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PubMed2001

Virus replication and evolution drive the kinetics and specificity of SIV-specific cytotoxic T lymphocytes.

SIV (simian immunodeficiency virus) infection of cynomolgus macaques provides an excellent model for investigating the basis of protective immunity against HIV (human immunodeficiency virus). We explored the protective role of cytotoxic T lymphocytes (CTL) against the pathogenic molecular clone SIVmac-J5. Vaccine-induced CTL precursors (CTLp) against Env, Gag or Nef did not protect macaques against intravenous challenge. However, detection of Rev-specific CTLp in infected macaques was associated with effective virus containment. Furthermore, CTL against an immunodominant Gag/p26 epitope (amino acids 242-250) resulted in the emergence of a mutant virus that uniformly replaced wild-type virus in the spleen and partially escaped recognition. During primary infection, CTLp detection in blood coincided with decreasing viremia. After 12 months, two outcomes emerged. In one group of macaques, persistent viremia was associated with high viral load in lymphoid organs and declining CD4+ T-cell counts. CTLp were maintained in asymptomatic macaques, but declined in the symptomatic phase of infection. In a second group, loss of detectable viremia was associated with low-level virus reservoirs in lymphoid organs, asymptomatic status and maintained CD4+ T-cell counts. CTLp peaked in the first 4 months of infection and subsequently declined in this group. These studies provide insights into the complex interplay between virus replication and host immunity.

Animals↗
PubMed1998

Identification of the leader-body junctions for the viral subgenomic mRNAs and organization of the simian hemorrhagic fever virus genome: evidence for gene duplication during arterivirus evolution.

Simian hemorrhagic fever virus (SHFV) was recently reclassified and assigned to the new virus family Arteriviridae. During replication, arteriviruses produce a 3' coterminal, nested set of subgenomic mRNAs (sgRNAs). These sgRNAs arise by discontinuous transcription, and each contains a 5' leader sequence which is joined to the body of the mRNA through a conserved junction sequence. Only the 5'-most open reading frame (ORF) is believed to be transcribed from each sgRNA. The SHFV genome encodes nine ORFs that are presumed to be expressed from sgRNAs. However, reverse transcription-PCR analysis with leader- and ORF-specific primers identified only eight sgRNA species. The consensus sequence 5'-UCNUUAACC-3' was identified as the junction motif. Our data suggest that sgRNA 2 may be bicistronic, expressing both ORF 2a and ORF 2b. SHFV encodes three more ORFs on its genome than the other arteriviruses. Comparative sequence analysis suggested that SHFV ORFs 2a, 2b, and 3 are related to ORFs 2 through 4 of the other arteriviruses. Evidence which suggests that SHFV ORFs 4 through 6 are related to ORFs 2a through 3 and may have resulted from a recombination event during virus evolution is presented.

Amino Acid Sequence↗
PubMed1982

Molecular evolution in papova viruses and in bacteriophages.

By comparing the DNA sequences of three eukaryotic papova viral genomes, we attempt to show the very close relative phylogeny among the viral species and their host species, and that therefore the viral species appear to have evolved with their hosts. A comparison of the DNA data also reveals that the rate of nucleotide substitutions at the third positions of codons is much faster than at the first and second positions, though the rate varies depending upon the genes. The estimated rates of amino acid substitutions in homologous genes among the three virus species appear to be considerably faster than the rates known for various vertebrate genes. The comparison reveals further that the rate of silent substitutions is faster than that of replacement substitutions. The DNA sequence data on bacteriophages phi X174 and G4 enable us to examine the patterns of nucleotide substitutions in overlapping genes as well as in nonoverlapping genes. It then becomes evident that overlapping genes have a quite different substitutional pattern with respect to the position of nucleotides in codons than do nonoverlapping sequences. In nonoverlapping regions the third positions usually change the fastest among the three codon positions. This pattern does not apply to overlapping genes, which are coded in the same region but with different reading frames. It will be shown that the younger of the two overlapping genes appears to be very tolerant to nucleotide substitutions at any codon position. Further more, the rate of substitution at each nucleotide site appears to be determined by the rate of the corresponding site in the older of the two overlapping genes.

