hepatitis C virus. Antiviral antibodies and the presence of viral RNA were analyzed throughout the course of the disease. After a weak initial response to a single viral epitope (c22-3), serology became negative, the infection remaining detectable by polymerase chain reaction only. This case demonstrates the potentially severe consequences of hepatitis C virus infection under immunosuppression. The incidence of this infection may be underestimated, as the presented case apparently would not have been detected if serology had been used for diagnosis.
Base Sequence↗
The theory of genotypic selection: predicting the direction of evolution as a consequence of G:U base pairing and the existence of non-pathogenic strains of HIV-1.
One aspect of the Theory of Genotypic Selection states that G:U base pairs are selected for function and structure. RNA secondary structures stabilised by G:U base pairs are suggested to be involved in the evolution of attenuated strains of polio virus. Asymmetric mutations (C-->U and A-->G) and convergent evolutionary solutions are explained as a direct consequence of G:U base pairing. The possibility of a naturally occurring attenuated strain of HIV-1 is predicted.
Base Composition↗
Homology-dependent gene silencing and host defense in plants.
Analyses of transgene silencing phenomena in plants and other organisms have revealed the existence of epigenetic silencing mechanisms that are based on recognition of nucleic acid sequence homology at either the DNA or RNA level. Common triggers of homology-dependent gene silencing include inverted DNA repeats and double-stranded RNA, a versatile silencing molecule that can induce both degradation of homologous RNA in the cytoplasm and methylation of homologous DNA sequences in the nucleus. Inverted repeats might be frequently associated with silencing because they can potentially interact in cis and in trans to trigger DNA methylation via homologous DNA pairing, or they can be transcribed to produce double-stranded RNA. Homology-dependent gene silencing mechanisms are ideally suited for countering natural parasitic sequences such as transposable elements and viruses, which are usually present in multiple copies and/or produce double-stranded RNA during replication. These silencing mechanisms can thus be regarded as host defense strategies to foreign or invasive nucleic acids. The high content of transposable elements and, in some cases, endogenous viruses in many plant genomes suggests that host defenses do not always prevail over invasive sequences. During evolution, slightly faulty genome defense responses probably allowed transposable elements and viral sequences to accumulate gradually in host chromosomes and to invade host genes. Possible beneficial consequences of this "foreign" DNA buildup include the establishment of genome defense-derived epigenetic control mechanisms for regulating host gene expression and acquired hereditary immunity to some viruses.
Animals↗
Viral evolution and insects as a possible virologic turning table.
Three lines of observation demonstrate the role of arthropods in transmission and evolution of viruses. a) Recent outbreaks of viruses from their niches took place and insects have played a major role in propagating the viruses. b) Examination of the list of viral families and their hosts shows that many infect invertebrates (I) and vertebrates (V) or (I) and plants (P) or all kingdoms (VIPs). This notion holds true irrespective of the genome type. At first glance the argument seems to be weak in the case of enveloped and non-enveloped RNA viruses with single-stranded (ss) segmented or non-segmented genomes of positive (+) or negative polarity. Here, there are several families infecting V or P only; no systematic relation to arthropods is found. c) In the non-enveloped plant viruses with ss RNA genomes there is a strong tendency for segmentation and individual packaging of the genome pieces. This is in contrast to ss+ RNA animal viruses and can only be explained by massive transmission by seed or insects or both, because individual packaging necessitates a multihit infection. Comparisons demonstrate relationships in the nonstructural proteins of double-stranded and ss+ RNA viruses irrespective of host range, segmentation, and envelope. Similar conclusions apply for the negative-stranded RNA viruses. Thus, viral supergroups can be created that infect V or P and exploit arthropods for infection or transmission or both. Examples of such relationships and explanations for viral evolution are reviewed and the arthropod orders important for cell culture are given.
Amino Acid Sequence↗
Evolution in the hypervariable region of hepatitis C virus in infants after vertical transmission.
To elucidate the clonal evolution of hepatitis C virus (HCV) during mother-to-infant transmission, we prospectively analyzed HCV clones of the hypervariable region in four HCV RNA-positive infants and compared them with those of the mother. Cord blood samples from three of the four infants were positive for the HCV RNA (< or =10(3) copies/mL), and all of the four infants had the HCV RNA titer of >10(6) copies/mL within 2 mo after birth. The hypervariable region clones detected in the infants were closely related to those in the respective mothers. The results suggest the perinatal transmission of HCV. The hypervariable region clones transmitted to infants were not a single selected clone or minor clones in the mother. None of the clones specific to the low-density fraction in the mother was transmitted to the infants. Moreover, the proportion of HCV in the low-density fraction was minimal in the first few months of life, but increased several months after birth in association with the elevation of alanine aminotransferase. These results suggest that the increase of HCV in the low-density fraction reflect the evolution of immune response in infants. We also demonstrated that the emergence of quasispecies in infants precedes the infantile antibody response.
