Molecular evolution of puumala hantavirus in Fennoscandia: phylogenetic analysis of strains from two recolonization routes, Karelia and Denmark

A fatal case of haemorrhagic fever with renal syndrome in Kursk Region, Russia, caused by a novel Puumala virus clade

Haemorrhagic fever with renal syndrome (HFRS) is the most widespread natural-focal human disease in the Russian Federation. In this study, we report virological assessment of a fatal case of HFRS-PUUV (Puumala virus) in the Kursk Region. The infection caused severe multiorgan failure and the maximum viral load was detected in the tissue of the spleen. Viral sequences were obtained from the patient's autopsy material and lung tissues of bank voles captured in the region. These sequences formed a new clade in the PUUV phylogenetic tree, an outgroup to all known Russian (RUS) lineage sequences. On the other hand viruses collected in the Kursk Region grouped with the RUS lineage and are separated from all other PUUV linages. We propose to nominate this novel group as W-RUS as the identified viruses were collected near the western Russian boundary. The recombination signals between their ancestors and RUS lineage representatives from the Volga region were revealed. The strain Samara_94/CG/2005 suggestively emerged as the result of reassortment between the ancestors of W-RUS and DTK-Ufa-97.

Orthohantaviruses, Emerging Zoonotic Pathogens

Orthohantaviruses give rise to the emerging infections such as of hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in Eurasia and the Americas, respectively. In this review we will provide a comprehensive analysis of orthohantaviruses distribution and circulation in Eurasia and address the genetic diversity and evolution of Puumala orthohantavirus (PUUV), which causes HFRS in this region. Current data indicate that the geographical location and migration of the natural hosts can lead to the orthohantaviruses genetic diversity as the rodents adapt to the new environmental conditions. The data shows that a high level of diversity characterizes the genome of orthohantaviruses, and the PUUV genome is the most divergent. The reasons for the high genome diversity are mainly caused by point mutations and reassortment, which occur in the genome segments. However, it still remains unclear whether this diversity is linked to the disease's severity. We anticipate that the information provided in this review will be useful for optimizing and developing preventive strategies of HFRS, an emerging zoonosis with potentially very high mortality rates.

Characterization of the Puumala orthohantavirus Strains in the Northwestern Region of the Republic of Tatarstan in Relation to the Clinical Manifestations in Hemorrhagic Fever With Renal Syndrome Patients

Over 1,000 cases of hemorrhagic fever with renal syndrome (HFRS) were recorded in the Republic of Tatarstan (RT) in 2015. HFRS is a zoonotic disease caused by several different Old World hantaviruses. In RT, Puumala orthohantavirus (PUUV) is a prevalent etiological agent of HFRS. We looked for the genetic link between the PUUV strains isolated from the bank voles and from the infected humans. In addition, possible correlation between the genetic makeup of the PUUV strain involved and different clinical picture of HFRS was investigated. Partial PUUV small (S) genome segment sequences were retrieved from 37 small animals captured in the northwestern region of RT in 2015. Phylogenetic analysis revealed that 34 PUUV sequences clustered with strains of the previously identified “Russia” (RUS) genetic lineage, while 3 remaining PUUV sequences clustered with the known lineage from Finland (FIN). Sequence comparisons showed that the majority of the S-segment sequences isolated in the current study displayed 98.2–100.0% sequence identity when compared with the strains isolated earlier from the HFRS patients hospitalized in Kazan city. HFRS patients infected with PUUV strains of either RUS or FIN genetic lineages were observed to have consistent differences in clinical presentation of the disease and laboratory findings. These findings indicated a strong genetic link between the infected bank voles and human HFRS cases from the same localities. Thus, S-segment sequences of the PUUV strains isolated from HFRS patients could serve as a molecular marker for determining the likely geographic area where infection occurred.

Phylogeography of Puumala orthohantavirus in Europe

Puumala virus is an RNA virus hosted by the bank vole (Myodes glareolus) and is today present in most European countries. Whilst it is generally accepted that hantaviruses have been tightly co-evolving with their hosts, Puumala virus (PUUV) evolutionary history is still controversial and so far has not been studied at the whole European level. This study attempts to reconstruct the phylogeographical spread of modern PUUV throughout Europe during the last postglacial period in the light of an upgraded dataset of complete PUUV small (S) segment sequences and by using most recent computational approaches. Taking advantage of the knowledge on the past migrations of its host, we identified at least three potential independent dispersal routes of PUUV during postglacial recolonization of Europe by the bank vole. From the Alpe-Adrian region (Balkan, Austria, and Hungary) to Western European countries (Germany, France, Belgium, and Netherland), and South Scandinavia. From the vicinity of Carpathian Mountains to the Baltic countries and to Poland, Russia, and Finland. The dissemination towards Denmark and North Scandinavia is more hypothetical and probably involved several independent streams from south and north Fennoscandia.

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus RNA by reverse transcription polymerase chain reaction (RT-PCR). Phylogenies inferred from the L-, M-, and S-segment sequences of 30 JMSV strains were compared with host mitochondrial cytochrome b. Viral clades largely corresponded to host clades, which were primarily structured by geography and were consistent with hypothesized post-glacial expansion. Despite an overall congruence between host and viral gene phylogenies at deeper scales, phylogenetic signals were recovered that also suggested a complex pattern of host switching and at least one reassortment event in the evolutionary history of JMSV. A fundamental understanding of how orthohantaviruses respond to periods of host population expansion, contraction, and secondary host contact is the key to establishing a framework for both more comprehensive understanding of orthohantavirus evolutionary dynamics and broader insights into host–pathogen systems.

