The Evolution of Vp1 Gene in Enterovirus C Species Sub-Group That Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

Genus Enterovirus (Family Picornaviridae,) consists of twelve species divided into genetically diverse types by their capsid protein VP1 coding sequences. Each enterovirus type can further be divided into intra-typic sub-clusters (genotypes). The aim of this study was to elucidate what leads to the emergence of novel enterovirus clades (types and genotypes). An evolutionary analysis was conducted for a sub-group of Enterovirus C species that contains types Coxsackievirus A21 (CVA-21), CVA-24, Enterovirus C95 (EV-C95), EV-C96 and EV-C99. VP1 gene datasets were collected and analysed to infer the phylogeny, rate of evolution, nucleotide and amino acid substitution patterns and signs of selection. In VP1 coding gene, high intra-typic sequence diversities and robust grouping into distinct genotypes within each type were detected. Within each type the majority of nucleotide substitutions were synonymous and the non-synonymous substitutions tended to cluster in distinct highly polymorphic sites. Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. Despite robust clustering to intra-typic genotypes, only few genotype-specific ‘signature’ amino acids were detected. In contrast, when different enterovirus types were compared, there was a clear tendency towards fixation of type-specific ‘signature’ amino acids. The results suggest that permanent fixation of type-specific amino acids is a hallmark associated with evolution of different enterovirus types, whereas neutral evolution and/or (frequency-dependent) positive selection in few highly polymorphic amino acid sites are the dominant forms of evolution when strains within an enterovirus type are compared.     

Evolutionary Dynamics and Temporal/Geographical Correlates of Recombination in the Human Enterovirus Echovirus Types 9, 11, and 30

The relationship between virus evolution and recombination in species B human enteroviruses was investigated through large-scale genetic analysis of echovirus type 9 (E9) and E11 isolates (n = 85 and 116) from 16 European, African, and Asian countries between 1995 and 2008. Cluster 1 E9 isolates and genotype D5 and A E11 isolates showed evidence of frequent recombination between the VP1 and 3Dpol regions, the latter falling into 23 (E9) and 43 (E11) clades interspersed phylogenetically with 46 3Dpol clades of E30 and with those of other species B serotypes. Remarkably, only 2 of the 112 3Dpol clades were shared by more than one serotype (E11 and E30), demonstrating an extremely large and genetically heterogeneous recombination pool of species B nonstructural-region variants. The likelihood of recombination increased with geographical separation and time, and both were correlated with VP1 divergence, whose substitution rates allowed recombination half-lives of 1.3, 9.8, and 3.1 years, respectively, for E9, E11, and E30 to be calculated. These marked differences in recombination dynamics matched epidemiological patterns of periodic epidemic cycles of 2 to 3 (E9) and 5 to 6 (E30) years and the longer-term endemic pattern of E11 infections. Phylotemporal analysis using a Bayesian Markov chain Monte Carlo method, which placed recombination events within the evolutionary reconstruction of VP1, showed a close relationship with VP1 lineage expansion, with defined recombination events that correlated with their epidemiological periodicity. Whether recombination events contribute directly to changes in transmissibility that drive epidemic behavior or occur stochastically during periodic population bottlenecks is an unresolved issue vital to future understanding of enterovirus molecular epidemiology and pathogenesis.Human enteroviruses (HEV) are single-stranded, positive-sense RNA viruses in the virus family Picornaviridae. Infections with these viruses are enterically transmitted and normally cause subclinical or mild symptoms, but they are also capable of causing a wide array of often severe disease presentations, including aseptic meningitis, encephalitis, and acute flaccid paralysis. Echovirus type 9 (E9) and E11 are serotypes of species B enteroviruses and are among the most common etiological agents of aseptic meningitis (14). The first epidemiological study of E9 investigated isolates obtained from sick children in 1995 (24). E9 is chiefly associated with mild infections affecting children over the age of 5 years and teenagers, although it can cause more severe syndromes in neonates and immunosuppressed patients (14). E11 infections, which predominantly affect infants less than 1 year old, have been associated with large outbreaks of uveitis in infants (15, 21), sepsis, and other neonatal systemic illnesses with high mortality rates (14, 23).Circulating strains and genotypes of E9 (2, 8, 11, 14) and E11 (4, 7, 21) have been characterized in many different countries through analysis of the structural genome regions, principally VP1. In common with other mammalian RNA viruses, both E9 and E11 show rapid accumulation of nucleotide substitutions over time, but their epidemiologies are distinct. E9 is associated with widespread, large-scale seasonal outbreaks and displays a regular epidemic pattern of outbreaks occurring approximately every 3 years (8, 14). Outbreaks of E11 are less common, occur irregularly, and often last for several years (14, 25).In contrast to time-related diversification observed in the capsid-encoding regions of the HEV genome, nonstructural region genes are subject to frequent recombination (7, 18, 19, 26, 30), leading to the concept of separate, modular evolution of the structural and nonstructural regions of the HEV genome (20). Recombination in the nonstructural gene region of HEV is limited to members of the same species (27). In a recent large-scale investigation of echovirus type 30 (E30) molecular epidemiology, phylogenetic analysis of the 3Dpol region revealed the existence of a number of discrete, bootstrap-supported clades, allowing circulating E30 variants to be classified into a series of distinct recombinant forms (RFs) (22). Individual RFs became very rapidly disseminated over large geographical distances through repeated cycles of emergence, dominance, and disappearance in a 3- to 5-year cycle.In the current study, we carried out parallel investigations of the molecular epidemiology and evolution of clinically presenting isolates of E9 and E11 collected in 16 countries in Europe, central Asia, Southeast Asia, and West Africa over a 14-year period. By comprehensive sequencing of these isolates in the structural (VP1) and nonstructural (3Dpol) genome regions, it was possible to explore the dynamics of sequence diversification and recombination. The turnover of individual recombinant groups and the phylogeographical correlates of recombination were determined and compared to those of E30, providing new insights into the nature of the global spread of these important viral pathogens and the role of recombination in enteroviral evolution.     

