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At least 505 records · Page 28Linked to original sources
PubMed1998

Influence of host species on the evolution of the nonstructural (NS) gene of influenza A viruses.

The matrix (M) and nonstructural (NS) genes of influenza A viruses each encode two overlapping proteins. In the M gene, evolution of one protein affects that of the other. To determine whether or not this evolutionary influence operating between the two M proteins also occurs in the NS gene, we sequenced the NS genes of 36 influenza A viruses isolated from a broad spectrum of animal species (wild and domestic birds, horses, pigs, humans, and sea mammals) and analyzed them phylogenetically, together with other previously published sequences. These analyses enabled us to conclude the following host species-related points that are not found in the other influenza A virus genes and their gene products. (1) The evolution of the two overlapping proteins encoded by the NS gene are lineage-dependent, unlike the M gene where evolutionary constraints on the Ml protein affect the evolution of the M2 protein (Ito et al.. J. Virol. 65 (1991) 5491 5498). (2) The gull-specific lineage contained nonH13 gull viruses and the non-gull avian lineage contained H13 gull viruses, indicating that the gull-specific lineage does not link to the H13 HA subtype in the NS gene unlike findings with other genes. (3) The branching topology of the recent equine lineage (H7N7 viruses isolated after 1973 and H3N8) indicates recent introduction of the NS, M, and PB2 genes into horses from avian sources by genetic reassortment.

Animals↗
PubMed2006

[Genome conservatism of phiKMV-like bacteriophages (T7 supergroup) active against Pseudomonas aeruginosa].

The T7-like phiKMV bacteriophage active on Pseudomonas aeruginosa was previously isolated by us and shown to have DNA resistant to many endonucleases. A loss of sensitive sites might be a consequence of a long phiKMV evolution on different hosts. To elucidate, whether this trait is shared by other similar phages, several new phiKMV-like phages were isolated from different sources and compared. All studied phiKMV-like phages formed three groups, insignificantly differing in the number and localization of endonuclease-sensitive DNA sites. This confirms that the present-day phages of this species have highly conserved genomes. Mutational "restoration" of the lost sites may be restricted by a lethal effect. The phiKMV-like phages were shown for the first time to increase the rate of in vitro accumulation of giant phiKZ-like phages of P. aeruginosa. This effect is characteristic only of phiKMV-like phages.

Bacteriophage Typing↗
PubMed2006

Molecular evolution of porcine circovirus type 2 genomes: phylogeny and clonality.

Porcine circoviruses (PCVs) type 1 (PCV1) and type 2 (PCV2) show high levels of nucleotide similarity, but PCV1 is considered non-pathogenic and PCV2 has been associated with several disease outcomes in pigs, mainly postweaning multisystemic wasting syndrome (PMWS). After exploring different topologies of the origin of PCVs, it was concluded that PCV1 and PCV2 seem to have a common origin. On the other hand, PCV2 could be divided into two groups (1 and 2) and eight clusters (1A to 1C and 2A to 2E), but none of those was apparently associated with disease status or geographic area. When phylogenetic trees constructed with the whole PCV2 genome, the cap or the rep genes were compared, some incongruence was identified. The possible existence of recombination was evaluated and cluster 1B was found to have a possible recombinant origin. Selective pressure was detected in all parts of the PCV2 genome, especially in the rep gene. Finally, the cap gene was the more suitable phylogenetic and epidemiological marker for PCV2, despite the fact that the virus can undergo recombination mainly within the first part of the rep region.

Animals↗
PubMed1999

Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory.

The comparative analysis of five completely sequenced Streptococcus thermophilus bacteriophage genomes demonstrated that their diversification was achieved by a combination of DNA recombination events and an accumulation of point mutations. The five phages included lytic and temperate phages, both pac site and cos site, from three distinct geographical areas. The units of genetic exchange were either large, comprising the entire morphogenesis gene cluster, excluding the putative tail fiber genes, or small, consisting of one or maximally two genes or even segments of a gene. Many indels were flanked by DNA repeats. Differences in a single putative tail fiber gene correlated with the host ranges of the phages. The predicted tail fiber protein consisted of highly conserved domains containing conspicuous glycine repeats interspersed with highly variable domains. As in the T-even coliphage adhesins, the glycine-containing domains were recombinational hot spots. Downstream of a highly conserved DNA replication region, all lytic phages showed a short duplication; in three isolates the origin of replication was repeated. The lytic phages could conceivably be derived from the temperate phages by deletion and multiple rearrangement events in the lysogeny module, giving rise to occasional selfish phages that defy the superinfection control systems of the corresponding temperate phages.

