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1.  Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts 
PLoS Pathogens  2016;12(12):e1006041.
The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.
Author Summary
Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.
doi:10.1371/journal.ppat.1006041
PMCID: PMC5158080  PMID: 27977811
2.  Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia 
Virology Journal  2016;13:206.
Biological invasions are a major threat to global biodiversity. Australia has experienced many invasive species, with the common carp (Cyprinus carpio L.) a prominent example. Cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biological control (biocontrol) agent for invasive carp in Australia. Safety and efficacy are critical factors in assessing the suitability of biocontrol agents, and extensive host-specificity testing suggests that CyHV-3 is safe. Efficacy depends on the relationship between virus transmissibility and virulence. Based on observations from natural outbreaks, as well as the biology of virus-host interactions, we hypothesize that (i) close contact between carp provides the most efficient transmission of virus, (ii) transmission occurs at regular aggregations of carp that favour recrudescence of latent virus, and (iii) the initially high virulence of CyHV-3 will decline following its release in Australia. We also suggest that the evolution of carp resistance to CyHV-3 will likely necessitate the future release of progressively more virulent strains of CyHV-3, and/or an additional broad-scale measure(s) to complement the effect of the virus. If the release of CyHV-3 does go ahead, longitudinal studies are required to track the evolution of a virus-host relationship from its inception, and particularly the complex interplay between transmission, virulence and host resistance.
doi:10.1186/s12985-016-0666-4
PMCID: PMC5146810  PMID: 27931224
Biological invasion; Cyprinus carpio; Cyprinid herpesvirus 3; Host specificity; Virulence; Transmission; Evolution; Virus
3.  Cell Walls and the Convergent Evolution of the Viral Envelope 
SUMMARY
Why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. The viral envelope serves several functions, including protecting the RNA or DNA molecule(s), evading recognition by the immune system, and facilitating virus entry. Despite these commonalities, viral envelopes come in a wide variety of shapes and configurations. The evolution of the viral envelope is made more puzzling by the fact that nonenveloped viruses are able to infect a diverse range of hosts across the tree of life. We reviewed the entry, transmission, and exit pathways of all (101) viral families on the 2013 International Committee on Taxonomy of Viruses (ICTV) list. By doing this, we revealed a strong association between the lack of a viral envelope and the presence of a cell wall in the hosts these viruses infect. We were able to propose a new hypothesis for the existence of enveloped and nonenveloped viruses, in which the latter represent an adaptation to cells surrounded by a cell wall, while the former are an adaptation to animal cells where cell walls are absent. In particular, cell walls inhibit viral entry and exit, as well as viral transport within an organism, all of which are critical waypoints for successful infection and spread. Finally, we discuss how this new model for the origin of the viral envelope impacts our overall understanding of virus evolution.
doi:10.1128/MMBR.00017-15
PMCID: PMC4651029  PMID: 26378223
4.  17th Century Variola Virus Reveals the Recent History of Smallpox 
Current Biology  2016;26(24):3407-3412.
Summary
Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1, 2, 3, 4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4, 5, 6, 7, 8, 9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4, 5, 6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.
Highlights
•Variola virus genome was reconstructed from a 17th century mummified child•The archival strain is basal to all 20th century strains, with same gene degradation•Molecular-clock analyses show that much of variola virus evolution occurred recently
Using ancient DNA sequences of variola virus recovered from the mummified remains of a 17th century child, Duggan et al. reconstruct the evolutionary history of smallpox. With the ancient strain, the genetic diversification of the smallpox virus is found to be more recent than previously supposed and concurrent with the onset of widespread vaccination.
doi:10.1016/j.cub.2016.10.061
PMCID: PMC5196022  PMID: 27939314
variola virus; smallpox; ancient DNA; Lithuanian Mummy Project; evolution; molecular clock; phylogeny
5.  Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species 
Scientific Reports  2016;6:38770.