BK Virus↗
PubMed1991

RNA viruses: genome structure and evolution.

The explosive pace of sequencing of RNA viruses is leading to rapid advances in our understanding of the evolution of these viruses and of the ways in which their genomes are organized and expressed. New insights are coming not only from genomic nucleotide sequence comparisons, but also from direct sequencing of transcribed mRNAs and of RNAs that serve as intermediates in replication.

Biological Evolution↗
PubMed1999

[Molecular evolution and genotype classification of TT virus].

Based on sequences data, TTV have a partial Rep protein motifs found among Circoviridae and the conserved region of parvoviral nonstructural polypeptides (NS)-1 genes, however we could not perform phylogenetic analyses among TTV and other viruses because of few similar sequences. Putative ORF2 among G2 and G4 encoded 49 aa because of in-frame stop codon, although that of G1 encoded 202 aa. Just down-stream of the stop codon, another putative new ORF(ORF3) were found around 150 aa. A phylogenetic analysis, using the ORF1 sequences of 93 TTV obtained from various geographical areas, indicated that the virus could be classified into six different genotypes. Further studies using more than 350 isolates obtained from DDBJ showed at least nine genotypes.

Amino Acid Sequence↗
PubMed1994

Human parainfluenza virus type 1 evolution combines cocirculation of strains and development of geographically restricted lineages.

The hemagglutinin neuraminidase (HN) glycoprotein of human parainfluenza virus type 1 (HPIV-1) mediates attachment to the host cell and is the target of protective antibody. Since the efficacy of a potential vaccine depends on antigenic constancy, the antigenic and genetic stability of the HPIV-1 HN glycoprotein was examined for 13 isolates obtained between 1981 and 1989. Antigenic analysis with a panel of 11 monoclonal antibodies demonstrated a single change among 3 isolates from 1989 that distinguished them from all other isolates. The HN genes from all 13 isolates and 13 previously published HN gene sequences shared > 95% homology. Evolutionary analysis demonstrated cocirculation of strains, without a dominant lineage. The 1989 isolates and the previously proposed subtype A isolates occupied distinct evolutionary branches, indicating geographically limited evolution. The slow rate of evolution and HN homogeneity may allow development of a single vaccine formulation for the prevention of disease.

Antigens, Viral↗
PubMed1994

Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays.

High mutation rates and strong selective pressures imposed on human immunodeficiency viruses in vivo result in the formation of pools of genetic variants known as quasispecies. DNA heteroduplex mobility and tracking analyses were used to monitor the generation of HIV sequence diversity, to estimate quasispecies complexity, and to assess the turnover of genetic variants to approach an understanding of the relationship between viral quasispecies evolution in vivo and disease progression. Proviral DNA pools were nearly homogeneous soon after sexual transmission. The emergence and clearance of individual variants then occurred at different rates in different individuals. High quasispecies complexity was found in long-term-infected, asymptomatic individuals, while rapid CD4+ cell decline and AIDS were often, but not always, associated with lower quasispecies complexity. Proviral genetic variation was often low following in vitro culture, because of the outgrowth of one or a few variants that often became more abundant only later as proviruses in peripheral blood mononuclear cells. These studies provide insight into the dynamics of human immunodeficiency virus sequence changes in vivo and illustrate the utility of heteroduplex analysis for the study of phenomena associated with rapid genetic changes.

Acquired Immunodeficiency Syndrome↗
PubMed2006

Dengue virus circulation and evolution in Mexico: a phylogenetic perspective.

