Co-infecting viruses of species Bovine rhinitis B virus (Picornaviridae) and Bovine nidovirus 1 (Tobaniviridae) identified for the first time from a post-mortem respiratory sample of a sheep (Ovis aries) in Hungary

In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time. The complete/nearly complete genomes of the identified viruses were determined using RT-PCR and Nanopore (MinION-Flonge) / Dye-terminator sequencing techniques. The results of detailed genomic and phylogenetic analyses indicate that the identified picornavirus most likely belongs to a type 4 genotype of species Bovine rhinitis B virus (BRBV-4, OR885914) of genus Aphthovirus, family Picornaviridae while the ovine nidovirus (OvNV, OR885915) - as a novel variant - could belong to the recently created Bovine nidovirus 1 (BoNV) species of genus Bostovirus, family Tobaniviridae. None of the identified viruses were detectable in the enteric samples using RT-PCR and generic screening primer pairs. Both viruses are well-known respiratory pathogens of cattle, but their presence was not demonstrated before in other animals, like sheep. Furthermore, neither BRBV-4 nor BoNVs were investigated in European cattle and/or sheep flocks, therefore it cannot be determined whether the presence of these viruses in sheep was a result of a single host species switch/spillover event or these viruses are circulating in not just cattle but sheep populations as well. Further studies required to investigate the spread of these viruses in Hungarian and European sheep and cattle populations and to identify their pathogenic potential in sheep.

Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary

In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.

Human orf virus (family Poxviridae) infection following a lamb bite in Hungary

Human orf disease (called ecthyma contagiosum or contagious/infectious pustular dermatitis in animals) was confirmed on the fingers of both hands of a 24-year-old female, after feeding diseased lambs with a nursing bottle in April 2023. In addition to skin symptoms, she had low-grade fever (37.6°C) and swollen lymph nodes in both axilla. The presence of orf virus (genus Parapoxvirus, family Poxviridae) was confirmed, and this strain, Baja/2023/HUN (OR372161-OR372163), was found to have > 98% nucleotide sequence identity to sheep-origin orf viruses in four tested genome regions (ORF011/B2L, ORF019, ORF020/VIR, and ORF056). This is the first report of a human case of infection with the neglected zoonotic orf virus in Hungary.

The genomic and epidemiological investigations of enteric viruses of domestic caprine (Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species

IMPORTANCE

Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.

Human cases of lymphocytic choriomeningitis virus (LCMV) infections in Hungary

Lymphocytic choriomeningitis (LCM) is a "neglected" rodent-borne viral zoonotic disease caused by lymphocytic choriomeningitis virus (LCMV) (family Arenaviridae). The aim of this retrospective clinical and laboratory study was to detect LCMV RNA, using RT-PCR, in cerebrospinal fluid samples collected from patients with central nervous system (CNS) infections of unknown aetiology from over a 12-year period in Hungary. Between 2009 and 2020, a total of 74 cerebrospinal fluid samples were tested using an in-house LCMV-specific RT-PCR-based method at the Department of Medical Microbiology and Immunology, University of Pécs. The mean age of the 74 patients included in our study was 24 years (min. 5, max. 74), with a predominance of men (44 [59.5%]; women, 30 [40.5%]). Two (2.7%) cerebrospinal fluid samples were found to be positive for LCMV RNA by RT-PCR and sequencing. The first LCMV case was a 5-year-old preschool boy who had a hamster bite on his left-hand finger, and the second LCMV case was a 74-year-old man who was living in a village and had incipient dementia and a previous permanent functional CNS impairment. The two detected LCMV strains (MW558451 and OM648933) from the year 2020 belonged to two different genetic lineages (I and II). These two cases of CNS inflammation of unknown origin represent the first published human LCMV infections confirmed by molecular methods in Hungary.

Molecular epidemiology and characterization of endemic, epidemic and imported hepatitis A virus (HAV) strains in Hungary (2003-2022)

Hepatitis A virus (HAV) is one of the most important etiological agents of acute viral hepatitis but comprehensive molecular epidemiological study with chrono-phylogeographical data are not available from Hungary.Between 2003 and 2022, a total of 8,307 HAV infections were registered officially in Hungary of which 400 (4.8%) HAV IgM antibody-positive serum samples were collected countrywide. HAV genomic RNA was successfully detected in 216/400 (54%) sera by RT-PCR subsequently confirmed by sequencing. The complete nucleotide sequences of VP1 region were determined in 32 representative HAV strains. Based on the sequence analysis, 150 (69.4%) strains were characterized as HAV sub-genotype IA and 66 (30.6%) as sub-genotype IB, respectively. Based on the combined epidemiological and molecular data, epidemic, endemic, and imported HAV strains were also characterized. The first two registered countrywide outbreaks started among men-sex-with men (MSM) in 2011 (sub-genotype IA) and 2021 (sub-genotype IB), the continuously circulating endemic/domestic HAV strain (sub-genotype IA) in East Hungary and the travel-related sub-genotype IB strains from Egypt should be highlighted. All HAV strains are deposited in the HAVNET database (https://www.rivm.nl/en/havnet).In this 20-year-long comprehensive molecular epidemiological study, we report the genetic characterization and geographic distribution of endemic, epidemic and imported HAV strains for the first time in Hungary with continuous co-circulation of sub-genotypes IA and IB HAV strains since 2003. These data provide basic information about the HAV situation in the country in an international context and can promote more effective national public health intervention strategies for the prevention of HAV transmissions and infections.