Rickettsiales are important zoonotic pathogens, causing severe disease in humans globally. Although mosquitoes are an important vector for diverse pathogens, with the exception of members of the genus Wolbachia little is known about their role in the transmission of Rickettsiales. Herein, Rickettsiales were identified by PCR in five species of mosquitoes (Anopheles sinensis, Armigeres subalbatus, Aedes albopictus, Culex quinquefasciatus and Cu. tritaeniorhynchus) collected from three Chinese provinces during 2014–2015. Subsequent phylogenetic analyses of the rrs, groEL and gltA genes revealed the presence of Anaplasma, Ehrlichia, Candidatus Neoehrlichia, and Rickettsia bacteria in mosquitoes, comprising nine documented and five tentative species bacteria, as well as three symbionts/endosybionts. In addition, bacteria were identified in mosquito eggs, larvae, and pupae sampled from aquatic environments. Hence, these data suggest that Rickettsiales circulate widely in mosquitoes in nature. Also of note was that Ehrlichia and Rickettsia bacteria were detected in each life stage of laboratory cultured mosquitoes, suggesting that Rickettsiales may be maintained in mosquitoes through both transstadial and transovarial transmission. In sum, these data indicate that mosquitoes may have played an important role in the transmission and evolution of Rickettsiales in nature.
doi:10.1038/srep38770
PMCID: PMC5146937  PMID: 27934910
6.  Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia 
Emerging Infectious Diseases  2016;22(12):2146-2148.
Dengue virus type 2 was isolated from a tourist who returned from Borneo to Australia. Phylogenetic analysis identified this virus as highly divergent and occupying a basal phylogenetic position relative to all known human and sylvatic dengue virus type 2 strains and the most divergent lineage not assigned to a new serotype.
doi:10.3201/eid2212.160813
PMCID: PMC5189156  PMID: 27869598
dengue virus; dengue virus type 2; DENV-2; viruses; traveler; divergence; phylogeny; evolution; sylvatic cycle; Borneo; Australia
7.  Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment 
Journal of Virology  2015;90(2):862-872.
ABSTRACT
The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers.
IMPORTANCE How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
doi:10.1128/JVI.02305-15
PMCID: PMC4702690  PMID: 26512086
8.  Human Adaptation of Ebola Virus during the West African Outbreak 
Cell  2016;167(4):1079-1087.e5.
Summary
The 2013–2016 outbreak of Ebola virus (EBOV) in West Africa was the largest recorded. It began following the cross-species transmission of EBOV from an animal reservoir, most likely bats, into humans, with phylogenetic analysis revealing the co-circulation of several viral lineages. We hypothesized that this prolonged human circulation led to genomic changes that increased viral transmissibility in humans. We generated a synthetic glycoprotein (GP) construct based on the earliest reported isolate and introduced amino acid substitutions that defined viral lineages. Mutant GPs were used to generate a panel of pseudoviruses, which were used to infect different human and bat cell lines. These data revealed that specific amino acid substitutions in the EBOV GP have increased tropism for human cells, while reducing tropism for bat cells. Such increased infectivity may have enhanced the ability of EBOV to transmit among humans and contributed to the wide geographic distribution of some viral lineages.
Graphical Abstract
Highlights
•EBOV adapted to humans during the West African outbreak•Amino acid substitutions in the EBOV glycoprotein increase human cell tropism•The same glycoprotein amino acid substitutions decrease tropism for bat cells
The Ebola virus acquired amino acid substitutions in its glycoprotein that increased its tropism for human cells during the West African outbreak of 2013–2016.
doi:10.1016/j.cell.2016.10.013
PMCID: PMC5101188  PMID: 27814505
Ebola virus; Makona; pseudovirus; tropism; human; bat; adaptation; evolution; epistasis
9.  Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States 
Journal of Virology  2016;90(4):1997-2007.
ABSTRACT
In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies.
IMPORTANCE Until recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.
doi:10.1128/JVI.02418-15
PMCID: PMC4733988  PMID: 26656685
10.  Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses 
Journal of Virology  2015;90(2):659-669.
ABSTRACT
Viruses of the family Flaviviridae are important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to the Flaviviridae in a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the known Flaviviridae (“flavi-like” viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with the Flaviviridae in the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of the Flaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that the Flaviviridae infect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated.
IMPORTANCE The family Flaviviridae of RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of the Flaviviridae has largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of the Flaviviridae and related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.
doi:10.1128/JVI.02036-15
PMCID: PMC4702705  PMID: 26491167
11.  A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene 
PLoS Pathogens  2016;12(9):e1005883.
