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At least 883 records · Page 49Linked to original sources
PubMed1988

Analysis of genetic variability and mapping of point mutations in influenza virus by the RNase A mismatch cleavage method.

We have applied the RNase A mismatch cleavage method to analyze genetic variability in RNA viruses by using influenza virus as a model system. Uniformly labeled RNA probes synthesized from a cloned hemagglutinin gene of a given viral strain were hybridized to RNA isolated from other strains of characterized or uncharacterized genetic composition. The RNA.RNA heteroduplexes containing a variable number of base mismatches were digested with RNase A, and the resistant products were analyzed by denaturing polyacrylamide gel electrophoresis. We show that many of these single base mismatches are cleaved by RNase A, generating unique and characteristic patterns of resistant RNA fragments specific for each of the different viral strains. Comparative analysis of the cleavage patterns allows a qualitative estimation of the genetic relatedness and evolution of field strains. We also show that cleavage by RNase A at single base mismatches can readily detect and localize point mutations present in monoclonal antibody-resistant variants. This method should have wide applications in the study of RNA viruses, not only for epidemiological analysis but also in some diagnostic problems, such as characterization of phenotypic mutants.

Animals↗
PubMed2002

1917 avian influenza virus sequences suggest that the 1918 pandemic virus did not acquire its hemagglutinin directly from birds.

Wild waterfowl captured between 1915 and 1919 were tested for influenza A virus RNA. One bird, captured in 1917, was infected with a virus of the same hemagglutinin (HA) subtype as that of the 1918 pandemic virus. The 1917 HA is more closely related to that of modern avian viruses than it is to that of the pandemic virus, suggesting (i) that there was little drift in avian sequences over the past 85 years and (ii) that the 1918 pandemic virus did not acquire its HA directly from a bird.

Animals↗
PubMed2004

Plasma RNA viral load is not associated with intrapatient quasispecies heterogeneity in HIV-1 infection.

The human immunodeficiency virus type 1 (HIV-1) viral set point has been associated with the rate of, disease progression and with the level of HIV-specific immune response. The analysis of the possible association between viral set point and quasispecies heterogeneity has important consequences in the understanding of HIV-1 in vivo evolution. In this study, we analyzed the association between intrapatient viral diversity and RNA viral load in 16 antiretroviral therapy-naive HIV-1-infected patients at a single time point, during the disease free period. Patients were separated into low and high viral load groups according to plasma RNA values. HIV-1 quasispecies complexity was assessed in the C2-V5 env region. The average intrapatient quasispecies heterogeneity in both groups was not significantly different (t-test, P > 0.05). However, while within the low viral load group both synonymous and non-synonymous mutations contribute to the variation observed, in the heterogeneity observed in the high viral load group there was an increase in the contribution of the non-synonymous mutations. Thus, this study show that although intrapatient quasispecies heterogeneity is not associated with viral set point in HIV-1 infection, some differences exist between the two groups in the pattern of mutation accumulation.

Amino Acid Substitution↗
PubMed2026

Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology.

Jamestown Canyon virus (JCV) is a historically understudied mosquito-borne virus of increasing concern in North America. We generated 658 whole-genome JCV sequences from northeast United States, including 84% (500/597) of all JCV-positive mosquitoes detected in Connecticut from 1997 to 2022. Then, we applied phylodynamic methods to demonstrate how mosquito phenology structures the maintenance and evolution of JCV. Our phylogenetic analyses estimate that JCV was introduced in the Northeast by at least the early 1700s, and the primary introductions of lineages A and B into Connecticut occurred during the mid-1800s to mid-1900s. Further, we estimate that JCV evolves at a rate of ∼3 × 10-5 substitutions per site per year (s/s/y), making it one of the slowest-evolving known RNA viruses, because the virus spends ∼10 months per year in evolutionary stasis while overwintering in mosquito eggs. To investigate ecological drivers of JCV spread in Connecticut, we paired discrete trait and continuous phylogeographic reconstructions with mosquito surveillance data. We estimate that JCV has a low diffusion rate of ∼30-60 km2/year, which is more similar to slow-moving tick-borne viruses than to other mosquito-borne viruses. We found that univoltine Aedes mosquitoes were likely to maintain the virus across years through overwintering in eggs, accounting for its slow evolution and dispersal, while multivoltine mosquitoes contributed to periodic bursts of spatial diffusion and amplification within seasons. We demonstrate the utility of dense sequencing and phylodynamics to disentangle complex transmission cycles, offering a framework for rapidly advancing our evolutionary and ecological knowledge of understudied viruses.