A novel mammarenavirus (family Arenaviridae) in hedgehogs (Erinaceus roumanicus) in Europe

In this study, a novel mammarenavirus (family Arenaviridae) was identified in a hedgehog (family Erinaceidae) in Hungary and genetically characterized. Mecsek Mountains virus (MEMV, OP191655, OP191656) was detected in nine (45%) out of 20 faecal specimens collected from a Northern white-breasted hedgehog (Erinaceus roumanicus). The L-segment proteins (RdRp and Z) and S-segment proteins (NP and GPC) of MEMV had 67.5%/70% and 74.6%/65.6% amino acid sequence identity, respectively, to the corresponding proteins of Alxa virus (species Mammarenavirus alashanense) identified recently in an anal swab from a three-toed jerboa (Dipus sagitta) in China. MEMV is the second known arenavirus endemic in Europe.

High seroprevalence of hepatitis E virus (HEV) in South Transdanubia, Hungary (2010-2022)

Hepatitis E virus (HEV) is an increasingly recognized etiological agent of acute, chronic and extrahepatic human infections with primarily zoonotic origin in Europe. Limited numbers of comprehensive population-based studies are available related to HEV seroepidemiology, especially from Central Europe.The aim of this study was to investigate the seroprevalence and trends of total and IgM antibodies against HEV in different age groups in the population of South Transdanubia, Hungary, within a thirteen years long period between the years 2010 and 2022.We retrospectively analysed the serological test results of HEV total and HEV IgM antibodies carried out by ELISA technique using Dia.Pro (Diagnostic Bioprobes, Italy) kit from serum samples collected from patients with or without hepatitis between January 1, 2010 and December 31, 2022.The number of tested samples (∑6,996 for total antibody and ∑6,582 for IgM) increased during the study period. The average HEV total and the IgM antibody seropositivities were 33% (2,307/6,996 samples) and 9.6% (642/6,582 samples), respectively, in the study population. The HEV total antibody seropositivity varied in different age groups between 3.9% (age group 1-5 years) and 58.6% (86-90 years) and showed an increasing positivity by age. At the age groups >50 years, nearly half (43%) of the population had antibodies against HEV. The HEV IgM positivity had an increasing trend of up to 13.9% in the age group 81-85 years.High HEV total and IgM antibody seroprevalence were detected in South Transdanubia, Hungary, confirming that this region is highly endemic for HEV infections in Europe.

Seroprevalence and genotype distribution of hepatitis A virus in the pre-vaccine era in South Transdanubia, Hungary (2010-2020)

In this study, the age-related seroprevalence of hepatitis A virus (HAV) infection was investigated in the population in South-Transdanubia, Southwest Hungary (Central Europe) between years 2010 and 2020. Up to the age of 40, the HAV seropositivity was less than 18% in all age groups indicating a low level of HAV endemicity in this part of the country in the covered study period. The HAV seropositivity started to increase at the age group 41-45 years, reaching the ∼50% at age group 56-60, and 75-80% at age group 66-70, respectively. A total of 43 (0.2%) of the 21,106 tested sera were HAV IgM-positive (the annual percentage range of HAV IgM-positivity was 0.046-0.6%). Total of 24 (55.8%) of the 43 HAV IgM-positive samples tested RT-PCR-positive confirmed as HAV sub-genotypes IA (N = 17; 70.8%) and IB (N = 7; 29.2%), respectively. Imported HAV infections (three cases from Romania, and one-one case from Austria and Italy), two small outbreaks and 11 cases of a genetically identical sub-genotype IA strain (GenBank number of the prototype strain: KM657825) from 2012 to 2014 were identified later connected directly to the enormous HAV outbreak initiated among men who have sex with men (MSM) at the end of 2011 in the capital Budapest. In summary, low endemicity but high and increased susceptibility for HAV infection was found in the population in Southwest Hungary, where repeated introduction of sub-genotypes IA and IB HAV strains were identified between 2010 and 2020.

Human-stool-associated tusavirus (Parvoviridae) in domestic goats and sheep

In this study, genetic counterparts of the human-stool-associated tusavirus (subfamily Parvovirinae, family Parvoviridae) with >97% and 95-100% amino acid sequence identity in the parvoviral NS1 and VP1 protein were identified in faecal specimens from domestic goats (Capra hircus) and sheep (Ovis aries) in Hungary. Eleven (17.8%) of the 62 faecal specimens from goats and 12 (25.5%) of the 47 from sheep both from less than 12 months old animals were positive for tusavirus DNA by PCR, while none of the specimens collected from cattle and swine were positive. Thus, it cannot be ruled out that tusavirus infection in humans is of zoonotic origin.