Evolution and postglacial colonization of Seewis hantavirus with Sorex araneus in Finland

Hantaviruses have co-existed with their hosts for millions of years. Seewis virus (SWSV), a soricomorph-borne hantavirus, is widespread in Eurasia, ranging from Central Siberia to Western Europe. To gain insight into the phylogeography and evolutionary history of SWSV in Finland, lung tissue samples of 225 common shrews (Sorex araneus) trapped from different parts of Finland were screened for the presence of SWSV RNA. Forty-two of the samples were positive. Partial small (S), medium (M) and large (L) segments of the virus were sequenced, and analyzed together with all SWSV sequences available in Genbank. The phylogenetic analysis of the partial S-segment sequences suggested that all Finnish SWSV strains shared their most recent common ancestor with the Eastern European strains, while the L-segment suggested multiple introductions. The difference between the L- and S-segment phylogenies implied that reassortment events play a role in the evolution of SWSV. Of the Finnish strains, variants from Eastern Finland occupied the root position in the phylogeny, and had the highest genetic diversity, supporting the hypothesis that SWSV reached Finland first form the east. During the spread in Finland, the virus has formed three separate lineages, identified here by correlation analysis of genetic versus geographic distance combined with median-joining network analysis. These results support the hypothesis that Finnish SWSV recolonized Finland with its host, the common shrew, from east after the last ice age 12,000-8000years ago, and then subsequently spread along emerging land bridges towards west or north with the migration and population expansion of its host.

Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery

Bunyaviridae family is the largest and most diverse family of RNA viruses. It has more than 350 members divided into five genera: Orthobunyavirus, Phlebovirus, Nairovirus, Hantavirus, and Tospovirus. They are present in the five continents, causing recurrent epidemics, epizootics, and considerable agricultural loss. The genome of bunyaviruses is divided into three segments of negative single-stranded RNA according to their relative size: L (Large), M (Medium) and S (Small) segment. Bunyaviridae RNA-dependent RNA polymerase (RdRp) is encoded by the L segment, and is in charge of the replication and transcription of the viral RNA in the cytoplasm of the infected cell. Viral RdRps share a characteristic right hand-like structure with three subdomains: finger, palm, and thumb subdomains that define the formation of the catalytic cavity. In addition to the N-terminal endonuclease domain, eight conserved motifs (A-H) have been identified in the RdRp of Bunyaviridae. In this review, we have summarized the recent insights from the structural and functional studies of RdRp to understand the roles of different motifs shared by RdRps, the mechanism of viral RNA replication, genome segment packaging by the nucleoprotein, cap-snatching, mRNA transcription, and other RNA mechanisms of bunyaviruses.

Reservoir-Driven Heterogeneous Distribution of Recorded Human Puumala virus Cases in South-West Germany

Endemic regions for Puumala virus (PUUV) are located in the most affected federal state Baden-Wuerttemberg, South-West Germany, where high numbers of notified human hantavirus disease cases have been occurring for a long time. The distribution of human cases in Baden-Wuerttemberg is, however, heterogeneous, with a high number of cases recorded during 2012 in four districts (H districts) but a low number or even no cases recorded in four other districts (L districts). Bank vole monitoring during 2012, following a beech (Fagus sylvatica) mast year, resulted in the trapping of 499 bank voles, the host of PUUV. Analyses indicated PUUV prevalences of 7-50% (serological) and 1.8-27.5% (molecular) in seven of eight districts, but an absence of PUUV in one L district. The PUUV prevalence differed significantly between bank voles in H and L districts. In the following year 2013, 161 bank voles were trapped, with reduced bank vole abundance in almost all investigated districts except one. In 2013, no PUUV infections were detected in voles from seven of eight districts. In conclusion, the linear modelling approach indicated that the heterogeneous distribution of human PUUV cases in South-West Germany was caused by different factors including the abundance of PUUV RNA-positive bank voles, as well as by the interaction of beech mast and the proportional coverage of beech and oak (Quercus spec.) forest per district. These results can aid developing local public health risk management measures and early warning models.

Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.

Hokkaido genotype of Puumala virus in the grey red-backed vole (Myodes rufocanus) and northern red-backed vole (Myodes rutilus) in Siberia

Three species of Myodes voles known to harbor hantaviruses include the bank vole (Myodes glareolus), which serves as the reservoir host of Puumala virus (PUUV), the prototype arvicolid rodent-borne hantavirus causing hemorrhagic fever with renal syndrome (HFRS) in Europe, and the grey red-backed vole (Myodes rufocanus) and royal vole (Myodes regulus) which carry two PUUV-like hantaviruses, designated Hokkaido virus (HOKV) and Muju virus (MUJV), respectively. To ascertain the hantavirus harbored by the northern red-backed vole (Myodes rutilus), we initially screened sera from 233 M. rutilus, as well as from 90 M. rufocanus and 110 M. glareolus, captured in western and eastern Siberia during June 2007 to October 2009, for anti-hantaviral antibodies. Thereafter, lung tissues from 44 seropositive voles were analyzed for hantavirus RNA by reverse transcription-polymerase chain reaction. Partial L-, M- and S-segment sequences, detected in M. rutilus and M. rufocanus, were closely related to HOKV, differing from previously published L-, M- and S-segment sequences of HOKV by 17.8-20.2%, 15.9-23.4% and 15.0-17.0% at the nucleotide level and 2.6-7.9%, 1.3-6.3% and 1.2-4.0% at the amino acid level, respectively. Alignment and comparison of hantavirus sequences from M. glareolus trapped in Tyumen Oblast showed very high sequence similarity to the Omsk lineage of PUUV. Phylogenetic analysis, using neighbor-joining, maximal likelihood and Bayesian methods, showed that HOKV strains shared a common ancestry with PUUV and exhibited geographic-specific clustering. This report provides the first molecular evidence that both M. rutilus and M. rufocanus harbor HOKV, which might represent a genetic variant of PUUV.

