PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses

Bacteriophage Taxonomy: A Continually Evolving Discipline

While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.

Patterns of Genetic Diversity among Alphasatellites Infecting Gossypium Species

Alphasatellites are small single-stranded circular DNA molecules associated with geminiviruses and nanoviruses. In this study, a meta-analysis of known alphasatellites isolated from the genus Gossypium (cotton) over the last two decades was performed. The phylogenetic and pairwise sequence identity analysis suggested that cotton-infecting begomoviruses were associated with at least 12 different alphasatellites globally. Three out of twelve alphasatellite were associated with cotton leaf curl geminiviruses but were not isolated from cotton plants. The cotton leaf curl Multan alphasatellite, which was initially isolated from cotton, has now been reported in several plant species, including monocot plants such as sugarcane. Our recombination analysis suggested that four alphasatellites, namely cotton leaf curl Lucknow alphasatellites, cotton leaf curl Multan alphasatellites, Ageratum yellow vein Indian alphasatellites and Ageratum enation alphasatellites, evolved through recombination. Additionally, high genetic variability was detected among the cotton-infecting alphasatellites at the genome level. The nucleotide substitution rate for the replication protein of alphasatellites (alpha-Rep) was estimated to be relatively high (~1.56 × 10−3). However, unlike other begomoviruses and satellites, the first codon position of alpha-Rep rapidly changed compared to the second and third codon positions. This study highlights the biodiversity and recombination of alphasatellites associated with the leaf curl diseases of cotton crops.

Perspective on taxonomic classification of uncultivated viruses

Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.

Two novel bornaviruses identified in colubrid and viperid snakes

We present the complete genome sequences of Caribbean watersnake bornavirus (CWBV) and Mexican black-tailed rattlesnake bornavirus (MRBV), which we identified in archived raw transcriptomic read data of a Caribbean watersnake (Tretanorhinus variabilis) and a Mexican black-tailed rattlesnake (Crotalus molossus nigrescens), respectively. The genomes of CWBV and MRBV have a length of about 8,900 nucleotides and comprise the complete coding regions and the untranslated regions. The overall genomic makeup and predicted gene content is typical for members of the genus Orthobornavirus within the family Bornaviridae. Alternative splicing was detected for the L and M genes. Based on a phylogenetic analysis of all viral proteins, we consider both viruses to be members of a single novel species within the genus Orthobornavirus. Both viruses form a distinct outgroup to all currently known orthobornaviruses. Based on the novel virus genomes, we furthermore identified closely related endogenous bornavirus-like nucleoprotein sequences in transcriptomic data of veiled chameleons (Chamaeleo calyptratus) and a common lancehead (Bothrops atrox).

Identification of Plant Viruses Infecting Pear Using RNA Sequencing

Asian pear (Pyrus pyrifolia) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar ('Singo') in Korea. From June 2017 to October 2019, leaf samples (n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of 'Singo.' The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.

Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices

With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.

VIRIDIC-A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses

Nucleotide-based intergenomic similarities are useful to understand how viruses are related with each other and to classify them. Here we have developed VIRIDIC, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities. When compared with other software, VIRIDIC gave the best agreement with the traditional algorithm, which is based on the percent identity between two genomes determined by BLASTN. Furthermore, VIRIDIC proved best at estimating the relatedness between more distantly-related phages, relatedness that other tools can significantly overestimate. In addition to the intergenomic similarities, VIRIDIC also calculates three indicators of the alignment ability to capture the relatedness between viruses: the aligned fractions for each genome in a pair and the length ratio between the two genomes. The main output of VIRIDIC is a heatmap integrating the intergenomic similarity values with information regarding the genome lengths and the aligned genome fraction. Additionally, VIRIDIC can group viruses into clusters, based on user-defined intergenomic similarity thresholds. The sensitivity of VIRIDIC is given by the BLASTN. Thus, it is able to capture relationships between viruses having in common even short genomic regions, with as low as 65% similarity. Below this similarity level, protein-based analyses should be used, as they are the best suited to capture distant relationships. VIRIDIC is available at viridic.icbm.de, both as a web-service and a stand-alone tool. It allows fast analysis of large phage genome datasets, especially in the stand-alone version, which can be run on the user's own servers and can be integrated in bioinformatics pipelines. VIRIDIC was developed having viruses of Bacteria and Archaea in mind; however, it could potentially be used for eukaryotic viruses as well, as long as they are monopartite.

