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Puumala Virus (PUUV) Genome Analysis

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Published: Tue, 12 Jun 2018



A key concern of any viral vaccine research is the tremendous genetic diversity of the virus

Hantaviruses are etiological agents generally known to cause two distinct human diseases: kidney affecting disease and heart affecting disease, haemorrhagic fever with renal syndrome (HFRS) sometimes called Nephropaphia epidemica (NE) in Eurasia and Americas hantavirus pulmonary syndrome (HPS) respectively. These viruses are heterologous (heterologous transmission from animals to humans (zoonosis)) which belong to the hantavirus genus, family Bunyavidae normally they make up four genera Hantavirus, Orthobunyavirus,  Nairovirus, Phlebovirus and Tospovirus. The genome of hantaviruses consist of three segments which are negative-strand of RNA, small (S) 1821-1830 nucleotides (nt), medium (M) 3682 nt and large (L) 6530-6562 nt encoding for nucleocapsid (N) protein, glycoprotein molecule (GPC) Gn, Gc proteins  and RNA-dependent RNA-polymerase, respectively.

This study characterises the full genome of a Russian hantavirus discovered both in infected humans and small animals, Puumala virus (PUUV). PUUV is considered a prime etiological agent of hemorrhagic fever with renal syndrome sometimes referred to nephropaphia epidemica in Russia and Eurasia. Mostly, all hantavirus diseases in human have a fatality rate ranging from mild to severe with an intriguingly percentage rate from 0.1% up to 50%,  the symptom outcome of the disease  heavily depend on the geographic location of an infected person.

Precisely, in the republic of Tatarstan, Russia the strain of Puumala virus has shown significance increase as human pathogens resulting to the acquiring of the status as emerging virus. PUUV in the republic of Tatarstan, Russia, has become a serious life-threatening hantavirus causing HFRS with high fatality rate of up to 12%, especially in the Volga region. The spectrum of illnesses caused by hantaviruses varies with the particular virus involved(Hantavirus infection: a global zoonotic challenge paper). It is reported that the high peak of Puumala virus comes with the high agricultural activities of this region during of which Bank vole mouse (Clethrionomys glareolus) the etiological agent of HFRS rapidly multiply. Normally, hantavirus, Puumala virus (PUUV) is transmitted to human by coming into contact with contaminated materials like faecal matter, blood dropped by an infected rodent and through aerosolised contaminated air and by bite of a carrier infected rodent. In the case of the strain of Puumala virus in the Republic of Tatarstan, Russia, the strain is dropped by notorious reservoir rodent specie found in the surrounding environment either near homes or in the fields, Bank vole mouse (Clethrionomys glareolus). It has to be noted here that most hantaviruses are transmitted to human by small animals themselves with an exceptional of Andes virus which can be transmitted from human to human. In South America the case of Andes virus has been reported to be transmitted from human to human.

Intriguingly, other species of hantaviruses, Dobrava-belgrade (DOBV) virus with its sub-species isolated in Europe, and Tula virus (TULV) are seriously detected and isolated in Russian and know to cause hemorrhagic fever with renal syndrome (HFRS) and in Europe the syndrome is called Nephropaphia epidemica. Dobrava-belgrade is known to be associated with yellow naked-mouse (Apodemus flavicollis) this specie is the most life-threatening hantavirus. Other dobrava-belgrade species, DOBV-Af, DOBV-Aa and DOBV-Ap are associated with A. flavicollis (Af), A. agrarious (Aa) and A. ponticus (Ap) respectively. All these species cause HFRS from mild to severe mode of disease.

PUUV form distinct phylogenetic leanage, in line with the natural host, bank vole (Clethrionomys glareolus). The strain of Puumala virus is heavily isolated in Ufa, Samara,…..parts of Russia both in human and small animals, in human as they thrive causing the dangerous form of human disease, hemorrhagic fever with renal syndrome (HFRS)



If you hear a feminine voice thinks of a beautiful lady, what if this time the feminine voice is of a man [1]. Hantaviruses have been limited to the genus hantavirus under bunyaviridae family which give rise to several number of species viruses Puumala virus (PUUV) [2], Dobrava virus (DOBV), Tula Virus, puumala virus (PUUV) Saaremaa virus (SAAV), and Seoul virus (SEOV) are commonly know hantaviruses to be circulating in Europe and Russia [3-5]. However, the agent rodents Hantaviruses are morphologically classified as follows; order rodential, families crecitidae and muridae. It’s now a known fact that rodents are not the only hantavirus reservoirs. Researchers have found hantaviruses insects which belong to the lipotyphra order, soriciodae family’s and Talpidae[6]. Further, with the recently isolated Bat-borne Hantavirus in China, laibin virus ( LBV) chyroptera order has given a strong predictive assumption that hanataviruses could be found in other animals like cow, [6]. The black beard tomb bat hantaviruses isolated in china gave a discrete relation to the previously known hantaviruses.