Life-long shedding of Puumala hantavirus in wild bank voles (Myodes glareolus)

The knowledge of viral shedding patterns and viraemia in the reservoir host species is a key factor in assessing the human risk of zoonotic viruses. The shedding of hantaviruses (family Bunyaviridae) by their host rodents has widely been studied experimentally, but rarely in natural settings. Here we present the dynamics of Puumala hantavirus (PUUV) shedding and viraemia in naturally infected wild bank voles (Myodes glareolus). In a monthly capture-mark-recapture study, we analysed 18 bank voles for the presence and relative quantity of PUUV RNA in the excreta and blood from 2 months before up to 8 months after seroconversion. The proportion of animals shedding PUUV RNA in saliva, urine and faeces peaked during the first month after seroconversion, but continued throughout the study period with only a slight decline. The quantity of shed PUUV in reverse transcription quantitative PCR (RT-qPCR) positive excreta was constant over time. In blood, PUUV RNA was present for up to 7 months but both the probability of viraemia and the virus load declined with time. Our findings contradict the current view of a decline in virus shedding after the acute phase and a short viraemic period in hantavirus infection - an assumption widely adopted in current epidemiological models. We suggest the life-long shedding as a means of hantaviruses to survive over host population bottlenecks, and to disperse in fragmented habitats where local host and/or virus populations face temporary extinctions. Our results indicate that the kinetics of pathogens in wild hosts may differ considerably from those observed in laboratory settings.

Hantaviruses in Finnish soricomorphs: evidence for two distinct hantaviruses carried by Sorex araneus suggesting ancient host-switch

Hantaviruses are emerging viruses carried by rodents, soricomorphs (shrews and moles) and bats. In Finland, Puumala virus (PUUV) was for years the only hantavirus detected. In 2009, however, Seewis virus (SWSV) was reported from archival common shrew (Sorex araneus) samples collected in 1982 in Finland. To elucidate the diversity of hantaviruses in soricomorphs in Finland, 180 individuals were screened, representing seven species captured from 2001 to 2012: hantavirus RNA was screened using RT-PCR, and hantaviral antigen using immunoblotting with polyclonal antibodies raised against truncated SWSV nucleocapsid protein. The overall hantavirus RNA prevalence was 14% (26/180), antigen could be demonstrated in 9 of 20 SWSV RT-PCR positive common shrews. Genetic analyses revealed that four soricomorph-borne hantaviruses circulate in Finland, including Boginia virus (BOGV) in water shrew (Neomys fodiens) and Asikkala virus (ASIV) in pygmy shrew (Sorex minutus). Interestingly, on two study sites, common shrews harbored strains of two different hantaviruses: Seewis virus and a new distinct, genetically distant (identity 57% at amino acid level) virus (Altai-like virus) which clusters together with viruses in the basal phylogroup I of hantaviruses with 62-67% identity at amino acid level. This is the first evidence of coexistence of two clearly distinct hantavirus species circulating simultaneously in one host species population. The findings suggest an ancient host-switching event from a yet unknown host to S. araneus. In addition, phylogenetic analyses of partial S and M segment sequences showed that SWSV in Finland represents a unique genotype in Europe.

Survey for hantaviruses, tick-borne encephalitis virus, and Rickettsia spp. in small rodents in Croatia

In Croatia, several rodent- and vector-borne agents are endemic and of medical importance. In this study, we investigated hantaviruses and, for the first time, tick-borne encephalitis virus (TBEV) and Rickettsia spp. in small wild rodents from two different sites (mountainous and lowland region) in Croatia. In total, 194 transudate and tissue samples from 170 rodents (A. flavicollis, n=115; A. agrarius, n=2; Myodes glareolus, n=53) were tested for antibodies by indirect immunofluorescence assays (IIFT) and for nucleic acids by conventional (hantaviruses) and real-time RT-/PCRs (TBEV and Rickettsia spp.). A total of 25.5% (24/94) of the rodents from the mountainous area revealed specific antibodies against hantaviruses. In all, 21.3% (20/94) of the samples from the mountainous area and 29.0% (9/31) from the lowland area yielded positive results for either Puumala virus (PUUV) or Dobrava-Belgrade virus (DOBV) using a conventional RT-PCR. All processed samples (n=194) were negative for TBEV by IIFT or real-time RT-PCR. Serological evidence of rickettsial infection was detected in 4.3% (4/94) rodents from the mountainous region. Another 3.2% (3/94) rodents were positive for Rickettsia spp. by real-time PCR. None of the rodents (n=76) from the lowland area were positive for Rickettsia spp. by real-time PCR. Dual infection of PUUV and Rickettsia spp. was found in one M. glareolus from the mountainous area by RT-PCR and real-time PCR, respectively. To our knowledge, this is the first detection of Rickettsia spp. in small rodents from Croatia. Phylogenetic analyses of S- and M-segment sequences obtained from the two study sites revealed well-supported subgroups in Croatian PUUV and DOBV. Although somewhat limited, our data showed occurrence and prevalence of PUUV, DOBV, and rickettsiae in Croatia. Further studies are warranted to confirm these data and to determine the Rickettsia species present in rodents in these areas.

Hantavirus reservoirs: current status with an emphasis on data from Brazil

Since the recognition of hantavirus as the agent responsible for haemorrhagic fever in Eurasia in the 1970s and, 20 years later, the descovery of hantavirus pulmonary syndrome in the Americas, the genus Hantavirus has been continually described throughout the World in a variety of wild animals. The diversity of wild animals infected with hantaviruses has only recently come into focus as a result of expanded wildlife studies. The known reservoirs are more than 80, belonging to 51 species of rodents, 7 bats (order Chiroptera) and 20 shrews and moles (order Soricomorpha). More than 80genetically related viruses have been classified within Hantavirus genus; 25 recognized as human pathogens responsible for a large spectrum of diseases in the Old and New World. In Brazil, where the diversity of mammals and especially rodents is considered one of the largest in the world, 9 hantavirus genotypes have been identified in 12 rodent species belonging to the genus Akodon, Calomys, Holochilus, Oligoryzomys, Oxymycterus, Necromys and Rattus. Considering the increasing number of animals that have been implicated as reservoirs of different hantaviruses, the understanding of this diversity is important for evaluating the risk of distinct hantavirus species as human pathogens.

Co-circulation of two Puumala hantavirus lineages in Latvia: a Russian lineage described previously and a novel Latvian lineage

Puumala hantavirus (PUUV) causes a mild form of haemorrhagic fever with renal syndrome in Europe. Seven genetic lineages of PUUV have thus far been recorded, which exhibit geographic structure within the distribution of its natural host, the bank vole (Myodes glareolus). This study presents evidence for two distinct PUUV lineages co-circulating in Latvia: one previously described from Russia and a novel one that appears to be endemic. The Latvian lineage (LAT) is considerably divergent and several amino acid markers make it easily distinguishable. Phylogenetic analysis suggested a possibility of different evolutionary histories for the PUUV genome segments of LAT.

