A viral quasispecies is a population structure of viruses with a large number of variant genomes (related by mutations). Quasispecies result from high mutation rates as mutants arise continually and change in relative frequency as viral replication and selection proceeds.
The theory predicts that a viral quasispecies at a low but evolutionarily neutral and highly connected (that is, flat) region in the fitness landscape will outcompete a quasispecies located at a higher but narrower fitness peak in which the surrounding mutants are unfit. This phenomenon has been called 'the quasispecies effect' or, more recently, the 'survival of the flattest'.
The term quasispecies was adopted from a theory of the origin of life in which primitive replicons consisted of mutant distributions, as found experimentally with present-day RNA viruses within their host. The theory provided a new definition of wild type when describing viruses, and a conceptual framework for a deeper understanding of the adaptive potential of RNA viruses than is offered by classical studies based on simplified consensus sequences.
The quasispecies model is most applicable when the genome size is limited and the mutation rate is high, and so is most relevant to RNA viruses (including important pathogens) because they have high mutation rates (approx one error per round of replication), though the concepts can apply to other biological entities such as reverse transcribing DNA viruses like hepatitis B. In such scenarios, complex distributions of closely related variant genomes are subjected to genetic variation, competition and selection, and may act as a unit of selection. Therefore, the evolutionary trajectory of the viral infection cannot be predicted solely from the characteristics of the fittest sequence. High mutation rates also place an upper limit compatible with inheritable information. Crossing such a limit leads to RNA virus extinction, a transition that is the basis of an antiviral design termed lethal mutagenesis, and of relevance to antiviral medicine.
The relevance of quasispecies in virology has been the subject of extended debate. However, standard clonal analyses and deep sequencing methodologies have confirmed the presence of myriads of mutant genomes in viral populations, and their participation in adaptive processes.
History
Quasispecies theory was developed in the 1970s by Manfred Eigen and Peter Schuster to explain self-organization and adaptability of primitive replicons (a term used to refer to any replicating entity), as an ingredient of hypercyclic organizations that link genotypic and phenotypic information, as an essential step in the origin of life. The theory portrayed early replicon populations as organized mutant spectra dominated by a master sequence, the one endowed with the highest fitness (replicative capacity) in the distribution. It introduced the notion of a mutant ensemble as a unit of selection, thus emphasizing the relevance of intra-population interactions to understand the response to selective constraints. One of its corollaries is the error threshold relationship, which marks the maximum mutation rate at which the master (or dominant) sequence can stabilize the mutant ensemble. Violation of the error threshold results in loss of dominance of the master sequence and drift of the population in sequence space.
The core quasispecies concepts are described by two fundamental equations: replication with production of error copies, and the error threshold relationship. They capture two major features of RNA viruses at the population level: the presence of a mutant spectrum, and the adverse effect of an increase of mutation rate on virus survival, each with several derivations.
The existence of a mutant spectrum was experimentally evidenced first by clonal analyses of RNA bacteriophage Qβ populations whose replication had been initiated by a single virus particle. Individual genomes differed from the consensus sequence in an average of one to two mutations per individual genome. Fitness of biological clones was inferior to that of the parental, uncloned population, a difference also documented for vesicular stomatitis virus (VSV). The replicative capacity of a population ensemble need not coincide with that of its individual components. The finding that a viral population was essentially a pool of mutants came at a time when mutations in general genetics were considered rare events, and virologists associated a viral genome with a defined nucleotide sequence, as still implied today in the contents of data banks. The cloud nature of Qβ was understood as a consequence of its high mutation rate, calculated in 10−4 mutations introduced per nucleotide copied, together with tolerance of individual genomes to accept an undetermined proportion of the newly arising mutations, despite fitness costs. The error rate estimated for bacteriophage Qβ has been confirmed, and is comparable to values calculated for other RNA viruses.
High mutation rates and quasispecies were verified for other RNA viruses based on dissection of viral populations by molecular or biological cloning, and sequence analysis of individual clones. John Holland and colleagues were the first to recognize that a rapidly evolving RNA world inserted in a DNA-based biosphere had multiple evolutionary and medical implications. Genome plasticity of RNA viruses had been suspected for many decades. Key early observations were variations in viral traits described by Findley in the 1930s, the studies of Granoff on transitions of plaque morphology of Newcastle disease virus, or the high frequency of conversions between drug resistance and dependence in Coxsackie A9 virus, among other studies with animal and plant viruses in the middle of the 20th century. When put in the context of present-day knowledge, we realize that these observations on phenotypic changes were the tip of the iceberg of an extremely complex reality of viral populations. High mutation rates and population heterogeneity characterize RNA viruses, with consequences for viral pathogenesis and the control of viral disease. Detailed studies on quasispecies dynamics in vivo have been performed with human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus.
Current scope The first mathematical formulation of quasispecies was deterministic; it assumed steady state mutant distributions in genetic equilibrium without perturbations derived from modifications of the environment or population size. These conditions are common in initial theoretical formulations of complex phenomena because they confer mathematical tractability. Since then, several extensions of the theory to non-equilibrium conditions with stochastic components have been developed, with the aim of finding general solutions for multi-peak fitness landscapes. These objectives approximate quasispecies to the real case of RNA viruses, which are compelled to deal with dramatic variations in population size and environment. Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations). New inputs into experimental quasispecies research have come from deep sequencing to probe viral and cellular populations, recognition of interactions within mutant spectra, models of viral population dynamics related to disease progression and pathogen transmission, and new teachings from fidelity variants of viruses. Here we summarize the main aspects of quasispecies dynamics, and recent developments relevant to virus evolution and pathogenesis.
Dynamic heterogeneity The molecular basis of high error rates is the limited template-copying fidelity of RNA-dependent RNA polymerases (RdRps) and RNA-dependent DNA polymerases (also termed reverse transcriptases, RTs). In addition, these enzymes are defective in proofreading because they lack a 3' to 5' exonuclease domain present in replicative cellular DNA polymerases. Also, postreplicative-repair pathways, abundant to correct genetic lesions in replicating cellular DNA, appear as ineffective for double-stranded RNA or RNA-DNA hybrids. The presence of a proofreading-repair activity in coronaviruses increases their copying accuracy in about 15-fold. This and other repair activities, that may act on standard RNA or retroviral genomes, do not prevent the formation of mutant spectra, although their amplitude may be lower than for other RNA viruses, at least in populations close to a clonal (single genome) origin. Quasispecies dynamics will operate in any viral or cellular system in which due to high mutation rates (as a result of low fidelity nucleic acid polymerases or environmental alterations) mutant spectra are rapidly generated.
Studies with different virus-host systems have established some general observations on the mechanisms of mutant generation, and implications of quasispecies dynamics. In RNA virus genetics when we speak of "a mutant" the entity we handle is a cloud of mutants in which the specific mutation to which we direct our attention is present in all (or the great majority of) individual genomes. There is no such a thing as "a" wild type or "a" mutant virus. They are always clouds of mutants. Changes in the relative dominance of components of mutant spectra are particularly severe during in vivo infections, with complex dynamics of intra-host heterogeneity and variations. Bioinformatic procedures have been developed to unveil the relationships among different but closely related genome types that may suggest some hierarchical order of mutation acquisition or identification of transmission clusters (examples are Partition Analysis of Quasispecies, PAQ or QUasispecies Evolution, Network-based Transmission Inference, QUENTIN).
Phenotypic reservoirs