Heavily depending on the geographical location of an infected person, the outcomes of hantavirus infection are well classified human diseases: haemorrhagic fever with renal syndrome (HFRS) sometimes referred to nephropathia epidemical mostly in Eurasia and hantavirus cardiopulmonary syndrome (HCPS) normally called hantavirus pulmonary syndrome in the Americas [7] (dissertation Nina Luteka 2010). [1] As the onset of the diseases advances the changes in the vascular permeability is highly noticed, defects in platelet function and acute thrombocytopenia intrinsically can also be observed which is associated with high fever and hemorrhage. However, with the global health threat of hantavirus it has triggered serious research mainly focusing on the vulnerability of the endothelial cells when attacked by hantaviruses. Needless to say, less viral cytopathic effect is observed on the endothelial cells after hantavirus infection. (dissertation Nina Luteka 2010). The mechanism underlying these drastically changes in platelet as the pathogen advances drastically pooling down the immune system and how the hantaviruses trigger interference in the immune system greatly remain futile and poorly understood.

hantaviruses have been discovered in insects which acts as the host vector (HO2), hantaviruses in the reservoirs cause asymptomatic completely they do not show any symptom in the natural host.

We characterized genome of puumala virus discovered both in human and rodents


Hantaviruses are zoonotic viruses that infect human through rodents contact; in rodents they don’t cause diseases but when human come into contact with infected rodent through smelling the excretes or inhalation of infected hair from the rodents induces human diseases known as; Hemorrhagic fever with renal syndrome found in Europe, the agent viruses for this disease are: Dobrava virus (DOBV)-Belgrade, Puumala, Saaremaa, Sochi, and Seoul virus which is recently reported [8],these viruses are considered to be old world viruses, Bulgaria is one of the country were Hemorrhagic with renal syndrome is endemic but the virus has never been found in the natural rodent reservoir [8] however, Eastern Russia, Korea and China has the highest cases of HFRS caused by HTNV, SEOV, and ASV.

Nephropathia epidemical diseases, a rodent disease found in human who gets infected after coming in contact with infected rodents and this disease has the symptoms of the hemorrhageic fever with renal syndrome which makes it to be referred to as same as hemorrhagic fever with renal syndrome [2] has continued to be life threatening in the republic of Tatarstan since its first identified in 1997. Epidemiological study on Nephropathia epidemical between 1997 and 2013 in the republic of Tatarstan, Russia gives an account that NE mostly affect male adults due to the agricultural activities during which myodes graleorus (bank vole) the natural reservoir of NE causing agents population increases [9]. It is revealed that the higher epidemic of hantaviruses in the Republic of Tatarstan is due to the supportive mating environment of small animals (bank voles) and increase in agriculture activities. Myodes galeorus shows high population rate during this time of agricultural activities and are a genetic variant prevalence for hantavirus in this region.

However, the severity (or the fatality, the outcome) and the kind of disease or the infection involved mainly depends on several factors;

  1. The place infection take place
  2. The pathogenicity of the agents
  3. The genetic makeup (or the genetic predisposition of the host)
  4. Diversity of the agents [1]
  5. Geographical of the infection acquired

Not all known rodent and insect hantaviruses cause disease in human [3] and the treatment for this dangerous hantavirus infection remains futile.

The reasons for the variation of severity between virus species/genotypes and in individual patients are not yet known. Diverse determinants concerning virusand patient-specific characteristics may play a role in the pathogenesis. Differences in the use of entry receptors, in the regulation of cytokine response and in viral replication were described to be associated with pathogenicity [8-11]. Studies with genetic reassortants in vitro and in animal models suggest molecular determinants to be responsible for virulence [5, 12]. However, the speciesspecific factors of hantaviruses that are responsible for pathogenicity and clinical picture are not identified so far. Interestingly, the pathogenicity of related viruses of DOBV genotypes differs enormously with case fatality rates (CFRs) between 0.3%-0.9% for DOBV genotype