Rate of evolution and molecular epidemiology of tick-borne encephalitis virus in Europe, including two isolations from the same focus 44 years apart

Tick-borne encephalitis virus (TBEV) is a member of the family Flaviviridae. It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of cases of meningoencephalitis in Europe annually, with an increasing trend. The increase may be attributed to a complex network of elements, including climatic, environmental and socio-economic factors. In an attempt to understand the evolutionary history and dispersal of TBEV, to existing genetic data we add two novel complete ORF sequences of TBEV strains from northern Europe and the completion of the genome of four others. Moreover, we provide a unique measure for the natural rate of evolution of TBEV by studying two isolations from the same forest on an island in Åland archipelago 44 years apart. For all isolates, we analysed the phylogeny, rate of evolution and probable time of radiation of the different TBEV strains. The results show that the two lineages of TBEV in different Ixodes species have evolved independently for approximately 3300 years. Notably, rapid radiation of TBEV-Eur occurred approximately 300 years ago, without the large-scale geographical clustering observed previously for the Siberian subtype. The measurements from the natural rate of evolution correlated with the estimates done by phylogenetic programs, demonstrating their robustness.

Genetic diversity and geographic distribution of hantaviruses in Russia

Haemorrhagic fever with renal syndrome (HFRS) is the most prevalent zoonotic disease in Russia. It is caused by several hantavirus species hosted by small rodents. We describe spatial and temporal patterns of HFRS incidence in the Russian Federation, and the geographic distribution of prevalent hantavirus species: Puumala (PUUV) and Dobrava (DOBV). Partial sequencing of nucleocapsid and glycoprotein genes of 117 PUUV strains and 78 DOBV strains revealed several distinct genetic subgroups. The RNA of Volga PUUV subgroup was detected in patients with HFRS and bank voles Myodes glareolus in the Volga Federal District, where the highest HFRS incidence rate has been registered yearly. The RNA of Siberian PUUV subgroup was found in M. glareolus in the trans-Ural Tyumen and Omsk Provinces, where human HFRS cases have been rare. During an HFRS outbreak in 2007 in the Central Federal District, when more than 1000 patients were affected, specific subgroups of DOBV were discovered in patients and rodents, mainly in the striped field mouse Apodemus agrarius. DOBV strains might have 8–9% of nucleotide difference although they were collected at places separated by 30–100 km. The RNA of a unique DOBV subgroup was discovered in the southern semi-desert Astrakhan Province, mainly in A. agrarius and tamarisk jird Meriones tamariscinus. No human HFRS cases were diagnosed in this province. Russian PUUV and DOBV strains have no close homologues among European strains. Our DOBV strains might be genetically grouped together with Central European DOBV strains isolated from A. agrarius, but not from Apodemus flavicollis. The Volga PUUV subgroup is to some extent similar to Baltic PUUV strain, and Finnish PUUV strains resemble the strains from the Siberian PUUV subgroup. Thus, PCRbased monitoring and typing provided the opportunity to delineate and expand the area of hantaviruses in Russia and to identify their new genetic variants.

Geo-spatial hotspots of hemorrhagic fever with renal syndrome and genetic characterization of Seoul variants in Beijing, China

BACKGROUND

Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, and has extended from rural areas to cities recently. Beijing metropolis is a novel affected region, where the HFRS incidence seems to be diverse from place to place.

METHODOLOGY/PRINCIPAL FINDINGS

The spatial scan analysis based on geographical information system (GIS) identified three geo-spatial "hotspots" of HFRS in Beijing when the passive surveillance data from 2004 to 2006 were used. The Relative Risk (RR) of the three "hotspots" was 5.45, 3.57 and 3.30, respectively. The Phylogenetic analysis based on entire coding region sequence of S segment and partial L segment sequence of Seoul virus (SEOV) revealed that the SEOV strains circulating in Beijing could be classified into at least three lineages regardless of their host origins. Two potential recombination events that happened in lineage #1 were detected and supported by comparative phylogenetic analysis. The SEOV strains in different lineages and strains with distinct special amino acid substitutions for N protein were partially associated with different spatial clustered areas of HFRS.

CONCLUSION/SIGNIFICANCE

Hotspots of HFRS were found in Beijing, a novel endemic region, where intervention should be enhanced. Our data suggested that the genetic variation and recombination of SEOV strains was related to the high risk areas of HFRS, which merited further investigation.

Hantaviruses and their hosts in Europe: reservoirs here and there, but not everywhere?

Five hantaviruses are known to circulate among rodents in Europe, and at least two among insectivores. Four (Dobrava, Saaremaa, Seoul, and Puumala [PUUV] viruses) are clearly associated with hemorrhagic fever with renal syndrome (HFRS). PUUV, the most common etiological agent of HFRS in Europe, is carried by the bank vole (Myodes glareolus), one of the most widespread and abundant mammal species in Europe. This host-virus system is among hantaviruses also the most studied one in Europe. However, HFRS incidence varies throughout the continent. The spatial as well as temporal variation in the occurrence of HFRS is linked to geographic differences in the population dynamics of the reservoir rodents in different biomes of Europe. While rodent abundance may follow mast seeding events in many parts of temperate Europe, in northern (N) Europe multiannual cycles in population density exist as the result of the interaction between rodent populations and specialist predator populations in a delayed density-dependent manner. The spatial distribution of hantaviruses further depends on parameters such as forest patch size and connectivity of the most suitable rodent habitats, and the conditions for the survival of the virus outside the host, as well as historical distribution patterns (phylogeographies) of hosts and viruses. In multiannually fluctuating populations of rodents, with population increases of great amplitude, one should expect a simultaneous build-up of recently hantavirus-infected (shedding) rodents. The increasing number of infectious, virus-shedding rodents leads to a rapid transmission of hantavirus across the rodent population, and to humans. Our review discusses these aspects for PUUV, the only European hantavirus for which there is a reasonable, yet still far from complete, ecological continental-wide understanding. We discuss how this information could translate to other European hantavirus-host systems, and where the most important questions lie for further research.

