Influence of mutagenesis and viral load on the sustained low-level replication of an RNA virus

Lethal mutagenesis is an antiviral strategy that aims to extinguish viruses as a consequence of enhanced mutation rates during virus replication. The molecular mechanisms that underlie virus extinction by mutagenic nucleoside analogues are not well understood. When mutagenic agents and antiviral inhibitors are administered sequentially or in combination, interconnected and often conflicting selective constraints can influence the fate of the virus either towards survival through selection of mutagen-escape or inhibitor-escape mutants or towards extinction. Here we report a study involving the mutagenesis of foot-and-mouth disease virus (FMDV) by the nucleoside analogue ribavirin (R) and the effect of R-mediated mutagenesis on the selection of FMDV mutants resistant to the inhibitor of RNA replication, guanidine hydrochloride (GU). The results show that under comparable (and low) viral load, an inhibitory activity by GU could not substitute for an equivalent inhibitory activity by R in driving FMDV to extinction. Both the prior history of R mutagenesis and the viral population size influenced the selection of GU-escape mutants. A sufficiently low viral load allowed continued viral replication without selection of inhibitor-escape mutants, irrespective of the history of mutagenesis. These observations imply that reductions of viral load as a result of a mutagenic treatment may provide an opportunity either for immune-mediated clearing of a virus or for an alternative antiviral intervention, even if extinction is not initially achieved.     

森林水源涵养功能的多尺度内涵、过程及计量方法

近年来国内森林生态系统服务功能研究较多,但应用价值不高,其科学性受到诸多质疑。从森林水源涵养功能的多尺度内涵、过程以及其计量方法出发,对国内外研究动态和发展趋势进行了总结分析,重新审视森林水源涵养功能的研究意义,探讨森林水源涵养功能的多尺度特征。从森林水源涵养功能作用的空间尺度上看,其拦蓄洪水削减洪峰的功能仅在较小尺度上有效,而调节径流的功能只有当森林土壤的入渗量超过蒸散量时,才可能有更多地下水补给河道径流,进而增加旱季河道流量。同时森林水源涵养功能也具有明显的时间尺度特征,具体表现为在次降水事件中,由于蒸散发量较小,森林水源涵养功能的物质量等于森林不同层次的截留量,在功能上表现为拦蓄降水;在长时间尺度上,由于林地蒸散要耗去大量水分,森林水源涵养功能的物质量等于森林不同层次的截留量减去林地蒸散发量,在功能上表现为净化水质和调节径流。大多数研究仅对单一林分的个别层次蓄水功能进行研究,缺乏流域尺度或者更大空间尺度的森林水源涵养功能研究。建议从区域降尺度到流域或将坡面尺度上推到流域,集中在流域尺度解决森林水源涵养空间异质性将是解决森林水源涵养功能尺度外推的有效办法。就目前国内流行的森林水源涵养功能计量方法而言,其与尺度及研究目的有较大相关性,在研究中应根据研究目的、研究尺度和可获取的数据情况选择合适的计量方法。研究突出了不同尺度作用下森林水文过程的复杂性及重要性,并结合森林与水关系的争论问题,分析目前国内对森林水源涵养功能研究的一些误区,提出森林水源涵养功能研究的一些关键科学问题及未来可能的发展方向,主要包括:1)明确界定森林水源涵养功能的边界,探索森林水源涵养功能计量的新方法;2)加强不同时空尺度关联的森林水源涵养功能研究,包括正确评价森林水源涵养功能的时空变异规律,森林生态系统水源涵养功能的尺度效应,森林水源涵养与下游水生态安全,森林水源涵养研究范式转变等核心问题。     

Phylogenomics and molecular evolution of foot-and-mouth disease virus

This report describes the use of Bayesian methods to analyze polyprotein coding region sequences (n = 217) obtained from GenBank to define the genome-wide phylogeny of foot and mouth disease virus (FMDV). The results strongly supported the monophyly of five FMDV serotypes, O, A, Asia 1, C, and SAT 3, while sequences for the two remaining FMDV serotypes, SAT 1 and SAT 2 did not separate into entirely distinct clades. The phylogenomic tree revealed three sister-group relationships, serotype O + Asia 1, A + C, and SAT 1 + 3 + 2, with a new branching pattern: {[(O, Asia 1), (A, C)], (SAT 1, 2, 3)}. Within each serotype, there was no apparent periodic, geographic, or host species influence on the evolution of global FMDVs. Analysis of the polyprotein coding region of these sequences provided evidence for the influence of purifying selection on the evolution of FMDV. Using a Bayesian coalescent approach, the evolutionary rate of FMDV isolates that circulated during the years 1932-2007 was estimated to be 1.46 × 10(-3) substitutions/site/year, and the most recent common ancestor of the virus existed approximately 481 years ago. Bayesian skyline plot revealed a population expansion in the early 20(th) century that was followed by a rapid decline in population size from the late 20(th) century to the present day. These findings provide new insights into the mechanisms that impact on the evolution of this important livestock pathogen.     