Kurkino and 14.5% for DOBV genotype Sochi [13]. In addition to severe courses that are linked to specific virus species or genotypes, several serious cases were reported for infection with PUUV that usually causes a milder form of hantavirus disease [14, 15]. These infections often involve extrarenal manifestations [16, 17]. From (Clinical characterization of two severe cases of hemorrhagic fever with renal syndrome (HFRS) caused by hantaviruses Puumala and Dobrava-Belgrade genotype Sochi paper)

Hantaviruses evolution

Hantaviruses within the family bunyaviridae are different from other member viruses in the sense that they are roboviruses (ROdent-BOrne viruses) signifying that they are hosted by small animals which act as the host reservoirs (vector). Other bunyaviridae virus members are arborviruses (arthropod viruses) transmitted by arthropod to human [10-12] . the circulation of hantaviruses throughout the continent has been triggerd by a number of activities which account for from human movements to the events of the world. These activities also account for the evolution of hantaviruses. However, it is believed that hantaviruses co-evolved together with their reservoirs animal more than 10 million years ago. The genetic diversity of hantaviruses came about by genetic mutation on the genome of the virus producing quasispecies which happened through deletions or insertion of new nucleotides. It is further, shown that the genetic diversity came about by reasortments of the same two viruses genome within the host and by the homologous recombination of the viruses with each other [12-14]. Evolution of hantavirus in the host (rodents) depends on the number of factors which greatly help them to thrive as they live within the host rodents or insects these factors include: the destict environment which act as a life supporting of rodent, there events that are believed to contribute to the evolvement of different kind of rodents, such as glaciations events.  Deglaciation events triggered the movements of rodents in the northern hemisphere southern hemisphere as the small animals migrated from one place to the other caused mutation to occurred in the host themselves and equally in the strain producing distinct kind of hantaviruses in the end causing permanent genetic variations in the population of the hantaviruses. Needless to say, human do not act as the host range of hantaviruses instead they are dead-end point of hantaviruses. Thereafter, hantaviruses do not evolve after infecting human vectors, its either they die together with the an infected body or they are wiped off from the human body.[11]


PUUV -circulating in Northern and Central Europe, Baltics, the part of Russia Europe and the Alpe- Adrian region;

  • High fever
  • Back pain
  • Renal impairment

DOBV- mostly circulating in Balkan countries and Alped-Adrian region has the following symptoms

  • Severe illness
  • Hemorrhage
  • High fever
  • Acute renal failure
  • Dialysis may be required
  • Fatality rate reaches 10%

PUUV -circulating in Northern and Central Europe, Baltics, the part of Russia Europe and the Alpe- Adrian region;

  • High fever
  • Back pain
  • Renal impairment

Structure (morphology)

The new era of elucidating the etiological agent of human disease hemorrhagic fever with renal syndrome (HFRS), emerged when the strain of puumala virus was isolated from the Bank vole (Clethrionomys glareolus) in Europe 199.., and the discovery of the four canners hantavirus in USA 1996. However, thanks to the famous and prolonged scientific work of Lee at el who isolated the first agent of Korean hemorrhagic fever, hantaan virus, from the autopsy lungs of striped field mice (apodemus agrarius) in 1978 after two decades of work [15]. Hantaviruses virion is lipid enveloped, covered and protected by polymorphic protein membrane nucleoprotein. The virion of hantavirus species are spherical shaped 80-110 nm in diameter [16-19]. Tripartite segmented negative-sense single stranded RNA genome comprising small (S), medium (M) and large (L) [20-22]. Small (S)-segment is the smallest segment and encodes for the nucleoprotein of 1821-1830 nucleotides the protein have 433 amino acids (aa) [22-24]. Medium (M)-segment encodes for the glycoprotein, large (L)-segment encodes for the RNA dependent RNA-polymerase (RdRp), of 3682 nt the glycoprotein precursor which covers the medium segment has 1148 amino acid, RdRp have 2156 aa, respectively [22-24] [6-10]. Furthermore, the small (S) segment however, has further an overlapping open reading frame (ORF) with a putative NSs protein of 90 aa [16, 20, 22, 24, 25]

The lipid envelope bounded with viral glycoproteins covers nucleocapsids and RNA dependent RNA-polymerase. 


The transmission of hantaviruses is done horizontally in specific human become affected by inhalation contaminated air, smelling of excreta of infected rodents and by direct contact with infected rodents. This can be realized through different situations: first domestication situation were an infected rodent happen to be in the house and leave some excreta, when in habitant come into contact with these materials they become infected, secondly through camping and agriculture this kind of situation amount to 70% of all kind of situation where people become infected.

