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PubMed2025

Molecular Evolution and Zoonotic Potential of Muju Virus (Orthohantavirus puumalaense) in Craseomys regulus, Republic of Korea.

Orthohantavirus puumalaense causes hemorrhagic fever with renal syndrome in Europe, with Puumala virus (PUUV) as its primary representative. Muju virus (MUJV), harbored by Craseomys regulus, an Arvicolinae rodent species endemic to the Republic of Korea (ROK), is also a genotype of O. puumalaense. However, their genomic diversity and zoonotic potential remain largely unknown. To investigate their prevalence, 185 voles were collected from 23 regions of the ROK between 2012 and 2023. Serological assays detected anti-PUUV immunoglobulin G antibodies in five samples (3.1%), whereas reverse-transcription polymerase chain reaction confirmed MUJV RNA in identical specimens (2.7%). Amplicon-based nanopore sequencing facilitates near-complete genome recovery, enabling high-resolution comparative analysis. Phylogenetic analysis revealed distinct genetic lineages in Gangwon and Jeollabuk Provinces. Evolutionary rate estimates indicated greater sequence divergence in the S and L segments than in the M segment. A zoonotic risk assessment revealed that most MUJV variants exhibited moderate-to-high spillover potential. The molecular detection of MUJV in Cheorwon, Gangwon Province, expands its known geographic range and provides the first molecular evidence of MUJV circulation in this region. These findings highlight the need for continued surveillance and seroprevalence studies of MUJV to assess its potential for human exposure and public health relevance in the ROK.

Animals↗
PubMed1984

Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families.

The amino acid sequences deduced from the nucleic acid sequences of several animal picornaviruses and cowpea mosaic virus (CPMV), a plant virus, were compared. Good homology was found between CPMV and the picornaviruses in the region of the picornavirus 2C (P2-X protein), VPg, 3C pro (proteinase) and 3D pol (RNA polymerase) regions. The CPMV B genome was found to have a similar gene organization to the picornaviruses. A comparison of the 3C pro (proteinase) regions of all of the available picornavirus sequences and CPMV allowed us to identify residues that are completely conserved; of these only two residues, Cys-147 and His-161 (poliovirus proteinase) could be the reactive residues of the active site of a proteinase with analogous mechanism to a known proteinase. We conclude that the proteinases encoded by these viruses are probably cysteine proteinases, mechanistically related, but not homologous to papain.

Amino Acid Sequence↗
PubMed2004

[Application of gene sequence cluster in research for H3 antigenic evolution of influenza A virus].

OBJECTIVE: Gene sequence data were clustered to explore evolution lineages of H3 antigen of influenza A virus. METHODS: All data of H3 RNA sequence in NCBI Genbank and Influenza sequence database were downloaded and aligned in ClustalX while two step cluster method were applied to explore the data. RESULTS: All sequences were aggregated into ten clusters, while seven of them mainly were human virus. Human virus and avian/other mammal virus were separated into different clusters distinctively, but coexisted into same clusters with swine virus. Time and host distribution were very distinctive in these clusters, but no geographic distribution features were found. CONCLUSION: With the interaction of human immunity system, H3 antigen mutated significantly every 5 - 7 years, and the speed of mutation had accelerated with the application of influenza vaccines in recent years. Mean while, human and swine influenza virus were not separated distinctly between clusters indicating that they had short inheritance distance. Result showed again that swine served as the mixer for antigenic recombination of different influenza virus.

Antigenic Variation↗
PubMed1990

Serial passage of infectious transcripts of a cucumber mosaic virus satellite RNA clone results in sequence heterogeneity.

Populations of the D-satellite RNA (D-sat) of cucumber mosaic virus (CMV) have a major site of heterogeneity at which a significant proportion of the molecules vary from each other. The generation of this heterogeneity was investigated by using infectious transcript RNA of a prototype D-sat clone as an inoculum of uniform sequence to initiate serial passages in five different host plant species. RNase protection assays indicated that heterogeneity at the same site seen in natural D-sat RNA populations developed within two to four passages in most of the hosts tested, and the proportion of the population exhibiting this heterogeneity accumulated to a much higher level in tobacco than in the other hosts. Characterization of the heterogeneity which developed in tobacco showed it to be qualitatively different from that in the original D-sat population. This analysis of a CMV satellite RNA is the first example in which infectious transcript RNA from a clone has been used to investigate the rapid generation and selection of heterogeneity in a genomic RNA population replicating in plants.