Animals↗
PubMed2004

Lack of evidence for protease evolution in HIV-1-infected patients after 2 years of successful highly active antiretroviral therapy.

The mechanisms involved in maintaining a latent replication-competent integrated human immunodeficiency virus type 1 (HIV-1) reservoir after successful highly active antiretroviral therapy (HAART) have not been fully described. The objective of this study was to assess whether low-level, persistent HIV-1 replication can be detected in the protease gene, in 10 HIV-1-infected patients who have undergone 2 years of successful HAART. Peripheral blood mononuclear cells (PBMCs) were collected from 10 HIV-1-infected patients receiving a triple-drug combination therapy (2 nucleoside analogues and 1 protease inhibitor). HIV-1 RNA levels and CD4+ and CD8+ T cell counts were longitudinally determined during a follow-up period of 108 weeks. Similarly, proviral fragments of the protease-coding region, obtained at baseline and at week 108 of HAART, were amplified by polymerase chain reaction from PBMCs, and 10-25 individual clones were sequenced for each time point. Only 1 of 271 individual protease clones showed a major resistance substitution (M46I [patient D]). Phylogenetic analysis revealed that, in all patients, the genetic distances from the deduced most recent common ancestor, in samples obtained at week 108 of HAART, were not longer than those in samples obtained at baseline. Moreover, the pattern of amino acid divergence during therapy showed an absence of positive selection in the protease-coding region. Taken together, these results show a lack of clinically relevant evolution in the protease-coding region after 2 years of successful HAART.

Amino Acid Sequence↗
PubMed2001

Evolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life.

The ubiquity of the dut gene in Eukarya, Eubacteria, and Archaea implies its existence in the last common ancestor of the three domains of life. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. The dUTPase is encoded as an auxiliary gene in the genomes of several DNA viruses and two distinct lineages of retroviruses. A comprehensive analysis of dUTPase amino acid sequence relationships explores the evolutionary dynamics of dut genes in viruses and their hosts. The data set was comprised of representative sequences from available Eukaryotes, Archaea, Eubacteria cells and viruses. A multiple alignment of these protein sequences was generated using a hidden Markov model (HMM) approach developed to align divergent data. Phylogenetic analysis revealed that horizontal transfer from hosts to virus genomes has occurred in all three domains of life. The evidence for horizontal transfers is particularly interesting in Eukaryotes as these dut genes have introns, while DNA virus dut genes do not. This implies an intermediary Retroid Agent facilitated the horizontal transfer process, via reverse transcription, between host mRNA and DNA viruses. The horizontal transfer of the dut gene from Eukaryotic, Eubacterial, and Archaeal organisms to both DNA and RNA viruses is the first documented case of host to pathogen transfer that has occurred in all three domains of life.

Amino Acid Sequence↗
PubMed1997

The three subunits of the polymerase and the nucleoprotein of influenza B virus are the minimum set of viral proteins required for expression of a model RNA template.