Amino Acid Sequence↗
PubMed2004

Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the development and validation of an oligonucleotide resequencing array for interrogating the entire 30-kb SARS-CoV genome in a rapid, cost-effective fashion. Using this platform, we sequenced SARS-CoV genomes from Vero cell culture isolates of 12 patients and directly from four patient tissues. The sequence obtained from the array is highly reproducible, accurate (>99.99% accuracy) and capable of identifying known and novel variants of SARS-CoV. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable, and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale, making this an ideal platform for the global monitoring of SARS-CoV and other small-genome pathogens.

Animals↗
PubMed2002

Origin and evolution of influenza virus hemagglutinin genes.

Influenza A, B, and C viruses are the etiological agents of influenza. Hemagglutinin (HA) is the major envelope glycoprotein of influenza A and B viruses, and hemagglutinin-esterase (HE) in influenza C viruses is a protein homologous to HA. Because influenza A virus pandemics in humans appear to occur when new subtypes of HA genes are introduced from aquatic birds that are known to be the natural reservoir of the viruses, an understanding of the origin and evolution of HA genes is of particular importance. We therefore conducted a phylogenetic analysis of HA and HE genes and showed that the influenza A and B virus HA genes diverged much earlier than the divergence between different subtypes of influenza A virus HA genes. The rate of amino acid substitution for A virus HAs from duck, a natural reservoir, was estimated to be 3.19 x 10(-4) per site per year, which was slower than that for human and swine A virus HAs but similar to that for influenza B and C virus HAs (HEs). Using this substitution rate from the duck, we estimated that the divergences between different subtypes of A virus HA genes occurred from several thousand to several hundred years ago. In particular, the earliest divergence time was estimated to be about 2,000 years ago. Also, the A virus HA gene diverged from the B virus HA gene about 4,000 years ago and from the C virus HE gene about 8,000 years ago. These time estimates are much earlier than the previous ones.

Amino Acid Sequence↗
PubMed2024

TMPRSS2-mediated SARS-CoV-2 uptake boosts innate immune activation, enhances cytopathology, and drives convergent virus evolution.

The accessory protease transmembrane protease serine 2 (TMPRSS2) enhances severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake into ACE2-expressing cells, although how increased entry impacts downstream viral and host processes remains unclear. To investigate this in more detail, we performed infection assays in engineered cells promoting ACE2-mediated entry with and without TMPRSS2 coexpression. Electron microscopy and inhibitor experiments indicated TMPRSS2-mediated cell entry was associated with increased virion internalization into endosomes, and partially dependent upon clathrin-mediated endocytosis. TMPRSS2 increased panvariant uptake efficiency and enhanced early rates of virus replication, transcription, and secretion, with variant-specific profiles observed. On the host side, transcriptional profiling confirmed the magnitude of infection-induced antiviral and proinflammatory responses were linked to uptake efficiency, with TMPRSS2-assisted entry boosting early antiviral responses. In addition, TMPRSS2-enhanced infections increased rates of cytopathology, apoptosis, and necrosis and modulated virus secretion kinetics in a variant-specific manner. On the virus side, convergent signatures of cell-uptake-dependent innate immune induction were recorded in viral genomes, manifesting as switches in dominant coupled Nsp3 residues whose frequencies were correlated to the magnitude of the cellular response to infection. Experimentally, we demonstrated that selected Nsp3 mutations conferred enhanced interferon antagonism. More broadly, we show that TMPRSS2 orthologues from evolutionarily diverse mammals facilitate panvariant enhancement of cell uptake. In summary, our study uncovers previously unreported associations, linking cell entry efficiency to innate immune activation kinetics, cell death rates, virus secretion dynamics, and convergent selection of viral mutations. These data expand our understanding of TMPRSS2's role in the SARS-CoV-2 life cycle and confirm its broader significance in zoonotic reservoirs and animal models.