Base Sequence↗
PubMed2000

[Evolution of hepatitis G in children with vertically transmitted HGV]

Background A new hepatitis-associated RNA virus, belonging to the Flaviviridae, has been recently discovered and called HGV (GBV-C). This virus has been shown to be transmitted parenterally. In this study we examined a group of children born to HCV infected women. Methods Between September 1994 and December 1998, we studied a cohort of 53 pregnant women, aged between 20 and 43 years. They were all HCV Ab and HCV RNA positive, with a diagnosis of chronic hepatitis. One patient was HbsAg positive and 4 patients (pts.) (7.5%) were HIV Ab positive. Anamnestic information revealed that: 28 pts. (52.8%) were IVDUs, 11 pts. (20.8%) had been haemotransfused and 14 pts. (26.4%) had no risk factors. We examined HGV RNA by RT nested PCR, using primers from the 5'UTR of HGV. Anti-HGV antibodies (anti-E2) were detected with an ELISA test using recombinant E2 protein. Ten of the 53 pregnant women (18.9%) were HGV RNA positive (32 other pts., 60.4%, were positive for anti-E2 antibodies). We monitored their children for 18-24 months (with clinicai and haematological controls), looking for HGV RNA, anti-E2 antibodies, HCV RNA and for ALT serum levels. Results Seven (70%) new-bom children proved HGV RNA positive at follow-up; all babies were HCV RNA negative at controls. Four of them were born vaginally; none of them was breast-fed. HGV RNA was first detectable at the 3rd month of life in 3 babies, and all babies were HGV RNA positive at the 6th month of life. Six babies (85.7%) remained positive during the observation period. One baby (14.3%) seroconverted at 10 months, developing anti E-2 antibodies and becoming HGV RNA negative. Four babies (57.1%) maintained normal ALT serum levels during the whole follow-up period, while 3 patients showed a low increase in ALT serum levels. The ALT values normalised at later controls. Conclusions HGV infection shows a very high (70%) rate of vertical transmission but a low and doubtful pathogenicity with asymptomatic evolution in babies. Patients who did not develop anti-E2 antibodies at the 12th month of life remained infected without persistent signs of hepatic failure.

Journal Article↗
PubMed1990

The polymerase gene of corona- and toroviruses: evidence for an evolutionary relationship.

In this paper we demonstrate that the organization of the polymerase gene of toroviruses and coronaviruses is similar. The polymerase gene of both virus families consists of at least two large ORFs (1a and 1b). Four domains of conserved amino acid sequences have been identified in nearly identical positions in the 3' ORF of the pol gene of toroviruses and coronaviruses. The most 3' conserved domain which is still unique for these viruses encodes a 33-kDA protein in MHV-A59, which is cleaved from a precursor protein. Expression of ORF1b of the pol gene of both virus families occurs by ribosomal frameshifting. A predicted stem-loop structure and pseudoknot are conserved in the ORF1a/ORF1b overlap of toro- and coronaviruses. On the basis of these results we postulate that toro- and coronaviruses are ancestrally more related to each other than to other families of positive stranded RNA viruses.

Amino Acid Sequence↗
PubMed2004

Modelling HIV-RNA viral load in vertically infected children.

Human immunodeficiency virus (HIV) ribo-nucleic acid (RNA) viral load is a measure of actively replicating virus and is used as a marker of disease progression. For a thorough understanding of the dynamics of the evolution of the virus in the early life of HIV-1 vertically infected children, it is important to elucidate the pattern of HIV-RNA viral load over age. An aspect of assay systems used in the quantification of RNA viral load is that they measure values above particular cut-off values for detection, below which the assays used are not sufficiently sensitive. In this way, measurements are potentially left-censored. Recent adult studies suggest that to adequately model RNA pattern over age, it is necessary to account for within-subject correlation, due to repeated measures, and censoring. The aim of this study, therefore, was to establish whether it is necessary to use complex methods to allow for repeated measures within individuals and censoring of the HIV-RNA viral load in children enrolled in a cohort study. The approach involved the identification of an appropriate model for the basic pattern of RNA viral load by age and subsequent assessment of various estimation procedures accounting for repeated measures and censoring in different ways. Methods developed by Hughes involving the expectation-maximization (EM) algorithm and the Gibbs sampler were taken as the benchmark for comparison of simpler alternatives. Other approaches considered involve linear mixed-effects and ordinary least squares in which censoring is dealt with informally by taking the cut-off value as absolute or taking the mid-point between cut-off and zero. Fractional polynomials provided a substantially superior approach for modelling the dynamics of viral load over age compared to conventional polynomials or change-point models. Allowing for repeated measures was necessary to improve the power of the likelihood ratio tests required to establish the final model, but methods beyond taking the mid-point for censored values did not further improve the fit. Although Hughes' methodology is the best approach, its implementation is not necessary for the identification of the optimal model.