Epidemics and Frequent Recombination within Species in Outbreaks of Human Enterovirus B-Associated Hand,Foot and Mouth Disease in Shandong China in 2010 and 2011

The epidemiology and molecular characteristics of human enterovirus B (HEV-B) associated with hand, foot and mouth disease (HFMD) outbreaks in China are not well known. In the present study, we tested 201 HEV isolates from 233 clinical specimens from patients with severe HFMD during 2010–2011 in Linyi, Shandong, China. Of the 201 isolates, 189 were fully typed and 18 corresponded to HEV-B species (six serotypes CVA9, CVB1, CVB4, Echo 6, Echo 25 and Echo 30) using sensitive semi-nested polymerase chain reaction analysis of VP1 gene sequences. Phylogenetic analysis based on the VP1 region showed that eight E30SD belonged to a novel sub-genogroup D2; E25SD belonged to a novel sub-genogroup D6; E6SD belonged to sub-lineage C6 and five CVB1SD belonged to subgroup 4C; and B4SD belonged sub-lineage D2. The full viral genomes of the CVB1SD, E6SD, E25SD and E30SD isolates were sequenced. Analysis of phylogenetic and similarity plots indicated that E25SD recombined with E25-HN-2, E30FDJS03 and E4AUS250 at noncontiguous P2A–P3D regions, while E30SD, E30FDJ03, E25-HN-2 and E9 DM had shared sequences in discrete regions of P2 and P3. Both E6SD and B1SD shared sequences with E1-HN, B4/GX/10, B5-HN, and A9-Alberta in contiguous regions of most of P2 and P3. Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points. In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup. Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.     

Whole Genomic Sequence and Replication Kinetics of a New Enterovirus C96 Isolated from Guangdong,China with a Different Cell Tropism

Enterovirus 96 (EV-C96) is a newly described serotype within the enterovirus C (EV-C) species, and its biological and pathological characters are largely unknown. In this study, we sequenced the whole genome of a novel EV-C96 strain that was isolated in 2011 from a patient with acute flaccid paralysis (AFP) in Guangdong province, China and characterized the properties of its infection. Sequence analysis revealed the close relationship between the EV-C96 strains isolated from the Guangdong and Shandong provinces of China, and suggested that recombination events occurred both between these EV-C96 strains and with other EV-C viruses. Moreover, the virus replication kinetics showed EV-C96 Guangdong strain replicated at a high rate in RD cells and presented a different cell tropism to other strains isolated from Shandong recently. These findings gave further insight into the evolutionary processes and extensive biodiversity of EV-C96.     