Aging↗
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↗
[Changes in the dynamics of viral infectious diseases].
Modern methods of molecular biology are suitable to analyse evolutionary processes in the area of infectious diseases. Visible expression of this evolution is the emergence of "new" infectious agents, e.g., canine parvovirus, the agent of the porcine reproductive and respiratory syndrome and phocine distemper virus. In addition a gradual change of disease syndromes may be observed, e.g., classical and African swine fever and myxoma. These processes are based on genomic changes of the respective infectious agents, i.e., point mutations and recombinations. Especially RNA viruses are prone to genomic change, and the plasticity of their genomes enables them to adapt to varying selective pressures. Human activities in agriculture, global commerce and tourism may enhance and precipitate microbial evolution.
Animals↗
Sequence variation and evolution of Cryphonectria hypovirus 1 (CHV-1) in Europe.
Cryphonectria hypovirus 1 (CHV-1) acts as a naturally occurring biological control agent for chestnut blight, a destructive fungal disease of chestnut trees, which has been introduced into Europe in the 1930s. We have determined partial nucleotide and deduced amino acid sequences of the ORF A of 47 CHV-1 isolates collected in Europe over a period of 28 years. Phylogenetic analysis revealed the presence of four groups or single viruses, which showed sequence divergences ranging from 11 to 19%. These results confirm the previous subtype classification based on RFLP markers, with the exception of the two CHV-1 subtypes E and D, which appear to be related closer than anticipated previously. Dates of divergences between CHV-1 subtypes, calculated from nucleotide substitution rates, indicate that the CHV-1 subtypes diverged several hundreds years ago. Our results suggest that the genetic variation among CHV-1 subtypes did not evolve in Europe and support the hypothesis of multiple introductions of CHV-1 into Europe.
Ascomycota↗
Evolution of enterovirus 70 in nature: all isolates were recently derived from a common ancestor.
The data of large RNase T1-resistant oligonucleotide mapping of enterovirus 70 (EV 70) previously reported (Takeda et al., Virology 134, 375-388, 1984) were subjected to further genetical analysis to estimate the evolutionary rate of genome RNA of EV 70 and to clarify the phylogenetic relationship among isolates. A proportion of common spots between strains decreased as the year elapsed and eventually, only seven spots were common to all the 16 isolates tested, indicating that the substitution is scattered throughout the genome. On the other hand, some specific sets of spots were conserved among geographically or epidemiologically related strains. Base sequence variation of the isolates was deduced according to Aaronson et al. (Nucleic Acids Res. 10, 237-246, 1982) from pariwise comparison of the common spots and used as a genetic distance between them. The base substitution rate of virus genome was estimated by regression analysis of the genetic distance of the isolates against the sampling time. A fairly constant and rapid rate was obtained; it was 1.83 X 10(-3)/base/year. Based on the substitution rate, genetic distance and sampling time of the strains, the phylogenetic tree of EV 70 was constructed using Unweighted Pair Group Method Using Arithmetic Averages (UPGMA) (Nei, Molecular Population Genetics and Evolution, North Holland, Amsterdam, 1975). The tree supports the previous hypothesis that evolution of EV 70 started from a single common ancestor. The time of its emergence was estimated to be 1967 +/- 15 months. The virus branched into many strains early during the first pandemic and has evolved in a divergent fashion, yielding genetically polymorphic viruses in the world.
Biological Evolution↗
Evolution of bacteriophage in continuous culture: a model system to test antiviral gene therapies for the emergence of phage escape mutants.
The emergence of viral escape mutants is usually a highly undesirable phenomenon. This phenomenon is frequently observed in antiviral drug applications for the treatment of viral infections and can undermine long-term therapeutic success. Here, we propose a strategy for evaluating a given antiviral approach in terms of its potential to provoke the appearance of resistant virus mutants. By use of Q beta RNA phage as a model system, the effect of an antiviral gene therapy, i.e., a virus-specific repressor protein expressed by a recombinant Escherichia coli host, was studied over the course of more than 100 generations. In 13 experiments carried out in parallel, 12 phage populations became resistant and 1 became extinct. Sequence analysis revealed that only two distinct phage mutants emerged in the 12 surviving phage populations. For both escape mutants, sequence variations located in the repressor binding site of the viral genomic RNA, which decrease affinity for the repressor protein, conferred resistance to translational repression. The results clearly suggest the feasibility of the proposed strategy for the evaluation of antiviral approaches in terms of their potential to allow resistant mutants to appear. In addition, the strategy proved to be a valuable tool for observing virus-specific molecular targets under the impact of antiviral drugs.
Allolevivirus↗