A global perspective on hantavirus ecology, epidemiology, and disease

Hantaviruses are enzootic viruses that maintain persistent infections in their rodent hosts without apparent disease symptoms. The spillover of these viruses to humans can lead to one of two serious illnesses, hantavirus pulmonary syndrome and hemorrhagic fever with renal syndrome. In recent years, there has been an improved understanding of the epidemiology, pathogenesis, and natural history of these viruses following an increase in the number of outbreaks in the Americas. In this review, current concepts regarding the ecology of and disease associated with these serious human pathogens are presented. Priorities for future research suggest an integration of the ecology and evolution of these and other host-virus ecosystems through modeling and hypothesis-driven research with the risk of emergence, host switching/spillover, and disease transmission to humans.

Associations between MHC genes and Puumala virus infection in Myodes glareolus are detected in wild populations, but not from experimental infection data

We analysed the influence of MHC class II Dqa and Drb genes on Puumala virus (PUUV) infection in bank voles (Myodes glareolus). We considered voles sampled in five European localities or derived from a previous experiment that showed variable infection success of PUUV. The genetic variation observed in the Dqa and Drb genes was assessed by using single-strand conformation polymorphism and pyrosequencing methods, respectively. Patterns were compared with those obtained from 13 microsatellites. We revealed significant genetic differentiation between PUUV-seronegative and -seropositive bank voles sampled in wild populations, at the Drb gene only. The absence of genetic differentiation observed at neutral microsatellites confirmed the important role of selective pressures in shaping these Drb patterns. Also, we found no significant associations between infection success and MHC alleles among laboratory-colonized bank voles, which is explained by a loss of genetic variability that occurred during the captivity of these voles.

Puumala hantavirus and Myodes glareolus in northern Europe: no evidence of co-divergence between genetic lineages of virus and host

The genus Hantavirus (family Bunyaviridae) includes negative-strand RNA viruses that are carried by persistently infected rodent and insectivore species. Puumala virus (PUUV), carried by bank voles (Myodes glareolus), is a pathogenic hantavirus that causes outbreaks of mild haemorrhagic fever with renal syndrome across Europe. In northern Europe, PUUV is represented by several genetic lineages that are maintained by distinct phylogroups of bank voles. The present study describes sequences of new PUUV strains recovered from northern and southern regions of Scandinavia and compares phylogenetic relationships between north-European PUUV strains and M. glareolus. This analysis revealed contradictions in phylogenetic clustering and remarkable differences in estimated divergence times between the lineages of PUUV and its host, suggesting that the established PUUV lineages did not co-diverge with the distinct phylogroups of M. glareolus that carry them at present.

Correlates of viral richness in bats (order Chiroptera)

Historic and contemporary host ecology and evolutionary dynamics have profound impacts on viral diversity, virulence, and associated disease emergence. Bats have been recognized as reservoirs for several emerging viral pathogens, and are unique among mammals in their vagility, potential for long-distance dispersal, and often very large, colonial populations. We investigate the relative influences of host ecology and population genetic structure for predictions of viral richness in relevant reservoir species. We test the hypothesis that host geographic range area, distribution, population genetic structure, migratory behavior, International Union for Conservation of Nature and Natural Resources (IUCN) threat status, body mass, and colony size, are associated with known viral richness in bats. We analyze host traits and viral richness in a generalized linear regression model framework, and include a correction for sampling effort and phylogeny. We find evidence that sampling effort, IUCN status, and population genetic structure correlate with observed viral species richness in bats, and that these associations are independent of phylogeny. This study is an important first step in understanding the mechanisms that promote viral richness in reservoir species, and may aid in predicting the emergence of viral zoonoses from bats.

Genetic analysis of Puumala hantavirus strains from Austria

Sequences of the Small (S) and the Medium (M) genome segments of Puumala hantavirus (PUUV) were recovered from bank voles Clethrionomys glareolus trapped at 2 locations, Klippitztörl (Carinthia) and Ernstbrunn (Lower Austria). Lung tissue samples from 12 rodents earlier found hantavirus antibody-positive were further screened for the presence of hantaviral N-antigen using immunoblotting. RNA purified from 7 N-Ag-positive samples was subjected to the reverse transcription-polymerase chain reaction with primers designed to recover the complete S segment sequence of PUUV. The amplicons of expected size (approximately 1800 bp) have been recovered from 2 samples, 1 from Klippitztörl and another from Ernstbrunn. From the same 2 samples, PCR amplicons corresponding to the partial M segment sequence (nt 2140 to 2594), have been prepared. The S and M amplicons were sequenced and subjected to genetic analyses. Recovered hantavirus genome sequences undoubtedly belonged to PUUV genotype and the corresponding wild-type hantavirus strains were designated as PUU/Klippitztörl/Cg9/1995 and PUU/Ernstbrunn/Cg641/1995. Phylogenetic analysis placed 2 Austrian PUUV strains within a distinct genetic lineage that also included strains from the neighbouring Slovenia and Croatia. This Alpe-Adrian lineage, previously designated as 'Balkan lineage', was well supported on both S and M phylogenetic trees.