The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3’-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.
Author Summary
Recombination is commonly reported in coronaviruses, and is an important mechanism by which these viruses generate genetic diversity. To date, however, most such recombination events involve homologous sequences among related viruses. We discovered a novel bat coronavirus that possesses a divergent but functional p10 gene that likely originated from, or shared the ancestry with, an ancestral non-enveloped orthoreovirus, thereby representing the outcome of heterologous recombination. We report herein a fusion-associated small transmembrane (FAST) protein encoded in an enveloped virus that arose through a putative inter-family recombination between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus. These findings shed important new light on the mechanisms of viral evolution and particularly the importance and scope of heterologous recombination.
doi:10.1371/journal.ppat.1005883
PMCID: PMC5038965  PMID: 27676249
12.  Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia 
Journal of Virology  2015;89(23):12217-12220.
To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.
doi:10.1128/JVI.01937-15
PMCID: PMC4645337  PMID: 26378178
13.  Cross-validation to select Bayesian hierarchical models in phylogenetics 
Background
Recent developments in Bayesian phylogenetic models have increased the range of inferences that can be drawn from molecular sequence data. Accordingly, model selection has become an important component of phylogenetic analysis. Methods of model selection generally consider the likelihood of the data under the model in question. In the context of Bayesian phylogenetics, the most common approach involves estimating the marginal likelihood, which is typically done by integrating the likelihood across model parameters, weighted by the prior. Although this method is accurate, it is sensitive to the presence of improper priors. We explored an alternative approach based on cross-validation that is widely used in evolutionary analysis. This involves comparing models according to their predictive performance.
Results
We analysed simulated data and a range of viral and bacterial data sets using a cross-validation approach to compare a variety of molecular clock and demographic models. Our results show that cross-validation can be effective in distinguishing between strict- and relaxed-clock models and in identifying demographic models that allow growth in population size over time. In most of our empirical data analyses, the model selected using cross-validation was able to match that selected using marginal-likelihood estimation. The accuracy of cross-validation appears to improve with longer sequence data, particularly when distinguishing between relaxed-clock models.
Conclusions
Cross-validation is a useful method for Bayesian phylogenetic model selection. This method can be readily implemented even when considering complex models where selecting an appropriate prior for all parameters may be difficult.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-016-0688-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-016-0688-y
PMCID: PMC4880944  PMID: 27230264
Model selection; Cross-validation; Bayesian phylogenetics; Molecular clock; Demographic models; Marginal likelihood
14.  Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy 
Infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) are the most important viral pathogens impacting rainbow trout farming. These viruses are persistent in Italy, where they are responsible for severe disease outbreaks (epizootics) that affect the profitability of the trout industry. Despite the importance of IHNV and VHSV, little is known about their evolution at a local scale, although this is likely to be important for virus eradication and control. To address this issue we performed a detailed molecular evolutionary and epidemiological analysis of IHNV and VHSV in trout farms from northern Italy. Full-length glycoprotein gene sequences of a selection of VHSV (n = 108) and IHNV (n = 89) strains were obtained. This revealed that Italian VHSV strains belong to sublineages Ia1 and Ia2 of genotype Ia and are distributed into 7 genetic clusters. In contrast, all Italian IHNV isolates fell within genogroup E, for which only a single genetic cluster was identified. More striking was that IHNV has evolved more rapidly than VHSV (mean rates of 11 and 7.3 × 10−4 nucleotide substitutions per site, per year, respectively), indicating that these viruses exhibit fundamentally different evolutionary dynamics. The time to the most recent common ancestor of both IHNV and VHSV was consistent with the first reports of these pathogens in Italy. By combining sequence data with epidemiological information it was possible to identify different patterns of virus spread among trout farms, in which adjacent facilities can be infected by either genetically similar or different viruses, and farms located in different water catchments can be infected by identical strains. Overall, these findings highlight the importance of combining molecular and epidemiological information to identify the determinants of IHN and VHS spread, and to provide data that is central to future surveillance strategies and possibly control.
doi:10.3389/fmicb.2016.01306
PMCID: PMC4994472  PMID: 27602026
VHSV; IHNV; phylogeny; evolution; molecular epidemiology
15.  Complexities of Estimating Evolutionary Rates in Viruses 
Journal of Virology  2016;90(4):2155.
doi:10.1128/JVI.02570-15
PMCID: PMC4734009  PMID: 26822594
16.  Comparative Phylodynamics of Rabbit Hemorrhagic Disease Virus in Australia and New Zealand 
Journal of Virology  2015;89(18):9548-9558.
