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Schoub Paul D. Griffiths Philip Mortimer. First published: Print ISBN: As before, the book provides a detailed account of the diagnosis and treatment of virus infections, with a stronger emphasis on clinical expertise and management. Each chapter deals with a single virus or group or viruses and is written by leading international experts in the field.
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The database currently provides access to molecular data of viruses including complete genomes of 14 viral families. Analytical and visualization tools for metadata-driven statistical sequence analysis, data filtering, analytical workflows and utility of personal workbench are provided to the users. Such annotations will be highly useful in subsequent analysis and model building. The challenges of managing dedicated resources for viral genomes are relatively different as compared to the genomic databases of model and other organisms.
The pace of sequencing and the quantum of genomic data being generated are affecting identification of reference genomes and annotations of genomes of strains and isolates. Additionally, to study the spatio-temporal evolution and to model the viral populations, it is desirable to tag metadata such as the place and date of isolation of viruses with the corresponding genomic entries.
While understanding the sequence—structure—function relationships, it has also resulted in the development of new areas of research such as phyloinformatics and immunoinformatics, which translates raw data into information. The information generated from these independent yet interlinked areas, when put together fits as pieces of jigsaw puzzle Figure 1 , leading to an improved understanding of the viral diseases and, thereby, the development of antiviral therapies.
Figure 1. Scope of research in virology enabled and augmented due to availability of NGS data. Unravelling mutational landscapes in viral quasispecies Viral quasispecies are mutant swarms generated mainly by RNA viruses during replication, which is known to be error-prone due to the lack of proofreading activity of RNA-dependent RNA polymerase. The resulting mosaic is a dynamic distribution of non-identical but related replicons that cannot be detected using conventional sequencing approaches.
Hence, quasispecies remained unexplored for a considerable time, even though the theoretical concept for quasispecies was put forth by Eigen in [ 55 ]. With the advent of NGS technologies, the generation of large genomic datasets became a reality. Due to the sequencing error issues, it was still tough to demarcate true genetic variations. Circular Sequencing CirSeq , a novel experimental approach that creates template of tandem repeats of circularized genomic RNA fragments has been developed by Andino's group [ 56 ].
CirSeq reduces the sequencing error drastically as the repeats get sequenced in a redundant manner for every genomic fragment. CirSeq was employed to study seven serial passages of Poliovirus replicated in HeLa cells. Mutation frequency was computed for every passage and their fitness was determined by mapping onto the 3D structure of proteins.
As expected, majority of the mutations detected were neutral substitutions, thus highlighting robustness as driving force for adaptation and evolution [ 56 ].
This study clearly delineates the viral mutations responsible for quasispecies structure and highlights the extent of genetic variation that can be maintained in a population. Microevolution in an evolving quasispecies population is responsible for the sequence diversity in Porcine reproductive and respiratory syndrome virus PRRSV.
PRRSV is the causative agent of late-term reproductive failure in sows and respiratory distress in pigs and hence has large economic impact. Genomic complexity of PRRSV due to multiple circulating genotypes results in antigenic diversity, which, in turn, is responsible for lack of effective vaccine development [ 57 ]. Sanger sequencing has identified open reading frames ORF5 and ORF7 as the polymorphic regions of the virus genome, encoding major immunogenic epitopes. By analysing nucleotide substitutions over time followed by comparative genomics with non-pathogenic variants, the role of mutation and selection in preserving the pathogenesis or fitness of PRRSV was well documented in this study.
Minority quasispecies refers to the memory genomes that were dominant at an earlier phase of quasispecies evolution and can play an important role in conferring drug resistance in viruses such as Human Immunodeficiency Virus type-1 HIV-1 and Influenza virus. Minority quasispecies of drug-resistant viruses can rapidly re-emerge as major populations after the reintroduction of drug pressure.
In case of HIV-1, presence of such low-frequency variants has been linked with early failure to the antiretroviral therapy [ 59 , 60 ]. Emergence of highly pathogenic subtype of Avian Influenza viruses HPAI has also been explained on the basis of low-frequency variants. Inter- and intra-host genetic diversity The rate of viral evolution and the effectiveness of its transmission are determined by inter- and intra-host genetic diversity.
Mutation rate and selection pressure ascertain viral diversity. Factors like mixed infections and random processes such as genetic drift and population bottlenecks also contribute to the genetic diversity of viruses both within and among hosts.
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Transmission fitness influences the effective spread of viruses and is responsible for its stable maintenance in the environment [ 62 ]. Population bottlenecks were investigated for this aphid-borne virus and are thought to occur during both inter-host vector transmission and systemic movement within an individual plant. ZYMV populations infecting cucumbers with and without vector were sequenced followed by de novo assembly and variant calling. Analysis revealed that the low-frequency mutants present in the initial population got fixed rapidly in vector-transmitted viruses, whereas the same continued to remain as minor variants in mechanically inoculated viruses.
Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges
In addition, regions known to be responsible for vector transmission were conserved in all samples. It is interesting to know that previous studies using Sanger sequencing of the coat protein of ZYMV, which is involved in interaction with aphids, could not detect mutations when transmitted between or within plants.
Such studies provide an insight into the complex dynamics of genetic diversity of an emerging viral infection with implications in disease management. Metagenomics involves sequencing of samples from diverse environments spanning across the biosphere [ 64 ].
The initial attempts at characterizing the viral metagenomes were more of an enumeration nature [ 65 ] and provided a glimpse of the enormous diversity underlying the previously unculturable communities.