SARS-CoV-2↗
PubMed2005

Each genomic RNA in HIV-1 heterozygous virus generate new virions.

Retrovirus are unique because they present two complete copies of the genomic RNA in each virion. It is believed that only one proviral DNA is formed from the two genomic RNAs. To check this hypothesis, we constructed two deleterious HIV-1 variants in gag gene which upon transfection in Cos-1 cells were able, by complementation, to form heterozygous viruses, used to infect MT4 cells in a plaque assay. Analysis of the proviral DNA of the eight plaques obtained indicated that five were recombinants between the two deleterious mutants. Three other plaques showed three bands corresponding to the reverse transcription of both strands of one heterozygous virion and to the recombination of the two genomes. These results demonstrate that the two genomic RNAs in HIV-1 heterozygous virions could be used in the generation of new viruses. This mechanism permits the recovery of deleterious mutants and enhances the evolutive potential of HIV-1.

Amino Acid Sequence↗
PubMed2000

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution.

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3'-untranslated region (3'-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis-Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3'-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis-D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

3' Untranslated Regions↗
PubMed1998

Evolution of Streptococcus thermophilus bacteriophage genomes by modular exchanges followed by point mutations and small deletions and insertions.

Comparative sequence analysis of 40% of the genomes from two prototype Streptococcus thermophilus bacteriophages (lytic group I phage phi Sfi19 and the cos site containing temperate phage phi Sfi21) suggested two processes in the evolution of their genomes. In a first evolutionarily distant phase the basic genome structure was apparently constituted by modular exchanges. Over the 17-kb-long DNA segment analyzed in the present report, we observed clusters of genes with similarity to genes from Leuconostoc oenos phage L10, Lactococcus lactis phage BK5-T, and Streptococcus pneumoniae phage Dp-1. A chimeric protein was predicted for orf 1291 which showed similarity to both phage BK5-T and phage Dp-1 proteins. The very large orf 1626 gene product showed similarity to two adjacent genes from the Lactobacillus delbrueckii phage LL-H and further phage proteins (Lactococcus lactis, Bacillus subtills). The similarities were localized to distinct parts of this apparently multifunctional protein. The putative phi Sfi19 lysin showed similarity to both lysins of phages and cellular enzymes. In a second, evolutionarily more recent, phase the S, thermophilus phage genomes apparently diversified by point mutations and small deletions/insertions. Over the investigated 17-kb DNA region phi Sfi19 differed from phi Sfi21 by 10% base pair changes, the majority of which were point mutations (mainly at the third codon position), while a third of the base pair differences were contributed by small deletions/insertions. The base pair changes were unevenly distributed. Over the Leuconostoc phage-related DNA the change rate was high, while over the Lactococcus and S. pneumoniae phage-related DNA the change rate was low. We speculate that the degree of base pair change could provide relative time scales for the modular exchange reactions observed in S. thermophilus phages.

Amino Acid Sequence↗
PubMed2003

Evolution of surface and nonstructural-1 genes of influenza B viruses isolated in the Province of Québec, Canada, during the 1998-2001 period.