BACKGROUND: Dengue is the most important arthropod-borne viral infection in the Americas. In the last decades a progressive increment in dengue severity has been observed in Mexico and other countries of the region. METHODS: Molecular epidemiological studies were conducted to investigate the viral determinants of the emergence of epidemic dengue, dengue hemorrhagic fever and dengue shock syndrome as major public health problems in Mexico. Bayesian phylogenetic analyses were conducted to determine the origin, persistence and geographical dispersion of the four serotypes of dengue virus (DENV) isolated in Mexico between 1980 and 2002. Tests for natural selection were also conducted. RESULTS: The origin of some, but not all, strains circulating in Mexico could be inferred. Frequent lineage replacements were observed and were likely due to stochastic events. In situ evolution was detected but not associated with natural selection. Recent changes in the incidence and severity of dengue were temporally associated with the introduction and circulation of different serotypes and genotypes of DENV. CONCLUSIONS: Introduction of new DENV genotypes and serotypes is a major risk factor for epidemic dengue and severe disease. Increased surveillance for such introductions is critical to allow public health authorities to intervene in impending epidemics.

Aedes↗
PubMed1997

The evolution of virus-induced apoptosis.

Viruses from several different families are able to exploit their host's cell death programmes so as to maximize viral fitness. Consideration of the evolution of such strategies has lead to the suggestion that the virus should inhibit apoptosis, in order to prolong the life of the cell and thereby maximize the number of progeny virions. The host, on the other hand, should stimulate apoptosis thereby inhibiting viral growth and blocking viral spread. For example, the function of the latent membrane protein I (LMPI) of the Epstein-Barr virus and the bcl-2 homologue gene A179L of African swine fever virus is to inhibit apoptosis. However, in other cases it is the virus that stimulates cell death or the host that benefits from inhibiting apoptosis, such as in fatal alphavirus encephalitis. This has been explained by assuming that virus-induced apoptosis in non-regenerating cells would be detrimental to the host. We present a mathematical framework for understanding virus-induced apoptosis which accounts for these two opposite solutions to virus infection with respect to the mode of virus replication and the life cycle of the target cell.

Apoptosis↗
PubMed2002

Phylogenetic evidence for adaptive evolution of dengue viruses in nature.

A maximum-likelihood approach was used to analyse selection pressures acting on genes from all four serotypes of dengue virus (DEN). A number of amino acid positions were identified within the envelope (E) glycoprotein that have been subject to relatively weak positive selection in both DEN-3 and DEN-4, as well as in two of the five genotypes of DEN-2. No positive selection was detected in DEN-1. In accordance with the function of the E protein as the major antigenic determinant of DEN, the majority of these sites were located in, or near to, potential T- or B-cell epitopes. A smaller number of selected sites was located in other well-defined functional domains of the E protein, suggesting that cell tropism and virus-mediated membrane fusion may also confer fitness advantages to DEN in nature. Several positively selected amino acid substitutions were also identified in the NS2B and NS5 genes of DEN-2, although the cause of this selection is unclear, whereas the capsid, membrane and non-structural genes NS1, NS2A, NS3 and NS4 were all subject to strong functional constraints. Hence, evidence was found for localized adaptive evolution in natural isolates of DEN, revealing that selection pressures differ among serotypes, genotypes and viral proteins.

Biological Evolution↗
PubMed2003

Role of viruses in human evolution.

The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long-standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N-glycolylneuraminic acid (Neu5Gc), a cell-surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development.

Animals↗
PubMed1995

Molecular evolution of influenza viruses.

There are two different mechanisms by which influenza viruses might evolve: (1) Because the RNA genome of influenza viruses is segmented, new strains can suddenly be produced by reassortment, as happens, for example, during antigenic shift, creating new pandemic strains. (2) New viruses evolve relatively slowly by stepwise mutation and selection, for example, during antigenic or genetic drift. Influenza A viruses were found in various vertebrate species, where they form reservoirs that do not easily mix. While human influenza A viruses do not spread in birds and vice versa, the species barrier to pigs is relatively low, so that pigs might function as "mixing vessels" for the creation of new pandemic reassortants in Southeast Asia, where the probability is greatest for double infection of pigs by human and avian influenza viruses. Phylogenetic studies revealed that about 100 years ago, an avian influenza A virus had crossed the species barrier, presumably first to pigs, and from there to humans, forming the new stable human and classical swine lineages. In 1979, again, an avian virus showed up in the North European swine population, forming another stable swine lineage. The North European swine isolates from 1979 until about 1985 were genetically extremely unstable. A hypothesis is put forward stating that a mutator mutation is necessary to enable influenza virus to cross the species barrier by providing the new host with sufficient variants from which it can select the best fitting ones. As long as the mutator mutation is still present, such a virus should be able to cross the species barrier a second time, as happened about 100 years ago. Although the most recent swine isolates from northern Germany are again genetically stable, we nevertheless should be on the lookout to see if a North European swine virus shows up in the human population in the near future.