Analysis of Puumala hantavirus in a bank vole population in northern Finland: evidence for co-circulation of two genetic lineages and frequent reassortment between strains

In this study, for the first time, two distinct genetic lineages of Puumala virus (PUUV) were found within a small sampling area and within a single host genetic lineage (Ural mtDNA) at Pallasjärvi, northern Finland. Lung tissue samples of 171 bank voles (Myodes glareolus) trapped in September 1998 were screened for the presence of PUUV nucleocapsid antigen and 25 were found to be positive. Partial sequences of the PUUV small (S), medium (M) and large (L) genome segments were recovered from these samples using RT-PCR. Phylogenetic analysis revealed two genetic groups of PUUV sequences that belonged to the Finnish and north Scandinavian lineages. This presented a unique opportunity to study inter-lineage reassortment in PUUV; indeed, 32 % of the studied bank voles appeared to carry reassortant virus genomes. Thus, the frequency of inter-lineage reassortment in PUUV was comparable to that of intra-lineage reassortment observed previously (Razzauti, M., Plyusnina, A., Henttonen, H. & Plyusnin, A. (2008). J Gen Virol 89, 1649-1660). Of six possible reassortant S/M/L combinations, only two were found at Pallasjärvi and, notably, in all reassortants, both S and L segments originated from the same genetic lineage, suggesting a non-random pattern for the reassortment. These findings are discussed in connection to PUUV evolution in Fennoscandia.

Detection, distribution, and genetic variability of European mountain ash ringspot-associated virus

European mountain ash ringspot-associated virus (EMARAV) was recently characterized from mountain ash (rowan) (Sorbus aucuparia) in Germany. The virus belongs tentatively to family Bunyaviridae but is not closely related to any classified virus. How commonly EMARAV occurs in ringspot disease (EMARSD) affected mountain ash trees was not reported and was investigated here. Virus-specific detection tools such as reverse transcription-polymerase chain reaction and dot blot hybridization using digoxigenin-labeled RNA probes were developed to test 73 mountain ash trees including 16 trees with no virus-like symptoms from 16 districts in Finland and Viipuri, Russia. All trees were infected with EMARAV. Hence, EMARAV is associated with EMARSD and can also cause latent infections in mountain ash. Symptom expression and the variable relative concentrations of viral RNA detected in leaves showed no correlation. Infectious EMARAV was detected also in dormant branches of trees in winter. Subsequently, genetic variability, geographical differentiation, and evolutionary selection pressures were investigated by analyzing RNA3 sequences from 17 isolates. The putative nucleocapsid (NP) gene sequence (944 nucleotides) showed little variability (identities 97 to 99%) and was under strong purifying selection. Amino acid substitutions were detected in two positions at the N terminus and one position at the C terminus of NP in four isolates. The 3' untranslated region (442 nucleotides) was more variable (identities 94 to 99%). Six isolates from a single sampling site exhibited as wide a genetic variability as isolates from sites that were hundreds of kilometers apart and no spatial differentiation of populations of EMARAV was observed.

Accumulation of point mutations and reassortment of genomic RNA segments are involved in the microevolution of Puumala hantavirus in a bank vole (Myodes glareolus) population

The genetic diversity of Puumala hantavirus (PUUV) was studied in a local population of its natural host, the bank vole (Myodes glareolus). The trapping area (2.5 x 2.5 km) at Konnevesi, Central Finland, included 14 trapping sites, at least 500 m apart; altogether, 147 voles were captured during May and October 2005. Partial sequences of the S, M and L viral genome segments were recovered from 40 animals. Seven, 12 and 17 variants were detected for the S, M and L sequences, respectively; these represent new wild-type PUUV strains that belong to the Finnish genetic lineage. The genetic diversity of PUUV strains from Konnevesi was 0.2-4.9 % for the S segment, 0.2-4.8 % for the M segment and 0.2-9.7 % for the L segment. Most nucleotide substitutions were synonymous and most deduced amino acid substitutions were conservative, probably due to strong stabilizing selection operating at the protein level. Based on both sequence markers and phylogenetic clustering, the S, M and L sequences could be assigned to two groups, 'A' and 'B'. Notably, not all bank voles carried S, M and L sequences belonging to the same group, i.e. S(A)M(A)L(A) or S(B)M(B)L(B). A substantial proportion (8/40, 20 %) of the newly characterized PUUV strains possessed reassortant genomes such as S(B)M(A)L(A), S(A)M(B)L(B) or S(B)M(A)L(B). These results suggest that at least some of the PUUV reassortants are viable and can survive in the presence of their parental strains.

Puumala hantavirus genetic variability in an endemic region (Northern Sweden)

Puumala hantavirus (PUUV), naturally harboured and shed by bank voles (Myodes [Clethrionomys] glareolus), is the etiological agent to nephropathia epidemica (NE), a mild haemorrhagic fever with renal syndrome. Both host and virus are found throughout much of the European continent and in northern Sweden NE is the second most prevalent serious febrile viral infection after influenza. The reliability of diagnostics by PCR depends on genetic variability for the detection of viral nucleic acids in unknown samples. In the present study we evaluated the genetic variability of PUUV isolated from bank voles in an area of northern Sweden highly endemic for NE. Genetic variability among bank voles was also investigated to evaluate co-evolutionary patterns. We found that the viral sequence appeared stable across the 80km study region, with the exception of the southernmost sampling site, which differed from its nearest neighbour by 7%, despite a geographical separation of only 10km. The southernmost sampling site demonstrated a higher degree of genetic similarity to PUUV previously isolated 100km south thereof; two locations appear to constitute a separate PUUV phylogenetic branch. In contrast to the viral genome, no phylogenetic variance was observed in the bank vole mtDNA in this study. Previous studies have shown that as a result of terrestrial mammals' postglacial re-colonization routes, bank voles and associated PUUV of a southern and a northern lineage established a dichotomous contact zone across the Scandinavian peninsula approximately 100-150km south of the present study sites. Our observations reveal evolutionary divergence of PUUV that has led to dissimilarities within the restricted geographical scale of the northern host re-colonization route as well. These results suggest either a static situation in which PUUV strains are regionally well adapted, or an ongoing process in which strains of PUUV circulate on a geographical scale not yet reliably described.