中国口蹄疫病毒同源重组研究

从GenBank数据库中获得在我国分离的16株口蹄疫病毒全基因组序列,进而运用常规的系统发生方法分析了这16株病毒的同源重组情况,发现5株重组毒株．这些重组病毒主要来源于亚洲Ⅰ型(Asia1)和O型病毒间的重组．这些重组事件的鉴定也表明口蹄疫病毒间的交叉感染在我国比较常见．另外,在我国还出现了由于Asia1型和O型病毒重组后导致病毒血清型发生转化的现象．这些结果解释了我国口蹄疫病毒(FMDV)遗传多样性和抗原多变性的成因,提示了我国在口蹄疫预防、治疗方面所面临的复杂局面．     

Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations

RNA viruses are widely used to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more rounds of infection, of which the later ones are at high m.o.i. Here, we develop a model of the competition between wild type (wt) and a mutant under a regime of alternating m.o.i. We assume that the mutant is deleterious when it infects cells on its own, but derives a selective advantage when rare and coinfecting with wt, because it can profit from superior protein products created by the wt. We find that, under these assumptions, replication at alternating low and high m.o.i. may lead to the stable coexistence of wt and mutant for a wide range of parameter settings. The predictions of our model are consistent with earlier observations of frequency-dependent selection in vesicular stomatitis virus and human immunodeficiency virus type 1. Our results suggest that frequency-dependent selection may be common in typical evolution experiments with viruses.     

口蹄疫病毒单克隆抗体的制备及应用研究进展

口蹄疫是严重影响全球政治经济的烈性动物传染病,快速诊断及有效防治对口蹄疫的防控具有重要意义。单克隆抗体具有高特异性、均质、活性单一等优点,在生物医学领域中有广泛用途。目前,国内外学者制备了多种抗口蹄疫病毒的单克隆抗体,并应用于口蹄疫病毒抗原定型、疫苗量化、抗体水平监测、自然感染与疫苗免疫动物的鉴别诊断,以及口蹄疫病毒抗原表位分析等方面。我们简要综述口蹄疫病毒单克隆抗体的制备及应用进展。     

多尺度植物色彩表征及其与人体响应的关系

色彩是人们对植物外观的第一印象,与植物视觉特征和人体响应关系密切,因此,对森林美景度提升和公众适宜性契合具有重要作用。结合色彩学形成的历史关键节点和1个世纪以来植物色彩的研究动态,将植物色彩研究的发展历程划分为萌芽、形成、发展和繁荣等4个阶段,并简介了各阶段的主要特点。同时,从植物器官、植物个体、植物群体(涵盖种群和群落)、整体景观等4个视觉尺度以及审美、生理与心理等3个影响层面,阐述与评价了植物色彩传达机制与人体响应关系的相关研究。在此基础上,围绕植物色彩特征提取中存在的色彩要素定量、特征因子选取、色彩量化方法等方面的不足之处,对未来研究方向进行展望,提出植物色彩尺度与公众响应关系剖析、较大尺度色彩评价因子的深入挖掘、色彩量化方法的多学科融入、公众对植物色彩响应关系综合比对、森林景观美景度提升实践等5个方向的发展趋势,以期为全面地了解植物色彩的传达机制与影响、科学地开展不同精度和尺度下的植物色彩研究提供参考。     

Effect of amino acid mutation at position 127 in 3A of a rabbitattenuated foot-and-mouth disease virus serotype Asia1 on viral replication and infection

An amino acid mutation(R127→I) in the 3A non-structural protein of an FMDV serotype Asia1 rabbit-attenuated ZB strain was previously found after attenuation of the virus. To explore the effects of this mutation on viral replication and infection, the amino acid residue isoleucine(I) was changed to arginine(R) in the infectious cDNA clone of the rabbit-attenuated ZB strain by sitedirected mutagenesis, and the R127-mutated virus was rescued. BHK monolayer cells and suckling mice were inoculated with the R127-mutated virus to test its growth property and pathogenicity, respectively. The effects of the R127 mutation on viral replication and virulence were analyzed. The data showed that there was a slight difference in plaque morphology between the R127-mutated and wild-type viruses. The growth rate of the mutated virus was lower in BHK-21 cells and its virulence in suckling mice was also attenuated. This study indicates that the R127 mutation in 3A may play an important role in FMDV replication in vitro and in pathogenicity in suckling mice.     