Species Diversity, Biogeography, and the Evolution of Biotas

SYNOPSIS. A central scientific problem for ecologists and systematistshas been to explain spatiotemporal patterns of species diversity.One aspect of this question is how to understand the taxonomicassembly of biotas and their included ecosystems and communities.Four processes add or subtract species from a region: speciation,extinction, biotic dispersion, and long-distance dispersal.Speciation and biotic dispersion are postulated to result inhistorically structured (hierarchical) species assemblages,whereas long-distance dispersal results in assemblages thatwould be expected to be historically unstructured (nonhierarchical).Continental biotas, as exemplified by the Australian avifauna,are historically structured: they are segregated into areasof endemism having hierarchical relationships that presumablyarose as a result of their history being dominated by cyclesof biotic dispersion and vicariance. It is also proposed thatthese latter two processes are necessary, and in many casesprobably sufficient, to explain the taxonomic composition ofcommunities within these areas of endemism. Long-distance dispersalappears to play a much more minor role in the assembly of eithercontinental biotas or their communities than current ecologicaltheory would predict.     

First Detection of an Enterovirus C99 in a Captive Chimpanzee with Acute Flaccid Paralysis,from the Tchimpounga Chimpanzee Rehabilitation Center,Republic of Congo

Enteroviruses, members of the Picornaviridae family, are ubiquitous viruses responsible for mild to severe infections in human populations around the world. In 2010 Pointe-Noire, Republic of Congo recorded an outbreak of acute flaccid paralysis (AFP) in the humans, caused by wild poliovirus type 1 (WPV1). One month later, in the Tchimpounga sanctuary near Pointe-Noire, a chimpanzee developed signs similar to AFP, with paralysis of the lower limbs. In the present work, we sought to identify the pathogen, including viral and bacterial agents, responsible for this illness. In order to identify the causative agent, we evaluated a fecal specimen by PCR and sequencing. A Human enterovirus C, specifically of the EV-C99 type was potentially responsible for the illness in this chimpanzee. To rule out other possible causative agents, we also investigated the bacteriome and the virome using next generation sequencing. The majority of bacterial reads obtained belonged to commensal bacteria (95%), and the mammalian virus reads matched mainly with viruses of the Picornaviridae family (99%), in which enteroviruses were the most abundant (99.6%). This study thus reports the first identification of a chimpanzee presenting AFP most likely caused by an enterovirus and demonstrates once again the cross-species transmission of a human pathogen to an ape.     

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.     

Linkage Between Virulence Genes, Compatibility Types and Sexual Recombination in the Swedish Population of Bremia lactucae

The host pathogen interaction between Lactuca sativa and Bremia lactucae fits a gene-for-gene model well. Twelve resistance genes of the host are matched by twelve genes for virulence in the pathogen. The evolution of the parasite involves drastic changes in virulence frequencies, and a great diversity in virulence even on a sub-poipulation level. Bremia is a heterothallic, obligate parasite, in which presence of two mating types is needed for sexual reproduction. Sexual recombination probably occurs frequently, indicated by simultaneous occurrence of mating types in commercial lettuce crops, zygote formation, and sufficiently high oospore germination. The pattern of variation agrees well with that of a diploid, out- crossing organism with frequent sexual recombination. Unexpected high frequencies of some of the unnecessary v-genes are probably due to genetic linkage with another "necessary" v-gene.     

The Role of Recombination in the Origin and Evolution of Alu Subfamilies

Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.     

Multilocus Evolution in Fire Ants: Effects of Selection, Gene Flow and Recombination

The reproductive success of individual fire ant queens (Solenopsis invicta) previously has been shown to be strongly influenced by their genotype at a single enzyme-encoding gene, designated Pgm-3. This paper presents evidence that a second, tightly linked gene, designated Gp-9, is under similarly strong selection in these ants. Selection appears to act independently on the two genes and is detectable in only one of the two social forms of this species (the ``polygyne' social form, in which nests contain multiple fertile queens). Strong directional selection on Pgm-3 in this form involves worker destruction of all queens with genotype Pgm-3(AA) before they reproduce. Selection on Gp-9 is more complex, involving both lethality of all Gp-9(bb) females and a strong or even complete survival advantage to reproductive queens with the heterozygous genotype Gp-9(Bb). Pgm-3 and Gp-9 are tightly linked (r(f) = 0.0016) and exhibit strong gametic phase disequilibrium in introduced populations in the U.S. This disequilibrium seems not to have stemmed from the founder event associated with the introduction, because the same associations of alleles found in the U.S. apparently occur also in two native populations in Argentina. Rather, selection acting independently on Pgm-3 and Gp-9, in conjunction with gene flow from the alternate, ``monogyne' social form (in which nests contain a single fertile queen), may explain the origin of disequilibrium between the two loci in polygyne fire ants.     

Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee,Apis mellifera

Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution.     

Co-Circulation and Genomic Recombination of Coxsackievirus A16 and Enterovirus 71 during a Large Outbreak of Hand,Foot, and Mouth Disease in Central China

A total of 1844 patients with hand, foot, and mouth disease (HFMD), most of them were children of age 1–3-year-old, in Central China were hospitalized from 2011 to 2012. Among them, 422 were infected with coxsackievirus A16 (CVA16), 334 were infected with enterovirus 71 (EV71), 38 were co-infected with EV71 and CVA16, and 35 were infected with other enteroviruses. Molecular epidemiology analysis revealed that EV71 and CVA16 were detected year-round, but EV71 circulated mainly in July and CVA16 circulated predominantly in November, and incidence of HFMD was reduced in January and February and increased in March. Clinical data showed that hyperglycemia and neurologic complications were significantly higher in EV71-infected patients, while upper respiratory tract infection and C-reactive protein were significantly higher in CVA16-associated patients. 124 EV71 and 80 CVA16 strains were isolated, among them 56 and 68 EV71 strains were C4a and C4b, while 25 and 55 CVA16 strains were B1a and B1b, respectively. Similarity plots and bootscan analyses based on entire genomic sequences revealed that the three C4a sub-genotype EV71 strains were recombinant with C4b sub-genotype EV71 in 2B–2C region, and the three CVA16 strains were recombinant with EV71 in 2A–2B region. Thus, CVA16 and EV71 were the major causative agents in a large HFMD outbreak in Central China. HFMD incidence was high for children among household contact and was detected year-round, but outbreak was seasonal dependent. CVA16 B1b and EV71 C4b reemerged and caused a large epidemic in China after a quiet period of many years. Moreover, EV71 and CVA16 were co-circulated during the outbreak, which may have contributed to the genomic recombination between the pathogens. It should gain more attention as there may be an upward trend in co-circulation of the two pathogens globally and the new role recombination plays in the emergence of new enterovirus variants.     

13C,Ontogeny, and the Paradox of Evolution

The accurate reading of two variants of genetic informatio n is mandatory to perform the ontogenetic program in highly organized multicellular organisms. Physicochemical differences between different portions of the cytoplasm of an egg are insufficient to discriminate these variants. A.A. Ivanov has shown that the formation of differences in the ¹³C isotope content of the DNA copies at early embryological stages is essential for the successful completion of development. Consideration of this fact and the fifth fundamental interaction (the interaction of the spins of macroscopic objects) sheds light on the tremendous delay of the Cambrian explosion.

     

Isolation of the Photoactive Reaction Center Complex that Contains Three Types of Fe-S Centers and a Cytochrome c Subunit from the Green Sulfur Bacterium Chlorobium limicola f. thiosulfatophilum, Strain Larsen

The photoactive reaction center (RC) complex from the greensulfur bacterium Chlorobium limicola f. thiosulfatophilum, strainLarsen, was isolated after solubilization and ammonium sulfatefractionation followed by ion-exchange chromatography. The spectrumof the complex was almost identical with that of the similarRC complex isolated by Feiler et al. [(1992) Biochemistry 31:2608–2614] except for the presence of cytochrome c₅₅₁instead of c₅₅₃ in the latter study. A molecular ratio of BChla to P840 of the isolated RC complex was assayed to be 25–35.SDSPAGE analysis revealed that the isolated complex containedthree major polypeptides with apparent molecular masses of 68,41 and 21 kDa, respectively. The 21-kDa polypeptide was identifiedto be a heme-binding protein by staining the gel for peroxidaseactivity. The cytochrome c₅₅₁ was oxidized by flash light ina biphasic manner with half times of 90 and 390 µs, respectively,that coincided with the reduction half times of P840⁺. Threedistinct iron-sulfur centers assigned to F_A, F_B and F_x, respectively,from their g-values were detected by EPR spectroscopy at cryogenictemperature. These results suggest that the present preparationcontains a minimal functional unit of the RC of this bacterium,and that this complex appears to lie on a evolutionary linebetween RC's of purple bacteria and photosystem I. (Received August 18, 1992; Accepted October 28, 1992)