Detection of phylogenetically distinct Puumala-like viruses from red-grey vole Clethrionomys rufocanus in China

In order to investigate whether Puumala virus (PUUV) or PUUV-like virus is present in China, Clethrionomys rufocanus and C. rutilus were captured in the Jilin province during the spring and autumn of 2002-2003 for detection of PUUV viral RNA by RT-PCR and confirmation of PUUV-positive antigens by an immunofluorescence assay. PUUV-positive RNA was identified in six out of 121 C. rufocanus but not in any of the 41 C. rutilus. Complete S and partial M sequences (nt 1,316-1,598 and 2,687-3,089) were amplified by RT-PCR directly from some of the antigen positive lung tissues and subjected to nucleic acid sequencing. It was found that the Chinese PUUV-like viruses were related most closely with the PUUV strains with 77.7-81.7% identity at the nucleotide level and 91.7-97% identity at the amino acid level for S segment, and with 77-78.8% identity at the nucleotide level and 91.5-92.6% identity at the amino acid level for the partial M segment (nt 1,316-1,598). Genetic analysis indicated that the Chinese PUUV-like viruses shared the highest level of identity with the viruses which circulate in C. rufocanus in the Far East region of Russia with 85.1-87.4% identity at the nucleotide level and 95.9% identity at the amino acid level for the partial M segment (nt 2,687-3,089), respectively. Phylogenetic analysis revealed that the Chinese PUUV-like viruses are distinct from those identified from Japan, South Korea, Europe or Russia. These results indicate that PUUV-like virus is present in China in addition to Hantaan, Seoul and Dabieshan viruses.

Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses

Phylogeographical partitioning of Sin Nombre and Monongahela viruses (hantaviruses) may reflect that of their primary rodent host, the deer mouse (Peromyscus maniculatus). Lack of a comprehensive assessment of phylogeographical variation of the host has precluded the possibility of predicting spatial limits of existing strains of these viruses or geographical regions where novel viral strains might emerge. The complete cytochrome b gene was sequenced for 206 deer mice collected from sites throughout North America to provide a foundation for future studies of spatial structure and evolution of this ubiquitous host. Bayesian analyses of these sequences partitioned deer mice into six largely allopatric lineages, some of which may represent unrecognized species. The geographical distributions of these lineages were probably shaped by Quaternary climatic events. Populations of mice were apparently restricted to refugia during glacial advances, where they experienced genetic divergence. Expansion of these populations, following climatic amelioration, brought genetically distinctive forms into contact. Occurrence of parallel changes in virus strains can now be explored in appropriate regions. In New Mexico, for example, near the location where Sin Nombre virus was first discovered, there are three genetically distinctive lineages of deer mice whose geographical ranges need to be delineated precisely. The phylogeography of P. maniculatus provides a framework for interpreting geographical variability, not only in hosts, but also in associated viral variants and disease transmission, and an opportunity to predict the potential geographical distribution of newly emerging viral strains.

Predicting the emergence of human hantavirus disease using a combination of viral dynamics and rodent demographic patterns

The paper proposes a model explaining the spatial variation in incidence of nephropathia epidemica in Europe. We take into account the rodent dynamic features and the replicative dynamics of the virus in animals, high in the acute phase of newly infected animals and low in the subsequent chronic phase. The model revealed that only vole populations with multi-annual fluctuations allow for simultaneously high numbers of infected rodents and high proportions of those rodents in the acute excretion phase during the culminating phase of population build-up. This leads to a brief peak in exceptionally high concentrations of virus in the environment, and thereby, to human exposure. Such a mechanism suggests that a slight ecological disturbance in animal-parasite systems could result in the emergence of human diseases. Thus, the potential risk for public health due to several zoonotic diseases may be greater than previously believed, based solely on the distribution of human cases.

Molecular epidemiology of tick-borne encephalitis virus in Ixodes ricinus ticks in Lithuania

In Lithuania, 171-645 serologically confirmed cases of tick-borne encephalitis occurred annually [Mickiene et al. (2001): Eur J Clin Microbiol Infect Dis 20:886-888] in 1993-1999, and the tick-borne encephalitis virus (TBEV) seroprevalence in the general population was found previously to be 3.0% [Juceviciene et al. (2002): J Clin Virol 25:23-27]. To assess the risk for TBEV virus infection in Lithuania and to characterize the agent a panel of 3,234 ticks combined into 436 pools [Juceviciene et al., 2005] were tested for presence of TBEV RNA by a nested RT-PCR targeting at the NS5 gene. Six pools were confirmed positive and the prevalence of the infected ticks was 0.2% (if one tick per pool [Juceviciene et al., 2005] was considered positive) and the proportion of positive tick pools was 1.4%. The prevalence of the infected ticks in the Panevezys, Siauliai, and Radviliskis regions (in central Lithuania) was 0.1%, 0.4%, and 1.7% corresponding with a higher TBE disease burden in these regions. The 252-nucleotide NS5-region amplicons, and a longer sequence (737 nucleotides) obtained from one sample from the PrM-E gene region, were sequenced. Phylogenetic analysis of the latter showed that all western type TBEV PrM-E sequences, including the Lithuanian strains, were monophyletic, showed no clustering and had very little variation. The NS5 sequences, although identical within one locality, did not show any mutations common to strains from the two Lithuanian regions, nor could any geographical clustering be found among western type TBEV strains from other areas.

A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes

RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in mutation rates of RNA viruses and to understand the source of such variation, we studied the synonymous substitution rate because synonymous substitution is exempt from functional constraints at the protein level, and its rate reflects the mutation rate to a great extent. We estimated the synonymous substitution rates for a total of 49 different species of RNA viruses, and we found that the rates had tremendous variation by 5 orders of magnitude (from 1.3 × 10⁻⁷ to 6.2 × 10⁻² /synonymous site/year). Comparing the synonymous substitution rates with the replication frequencies and replication error rates for the RNA viruses, we found that the main source of the rate variation was differences in the replication frequency because the rates of replication error were roughly constant over different RNA viruses. Moreover, we examined a relationship between viral life strategies and synonymous substitution rates to understand which viral life strategies affect replication frequencies. The results show that the variation of synonymous substitution rates has been influenced most by either the difference in the infection modes or the differences in the transmission modes. In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes.