The genes encoding the nucleoprotein, PB1, PB2, and PA proteins of the influenza virus strain B/Panamá/45/90 have been cloned under control of the T7 RNA polymerase promoter of plasmid pGEM-3. Transfection of the recombinant plasmids obtained into mammalian cells, which had been infected with a vaccinia virus encoding the T7 RNA polymerase, resulted in expression of the expected influenza B virus polypeptides. Moreover, it is shown that coexpression of the four recombinant core proteins in COS-1 cells reconstituted a functional polymerase capable of expressing a synthetic influenza B virus-like CAT RNA. By using the influenza B virus recombinant plasmids and a set of pGEM-derived plasmids encoding the homologous core proteins of the influenza A virus A/Victoria/3/75 (I. Mena et al. (1994). J. Gen. Virol. 75, 2109-2114), the capabilities of homo- and heterotypic mixtures of the four core proteins to express synthetic type A and B CAT RNAs were analyzed. Both the influenza A and B virus polymerases were active in expressing, albeit with reduced efficiencies, the heterotypic model CAT RNAs. However, none of all possible heterotypic mixtures of the core proteins reconstituted a functional polymerase. In order to fully characterize the recombinant plasmids obtained, the nucleotide sequences of the cloned genes were determined and compared to sequences of other type B virus isolates. The results obtained from these latter analyses are discussed in terms of the conservation and evolution of the influenza B virus core genes.

Amino Acid Sequence↗
PubMed1994

Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. Significance for the evolution of tobamoviruses.

Cucumber green mottle mosaic virus (CGMMV) is a rod-shaped virus of the tobacco mosaic virus (TMV) group. The structure of cucumber green mottle mosaic virus has been determined by fiber diffraction methods at 3.4 A resolution, and refined by molecular dynamics methods to an R factor of 0.093. Disassembly of TMV is driven by the mutual repulsion of intersubunit carboxyl-carboxylate pairs, but one of these pairs is not conserved in CGMMV. An alternative pair, located about 5 A from the site of the TMV pair, has been found in CGMMV. Comparison of the two structures suggests that the carboxylate groups are free to migrate in the subunit interfaces during evolution.

Biological Evolution↗
PubMed1995

Aura virus is a New World representative of Sindbis-like viruses.

Aura virus is an alphavirus present in Brazil and Argentina that is serologically related to Sindbis virus (present throughout the Old World) and to Western equine encephalitis (WEE) virus (present in the Americas). We have previously shown that WEE is a recombinant virus whose glycoproteins and part of whose 3' nontranslated region (NTR) are derived from a Sindbis-like virus, but the remainder of whose genome is derived from Eastern equine encephalitis (EEE) virus. We show here that Aura virus is a Sindbis-like virus that shares considerable organizational and sequence identity with Sindbis virus. Certain nucleotide sequence elements present in Aura RNA that are believed to function as promoters are almost identical to their Sindbis counterparts, repeated elements in the 3' nontranslated region are shared with Sindbis virus, and important antigenic epitopes are conserved between the two viruses. Despite their close relationship, the two viruses have diverged significantly, sharing 73% amino acid sequence identity in the nonstructural proteins and 62% identity in the structural proteins. This is about the same as the identities between EEE and Venezuelan equine encephalitis virus, whose promoter elements, 3' NTRs, and antigenic epitopes have diverged more radically, such that these two viruses are considered to belong to different subgroups. Importantly, the glycoproteins of WEE are more closely related to those of Sindbis than to those of Aura virus. From this we propose that an ancestral Sindbis-like virus present in the Americas (probably South America) diverged 1000-2000 years ago into a lineage that gave rise to Aura virus and a lineage that gave rise to Sindbis virus and to the Sindbis-like parent of WEE. At some time after this divergence, a Sindbis-like virus belonging to the latter lineage was transferred to the Old World where it gave rise to Sindbis viruses distributed throughout the Old World, and in a separate event a Sindbis-like virus belonging to the same lineage underwent recombination with EEE to give rise to WEE.

Alphavirus↗
PubMed1994

De novo generation and accumulation of tomato bushy stunt virus defective interfering RNAs without serial host passage.

