Quasispecies theory in the context of population genetics

BACKGROUND: A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory. RESULTS: I review the pertinent literature, and demonstrate for a number of cases that the quasispecies concept is equivalent to the concept of mutation-selection balance developed in population genetics, and that there is no disagreement between the population genetics of haploid, asexually-replicating organisms and quasispecies theory. CONCLUSION: Since quasispecies theory and mutation-selection balance are two sides of the same medal, the discussion about which is more appropriate to describe virus evolution is moot. In future work on virus evolution, we would do good to focus on the important questions, such as whether we can develop accurate, quantitative models of virus evolution, and to leave aside discussions about the relative merits of perfectly equivalent concepts

Single genome sequencing of near full-length HIV-1 RNA using a limiting dilution approach

Sequencing very long stretches of the HIV-1 genome can advance studies on virus evolution and in vivo recombination but remains technically challenging. We developed an efficient procedure to sequence near full-length HIV-1 RNA using a two-amplicon approach. The whole genome was successfully amplified for 107 (88%) of 121 plasma samples including samples from patients infected with HIV-1 subtype A1, B, C, D, F1, G, H, CRF01_AE and CRF02_AG. For the 17 samples with a viral load below 1000 c/ml and the 104 samples with a viral load above 1000 c/ml, the amplification efficiency was respectively 53% and 94%. The sensitivity of the method was further evaluated using limiting dilution of RNA extracted from a plasma pool containing an equimolar mixture of three HIV-1 subtypes (B, C and CRF02_AG) and diluted before and after cDNA generation. Both RNA and cDNA dilution showed comparable sensitivity and equal accuracy in reflecting the subtype distribution of the plasma pool. One single event of in vitro recombination was detected amongst the 41 sequences obtained after cDNA dilution but no indications for in vitro recombination were found after RNA dilution. In conclusion, a two-amplicon strategy and limiting dilution of viral RNA followed by reverse transcription, nested PCR and Sanger sequencing, allows near full genome sequencing of individual HIV-1 RNA molecules. This method will be a valuable tool in the study of virus evolution and recombination

Virus evolution : the emergence of new ideas (and re-emergence of old ones)

Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms appearing daily in the H5N1 avian flu virus [1], than to the fundamental interrogation: where do viruses come from? This situation is now rapidly changing, due to the coincidence of bold new ideas (and sometimes the revival of old ones), the unexpected features exhibited by recently isolated spectacular viruses [2] (see at URL: www.giantvirus.org), as well as the steady increase of genomic sequences for 'regular' viruses and cellular organisms enhancing the power of comparative genomics [3]. After being considered non-living and relegated in the wings by a majority of biologists, viruses are now pushed back on the center stage: they might have been at the origin of DNA, of the eukaryotic cell, and even of today's partition of biological organisms into 3 domains of life: bacteria, archaea and eukarya. Here, I quickly survey some of the recent discoveries and the new evolutionary thoughts they have prompted, before adding to the confusion with one interrogation of my own: what if we totally missed the true nature of (at least some) viruses?Comment: submitte

Variation and evolution of plant virus populations

Over the last 15 years, interest in plant virus evolution has re-emerged, as shown by the increasing number of papers published on this subject. In recent times, research in plant virus evolution has been viewed from a molecular, rather than populational, standpoint, and there is a need for work aimed at understanding the processes involved in plant virus evolution. However, accumulated data from analyses of experimental and natural populations of plant viruses are beginning to delineate some trends that often run contrary to accepted opinion: (1) high mutation rates are not necessarily adaptive, as a large fraction of the mutations are deleterious or lethal; (2) in spite of high potential for genetic variation, populations of plant viruses are not highly variable, and genetic stability is the rule rather than the exception; (3) the degree of constriction of genetic variation in virus-encoded proteins is similar to that in their eukaryotic hosts and vectors; and (4) in spite of huge census sizes of plant virus populations, selection is not the sole factor that shapes their evolution, and genetic drift may be important. Here, we review recent advances in understanding plant virus evolution, and describe the experimental and analytical methods most suited to this purpose

Introduction of RNA virus evolution

Lots of viruses, in particular RNA viruses, have high mutation rates and relatively short generation times. Particle stability during infection in nature or in laboratory triggers the evolutionary event toward different mechanisms such as genome segmentation, point mutation and  recombination. The frequency of mutant genomes increase and modify  the previous distribution, which, consequently, lead to emergence of a new infectious particle. Mutation and selection are the most fundamental processes in evolution. High mutation rate of RNA viruses has an important role in viral fitness. Therefore, it increase our understanding about molecular biology of viral infections and their evolution by selection, mutation could reliably  determine our ability to challenge destructive viruses. This review focuses on existing impressions of genetic organization and mechanisms of RNA viruses evolution

Virus evolution in Wolbachia-infected Drosophila

Wolbachia, a common vertically transmitted symbiont, can protect insects against viral infection and prevent mosquitoes from transmitting viral pathogens. For this reason, Wolbachia-infected mosquitoes are being released to prevent the transmission of dengue and other arboviruses. An important question for the long-term success of these programmes is whether viruses can evolve to escape the antiviral effects of Wolbachia. We have found that Wolbachia altered the outcome of competition between strains of the DCV virus in Drosophila. However, Wolbachia still effectively blocked the virus genotypes that were favoured in the presence of the symbiont. We conclude that Wolbachia did cause an evolutionary response in viruses, but this has little or no impact on the effectiveness of virus blocking

Virus evolution in Wolbachia-infected Drosophila

Wolbachia, a common vertically transmitted symbiont, can protect insects against viral infection and prevent mosquitoes from transmitting viral pathogens. For this reason, Wolbachia-infected mosquitoes are being released to prevent the transmission of dengue and other arboviruses. An important question for the long-term success of these programmes is whether viruses can evolve to escape the antiviral effects of Wolbachia. We have found that Wolbachia altered the outcome of competition between strains of the DCV virus in Drosophila. However, Wolbachia still effectively blocked the virus genotypes that were favoured in the presence of the symbiont. We conclude that Wolbachia did cause an evolutionary response in viruses, but this has little or no impact on the effectiveness of virus blocking