ABSTRACT
The introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand during the 1990s as a means of controlling feral rabbits is an important case study in viral emergence. Both epidemics are exceptional in that the founder viruses share an origin and the timing of their release is known, providing a unique opportunity to compare the evolution of a single virus in distinct naive populations. We examined the evolution and spread of RHDV in Australia and New Zealand through a genome-wide evolutionary analysis, including data from 28 newly sequenced RHDV field isolates. Following the release of the Australian inoculum strain into New Zealand, no subsequent mixing of the populations occurred, with viruses from both countries forming distinct groups. Strikingly, the rate of evolution in the capsid gene was higher in the Australian viruses than in those from New Zealand, most likely due to the presence of transient deleterious mutations in the former. However, estimates of both substitution rates and population dynamics were strongly sample dependent, such that small changes in sample composition had an important impact on evolutionary parameters. Phylogeographic analysis revealed a clear spatial structure in the Australian RHDV strains, with a major division between those viruses from western and eastern states. Importantly, RHDV sequences from the state where the virus was first released, South Australia, had the greatest diversity and were diffuse throughout both geographic lineages, such that this region was likely a source population for the subsequent spread of the virus across the country.
IMPORTANCE Most studies of viral emergence lack detailed knowledge about which strains were founders for the outbreak or when these events occurred. Hence, the human-mediated introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand from known starting stocks provides a unique opportunity to understand viral evolution and emergence. Within Australia, we revealed a major phylogenetic division between viruses sampled from the east and west of the country, with both regions likely seeded by viruses from South Australia. Despite their common origins, marked differences in evolutionary rates were observed between the Australian and New Zealand RHDV, which led to conflicting conclusions about population growth rates. An analysis of mutational patterns suggested that evolutionary rates have been elevated in the Australian viruses, at least in part due to the presence of low-fitness (deleterious) variants that have yet to be selectively purged.
doi:10.1128/JVI.01100-15
PMCID: PMC4542356  PMID: 26157125
17.  Quantifying influenza virus diversity and transmission in humans 
Nature genetics  2016;48(2):195-200.
Influenza A virus is characterized by high genetic diversity.1–3 However, most of what we know about influenza evolution has come from consensus sequences sampled at the epidemiological scale4 that only represent the dominant virus lineage within each infected host. Less is known about the extent of intra-host virus diversity and what proportion is transmitted between individuals.5 To characterize those virus variants that achieve sustainable transmission in new hosts, we examined intra-host virus genetic diversity within household donor/recipient pairs from the first wave of the 2009 H1N1 pandemic when seasonal H3N2 was co-circulating. While the same variants were found in multiple members of the community, the relative frequencies of variants fluctuated, with patterns of genetic variation more similar within than between households. We estimated the effective population size of influenza A virus across donor/recipient pairs to be approximately 100–200 contributing members, which enabled the transmission of multiple lineages including antigenic variants.
doi:10.1038/ng.3479
PMCID: PMC4731279  PMID: 26727660
Influenza A virus; evolution; diversity; virus transmission; next generation sequencing
18.  Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range 
Journal of Virology  2015;90(2):753-767.