Studies were initiated to monitor generation and accumulation of defective interfering (DI) RNAs associated with tomato bushy stunt virus (TBSV) in the absence of serial, high multiplicity of infection passage. Infections were initiated in Nicotiana clevelandii host plants and protoplast cell suspensions by inoculation with in vitro-synthesized infectious TBSV RNA transcripts containing a genomic marker. The infections were then assayed for DI-size RNAs by both Northern blot analysis and reverse transcription coupled with PCR amplification. DI-size RNAs could not be detected by Northern blot analysis in either plants or protoplasts after an evident viral infection. However, RT-PCR amplification permitted the isolation of DI-size cDNAs (600-700 nt) from plant, but not protoplast, infections as early as 8 days postinoculation. Sequence analysis of these DI-size cDNA clones revealed that they contained the four conserved regions found in all previously identified competent DI RNAs. Several DI RNA clones contained the genomic marker which confirmed their de novo generation from the input transcript inoculum. A comparison of the nucleotide sequence of these clones to previously sequenced DI RNAs, isolated from plants after multiple passages, showed that differences existed at the junctions between regions. These results demonstrate that a heterogeneous population of DI RNAs accumulated in plants in the absence of serial host passage. In addition, the similarity of these DI RNAs to previously characterized DI RNAs that accumulate upon passage indicates that evolution can occur very rapidly within the initially inoculated plant.

Base Sequence↗
PubMed2006

Sexually transmitted acute infection with a clustered genotype 4 hepatitis C virus in HIV-1-infected men and inefficacy of early antiviral therapy.

BACKGROUND: Recent studies have suggested an increased risk of acute hepatitis C (HCV) infection in homosexual HIV-infected men and that early treatment with standard or pegylated interferon-alfa, alone or associated with ribavirin, significantly reduces the risk of chronic evolution in HIV-infected patients. METHODS: A retrospective analysis of 12 HIV-infected patients who were consecutively diagnosed as developing acute HCV infection, defined by both seroconversion of anti-HCV antibodies and detection of serum HCV RNA in those with previous negative results. Ten of these patients received early antiviral treatment with standard or pegylated interferon-alfa, alone or associated with ribavirin. RESULTS: The only risk factor in these patients was unprotected sexual intercourse with men. Acute HCV infection was asymptomatic in 10 patients, and the HCV genotype was 4d in 10 patients. The 10 genotype 4d viruses formed a monophylogenetic group and clustered separately from other local sequences of HCV genotype 4d, suggesting a common source of infection. None of the 10 patients who were treated early with antiviral therapy had a sustained virological response, as defined by undetectable HCV RNA 6 months after therapy. CONCLUSIONS: There is a risk of sexual transmission of HCV in HIV-infected men who have sex with men; the cluster of HCV genotype 4d suggested a common source of infection and a failure in prevention counselling. Early treatment with standard interferon-alfa failed to prevent chronic evolution of HCV infection in this particular group of HIV-infected patients who had acquired this peculiar cluster of genotype 4 strains.

Acute Disease↗
PubMed2006

Complete genome analysis of 33 ecologically and biologically diverse Rift Valley fever virus strains reveals widespread virus movement and low genetic diversity due to recent common ancestry.

Rift Valley fever (RVF) virus is a mosquito-borne RNA virus responsible for large explosive outbreaks of acute febrile disease in humans and livestock in Africa with significant mortality and economic impact. The successful high-throughput generation of the complete genome sequence was achieved for 33 diverse RVF virus strains collected from throughout Africa and Saudi Arabia from 1944 to 2000, including strains differing in pathogenicity in disease models. While several distinct virus genetic lineages were determined, which approximately correlate with geographic origin, multiple exceptions indicative of long-distance virus movement have been found. Virus strains isolated within an epidemic (e.g., Mauritania, 1987, or Egypt, 1977 to 1978) exhibit little diversity, while those in enzootic settings (e.g., 1970s Zimbabwe) can be highly diverse. In addition, the large Saudi Arabian RVF outbreak in 2000 appears to have involved virus introduction from East Africa, based on the close ancestral relationship of a 1998 East African virus. Virus genetic diversity was low (approximately 5%) and primarily involved accumulation of mutations at an average of 2.9 x 10(-4) substitutions/site/year, although some evidence of RNA segment reassortment was found. Bayesian analysis of current RVF virus genetic diversity places the most recent common ancestor of these viruses in the late 1800s, the colonial period in Africa, a time of dramatic changes in agricultural practices and introduction of nonindigenous livestock breeds. In addition to insights into the evolution and ecology of RVF virus, these genomic data also provide a foundation for the design of molecular detection assays and prototype vaccines useful in combating this important disease.