Relationships between stream macroinvertebrates and environmental variables at multiple spatial scales

1. Aquatic communities are structured by multiple forces, and identifying the driving factors over multispatial scales is an important research issue. The East Asian monsoon region is globally one of the richest environments in terms of biodiversity, and is undergoing rapid human development, yet the river ecosystems in this region have not been well studied. We applied a hierarchical framework to incorporate regional and local environmental effects on stream macroinvertebrate communities in this region. The knowledge gained is expected to improve the understanding of the importance of spatial scale on regional and local diversity in the East Asian monsoon region. 2. A national data set of benthic macroinvertebrates and environmental variables (geographical, land‐use, hydrological, substratum and physicochemical elements) in Korean rivers was used to determine the habitat preferences of macroinvertebrates. 3. Latitude, proportion of forest coverage, riffle habitat, silt substratum and temperature were the most important determinants for the ordinations of macroinvertebrate communities in each category evaluated by canonical correspondence analysis (CCA). The optimal habitats for stream macroinvertebrates are not the same for all species, and overall community metrics and abundance of sensitive species tended to be lower in open agricultural and urban streams than in forested streams. The sensitivity of mayflies and stoneflies to anthropogenic disturbances implicated them as good indicators to assess the effects of urban and agricultural activities. 4. A partial CCA was used to evaluate the relative importance of macrohabitat and microhabitat variables on community composition at three spatial scales (whole country, the large Han River basin and two small sub‐basins in the lowlands and highlands). The majority of community variation (17–22% for each environmental element) was explained by macrohabitat variables at the regional spatial scale. In contrast, large proportions (15–18%) were explained by microhabitat variables at the local spatial scale. 5. Our findings indicate that the relative importance of habitat scales should be determined by geographical size and that comprehensive understanding of multispatial scale patterns can be important for implementing sound biodiversity conservation programmes.     

Fitness increase of memory genomes in a viral quasispecies

Viral quasispecies may contain a subset of minority genomes that reflect those genomic sequences that were dominant at an early phase of quasispecies evolution. Such minority genomes are referred to as memory in viral quasispecies. A memory marker previously characterized in foot-and-mouth disease virus (FMDV) is an internal oligoadenylate tract of variable length that became dominant upon serial plaque-to-plaque transfers of FMDV clones. During large population passages, genomes with internal oligoadenylate were outcompeted by wild-type revertants but remained in the mutant spectra as memory genomes. Here, we report a quantification of relative fitness of several FMDV clones, harboring internal oligoadenylate tracts of different length, and that were retrieved at early or late times (passage number) after implementation of memory. The results show that for any given length range of the oligoadenylate, maintenance in memory resulted in an increase in relative fitness, comparable to the increase undergone by the entire population. The fitness increase is in agreement with the Red Queen hypothesis, and implies a replicative memory mechanism. Thus, permanence of memory genomes may be a source of high fitness variants despite their initial low fitness, and despite having remained hidden in mutant spectra. This reinforces the interest of diagnosing minority genomes during chronic human and animal viral infections.     

Effect of amino acid mutation at position 127 in 3A of a rabbit-attenuated foot-and-mouth disease virus serotype Asia1 on viral replication and infection

An amino acid mutation(R127→I) in the 3A non-structural protein of an FMDV serotype Asia1 rabbit-attenuated ZB strain was previously found after attenuation of the virus. To explore the effects of this mutation on viral replication and infection, the amino acid residue isoleucine(I) was changed to arginine(R) in the infectious cDNA clone of the rabbit-attenuated ZB strain by sitedirected mutagenesis, and the R127-mutated virus was rescued. BHK monolayer cells and suckling mice were inoculated with the R127-mutated virus to test its growth property and pathogenicity, respectively. The effects of the R127 mutation on viral replication and virulence were analyzed. The data showed that there was a slight difference in plaque morphology between the R127-mutated and wild-type viruses. The growth rate of the mutated virus was lower in BHK-21 cells and its virulence in suckling mice was also attenuated. This study indicates that the R127 mutation in 3A may play an important role in FMDV replication in vitro and in pathogenicity in suckling mice.     

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus

Estimating detailed transmission trees that reflect the relationships between infected individuals or populations during a disease outbreak often provides valuable insights into both the nature of disease transmission and the overall dynamics of the underlying epidemiological process. These trees may be based on epidemiological data that relate to the timing of infection and infectiousness, or genetic data that show the genetic relatedness of pathogens isolated from infected individuals. Genetic data are becoming increasingly important in the estimation of transmission trees of viral pathogens due to their inherently high mutation rate. Here, we propose a maximum-likelihood approach that allows epidemiological and genetic data to be combined within the same analysis to infer probable transmission trees. We apply this approach to data from 20 farms infected during the 2001 UK foot-and-mouth disease outbreak, using complete viral genome sequences from each infected farm and information on when farms were first estimated to have developed clinical disease and when livestock on these farms were culled. Incorporating known infection links due to animal movement prior to imposition of the national movement ban results in the reduction of the number of trees from 41472 that are consistent with the genetic data to 1728, of which just 4 represent more than 95% of the total likelihood calculated using a model that accounts for the epidemiological data. These trees differ in several ways from those constructed prior to the availability of genetic data.     