NGS has paved way for extensive characterization of the functional role of virome in hosts harbouring them [ 66 , 67 ]. Two major methods based on 'sequence-similarity' and 'sequence composition' are usually used for categorization of samples in metagenomics.
In a major study involving analysis of dsDNA viruses from 43 ocean samples obtained from across the globe revealed several intriguing observations [ 69 ]. Genes shared across different samples were used as 'core genes' for comparison. As viruses rely on the host machinery to replicate, a direct relationship was observed between the community structures of both viruses and hosts. Environmental factors like salinity also influenced the viral persistence and hence their diversity.
Technological advances in viral metagenomics would help to unravel the underlying rules of viral evolution and ecology, the so-called 'Genomic rulebook of viruses' [ 70 ]. Genotype—phenotype correlation studies 3. Receptor switching A key event during any viral infection is the interaction of viruses with the host receptors on the plasma membrane.
This serves as an entry point for viruses to access resources of the host cell and is very crucial for tropism. This interaction is known to be very specific and is responsible for activation of the signalling processes that recruit cellular machinery of the host for viral replication. The specificity of receptor binding defines host range that a virus can infect and the extent of tissue tropism that a virus can display. HIV-1 enters the target host cell by binding to CD4 receptor along with a co-receptor in majority of cases, chemokine C-C motif receptor 5 CCR5 using its spike protein.
However, due to the low resolution of these procedures, this transition could not be captured effectively. NGS of the variable loop region V3 of the envelope gene containing determinants of co-receptor usage revealed the stepwise mutational pathway involved in the transition from CCR5 to CXCR4 [ 71 ].
The observation of the low-frequency intermediate variants provided an insight into the fitness landscape of HIV-1 and provided clues to tackle the disease progression in a rational manner. The amino acid changes in haemagglutinin protein GE and GN were observed to be associated with the immune escape [ 72 ]. Bioinformatics methods for viral genomics Bioinformatics approaches help to estimate and analyse population diversity by studying genetic recombination, mutation, selection and, thereby, assist in correlation of genotype to phenotype.
The methods relevant to these aspects are discussed below with emphasis on the analysis of viral populations.
Methods for quasispecies reconstruction Quasispecies reconstruction refers to the estimation of number of viral variants and their frequency. Each viral variant in a quasispecies is considered as a haplotype. It can detect viral haplotypes with frequencies as low as 0. It performs pairwise alignment of all reads to the reference sequence and generates a multiple sequence alignment MSA. Error correction local haplotype reconstruction : Using MSA as a starting point, a set of overlapping windows is analysed by employing a model-based probabilistic clustering algorithm to obtain i haplotype sequences, ii their frequencies, iii corrected reads and iv posterior probability of the reconstruction.
Global haplotype reconstruction: The set of corrected reads is analysed under parsimony principle, which results in identification of set of unique reads of maximum length. Frequency estimation: Using maximum likelihood ML and expectation maximization algorithm, the frequencies of the reconstructed haplotypes are estimated. Algorithm steps: Overlaps between the reference genome and reads are generated in terms of k-mers.
Mapping of k-mers is then carried out to obtain genomic co-ordinates. Generates a multinomial distribution based on the alignment scores of true matches along with the matches with randomly shuffled reads. Coverage, nucleotide content and entropy of each mapped genomic position are then calculated. Errors are corrected based on Poisson distribution model, parameterized differently for homopolymeric and non-homopolymeric regions.
Reconstruction of quasispecies is carried out using the sliding window approach by calculating maximal coverage and read diversity, which reduces the false positives, i. QuasiRecomb Principle: It employs the jumping Hidden Markov Model HMM -based probabilistic statistics for inference of viral quasispecies, especially for estimating the intra-patient viral haplotype distribution [ 75 ].
This method assumes that the true genetic diversity is generated by a few sequences called generators through mutation and recombination, and that the observed diversity results from additional sequencing errors. Algorithm steps: Distribution of haplotypes in a given population is modelled to account for either point mutation or recombination in the form of probability tables and jumping HMM states respectively.
Expectation maximization algorithm is used to estimate posterior probabilities associated with rare events of mutation and recombination. Methods to study viral population genetics Genetic structure of a population refers to the number of distinct subpopulations, identified using a characteristic set of allele frequencies [ 76 ].
The program can infer the genetic structure in haploid, diploid and polyploid species [ 78 ]. It assigns individuals to subpopulations based on likelihood estimates. In case of haploids, the program assumes that the loci are in linkage equilibrium or only weakly linked [ 78 ].
The program accounts for recombination by incorporating ancestry models such as admixture and linkage models. An admixed strain is assigned with a membership score to belong to two or more subpopulations, to indicate its mixed ancestry.
Linkage model is an extension of admixture model to account for weak linkage that arises as a result of admixture linkage disequilibrium LD. Input genotype data: A wide range of markers such as multi-locus genotype data, microsatellites, SNPs can be used as an input.
In case of viruses, the polymorphic sites or more specifically the parsimony-informative PIs sites obtained from genome-based alignment are suitable markers for population genetic analyses. A PI site contains at least two types of nucleotide bases and at least two of which occur with a minimum frequency of two.Population genomic study of Hepatitis B virus HBV was carried out using both admixture and linkage models with burn-in of 20, and burn-length of 40, Metagenomics involves sequencing of samples from diverse environments spanning across the biosphere [ 64 ].
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