ABSTRACT
Sylvatic carnivores, such as raccoons, have recently been recognized as important hosts in the evolution of canine parvovirus (CPV), a pandemic pathogen of domestic dogs. Although viruses from raccoons do not efficiently bind the dog transferrin receptor (TfR) or infect dog cells, a single mutation changing an aspartic acid to a glycine at capsid (VP2) position 300 in the prototype raccoon CPV allows dog cell infection. Because VP2 position 300 exhibits extensive amino acid variation among the carnivore parvoviruses, we further investigated its role in determining host range by analyzing its diversity and evolution in nature and by creating a comprehensive set of VP2 position 300 mutants in infectious clones. Notably, some position 300 residues rendered CPV noninfectious for dog, but not cat or fox, cells. Changes of adjacent residues (residues 299 and 301) were also observed often after cell culture passage in different hosts, and some of the mutations mimicked changes seen in viruses recovered from natural infections of alternative hosts, suggesting that compensatory mutations were selected to accommodate the new residue at position 300. Analysis of the TfRs of carnivore hosts used in the experimental evolution studies demonstrated that their glycosylation patterns varied, including a glycan present only on the domestic dog TfR that dictates susceptibility to parvoviruses. Overall, there were significant differences in the abilities of viruses with alternative position 300 residues to bind TfRs and infect different carnivore hosts, demonstrating that the process of infection is highly host dependent and that VP2 position 300 is a key determinant of host range.
IMPORTANCE Although the emergence and pandemic spread of canine parvovirus (CPV) are well documented, the carnivore hosts and evolutionary pathways involved in its emergence remain enigmatic. We recently demonstrated that a region in the capsid structure of CPV, centered around VP2 position 300, varies after transfer to alternative carnivore hosts and may allow infection of previously nonsusceptible hosts in vitro. Here we show that VP2 position 300 is the most variable residue in the parvovirus capsid in nature, suggesting that it is a critical determinant in the cross-species transfer of viruses between different carnivores due to its interactions with the transferrin receptor to mediate infection. To this end, we demonstrated that there are substantial differences in receptor binding and infectivity of various VP2 position 300 mutants for different carnivore species and that single mutations in this region can influence whether a host is susceptible or refractory to virus infection.
doi:10.1128/JVI.02636-15
PMCID: PMC4702700  PMID: 26512077
19.  Ledantevirus: A Proposed New Genus in the Rhabdoviridae Has A Strong Ecological Association with Bats 
The Le Dantec serogroup of rhabdoviruses comprises Le Dantec virus from a human with encephalitis and Keuriliba virus from rodents, each isolated in Senegal. The Kern Canyon serogroup comprises a loosely connected set of rhabdoviruses many of which have been isolated from bats, including Kern Canyon virus from California, Nkolbisson virus from Cameroon, Central African Republic, and Cote d'Ivoire, Kolente virus from Guinea, Mount Elgon bat and Fikirini viruses from Kenya, and Oita virus from Japan. Fukuoka virus isolated from mosquitoes, midges, and cattle in Japan, Barur virus from a rodent in India and Nishimuro virus from pigs in Japan have also been linked genetically or serologically to this group. Here, we analyze the genome sequences and phylogenetic relationships of this set of viruses. We show that they form three subgroups within a monophyletic group, which we propose should constitute the new genus Ledantevirus.
doi:10.4269/ajtmh.14-0606
PMCID: PMC4347348  PMID: 25487727
20.  Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus 
eLife  null;5:e12994.
The 14th–18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague’s persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
DOI: http://dx.doi.org/10.7554/eLife.12994.001
eLife digest
A bacterium called Yersina pestis is responsible for numerous human outbreaks of plague throughout history. It is carried by rats and other rodents and can spread to humans causing what we conventionally refer to as plague. The most notorious of these plague outbreaks – the Black Death – claimed millions of lives in Europe in the mid-14th century. Several other plague outbreaks emerged in Europe over the next 400 years. Then, there was a large gap before the plague re-emerged as threat in the 19th century and it continues to infect humans today, though on a smaller scale.
Scientists have extensively studied Y. pestis to understand its origin and how it evolved to become such a deadly threat. These studies led to the assumption that the plague outbreaks of the 14–18th centuries likely originated in rodents in Asia and spread along trade routes to other parts of the world. However, it is not clear why the plague persisted in Europe for 400 years after the Black Death. Could the bacteria have gained a foothold in local rodents instead of being reintroduced from Asia each time? If it did, why did it then disappear for such a long period from the end of the 18th century?
To help answer these questions, Bos, Herbig et al. sequenced the DNA of Y. pestis samples collected from the teeth of five individuals who died of plague during the last major European outbreak of plague in 1722 in Marseille, France. The DNA sequences of these bacterial samples were then compared with the DNA sequences of modern day Y. pestis and other historical samples of the bacteria. The results showed the bacteria in the Marseille outbreak likely evolved from the strain that caused the Black Death back in the 14th century.