Genetic variability of New Zealand seagrass (Zostera muelleri) assessed at multiple spatial scales

We conducted RAPD analyses at multiple spatial scales to contribute to the conservation and future restoration of New Zealand's seagrass, Zostera muelleri Irmisch ex Asch. (Zosteraceae). Initially we focused on fine-scale genetic variation within two estuaries on the North Island, one on the East coast the other on the West coast. Within each estuary individuals were genetically similar, however, there was clear genetic separation between the two sites (genetic distance D = 0.2965). Genetic variation within a sampling location (m scale) was similar to that observed among sampling locations (km scale) within a site (21% and 28%, respectively) and smaller than that observed between sites (51%). We then expanded our sampling to include a further six populations distributed across almost the entire latitudinal (ca. 15°) gradient of the North and South Islands. At this scale genetic differences were closely correlated with coastal currents. There was a clear separation between North Island and South Island populations and further separation between the East and West coast populations of each Island. Sites located along the same section of coastline were more genetically similar than those from the opposite coast and other Island. Genetic similarity was highest within each of the sites, indicating a low degree of gene flow between populations. We recommend that any future restoration and conservation projects use only locally eco-sourced materials for population augmentations.     

The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance--a review

We review evidence that cloned (or uncloned) populations of most RNA viruses do not consist of a single genome species of defined sequence, but rather of heterogeneous mixtures of related genomes (quasispecies). Due to very high mutation rates, genomes of a quasispecies virus population share a consensus sequence but differ from each other and from the consensus sequence by one, several, or many mutations. Viral genome analyses by sequencing, fingerprinting, cDNA cloning etc. indicate that most viral RNA populations (quasispecies) contain all possible single and double genomic site mutations and varying proportions of triple, quadruple, etc. site mutations. This quasispecies structure of RNA virus populations has many important theoretical and practical implications because mutations at only one or a few sites may alter the phenotype of an RNA virus.     

Single amino acid substitution of VP1 N17D or VP2 H145Y confers acid-resistant phenotype of type Asia1 foot-and-mouth disease virus

Infection by foot-and-mouth disease virus (FMDV) is triggered by the acidic pH in endosomes after virus uptake by receptor-mediated endocytosis. However, dissociation of the FMDV 146S particle in mildly acidic conditions renders inactivated foot-and-mouth disease (FMD) vaccines much less effective. Type Asia1 FMDV mutants with increased resistance to acid inactivation were selected to study the molecular basis of viral resistance to acid-induced disassembly and improve the acid stability of FMDV. Sequencing of capsid-coding regions revealed four amino acid replacements (VP1 N17D, VP2 H145Y, VP2 G192D, and VP3 K153E) in the viral population of the acid-selected 10th passage. We performed single or combined mutagenesis using a reverse genetic system, and our results provide direct experimental evidence that VP2 H145Y or VP1 N17D substitution confers an acid-resistant phenotype to type Asia1 FMDV.     

Targeting of genomic and negative‐sense strands of viral RNA contributes to antiviral resistance mediated by artificial miRNAs and promotes the emergence of complex viral populations

Technology based on artificial small RNAs, including artificial microRNAs (amiRNAs), exploits natural RNA silencing mechanisms to achieve silencing of endogenous genes or pathogens. This technology has been successfully employed to generate resistance against different eukaryotic viruses. However, information about viral RNA molecules effectively targeted by these small RNAs is rather conflicting, and factors contributing to the selection of virus mutants escaping the antiviral activity of virus‐specific small RNAs have not been studied in detail. In this work, we transformed Nicotiana benthamiana plants with amiRNA constructs designed against the potyvirus plum pox virus (PPV), a positive‐sense RNA virus, and obtained lines highly resistant to PPV infection and others showing partial resistance. These lines have allowed us to verify that amiRNA directed against genomic RNA is more efficient than amiRNA targeting its complementary strand. However, we also provide evidence that the negative‐sense RNA strand is cleaved by the amiRNA‐guided RNA silencing machinery. Our results show that the selection pressure posed by the amiRNA action on both viral RNA strands causes an evolutionary explosion that results in the emergence of a broad range of virus variants, which can further expand in the presence, and even in the absence, of antiviral challenges.