After 2 minor winter seasons, influenza B viruses were predominantly isolated in the Province of Quebec, Canada, during the 2000-2001 season representing 74% of laboratory-confirmed influenza viruses. We performed an antigenic study of the hemagglutinin (HA) protein and a molecular characterization of the HA1 region, nonstructural-1 (NS1) and neuraminidase (NA)/NB genes of 20 influenza B strains isolated in the Province of Quebec during the 1998-2001 period. Our isolates were compared to recent vaccine strains (B/Harbin/7/94 in 1998-1999, B/Yamanashi/166/98 in 1999-2000 and 2000-2001, and B/Sichuan/379/99 in 2001-2002). The hemagglutination inhibition (HI) test revealed that all isolates were different from B/Harbin/7/94 and were more related to the 2 other vaccine strains although precise identification was often impossible. Molecular analysis of the HA1 gene revealed that both B/Yamanashi/166/98-like and B/Sichuan/379/99-like isolates co-circulated during the 1998-1999 season whereas isolates from the 2 subsequent years were more related to B/Sichuan/379/99. Most isolates (8/9) of the 2000-2001 season contained a N126D substitution recently associated with altered antigenicity in recent influenza B/Yamagata/16/88-related viruses. Although the HA1 and NS1 protein sequences of viruses isolated during the 1998-1999 season were clearly different from those of the respective vaccine strain (B/Harbin/7/94), the NA protein sequence of those isolates was slightly more related to B/Harbin/7/94 than B/Yamanashi/166/98 suggesting distinct patterns of evolution for these genes. This study confirms the importance of a detailed molecular analysis for understanding the evolution of influenza B viruses.

Antigenic Variation↗
PubMed2000

Distribution and evolution of bacteriophage WO in Wolbachia, the endosymbiont causing sexual alterations in arthropods.

Wolbachia are obligatory intracellular and maternally inherited bacteria, known to infect many species of arthropod. In this study, we discovered a bacteriophage-like genetic element in Wolbachia, which was tentatively named bacteriophage WO. The phylogenetic tree based on phage WO genes of several Wolbachia strains was not congruent with that based on chromosomal genes of the same strains, suggesting that phage WO was active and horizontally transmitted among various Wolbachia strains. All the strains of Wolbachia used in this study were infected with phage WO. Although the phage genome contained genes of diverse origins, the average G+C content and codon usage of these genes were quite similar to those of a chromosomal gene of Wolbachia. These results raised the possibility that phage WO has been associated with Wolbachia for a very long time, conferring some benefit to its hosts. The evolution and possible roles of phage WO in various reproductive alterations of insects caused by Wolbachia are discussed.

Amino Acid Sequence↗
PubMed1999

Macropodid herpesviruses 1 and 2 occupy unexpected molecular phylogenic positions within the Alphaherpesvirinae.

The molecular phylogeny of macropodid herpesviruses 1 and 2 (MaHV-1 and -2) has been investigated by cloning and sequencing the genes encoding glycoprotein B from both viruses. Phylogenetic reconstructions based on the putative amino acid sequences of glycoprotein B indicate that MaHV-1 and -2 are most closely related to the subfamily Alphaherpesvirinae. Within the Alphaherpesvirinae, MaHV-1 and -2 are closely associated with those herpesviruses that infect primates. This phylogenetic relationship does not fit the constraints of the proposed co-evolution theory described for other members of the Alphaherpesvirinae which have mammalian hosts.

Alphaherpesvirinae↗
PubMed2000

Genetic evolution of GB virus C/hepatitis G virus (GBV-C/HGV) under interferon pressure.

The epidemiology and clinical features of chronic GBV-C/HGV infection have largely been explored, but there is little information about the mechanisms enabling GBV-C/HGV to cause persistent infection. Since analysis of the genomic variation of GBV-C/HGV under interferon pressure might provide some insight into this issue, we analyzed the nucleotide sequence variation of the 5'NC and NS3 regions in GBV-C/HGV isolates obtained sequentially from seven patients co-infected with HCV and treated with interferon. A reduction of GBV-C/HGV-RNA serum level below the detection limit of the RT-PCR assay was observed during treatment in all patients, but upon interferon withdrawal, viral RNA remained undetectable in only two patients. Among the five patients who did not clear GBV-C/HGV-RNA, viral strains emerging after treatment were identical to those present at baseline in three cases. In a further case, in whom GBV-C/HGV-RNA re-emerged during therapy (breakthrough episode), several mutations appeared in relapse samples. In the remaining patient, with a mixed infection before therapy, only one of the two GBV-C/HGV strains present at baseline was detected upon treatment withdrawal. These data raise the possibility that positive selection may act over GBV-C/HGV genome during interferon therapy, and contribute to persistence of infection with this virus.

Base Sequence↗
PubMed2002

Replication advantage and host factor-independent phenotypes attributable to a common naturally occurring capsid mutation (I97L) in human hepatitis B virus.