Animals↗
PubMed1990

Molecular evolution and distribution of dengue viruses type 1 and 2 in nature.

During the past several decades, dengue viruses have progressively extended their geographic distribution, and are currently some of the most important mosquito-borne viruses associated with human illness. Determining the genetic variability and transmission patterns of these RNA viruses is crucial in developing effective control strategies for the disease. Primer-extension sequencing of less than 3% of the dengue genome (across the E/NS1 gene junction) provided sufficient information for estimating genetic relationships among 40 dengue type 1 and 40 type 2 virus isolates from diverse geographic areas and hosts. A quantitative comparison of these 240-nucleotide-long sequences revealed previously unrecognized evolutionary relationships between disease outbreaks. Five distinct virus genotypic groups were detected for each of the two serotypes. The evolutionary rates of epidemic dengue viruses of types 1 and 2 were similar, although the transmission pathways of these viruses around the world are different. For dengue type 2, one genotypic group represents an isolated, forest virus cycle which seems to have evolved independently in West Africa. This is the first genetic evidence of the existence of a sylvatic cycle of dengue virus, which is clearly distinct from outbreak viruses.

Amino Acid Sequence↗
PubMed1997

Molecular evolution and phylogeny of satellite RNA associated with bamboo mosaic potexvirus.

Satellite RNA of bamboo mosaic potexvirus (satBaMV) is a linear RNA molecule which encodes a 20-kDa nonstructural protein. Sequences of seven different satBaMV isolates from bamboo hosts in three genera showed 0.7% to 7.5% base variation which spanned the whole RNA molecule. However, the putative 20-kDa open reading frame was all preserved in these isolates. The phylogenetic relationship based on the nucleotide sequence did not show particular grouping of satBaMV from the host in one genus; neither was the grouping of satBaMV evident by location of sampling. Putative secondary structures of the 3' untranslated regions showed a basic pattern with conserved hexanucleotides (ACCUAA) and polyadenylation signal (AAUAAA) located in the loop regions. Although the satBaMV-encoded 20-kDa protein is a nonstructural protein, its predicted secondary structure contains eight-stranded beta-sheets which may form "jelly-roll" structure similar to that found in capsid protein encoded by satellite virus of panicum mosaic virus.

Amino Acid Sequence↗
PubMed2006

Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004.

Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and 2004. They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains. Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes. Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other. Genotype II included 6 strains that were isolated in the 1990s in China. Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates. Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances. The Massachusetts serotype was present in China in 1990s and was in a separate genotype. Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI. Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII). IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%. The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines. IBVs showing various genetic differences are cocirculating in China.

Animals↗
PubMed1989

Evolutionary pathways of the PA genes of influenza A viruses.

Nucleotide sequences of the PA genes of influenza A viruses, isolated from a variety of host species, were analyzed to determine the evolutionary pathways of these genes and the host specificity of the genes. Results of maximum parsimony analysis of the nucleotide sequences indicate at least five lineages for the PA genes. Those from human strains represent a single lineage, whereas the avian genes appear to have evolved as two lineages--one comprising genes from many kinds of birds (e.g., chickens, turkeys, shorebirds, and ducks) and the other comprising only genes from gulls. H3N2 swine influenza virus PA genes are closely related to the currently circulating duck virus PA gene. By contrast, the H1N1 swine and equine virus PA genes appear to have evolved along independent lineages. Comparison of predicted amino acid sequences disclosed 10 amino acid substitutions in the PA proteins of all avian and H3N2 swine viruses that distinguished them from human viruses. The H1N1 swine viruses seem to be chimeras between human and avian viruses and they contain 8 amino acids not shared by other viruses. The equine viruses also appear to show their own amino acid substitutions. These findings indicate that the PA genes of influenza A viruses have evolved in different pathways defined by apparently unique amino acid substitutions and host specificities. They also indicate that influenza A viruses have been transmitted from avian to mammalian species.

Amino Acid Sequence↗