Natural reservoir

Puumala virus is known to be harbored by the wild small animal called bank vole, myodes glareolus, DOBV, yellow field mouse; apodemus flavicollis, HTNV and a SAAV striped field mouse, apodemus agrarius (koreae and agrarius, respectively). SOCHV caused by black sea mouse, Apodemus ponticus; ASV Korean mouse field, apodemus penisulae; SEOV Norway rats, rattus norvegicus [3, 8]

Hantavirus history

Within a century modern world renascence between 1900 and 2000 the world witnessed the two major outbreak of diseases designated hemorrhagic fever with renal syndrome, sometimes referred to nephropathia epidenmica and cardiopulmonary syndrome all presumably caused by small animal rodents. The outbreak caused global human health threat before its agents where properly defined. It became an emerging potential human biological weapon disease because of its mass infections and its anthropoid vector which lead to the virus to thrive in its host reservoirs, without showing any sign of infection. The health hazardous outbreak led to the discovery of hantaviruses worldwide later categorized into two old and new world hantaviruses. Needless, to claim that hantaviruses evolutionarised only between this period, the signs and symptoms of these etiological agents disease in human hantavirus cardiopulmonary syndrome and hemorrhagic fever with renal syndrome where long ago described noticed and can be seen in Chinese literature of 10th century and the Russian archives show the description of the disease as early as 1913 in Vladivastok. Lee et al, while working on the early reported severe or mild form of hemorrhagic fever, isolated the etiological agent believed to have induced high fever called Korean hemorrhagic fever near Hantaan River, Korea in 1978. The initial isolation of the agent of KHF led to the designating name hantavirus derived from the hantaan river the place where it was discovered. The highly published anticipated discovery of 1978 proved the earlier noticed hemorrhagic fever in 1951-1953 and gave the new era in the understanding of etiological agents human disease, HFRS and HPS in the world of health hazardous biological weapon. Needless, to say more than 3000 UN soldiers were diagnosed with high fever in the course of Korean War which lasted for 3- 4 years from 1951-53. Throughout, decades of research these zoonosis viruses were not well known However, after thorough research, until late 1981 the virus was known to have its own clade and belonged to bunyaviridae family, unlike other viruses hantaviruses research revealed that they did not have arthropod vector, hence they formed their own genus of hantavirus in the family bunyavidae and they exclusively maintained their residing reservoir rodents. Hence the new zoonotic Hantavirus emerged and was restricted to the old world viruses. This was proved wrong in 1993, the world experienced the outbreak of hantaviruses related diseases which triggered the malfunction of the respiratory system, high fever and severe heart damage in the unfortunate patients infected with hantaviruses. This lead to the conviction of world researchers that hantaviruses are actively circulating in the region earlier than there isolation in 1993, in the four corners of the Americas.

Seoul virus transmitted by rat-borne mouse in Asia was described, an etiological agent specie of hantavirus causing HFRS in 1980 after the description of hantaan virus from striped field mouse (Apodemus agrarius) which started in 1976. This pioneered discovery came after a carefully long research and isolating the virus from the rat-borne mouse captured in the demilitarized battle field of Korea. The etiological agent of nephropaphia epidemical characterized in Europe was termed puumala virus, isolated from a bank vole striped field mouse initially called clethrionomys glareolus and later renamed myodes glareolus. 25 years later, the etiological agent of human disease hantavirus cardiopulmonary syndrome, Hantaan virus was identified from…..after the four corner outbreak in the united state in 1993 and this led to the discovery of another hantavirus specie called no name virus later renamed Sin Nombre virus. It is estimated that there hantavirus cases yearly go beyond 1500000 globally, with almost half of these cases occurs in the people’s republic of china. Since the definition of hantaviruses more than 22 species of hantaviruses known to be pathogen in humans have been clearly categorized and accepted by the international Committee of Virus Taxonomy. With the suspicions of been engineered spread the Center of Disease Control and Prevention (CDC) warn of hantaviruses to be possible potential biological weapons.

The world health organization  in 1983 initiated the use of HFRS to represent all etiological symptomatic diseases believed to cause HFRS restricted in the Eurasia later called old world. Mostly, HFRS displayed symptoms such as chills, headache, high fever, generalized myalgia, back and abdominal pain and hemorrhagic presentation. Because of its epidemiological and worldwide distribution, hemorrhagic fever with renal syndrome initially had several names before 1983. Most terms used were epidemic hemorrhagic fever, Korean hemorrhagic fever and the alike symptomatic disease was called nephropathia epidemica in china, Korea and (USSR, Scandinavia and Europe) respectively.