Exploiting the Legacy of the Arbovirus Hunters

In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.

Prevalence and Diversity Analysis of Candidate Prophages to Provide An Understanding on Their Roles in Bacillus Thuringiensis

Bacillus thuringiensis (Bt) is widely used in producing biological insecticides. Phage contaminations during Bt fermentation can cause severe losses of yields. Lots of strategies have been engaged to control extrinsic phage contamination during Bt fermentation, but their effectiveness is low. In this study, the candidate endogenous prophages (prophages) in 61 Bt chromosomes that had been deposited in GenBank database were analyzed. The results revealed that all chromosomes contained prophage regions, and 398 candidate prophage regions were predicted, including 135 putative complete prophages and 263 incomplete prophage regions. These putative complete prophages showed highly diverse genetic backgrounds. The inducibility of the prophages of ten Bt strains (4AJ1, 4BD1, HD-1, HD-29, HD-73, HD-521, BMB171, 4CC1, CT-43, and HD-1011) was tested, and the results showed that seven of the ten strains’ prophages were inducible. These induced phages belonged to the Siphoviridae family and exhibited a broad host spectrum against the non-original strains. The culture supernatants of the two strains (BMB171, 4CC1) could lyse Bt cells, but no virions were observed, which was speculated to be caused by lysin. The functional analysis of the putative complete prophage proteins indicated that some proteins, such as antibiotic resistance-associated proteins and restriction endonucleases, might increase the fitness of the Bt strains to different environments. The findings of this study provided understanding on the high prevalence and diversity of Bt prophages, as well as pointed out the role of prophages in the life cycle of Bt.

Transcriptome-wide identification and competitive disruption of sacum-binding partners in human colorectal cancer

Human sacum is regulatory adaptor protein involved in cellular signaling network of colorectal cancer. Molecular evidences suggest that the protein is integrated into oncogenic signaling network by binding to SH3-containing proteins through its proline-rich motifs. In this study, we have performed a transcriptome-wide analysis and identification of sacum-binding partners in the genome profile of human colorectal cancer. The sacum-binding potency of SH3-containing proteins found in colorectal cancer was investigated by using bioinformatics modeling and intermolecular binding analysis. With the protocol we were able to predict those high-affinity domain binders of the proline-rich peptides of human sacum in a high-throughput manner, and to analyze sequence-specific interaction in the domain-peptide recognition at molecular level. Consequently, a number of putative domain binders with both high affinity and specificity were identified, from which the Src SH3 domain was selected as a case study and tested for its binding activity towards the sacum peptides. We also designed two peptide variants that may have potent capability to competitively disrupt sacum interaction with its partners.

Transcriptome-wide identification and competitive disruption of sacum-binding partners in human colorectal cancer

Human sacum is regulatory adaptor protein involved in cellular signaling network of colorectal cancer. Molecular evidence suggests that the protein is integrated into oncogenic signaling network by binding to SH3-containing proteins through its proline-rich motifs. In this study, we have performed a transcriptome-wide analysis and identification of sacum-binding partners in the genome profile of human colorectal cancer. The sacum-binding potency of SH3-containing proteins found in colorectal cancer was investigated by using bioinformatics modeling and intermolecular binding analysis. With the protocol we were able to predict those high-affinity domain binders of the proline-rich peptides of human sacum in a high-throughput manner, and to analyze sequence-specific interaction in the domain-peptide recognition at molecular level. Consequently, a number of putative domain binders with both high affinity and specificity were identified, from which the Src SH3 domain was selected as a case study and tested for its binding activity towards the sacum peptides. We also designed two peptide variants that may have potent capability to competitively disrupt sacum interaction with its partners.

Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55–58% sequence diversity threshold range for genera and at the 23–36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

Guide to the Correct Use of Filoviral Nomenclature

The International Committee on Taxonomy of Viruses (ICTV) currently recognizes three genera and seven species as part of the mononegaviral family Filoviridae. Eight distinct filoviruses (Bundibugyo virus, Ebola virus, Lloviu virus, Marburg virus, Ravn virus, Reston virus, Sudan virus, and Taï Forest virus) have been assigned to these seven species. This chapter briefly summarizes the status quo of filovirus classification and focuses on the importance of differentiating between filoviral species and filoviruses and the correct use of taxonomic and vernacular filovirus names and abbreviations in written and oral discourse.

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Background

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods.

Results

We propose a supervised method based on a genetic algorithm to identify small genomic subsequences that discriminate among different species. The method identifies multiple subsequences of bounded length with the same information power in a given genomic region. The algorithm has been successfully evaluated through its integration into a rule-based classification framework and applied to three different biological data sets: Influenza, Polyoma, and Rhino virus sequences.

Conclusions

We discover a large number of small subsequences that can be used to identify each virus type with high accuracy and low computational time, and moreover help to characterize different genomic regions. Bounding their length to 20, our method found 1164 characterizing subsequences for all the Influenza virus subtypes, 194 for all the Polyoma viruses, and 11 for Rhino viruses. The abundance of small separating subsequences extracted for each genomic region may be an important support for quick and robust virus identification.

Finally, useful biological information can be derived by the relative location and abundance of such subsequences along the different regions.

Electronic supplementary material

The online version of this article (doi:10.1186/s13040-016-0116-2) contains supplementary material, which is available to authorized users.

Neglected filoviruses

Eight viruses are currently assigned to the family Filoviridae Marburg virus, Sudan virus and, in particular, Ebola virus have received the most attention both by researchers and the public from 1967 to 2013. During this period, natural human filovirus disease outbreaks occurred sporadically in Equatorial Africa and, despite high case-fatality rates, never included more than several dozen to a few hundred infections per outbreak. Research emphasis shifted almost exclusively to Ebola virus in 2014, when this virus was identified as the cause of an outbreak that has thus far involved more than 28 646 people and caused more than 11 323 deaths in Western Africa. Consequently, major efforts are currently underway to develop licensed medical countermeasures against Ebola virus infection. However, the ecology of and mechanisms behind Ebola virus emergence are as little understood as they are for all other filoviruses. Consequently, the possibility of the future occurrence of a large disease outbreak caused by other less characterized filoviruses (i.e. Bundibugyo virus, Lloviu virus, Ravn virus, Reston virus and Taï Forest virus) is impossible to rule out. Yet, for many of these viruses, not even rudimentary research tools are available, let alone medical countermeasures. This review summarizes the current knowledge on these less well-characterized filoviruses.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Methods for virus classification and the challenge of incorporating metagenomic sequence data

The division of viruses into orders, families, genera and species provides a classification framework that seeks to organize and make sense of the diversity of viruses infecting animals, plants and bacteria. Classifications are based on similarities in genome structure and organization, the presence of homologous genes and sequence motifs and at lower levels such as species, host range, nucleotide and antigenic relatedness and epidemiology. Classification below the level of family must also be consistent with phylogeny and virus evolutionary histories. Recently developed methods such as PASC, DEMaRC and NVR offer alternative strategies for genus and species assignments that are based purely on degrees of divergence between genome sequences. They offer the possibility of automating classification of the vast number of novel virus sequences being generated by next-generation metagenomic sequencing. However, distance-based methods struggle to deal with the complex evolutionary history of virus genomes that are shuffled by recombination and reassortment, and where taxonomic lineages evolve at different rates. In biological terms, classifications based on sequence distances alone are also arbitrary whereas the current system of virus taxonomy is of utility precisely because it is primarily based upon phenotypic characteristics. However, a separate system is clearly needed by which virus variants that lack biological information might be incorporated into the ICTV classification even if based solely on sequence relationships to existing taxa. For these, simplified taxonomic proposals and naming conventions represent a practical way to expand the existing virus classification and catalogue our rapidly increasing knowledge of virus diversity.

Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species membership, associated outbreaks, and transmission chains

Genome-similarity based codes were assigned to individual ebolavirus isolates. Codes were found to be informative of phylogenetic and epidemiological relationships. It is proposed that such codes should be assigned to every genome-sequenced virus to complement current viral taxonomy.