The comparisons showed that the strain isolated from the teeth is not found today, and may be extinct. This suggests that a historical reservoir for plague existed somewhere, perhaps in Asia, or perhaps in Europe itself, and was able to cause outbreaks up until the 18th century.Bos, Herbig et al.’s findings may help researchers trying to control the current outbreaks of the plague in Madagascar and other places.
DOI: http://dx.doi.org/10.7554/eLife.12994.002
doi:10.7554/eLife.12994
PMCID: PMC4798955  PMID: 26795402
ancient DNA; yersinia pestis; pathogen genomics; microbial evolution; epidemiology; human history; Other
21.  Dengue viruses cluster antigenically but not as discrete serotypes 
Science (New York, N.Y.)  2015;349(6254):1338-1343.
The four genetically divergent dengue virus (DENV) types are traditionally classified as serotypes. Antigenic and genetic differences among the DENV types influence disease outcome, vaccine-induced protection, epidemic magnitude, and viral evolution. We characterized antigenic diversity in the DENV types by antigenic maps constructed from neutralizing antibody titers obtained from African green monkeys and after human vaccination and natural infections. Genetically, geographically, and temporally, diverse DENV isolates clustered loosely by type, but we found many are as similar antigenically to a virus of a different type as to some viruses of the same type. Primary infection antisera did not neutralize all viruses of the same DENV type any better than other types did up to two years after infection and did not show improved neutralization to homologous type isolates. That the canonical DENV types are not antigenically homogenous has implications for vaccination and research on the dynamics of immunity, disease, and the evolution of DENV.
doi:10.1126/science.aac5017
PMCID: PMC4876809  PMID: 26383952
22.  Assessing the epidemiological impact of Wolbachia deployment for dengue control 
The Lancet. Infectious diseases  2015;15(7):862-866.
Summary
Dengue viruses cause more human morbidity and mortality than any other arthropod-borne virus. Dengue prevention relies primarily on vector control but the failure of traditional methods has promoted the development of novel entomological approaches. Although use of the intracellular bacterium Wolbachia to control mosquito populations was proposed half a century ago, it has only gained significant interest as a potential agent of dengue control in the last decade. Here, we review the evidence that supports a practical approach for dengue reduction through field release of Wolbachia-infected mosquitoes and discuss the additional studies that must be conducted before the strategy can be validated and operationally implemented. A critical next step is to assess the efficacy of Wolbachia deployment in reducing dengue virus transmission. We argue that a cluster-randomized trial is currently premature because Wolbachia strain choice for release as well as deployment strategies are still being optimized. We therefore present a pragmatic approach to acquiring preliminary evidence of efficacy via a suite of complementary methodologies: prospective cohort study, geographical cluster investigation, virus phylogenetic analysis, virus surveillance in mosquitoes, and vector competence assays. This multi-pronged approach could provide valuable intermediate evidence of efficacy to justify a future cluster-randomized trial.
doi:10.1016/S1473-3099(15)00091-2
PMCID: PMC4824166  PMID: 26051887
24.  Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses 
eLife  null;4:e05378.
Although arthropods are important viral vectors, the biodiversity of arthropod viruses, as well as the role that arthropods have played in viral origins and evolution, is unclear. Through RNA sequencing of 70 arthropod species we discovered 112 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses, a number of which are also present as endogenous genomic copies. With this greatly enriched diversity we revealed that arthropods contain viruses that fall basal to major virus groups, including the vertebrate-specific arenaviruses, filoviruses, hantaviruses, influenza viruses, lyssaviruses, and paramyxoviruses. We similarly documented a remarkable diversity of genome structures in arthropod viruses, including a putative circular form, that sheds new light on the evolution of genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution.
DOI: http://dx.doi.org/10.7554/eLife.05378.001
eLife digest
Many illnesses, including influenza, hemorrhagic fever, and rabies, are caused by a group of viruses called negative-sense RNA viruses. The genetic information—or genome—of these viruses is encoded in strands of RNA that must be copied before they can be translated into the proteins needed to build new viruses. It is currently known that there are at least eight different families of these viruses, which have a wide range of shapes and sizes and arrange their RNA in different ways.
