There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to ...eukaryotes.
A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage.Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events.RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variability.For each program, results can be plotted in real time during analysis through an integrated graphics package, providing publication quality graphs. Results can be also directed to tabulated datafiles for import into spreadsheet or database programs for further analysis.
SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research.
In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of ...host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus-host interactions may represent key components in establishing its 'ecological niche' in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.
Recent discoveries of contemporary genotypes of hepatitis B virus and parvovirus B19 in ancient human remains demonstrate that little genetic change has occurred in these viruses over 4,500-6,000 ...years. Endogenous viral elements in host genomes provide separate evidence that viruses similar to many major contemporary groups circulated 100 million years ago or earlier. In this Opinion article, we argue that the extraordinary conservation of virus genome sequences is best explained by a niche-filling model in which fitness optimization is rapidly achieved in their specific hosts. Whereas short-term substitution rates reflect the accumulation of tolerated sequence changes within adapted genomes, longer-term rates increasingly resemble those of their hosts as the evolving niche moulds and effectively imprisons the virus in co-adapted virus-host relationships. Contrastingly, viruses that jump hosts undergo strong and stringent adaptive selection as they maximize their fit to their new niche. This adaptive capability may paradoxically create evolutionary stasis in long-term host relationships. While viruses can evolve and adapt rapidly, their hosts may ultimately shape their longer-term evolution.
Poliovirus is known to most people in the world as the cause of polio, a devastating paralytic disease from the past. Success in polio eradication has understandably translated into stricter ...containment plans for poliovirus, coordinated by WHO. In this Personal View, we discuss the impact of recent biosafety level 3+ guidelines for handling potential poliovirus-containing diagnostic specimens, which has resulted in closure of many national WHO poliovirus reference laboratories. This reduction in laboratory capacity has a knock-on effect of capability to detect and characterise non-polio enteroviruses in samples obtained from patients with neurological symptoms. The development is of concern given the widespread circulation of non-polio enteroviruses, their role as the most common cause of meningitis worldwide, and their involvement in other severe neurological conditions, such as acute flaccid myelitis and encephalitis. These disease presentations have increased substantially in the past decade, and have been associated with major outbreaks of enterovirus D68 and enterovirus A71, leaving many who survived with lasting paralysis and disabilities. To address this growing gap in diagnostic and surveillance capability, we have established the European Non-Poliovirus Enterovirus Network (also known as ENPEN) as a supra-national, non-commercial, core reference consortium. Our consortium will develop, test, and implement generic surveillance platforms for non-polio enteroviruses and other emerging viral diseases.
Tall (taller than 300 ft 91m), supertall (taller than 984 ft 300 m), and megatall (taller than 1968 ft 600 m) buildings present unique and formidable challenges to architects and engineers because of ...their size, location in major urban areas, and the multiple, complex occupancies they often contain. The Second Edition of this book is a unique reference for owners; architects; and mechanical, structural, and electrical engineers as well as other specialized consultants involved in designing systems for these buildings. Expanded since the first edition published in 2015, this new design guide covers broadened scope and updated content that reflects current standards and industry practices, including major sections on architectural design, indoor air quality (IAQ) and thermal comfort, vertical transportation, life safety, residential occupancy needs, and intelligent buildings and controls, Also included are appendices with examples documenting climatic calculation for four representative climates, energy analysis, and HVAC design criteria and systems descriptions for a multiple-tenant office building. There are also nine new case studies illustrating real-world tall buildings across the globe.
In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species
, family
) for which complete genome sequences are available (Smith
., 2016). ...This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.
The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus ...descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data.
The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called 'Genome Relationships Applied to Virus Taxonomy' (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy.
A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.
Role of atmospheric oxidation in recent methane growth Rigby, Matthew; Montzka, Stephen A.; Prinn, Ronald G. ...
Proceedings of the National Academy of Sciences - PNAS,
05/2017, Volume:
114, Issue:
21
Journal Article
Peer reviewed
Open access
The growth in global methane (CH₄) concentration, which had been ongoing since the industrial revolution, stalled around the year 2000 before resuming globally in 2007. We evaluate the role of the ...hydroxyl radical (OH), the major CH₄ sink, in the recent CH₄ growth. We also examine the influence of systematic uncertainties in OH concentrations on CH₄ emissions inferred from atmospheric observations. We use observations of 1,1,1-trichloroethane (CH₃CCl₃), which is lost primarily through reaction with OH, to estimate OH levels as well as CH₃CCl₃ emissions, which have uncertainty that previously limited the accuracy of OH estimates. We find a 64–70% probability that a decline in OH has contributed to the post-2007 methane rise. Our median solution suggests that CH₄ emissions increased relatively steadily during the late 1990s and early 2000s, after which growth was more modest. This solution obviates the need for a sudden statistically significant change in total CH₄ emissions around the year 2007 to explain the atmospheric observations and can explain some of the decline in the atmospheric 13CH₄/12CH₄ ratio and the recent growth in C₂H₆. Our approach indicates that significant OH-related uncertainties in the CH₄ budget remain, and we find that it is not possible to implicate, with a high degree of confidence, rapid global CH₄ emissions changes as the primary driver of recent trends when our inferred OH trends and these uncertainties are considered.
The Flaviviridae is a family of small enveloped viruses with RNA genomes of 9000-13 000 bases. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C ...virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g. yellow fever virus, dengue virus). This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) report on the taxonomy of the Flaviviridae, which is available at www.ictv.global/report/flaviviridae.
The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive ...fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, proposed to be driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 36 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including
Picornaviridae
,
Flaviviridae
,
Matonaviridae
,
Caliciviridae
and
Coronaviridae
) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x–7.5x), with a consistently observed favoured 5’ U upstream context. The presence of genome scale RNA secondary structure (GORS) was the only other genomic or structural parameter significantly associated with C->U/U->C transition asymmetries by multivariable analysis (ANOVA), potentially reflecting RNA structure dependence of sites targeted for C->U mutations. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, potentially paralleling extensive homoplasy of this transition reported in SARS-CoV-2. Although mechanisms remain to be functionally characterised, excess C->U substitutions accounted for 11–14% of standing sequence variability of structured viruses and may therefore represent a potent driver of their sequence diversification and longer-term evolution.
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