Algorithms↗
PubMed2005

RNA recombination of hepatitis delta virus in natural mixed-genotype infection and transfected cultured cells.

Most RNA viruses encode their own RNA polymerases for genome replication, and increasing numbers of them appear to be capable of undergoing RNA recombination. Here, we provide the first report of intergenotypic recombination in hepatitis delta virus (HDV), the only animal RNA virus that requires host RNA polymerase(s) for viral replication. In vivo, we analyzed RNA species derived from the serum of a patient with mixed genotype I and genotype IIb HDV infection by using multiple restriction fragment length polymorphism (RFLP) assays and sequence analysis of cloned reverse transcription (RT)-PCR products. Six HDV recombinants were isolated from 101 tested clones, and HDV recombination in this patient was further confirmed by RT-PCR with genotype-specific primer pairs. Analysis of the recombination junctions suggested that the HDV genome rearrangement occurred through faithful homologous recombination. We then used an RNA cotransfection cell culture system to investigate HDV RNA recombination in vitro. We found that HDV recombinants could indeed be detected in the transfected cells; some of these possessed recombination junctions identical to those identified in vivo. Furthermore, using a PCR-independent RNase protection assay, we were able to readily identify the recombined HDV RNA species in cultured cells. Taken together, our results demonstrate that HDV RNA recombination occurs in both natural HDV infections and cultured cells, thereby presenting a novel mechanism for HDV evolution.

Amino Acid Sequence↗
PubMed2002

Molecular basis of adaptive convergence in experimental populations of RNA viruses.

Characterizing the molecular basis of adaptation is one of the most important goals in modern evolutionary genetics. Here, we report a full-genome sequence analysis of 21 independent populations of vesicular stomatitis ribovirus evolved on the same cell type but under different demographic regimes. Each demographic regime differed in the effective viral population size. Evolutionary convergences are widespread both at synonymous and nonsynonymous replacements as well as in an intergenic region. We also found evidence for epistasis among sites of the same and different loci. We explain convergences as the consequence of four factors: (1) environmental homogeneity that supposes an identical challenge for each population, (2) structural constraints within the genome, (3) epistatic interactions among sites that create the observed pattern of covariation, and (4) the phenomenon of clonal interference among competing genotypes carrying different beneficial mutations. Using these convergences, we have been able to estimate the fitness contribution of the identified mutations and epistatic groups. Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations.

Epistasis, Genetic↗
PubMed1998

The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily.

BACKGROUND: Tobacco ringspot virus (TRSV) is a member of the nepovirus genus of icosahedral RNA plant viruses that cause disease in fruit crops. Nepoviruses, comoviruses and picornaviruses are classified in the picornavirus superfamily. Crystal structures of comoviruses and picornaviruses and the molecular mass of the TRSV subunit (sufficient to accommodate three beta-barrel domains) suggested that nepoviruses may represent a link in the evolution of the picornavirus capsids from a T = 3 icosahedral virus. This evolutionary process is thought to involve triplication of the capsid protein gene, to encode a three-domain polyprotein, followed by development of cleavage sites in the interdomain linking regions. Structural studies on TRSV were initiated to determine if the TRSV subunit corresponds to the proposed uncleaved three-domain polyprotein. RESULTS: The 3.5 A resolution structure of TRSV shows that the capsid protein consists of three beta-barrel domains covalently linked by extended polypeptides. The order of connectivity of the domains in TRSV confirms the proposed connectivity for the precleaved comovirus and picornavirus capsid polyprotein. Structural differences between equivalent domains in TRSV and comoviruses are confined to the external surface loops, interdomain connecting polypeptides and N termini. The three different domains within TRSV and comoviruses are more closely related at the structural level than the three individual domains within picornaviruses. CONCLUSIONS: The structural results confirm the notion of divergent evolution of the capsid polyproteins of nepoviruses, comoviruses and picornaviruses from a common ancestor. A number of residues were found to be conserved among various nepoviruses, some of which stabilize the quaternary structure of the three domains in the TRSV capsid protein subunit. Two conserved regions were identified on the external surface of TRSV, however, mutational studies will be needed to understand their functional significance. Nepoviruses transmitted by the same nematode species do not share regions with similar amino acid composition on the viral surface.