Genetic similarity of Puumala viruses found in Finland and western Siberia and of the mitochondrial DNA of their rodent hosts suggests a common evolutionary origin

A total of 678 small mammals representing eight species were trapped in western Siberia in 1999-2000 and assayed for the presence of hantaviruses. Eighteen animals, all Clethrionomys species, were antigen positive by enzyme-linked immunosorbent assay (ELISA). Small and medium genome segments were recovered by RT-PCR from six samples from Clethrionomys glareolus and three from Clethrionomys rufocanus. Sequence comparison and phylogenetic analysis revealed that these hantaviruses were Puumala virus and were similar to hantavirus strains from Finland. To confirm these data, partial nucleotide sequences of the rodent hosts' cytochrome b genes were obtained, as well as several sequences from genes from rodents trapped at different localities of European Russia and western Siberia. The cytochrome b sequences of Siberian bank voles were similar to sequences of C. glareolus, trapped in Finland. These data suggest that the Puumala hantaviruses, as well as their rodent hosts, share a common evolutionary history. We propose that these rodents and viruses may be descendents of a population of bank voles that expanded northward from southern refugia during one of the interglacial periods.

Hantavirus infections in Europe

Hantaviruses are enveloped RNA viruses each carried by a specific rodent species. Three hantaviruses, Puumala, Dobrava, and Saaremaa viruses, are known to cause haemorrhagic fever with renal syndrome. In Europe. Puumala causes a generally mild disease, nephropathia epidemica, which presents most commonly with fever, headache, gastrointestinal symptoms, impaired renal function, and blurred vision, whereas Dobrava infections often also have haemorrhagic complications. There are few available data about the clinical picture of confirmed Saaremaa infections, but epidemiological evidence suggests that it is less pathogenic than Dobrava, and that Saaremaa infections are more similar to nephropathia epidemica caused by Puumala. Along with its rodent host, the bank vole (Clethrionomys glareolus), Puumala is reported throughout most of Europe (excluding the Mediterranean region), whereas Dobrava, carried by the yellow-necked mouse (Apodemus flavicollis), and Saaremaa, carried by the striped field mouse (Apodemus agrarius), are reported mainly in eastern and central Europe. The diagnosis of acute hantavirus infection is based on the detection of virus-specific IgM. Whereas Puumala is distinct, Dobrava and Saaremaa are genetically and antigenically very closely related and were previously thought to be variants of the same virus. Typing of a specific hantavirus infection requires neutralisation antibody assays or reverse transcriptase PCR and sequencing.

Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses

Recombination is increasingly seen as an important means of shaping genetic diversity in RNA viruses. However, observed recombination frequencies vary widely among those viruses studied to date, with only sporadic occurrences reported in RNA viruses with negative-sense genomes. To determine the extent of homologous recombination in negative-sense RNA viruses, phylogenetic analyses of 79 gene sequence alignments from 35 negative-sense RNA viruses (a total of 2154 sequences) were carried out. Powerful evidence was found for recombination, in the form of incongruent phylogenetic trees between different gene regions, in only five sequences from Hantaan virus, Mumps virus and Newcastle disease virus. This is the first report of recombination in these viruses. More tentative evidence for recombination, where conflicting phylogenetic trees were observed (but were without strong bootstrap support) and/or where putative recombinant regions were very short, was found in three alignments from La Crosse virus and Puumala virus. Finally, patterns of sequence variation compatible with the action of recombination, but not definitive evidence for this process, were observed in a further ten viruses: Canine distemper virus, Crimean-Congo haemorrhagic fever virus, Influenza A virus, Influenza B virus, Influenza C virus, Lassa virus, Pirital virus, Rabies virus, Rift Valley Fever virus and Vesicular stomatitis virus. The possibility of recombination in these viruses should be investigated further. Overall, this study reveals that rates of homologous recombination in negative-sense RNA viruses are very much lower than those of mutation, with many viruses seemingly clonal on current data. Consequently, recombination rate is unlikely to be a trait that is set by natural selection to create advantageous or purge deleterious mutations.

Distribution of Puumala hantavirus in Denmark: analysis of bank voles (Clethrionomys glareolus) from Fyn and Jutland

The majority of hantaviral infections in Denmark since 1957 have occurred on the island of Fyn. We have recently shown the presence of Puumala hantavirus (PUUV) in bank voles (Clethrionomys glareolus) on Fyn. To learn more about the distribution and prevalence of PUUV in Denmark, 310 small mammals, belonging to six rodent and two insectivore species, were trapped in four localities on Fyn and three localities on the Jutland Peninsula (mainland Denmark), where only a few cases of nephropathia epidemica (NE) have been confirmed so far. Serum samples (heart extracts) from all animals were initially analyzed for the presence of hantavirus-specific antibodies (Ab) by enzyme immunoassay, and lung tissue samples of bank voles for the presence of the viral nucleocapsid protein antigen by immunoblotting. Altogether 11 Ab-positive rodents were found, all of them bank voles from Fyn. PUUV genome sequences (nucleotides 2,168-2,569 from the medium genomic segment) were recovered by reverse transcription-polymerase chain reaction from seven bank voles. They showed an overall diversity up to 5% and formed a well-supported genetic lineage on the phylogenetic tree with a clustering of two strains from southeastern Fyn together and a separation from the one strain from western Fyn. Our data confirmed the circulation of PUUV in both the southeastern and western parts of the island, known to have the highest numbers of human NE cases.

Molecular evolution of Puumala hantavirus

Puumala virus (PUUV) is a negative-stranded RNA virus in the genus Hantavirus, family Bunyaviridae. In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several European countries, Russia, and Japan, the largest set available thus far for hantaviruses. The results show that PUUV sequences form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants is observed. The overall phylogeny of PUUV is star-like, suggesting an early split of genetic lineages. The individual PUUV lineages appear to be independent, with the only exception to this being the Finnish and the Russian lineages that are closely connected to each other. Two strains of PUUV-like virus from Japan form the most ancestral lineage diverging from PUUV. Recombination points within the S segment were searched for and evidence for intralineage recombination events was seen in the Finnish, Russian, Danish, and Belgian lineages of PUUV. Molecular clock analysis showed that PUUV is a stable virus, evolving slowly at a rate of 0.7 x 10(-7) to 2.2 x 10(-6) nt substitutions per site per year.