| PERSPECTIVES Evolutionary Virology at 40 Jemma L. Geoghegan* and Edward C. Holmes†,‡,§,**,1 *Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia and †Marie Bashir Institute for Infectious Diseases and Biosecurity, ‡Charles Perkins Centre, §School of Life and Environmental Sciences, and **Sydney Medical School, The University of Sydney, New South Wales 2006, Australia ORCID IDs: 0000-0003-0970-0153 (J.L.G.); 0000-0001-9596-3552 (E.C.H.) ABSTRACT RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus–host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequenc- ing and metagenomics. KEYWORDS virus; evolution; phylodynamics; phylogeny; metagenomics; quasispecies Introduction: Life at 40 highlighted that RNA viruses have an innate capacity to evolve rapidly. However, they initiated two very different THE year 2018 marks the 40th anniversary of the first pub- avenues of investigation that have effectively run in parallel lished studies on the evolution of viruses. The field of evolu- ever since (Figure 1). tionary virology was inaugurated with two key papers that The paper by Domingo et al. (1978) marks the beginning shaped the way virus evolution was studied in subsequent of experimental studies of RNA virus evolution, in which evo- decades. The first was an experimental study by Domingo and lutionary processes in the short-term are analyzed by either colleagues that showed that individual populations of RNA fi viruses carried abundant genetic variation (Domingo et al. in vitro or in vivo laboratory infections. Arguably the de ning fi 1978). The second, by Palese and co-workers, considered theme of this eld is the idea that the exceptionally high variants of human influenza virus sampled from different mutation rate in RNA viruses means that they evolve accord- “ ” patients to reveal the nature of genetic differences be- ing to a form of group selection known as the quasispecies tween RNA viruses at the interhost, epidemiological scale (Domingo et al. 1978, 2012; Andino and Domingo 2015) (Nakajima et al. 1978; and later Young et al. 1979). These (Box 1). Indeed, the quasispecies concept has become so studies shared a similar theme, understanding the extent widely adopted that it is often cited whenever genetic varia- of genetic variation within and between RNA virus popula- tion is encountered in a viral population, and has even been tions, both utilized oligonucleotide fingerprinting, and both used in nonviral systems (Kuipers et al. 2000; Webb and Blaser 2002; Tannenbaum and Fontanari 2008). In contrast, Copyright © 2018 by the Genetics Society of America the study by Palese and colleagues, with later work by Walter doi: https://doi.org/10.1534/genetics.118.301556 Fitch (Buonagurio et al. 1986; Yamashita et al. 1988; Fitch Manuscript received July 13, 2018; accepted for publication August 31, 2018. 1Corresponding author: School of Life and Environmental Sciences, The University et al. 1991), pioneered comparative studies of RNA virus of Sydney, Sydney, NSW 2006, Australia. E-mail: [email protected] populations that involves the analysis of gene sequences (or Genetics, Vol. 210, 1151–1162 December 2018 1151 the generation and fixation of mutations over time periods amenable to direct human observation, in contrast to most evolutionary changes that occur in higher organisms. Hence, RNA viruses provide a useful natural laboratory to visualize evolutionary processes in real time, including during single- disease outbreaks (Gire et al. 2014). The utility of RNA viruses in experimental assays is enhanced by their small genomes, in which mutations often result in major pheno- typic effects (Moya et al. 2000). It should therefore come as no surprise that RNA viruses have been used to test a variety of evolutionary theories (Turner and Chao 1999) and are powerful exemplars in the development of new methods of bioinformatic analysis (Lemey et al. 2009; Kühnert et al. 2014; To et al. 2016). Although there is also a large amount Figure 1 Approaches to studying RNA virus evolution. The Venn diagram of literature on the evolution of DNA viruses, their usually illustrates the two historical, and largely parallel, strands of research in lower rates of evolutionary change (Duffy et al. 2008) means virus evolution—the experimental and the comparative—that arose in the that they are generally less suited for use as model systems late 1970s. They generally only overlap in the study of a limited number and they will not be considered here. of interhost virus transmission events that often involve a substantial population bottleneck. Through the use of in vitro or in vivo model sys- To achieve a holistic understanding of RNA virus evolution tems, experimental studies largely focus on evolution in the short-term, it is important to bridge the divide between studies based on particularly that which occurs within individual hosts. In contrast, com- experimental approaches and those that utilize comparative, parative approaches deal with interhost, epidemiological-scale dynamics and usually phylogenetic, methods (Figure 1). Experimental that entail multiple rounds of interhost transmission and are usually based approaches are strongly focused toward studying evolution- on phylogenetic analyses. We suggest that a new evolutionary genetics approach is required to bridge this divide. ary change at the intrahost scale, which only represents a tiny, albeit hugely important, component of the overall evo- lutionary process. They also risk establishing inaccurate gen- other genetic markers) sampled from different individuals in eral rules for RNA virus evolution if they are founded on the a population. From this arose the modern science of molec- analysis of a limited number of case studies. For example, ular epidemiology, in which phylogenetic analysis is used to while poliovirus has been one of the mainstays of experimen- reveal evolutionary relationships among virus sequences tal approaches to studying viral evolution [for example, sampled from different individuals, often during disease out- Vignuzzi et al. (2006) and Stern et al. (2017)] and has pro- breaks, in turn leading to inferences on the underlying pat- vided a wealth of valuable biological data (Regoes et al. terns and processes of virus evolution (Holmes 2009; 2005), the evolution of poliovirus in the laboratory may not Moratorio and Vignuzzi 2018). always reflect that in nature and it is mistaken to think that it An unfortunate by-product of this siloed approach has been is representative of all viruses. RNA viruses vary widely, hav- the coexistence of two views of RNA virus evolution that are ing markedly different genome structures and replication often more antagonistic than complementary.We believe that cycles, infecting different hosts, possessing different propen- these differing world views are, in part, a reflection of their sities for disease, and experiencing variable rates of mutation contrasting methodological perspectives. With the ability of and recombination. next-generation sequencing and metagenomics to rapidly There is a similar danger in generalizing results from generate vast amounts of gene sequence data, from within experimental systems that do not reflect the natural host individual hosts to global populations (Firth and Lipkin 2013; range of the virus in question. For example, the textbook Willner and Hugenholtz 2013; Zhang et al. 2018), we suggest example of the evolution of pathogen virulence involves the that the time is right to bring the experimental and the com- release of myxomavirus (MYXV; a double-stranded DNA parative approaches together. Herein, we set out a frame- virus) as a biological control against European rabbits in work for this new synthesis, outlining some of the key Australia (Kerr et al. 2012). Experimental approaches using outcomes of the last 40 years of virus evolution research, cell culture have been used in determining which mutations noting areas of agreement and continuing contention, and in the MYXV genome might be responsible for the profound establishing a potential