Hantaviruses clinical presentation

Normally incubation of Hantaviruses human infection takes 2 to 3 weeks. The results of infection are the two distinct severe or mild forms of diseases: hemorrhagic renal with renal syndrome (HFRS) in the Eurasian countries and Hantavirus pulmonary syndrome in the American Countries. HFRS and Nephropaphia Epidemical are the severe form of hemorrhagic fever developed when infected with Euraisan kinds of Hantaviruses, patients present kidney failure, high fever, and internal bleeding as the main symptoms which results to the death of the patient[7]. Apart from kidney failure and high fever, affected humans present symptoms which include chills, vomiting, headache, dizziness, nausea, non-productive cough, gastrointestinal symptoms. A half percent of the patients display prolonged diarrhea, malaise and lightheadness, other presentations include back pain, arthralgias, abdominal pain, and shortness of breath, tachiypnea, tachycardia and fever. However, the main cause of death is the development of disseminated intravascular congulation and internal bleeding.

Table 1.  Clinical manifestation of Hemorrhagic Fever with renal syndrome [HemorrhagicFeverwithRenalSyndrome:PathogenesisandClinicalPicture

Hong Jiang 1, HongDu1, LiM.Wang2, PingZ.Wang1* and XueF.Bai 1*]

Incubation period takes 2-3 weeks


Phase 1. Febrile




Conjuctival injection




Present of antibodies IgM

Eye pain

Platelet decreased

Petechial rash

Immune complexes




Conjuctival injection




Present of antibodies IgM

Phase 2.



Complement activation


Disseminated intrascular congulation


Vascular leakage


Acute shock

Phase 3.


Disseminated intrasecular congulation (DI)


Kidney failure


Phase 4.


Improved renal function

Pulmonary complication


Death or improvement

Phase 5.


Recovery period

Table 2. Bunyavidae family classifications

Common Reservoir



Common Species

Country endemic

Animal vertebrate


Bunyamwera virus

La Crosse virus

Tahyna virus

Akabane virus

Oropouche virus

Animal vertebrate


Hantaan virus

Sin Nombre virus

Andes virus

Puumala, Dobrava



Animal vertebrate


Dugbe virus Crimean-Congo hemorrhagic fever virus

Nairobi sheep disease virus

Eurasia, Africa

Animal vertebrate


Rift Valley fever virus

Rift Valley fever virus

Sandly fever-Sicilian virus



Tomato spotted wilt virus

Tomato spotted wilt virus

Table 3: Hantaviruses genus classification


Endemic area and reservoir distribution


Rodent vector

Mortality (%)

Puumala (PUUV)

Eurasia (Old World)


Bank vole (Clethrionomys glareolus)


Dobrava-Belgrade (DOBV)

South and East Europe, Balkan countries and the middle East (Old World)


Yellow naked-mouse (Apodemus flavicollis)


Dobrava (DOBV)

Central, East and north of Europe (Old World)


Striped field mouse (Apodemus agrarius)


Hantaan (HTN)

Central, East and north of Europe, Eastern Russia,Tien Shan Mtns Caucasian,  China, north and south Korea (Old World)


Striped field mouse (Apodemus agrarius)


Seoul (SEOV)

World Wide (Old World)


Rattus norvegicus and rattus


Tula (TUL)

Europe (Old World)


Microtus arvalis



Eastern Russia, Eastern Asia and Siberia (Old World)


Korean field mouse (Apodemus peninsula)


Andes (ANDV)

South America (Argentina, Uruguay, Chile) (New World)


Oligoryzomys longicaudatus


Sin Nombre (SN)

USA, Canada (New World)


Peromyscus maniculatus



Prospect Hill(PH)

(New World) USA, Canada


Mricrotus pennsylvanicus

(Meadow vole)

New York (NY)

(New World) USA, Canada


Peromyscus  leucopus


Khabarosk (KHB)

Russia , Asia (Old World)


Microtus fortis (reed vole)


Thottapalayam (TPM)

India, Afghanistan, Pakistan, China, Japan (Old World)


Suncus murinus

(musk shrew)


USA, Mexico, Canada (New World)


Peromyscus maniculatus

(Deer mouse)


Black Creen Canal (BCCV)

USA, Venesuala, Peru, (New World)


Sigmodon hispidus


Bayou  (BAYV)

USA (Louisiana), (New World)


Oryzomys palustris


(Rice rat)


Araraquara (ARAV)

South America (Brazil) (New World)


Bolomys lasiurus



USA (New World)


Sigmodon hispidus



South America (Argentina), Brazil

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