Mutations of human hepatitis B virus (HBV) occur frequently within the capsid (core) protein in natural infections. The most frequent mutation of the core protein in HBV from Southeast Asia occurs at amino acid 97, changing an isoleucine (I) to a leucine (L). In our systematic study of virus-host interactions, we have examined the replication efficiency of a site-directed mutant, I97L, and its parental wild-type HBV in several different hepatoma cell lines. Interestingly, we found that this capsid variant replicated in human Huh7 hepatoma cells approximately 4.8-fold better than its parental wild-type HBV. A similar phenomenon was observed in another hepatoma cell line, J3. In addition, the level of encapsidated RNA pregenome in mutant I97L was about 5.7-fold higher than that of the wild-type HBV in Huh7 cells. Unlike Huh7 cells, no significant difference in viral DNA replication between the same I97L mutant and its parental wild-type HBV was observed in HepG2, a human hepatoblastoma cell line. This finding of a profound replication advantage for mutant I97L in Huh7 and J3 cells but not in HepG2 cells may have important implications for the emergence of this mutant in chronic HBV carriers. We speculate here that the mutation confers a host factor-independent growth advantage for the survival of HBV variants in gradually dedifferentiating hepatocytes and thus helps prolong viral persistence.

Amino Acid Substitution↗
PubMed1991

An evolutionary view of viral regulatory genes.

It is my great honor to dedicate this article to Professor Ludwig C. Yen at the occasion of the Annual Meeting of the Chinese Society of Microbiology, commemorating his 101st Birthday. I have had the privilege of being one of the earliest students of Professor Yen, and as a staff member working for 16 years under him, I have been benefited enormously from his teachings. I am most grateful to Dr. Czausiung Yang and the executive board members of the Chinese Society of Microbiology for giving me this opportunity to present some of my research activities which would be relevant to Professor Yen's teachings. Introduction to the evolutionary view of host-parasite relationship was one of the many contributions Professor Yen made to enlighten students and colleagues as early as in 1940. As promulgated by Professor Yen, natural history of infectious diseases has witnessed the reality of Theobald Smith's premise, "pathogenicity of microorganisms is an accident in the evolutionary processes of host-parasite relationship, and the outcome of evolutionary forces is a modus vivendi (a feasible compromise) according to which the parasite and the host reach some sort of equilibrium which permits the survival of both"(1). These evolutionary concept has since become a common knowledge for modern students of infectious diseases. The natural history of recently discovered human retroviruses such as HTLVs (human T-lymphotropic viruses) and HIVs (human immunodeficiency viruses) has amply demonstrated the truth of the premise. I shall review some results of our research which would be of relevance to the evolution of viral quasispecies and variants, viral oncogenes, and the cellular as well as viral regulatory genes. I shall focus on the roles played by these genes in the delicate and complex balance of host-virus relationships, and on their association with cellular differentiation and oncogenesis.

Biological Evolution↗
PubMed2002

Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples.

We analyzed the reverse transcriptase (RT) and protease sequences of HIV-1 isolates obtained over 7 years from two couples with known transmission histories. Phylogenetic trees constructed from the sequence data reflected the known transmission histories, despite the fact that the drug resistance mutations were most consistent with the drug treatment histories. However, the RT sequences from one couple diverged by 2.9% even before therapy was begun, and three (0.9%) of 339 unrelated individuals had viruses that shared a common ancestor with sequences from the recipient member of the couple but not with sequences from the transmitter. The divergence between the first two isolates from this couple is consistent with a pretransmission interval during which the transmitter developed a heterogeneous virus population. The closeness between the three controls and the recipient's first RT sequence may indicate slower evolution on the branches of the control sequences. Although the RT and protease genes contain phylogenetic information, they are suboptimal for reconstructing transmission history because the genetic distance between RT and protease isolates from unrelated individuals may occasionally approximate the distance between RT and protease isolates from related individuals.

Amino Acid Sequence↗
PubMed2001

Directed evolution of polymerase function by compartmentalized self-replication.

We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

DNA-Directed DNA Polymerase↗