Background. Developing a universal standardized microbial typing and nomenclature system that provides phylogenetic and epidemiological information in real time has never been as urgent in public health as it is today. We previously proposed to use genome similarity as the basis for immediate and precise typing and naming of individual organisms or viruses. In this study, we tested the validity of the proposed system and applied it to the epidemiology of infectious diseases using Ebola virus disease (EVD) outbreaks as the example.

Methods. One hundred twenty-eight publicly available ebolavirus genomes were compared with each other, and average nucleotide identity (ANI) was calculated. The ANI was then used to assign unique codes, hereafter referred to as Life Identification Numbers (LINs), to every viral isolate, whereby each LIN consisted of a series of positions reflecting increasing genome similarity. Congruence of LINs with phylogenetic and epidemiological relationships was then determined.

Results. Assigned LINs correlate with phylogeny at the species and infraspecies level and can even identify some individual transmission chains during the 2014–2015 EVD epidemic in West Africa.

Conclusions. Life Identification Numbers can provide a fast, automated, standardized, and scalable approach to precisely identify and name viral isolates upon genome sequence submission, facilitating unambiguous communication during disease epidemics among clinicians, epidemiologists, and governments.

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification

The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool's database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool ( http://www.ncbi.nlm.nih.gov/sutils/pasc/ ) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.

NCBI viral genomes resource

Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

Discussions and decisions of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group, January 2012–June 2013

The International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group prepares proposals on the classification and nomenclature of filoviruses to reflect current knowledge or to correct disagreements with the International Code of Virus Classification and Nomenclature (ICVCN). In recent years, filovirus taxonomy has been corrected and updated, but parts of it remain controversial, and several topics remain to be debated. This article summarizes the decisions and discussion of the currently acting ICTV Filoviridae Study Group since its inauguration in January 2012.

Filoviruses in bats: current knowledge and future directions

Filoviruses, including Ebolavirus and Marburgvirus, pose significant threats to public health and species conservation by causing hemorrhagic fever outbreaks with high mortality rates. Since the first outbreak in 1967, their origins, natural history, and ecology remained elusive until recent studies linked them through molecular, serological, and virological studies to bats. We review the ecology, epidemiology, and natural history of these systems, drawing on examples from other bat-borne zoonoses, and highlight key areas for future research. We compare and contrast results from ecological and virological studies of bats and filoviruses with those of other systems. We also highlight how advanced methods, such as more recent serological assays, can be interlinked with flexible statistical methods and experimental studies to inform the field studies necessary to understand filovirus persistence in wildlife populations and cross-species transmission leading to outbreaks. We highlight the need for a more unified, global surveillance strategy for filoviruses in wildlife, and advocate for more integrated, multi-disciplinary approaches to understand dynamics in bat populations to ultimately mitigate or prevent potentially devastating disease outbreaks.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

Phylogenetic relationships, recombination analysis, and genetic variability among diverse variants of tomato yellow leaf curl virus in Iran and the Arabian Peninsula: further support for a TYLCV center of diversity

The discovery of five strains of TYLCV in Iran, including the most well-known and widespread, TYLCV-IL, spurred a detailed study of the full-length genomes of additional TYLCV field isolates and an in-depth analysis of phylogenetic relationships, extent of recombination, and genetic variability of TYLCV isolates within Iran and throughout the Arabian Peninsula. Phylogenetic analysis of complete genome sequences of TYLCV isolates from Iran and other countries revealed four monophyletic clusters could be differentiated based on geographical origin, indicating that recent dispersal of these populations (by the vector or by humans) from these four regions has occurred minimally, or not at all. Genetic analysis revealed that TYLCV-IL isolates from southern Iran possessed greater genetic variability than the northeastern isolates, a pattern that may be reflective of evolution driven by geographically dependent isolation. Similarly, isolates of TYLCV-OM originating from Oman showed greater genetic variability than TYLCV-OM variants from Iran. Major recombination events, which were detected in all strains of TYLCV had breakpoints initiating in the C1, C1/C4, C2/C3 and V1 open reading frames (ORFs) and ending at the non-coding region and the C1, C1/C2 and C3 ORFs. Hence, these regions have consistently served as hot spots for recombination worldwide during the evolution of all currently recognized isolates and strains of TYLCV.