Amino Acid Sequence↗
PubMed1979

Wild mouse RNA tumor viruses. A nongenetically transmitted virus group closely related to exogenous leukemia viruses of laboratory mouse strains.

Type-C RNA viruses isolated from wild mice are causative of naturally occurring neoplasia and neurologic diseases. Biochemical and immunologic characterization of this virus group revealed that amphotropic viruses isolated from wild mice trapped in separate geographical areas are indistinguishable, whereas amphotropic and ecotropic viruses naturally infecting the same animal are env gene variants. Molecular hybridization studies established that neither host range variant is endogenous to the Mus musculus genome, although each demonstrates partial nucleotide sequence homology. Wild mouse type-C viruses exhibited much closer molecular and antigenic relatedness to the exogenous virus subgroup (Friend-, Moloney-, and Rauscher-MuLV) than to prototype endogenous viruses isolated from laboratory mouse strains. The evidence indicates that exogenous mouse type-C viruses have been maintained in nature over a long period of evolution as a separate virus group, causative of tumors in mice by a mechanism solely involving their transmission as infectious agents.

Animal Population Groups↗
PubMed2000

RNA structure. Ribozyme evolution at the crossroads.

Molecules that have similar sequences usually adopt the same structures and have the same functions. In his Perspective, Joyce explains that this is not always the case. In a remarkable study (Schultes and Bartel), an RNA sequence has been designed that can adopt two different structures, each with a different catalytic function. Joyce details how this study sheds light on the evolution of enzymes.

Base Pairing↗
PubMed1990

Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 3.

The nucleotide sequence of RNA 3 of two subgroup I strains of cucumber mosaic virus (CMV), Fny-CMV and M-CMV, was determined and compared at both the nucleic acid and protein level with the previously determined, corresponding (partial) sequences of RNA 3 of five other subgroup I strains: C-CMV, D-CMV, I17F-CMV, O-CMV and Y-CMV. Fny-CMV RNA 3 is composed of 2216 nucleotides (nt) and M-CMV RNA 3 2214 nt. Both RNAs contain two open reading frames, the 3a gene and the coat protein gene. These RNAs showed very little nucleotide sequence divergence, either from each other or from the five other subgroup I strains. The nucleotide sequence variation observed was two to 13 differences in the 120 to 123 nt 5' non-translated regions, six to 17 differences in the 840 nt 3a genes, two to 15 differences in the 296 to 299 nt intergenic regions, three to 25 differences in the 657 nt coat protein genes and two to 10 differences in the 299 to 303 nt 3' non-translated regions. Protein sequence similarity was also high, with one to four differences in the 279 amino acids of the 3a proteins and two to 13 differences in the 218 amino acids of the coat proteins. Limited nucleotide sequence variation among nine strains of CMV was also shown using an RNA protection assay and a probe specific for Fny-CMV RNA 3. The limited variation shown by RNA 3 of strains of CMV with different passage histories, isolated in different countries over a 50 year period, suggests that the maintenance of the highly conserved nucleotide sequence may be important for other viral RNA functions or interactions.

Amino Acid Sequence↗
PubMed2006

Cardiovirus leader proteins are functionally interchangeable and have evolved to adapt to virus replication fitness.

The leader (L) proteins encoded by picornaviruses of the genus Cardiovirus [Theiler's murine encephalomyelitis virus (TMEV) and Encephalomyocarditis virus (EMCV)] are small proteins thought to exert important functions in virus-host interactions. The L protein of persistent TMEV strains was shown to be dispensable for virus replication in vitro, but crucial for long-term persistence of the virus in the central nervous system of the mouse. The phenotype of chimeric viruses generated by exchanging the L-coding regions was analysed and it was shown that the L proteins of neurovirulent and persistent TMEV strains are functionally interchangeable in vitro and in vivo, despite the fact that L is the second most divergent protein encoded by these viruses after the L* protein. The L protein encoded by EMCV and Mengo virus (an EMCV strain) shares about 35 % amino acid identity with that of TMEV. It differs from the latter by lacking a serine/threonine-rich C-terminal domain and by carrying phosphorylated residues not conserved in the TMEV L protein. Our data show that, in spite of these differences, the L protein of Mengo virus shares, with that of TMEV, the ability to inhibit the transcription of type I interferon, cytokine and chemokine genes and to interfere with nucleocytoplasmic trafficking of host-cell proteins. Interestingly, analysis of viral RNA replication of the recombinant viruses raised the hypothesis that L proteins of TMEV and EMCV diverged during evolution to adapt to the different replication fitness of these viruses.