Insects, spiders, and other arthropods carry many different RNA viruses. Many of these viruses have not previously been studied, and those that have been studied so far are mainly those that cause diseases in humans and other vertebrates. Researchers therefore only know a limited amount about the diversity of the negative-sense RNA viruses that arthropods harbor and how these viruses evolved. Studying how viruses evolve helps scientists to understand what makes some viruses deadly and others harmless and can also help develop treatments or vaccines for the diseases caused by the viruses.
Li, Shi, Tian, Lin, Kang et al. collected 70 species of insects, spiders, centipedes, and other arthropods in China and sequenced all the negative-sense RNA viruses in the creatures. This revealed an enormous number of negative-sense RNA viruses, including 112 new viruses. Many of the newly discovered arthropod viruses appear to be the ancestors of disease-causing viruses, including influenza viruses and the filoviruses—the group that includes the Ebola virus. Indeed, it appears that arthropods host many—if not all—of the negative-sense RNA viruses that cause disease in vertebrates and plants.
While documenting the new RNA viruses and how they are related to each other, Li et al. found many different genome structures. Some genomes were segmented, which may play an important role in evolution as segments can be easily swapped to create new genetic combinations. Non-segmented and circular genomes were also found. This genetic diversity suggests that arthropods are likely to have played a key role in the evolution of new viruses by acting as a site where many different viruses can interact and exchange genetic information.
DOI: http://dx.doi.org/10.7554/eLife.05378.002
doi:10.7554/eLife.05378
PMCID: PMC4384744  PMID: 25633976
RNA virus; evolution; arthropods; segmentation; negative-sense; phylogeny; viruses
25.  The contrasting phylodynamics of human influenza B viruses 
eLife  null;4:e05055.
A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.
DOI: http://dx.doi.org/10.7554/eLife.05055.001
eLife digest
To develop new therapies against infections caused by a virus, it is important to understand the virus's history—where, when, and why it has caused disease and how it has changed over time. For example, new human strains of the influenza type A virus originate from strains that infect animals and rapidly can become common in human populations. In contrast, influenza type B virus strains almost exclusively infect humans and are continuously present in human populations. Both types have a detrimental impact on global health, but the type B viruses are less well understood, partly because outbreaks have not been as extensively documented.
Vijaykrishna et al. have now investigated the history of the two strains of the influenza type B virus—called Victoria and Yamagata—that currently circulate in humans. To do this, they inspected the genetic sequences of 908 viruses taken from samples of confirmed type B infections collected across Australia and New Zealand over 13 years.
Individual virus particles of the same strain have genetic sequences that are very similar, but not completely identical. Vijaykrishna et al. showed that the diversity of the genetic sequences from the Victoria strain fluctuated between seasons, and particular genetic variants of Victoria only persisted in the population for 1–3 years. This indicates that Victoria viruses are under a lot of pressure to evolve, which results in so-called ‘bottlenecks’ whereby only the viruses carrying particular varieties of genetic sequence survive. This fluctuating pattern resembles that of the better-understood type A seasonal flu strain H3N2.
On the other hand, there was little change in the genetic diversity of the Yamagata strains sampled over the same 13-year period. The Yamagata viruses have diversified to a greater extent and several different ‘varieties’ of the virus tend to circulate together for long periods of time. For example, the three varieties of Yamagata virus circulating in 2013 evolved from a common parent virus that was circulating around 10 years ago.
Vijaykrishna et al. found that between disease outbreaks, there was greater variation in the ability of Victoria viruses to be transmitted in humans, but that they were generally more easily transmitted than the Yamagata viruses. Victoria viruses tend to infect younger patients than Yamagata viruses, which is thought to be due to differences in the molecules that help the viruses enter the cells of the respiratory tract.
These findings suggests that it might be possible to eradicate the more slowly evolving influenza B Yamagata virus through mass vaccination programs using existing vaccines. This would then allow researchers to focus on developing effective vaccines to target the other strains of influenza virus.
DOI: http://dx.doi.org/10.7554/eLife.05055.002
doi:10.7554/eLife.05055
PMCID: PMC4383373  PMID: 25594904
influenza virus; evolution; epidemiology; antigenic drift; human; viruses

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