Animals↗
PubMed2026

Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.

The Mediterranean population of tomato leaf curl New Delhi virus (ToLCNDV-ES) is characterized by a high genetic uniformity, distinguishing it from its Asian counterparts. ToLCNDV-ES is thought to have a monophyletic origin, likely resulting from a single recombination event, prior to its spread throughout the Mediterranean region. Following its first detection in southeastern France in 2020, ToLCNDV-ES re-emerged in France in 2022. Our analysis based on advanced long-read sequencing, circular DNA profiling, and phylogeny indicates both local persistence of French ToLCNDV-ES and multiple independent introduction events. Signatures of positive selection were identified in French ToLCNDV-ES populations, whereas no clear evidence of recombination was found. Bayesian time-structured phylogenetic analyses suggest that introductions in France occurred between 2018 and 2021 from the major ToLCNDV-ES clade, while several Italian ToLCNDV-ES isolates diverged prior to the virus introduction in the Mediterranean basin. Overall, this study demonstrates the value of an optimized long-read sequencing approach for resolving circular DNA virus diversity, and sheds light on the complex evolutionary history of ToLCNDV-ES in the Mediterranean Basin, particularly in southeastern France.

France↗
PubMed1994

Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions.

For pathogenic viruses such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human influenza A virus, and human T-cell leukemia virus type I (HTLV-I), the evolutionary features were briefly reviewed with special reference to the rates of synonymous and nonsynonymous substitutions. In particular, these rates were discussed in connection with the neutral theory of molecular evolution. It was common to all the five pathogenic viruses that the rate of synonymous substitution was higher than that of nonsynonymous substitution particularly when the entire gene regions were compared between different isolates. This suggests that the viral proteins are quite conservative to functional and structural changes even though most of these viral genomes are evolving at a speed extraordinarily higher than their host genomes. Thus, this feature is consistent with the neutral theory. However, it is also pointed out that positive selection may be operating on some specific sites such as antigenic sites in order for the pathogenic viruses to escape from the host immune system.

Base Sequence↗
PubMed2006

Continuing evolution of H9 influenza viruses in Korean poultry.

We analyzed the evolution of H9 influenza viruses isolated from Korean chicken farms from 2002 to 2004. Korean H9 viruses formed two antigenically distinct groups: those isolated from 1996 to mid-2003, and those isolated from late 2003 through 2004. Most of the 2004 isolates showed greater cross-reactivity with the second group than with the first group. Phylogenetic analysis of the 12 viruses studied revealed three genotypes of H9N2 viruses and showed that reassortment had occurred. One isolate, Ck/Kor/164/04, belonged to the H9N8 subtype. Its HA and PB1 genes were similar to those of the H9N2 viruses, but its other genes were closely related to H3N8 viruses. This report is the first (to our knowledge) of H9N8 infection in this host. The pathogenicity of the early isolates altered due to antigenic drift and reassortment, leading to H9 avian influenza viruses in Korea that potentially can expand their host range to mammalians.

Animals↗
PubMed1980

Evolution of RNA viruses.

These arguments lead to the suggestion that four independent evolutionary lines exist within the general group of RNA viruses. These are positive strand viruses, negative strand viruses, double stranded viruses, and retroviruses. Three of the viral systems may well have shared genes but the double-stranded RNA viruses appear to represent a very different evolutionary line.

Biological Evolution↗