Adaptation, Physiological↗
PubMed2005

Foot-and-mouth disease virus evolution: exploring pathways towards virus extinction.

Foot-and-mouth disease virus (FMDV) is genetically and phenotypically variable. As a typical RNA virus, FMDV follows a quasispecies dynamics, with the many biological implications of such a dynamics. Mutant spectra provide a reservoir of FMDV variants, and minority subpopulations may become dominant in response to environmental demands or as a result of statistical fluctuations in population size. Accumulation of mutations in the FMDV genome occurs upon subjecting viral populations to repeated bottleneck events and upon viral replication in the presence of mutagenic base or nucleoside analogs. During serial bottleneck passages, FMDV survive during extended rounds of replication maintaining low average relative fitness, despite linear accumulation of mutations in the consensus genomic sequence. The critical event is the occurrence of a low frequency of compensatory mutations. In contrast, upon replication in the presence of mutagens, the complexity of mutant spectra increases, apparently no compensatory mutations can express their fitness-enhancing potential, and the virus can cross an error threshold for maintenance of genetic information, resulting in virus extinction. Low relative fitness and low viral load favor FMDV extinction in cell culture. The comparison of the molecular basis of resistance to extinction upon bottleneck passage and extinction by enhanced mutagenesis is providing new insights in the understanding of quasispecies dynamics. Such a comparison is contributing to the development of new antiviral strategies based on the transition of viral replication into error catastrophe.

Biological Evolution↗
PubMed1998

In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system.

BACKGROUND: One of the key issues in the investigation of evolution is how complex systems evolved from simple chemical replicators. Theoretical work proposed several models in which complex replicating systems are kinetically stabilized. The development of powerful isothermal amplification technique allows complex nucleic acid based evolving in vitro systems to be set up, which may then serve to verify experimentally current theories of evolution. Recently such a system based on the 3SR (self-sustained sequence replication) reaction has been established to investigate the evolution of cooperation: the trans-cooperatively coupled CATCH (cooperative amplification by cross hybridization). RESULTS: Over four rounds of serial transfer, the cooperatively coupled two species CATCH system evolved into a more complex cooperative four species system, which then was overgrown by CATCH-derived RNA-Z-like hairpin species. In contrast to the classical RNA-Z species, these molecules have complementary loop sequences and self-amplify using a dual mechanism that includes concentration-dependent phases of noncooperative and cooperative amplification. CONCLUSIONS: The evolution of a cooperative system, under conditions that were alternately unfavorable and favorable for cooperative amplification, led to a system showing facultative cooperation. This principle of facultative cooperation preserves the complexity of the system investigated and could have general implications for the evolution and stabilization of cooperation under oscillating reaction conditions.

Alfalfa mosaic virus↗
PubMed1999

Porcine reproductive and respiratory syndrome virus comparison: divergent evolution on two continents.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a recently described arterivirus responsible for disease in swine worldwide. Comparative sequence analysis of 3'-terminal structural genes of the single-stranded RNA viral genome revealed the presence of two genotypic classes of PRRSV, represented by the prototype North American and European strains, VR-2332 and Lelystad virus (LV), respectively. To better understand the evolution and pathogenicity of PRRSV, we obtained the 12,066-base 5'-terminal nucleotide sequence of VR-2332, encoding the viral replication activities, and compared it to those of LV and other arteriviruses. VR-2332 and LV differ markedly in the 5' leader and sections of the open reading frame (ORF) 1a region. The ORF 1b sequence was nearly colinear but varied in similarity of proteins encoded in identified regions. Furthermore, molecular and biochemical analysis of subgenomic mRNA (sgmRNA) processing revealed extensive variation in the number of sgmRNAs which may be generated during infection and in the lengths of noncoding sequence between leader-body junctions and the translation-initiating codon AUG. In addition, VR-2332 and LV select different leader-body junction sites from a pool of similar candidate sites to produce sgmRNA 7, encoding the viral nucleocapsid protein. The presence of substantial variations across the entire genome and in sgmRNA processing indicates that PRRSV has evolved independently on separate continents. The near-simultaneous global emergence of a new swine disease caused by divergently evolved viruses suggests that changes in swine husbandry and management may have contributed to the emergence of PRRS.

5' Untranslated Regions↗