A novel parvovirus (family Parvoviridae) in a freshwater fish, zander (Sander lucioperca)

In this study, a novel parvovirus (zander/M5/2015/HUN, OK236393) was detected in faecal specimens from a fish – zander or pikeperch (Sander lucioperca) – and genetically characterized using viral metagenomics and PCR methods. The NS1 and VP1 proteins of zander/M5/2015/HUN share <30% aa sequence identity, respectively, with the corresponding proteins of known members of the family Parvoviridae. Out of 62 faecal specimens collected from 13 freshwater fish species, three (4.8%) samples were positive by PCR for the novel parvovirus – all from zander. This is the second parvovirus detected in fish – after the disease-causing tilapia parvovirus of the subfamily Hamaparvovirinae – and it potentially represents a novel genus in the subfamily Parvovirinae.

Development and Large-Scale Testing of a Novel One-Step Triplex RT-qPCR Assay for Simultaneous Detection of “Neurotropic” Porcine Sapeloviruses, Teschoviruses (Picornaviridae) and Type 3 Porcine Astroviruses (Astroviridae) in Various Samples including Nasal Swabs

Porcine sapeloviruses, teschoviruses of family Picornaviridae and type 3 porcine astroviruses of family Astroviridae are (re-)emerging enteric pathogens that could be associated with severe, disseminated infections in swine, affecting multiple organs including the central nervous system (CNS). Furthermore, small-scale pioneer studies indicate the presence of these viruses in porcine nasal samples to various extents. The laboratory diagnostics are predominantly based on the detection of the viral RNA from faecal and tissue samples using different nucleic-acid-based techniques such as RT-qPCR. In this study, a novel highly sensitive one-step triplex RT-qPCR assay was introduced which can detect all known types of neurotropic sapelo-, tescho- and type 3 astroviruses in multiple types of samples of swine. The assay was evaluated using in vitro synthesized RNA standards and a total of 142 archived RNA samples including known sapelo-, tescho- and type 3 astrovirus positive and negative CNS, enteric and nasal specimens. The results of a large-scale epidemiological investigation of these viruses on n = 473 nasal swab samples from n = 28 industrial-type swine farms in Hungary indicate that all three neurotropic viruses, especially type 3 astroviruses, are widespread and endemically present on most of the investigated farms.

Genome characterization, prevalence and tissue distribution of astrovirus, hepevirus and norovirus among wild and laboratory rats (Rattus norvegicus) and mice (Mus musculus) in Hungary

Rodents including rats are reservoir of several pathogens capable of affecting human health. In this study, faecal and different organ specimens from free-living Norway rats (Rattus norvegicus) (N = 18) and faecal samples from laboratory rodents (rats N = 21 and mice N = 20) collected from different geographic areas in Hungary between 2017 and 2020 were investigated by viral metagenomics and conventional RT-PCR methods. The complete genome of three different RNA viruses, rat astrovirus, rat norovirus and rat hepevirus were characterized and analysed in detail. Rat norovirus was detected in faecal (17.6%, 3/17) and kidney (7.1%, 1/14) samples; rat astrovirus in faecal (23.5%, 4/17) and spleen (13.3%, 2/15) samples, and rat hepevirus in 43% to 67% the faecal, liver, kidney, lung, heart, muscle, brain and blood samples from Norway rats, respectively. Rat norovirus was also identifiable in 5% (1/21) of laboratory rats and rat astrovirus in 40% (8/20) of faecal samples from laboratory mice. Co-infections were found in 28% (5/18) wild Norway rats. The highest RNA viral load of astrovirus (1.81 × 108 copy/g) and norovirus (3.49 × 107 copy/g) were measured in faecal samples; while the highest RNA viral load of hepevirus (1.16 × 109 copy/g) was found in liver samples of Norway rats, respectively. This study confirms the wide geographic distribution and high prevalence of astrovirus, norovirus and hepevirus among wild rats in Hungary with confirmation of different organ involvement of as well as the detection of norovirus and astrovirus in laboratory rats and mice, respectively. This finding further strengthens the role of rodents in the spread of viral pathogens especially infecting human.

Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTR^IRES-?/P1(VP0-VP3-VP1)/P2(2A₁^NPG↓P-2A₂^H-box/NC-2B-2C)/P3(3A-3B^VPg-3C^Pro-3D^Pol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms

All of the known porcine sapeloviruses (PSVs) currently belong to a single genotype in the genus Sapelovirus (family Picornaviridae). Here, the complete genome of a second, possibly recombinant, genotype of PSV strain SZ1M-F/PSV/HUN2013 (MN807752) from a faecal sample of a paraplegic pig in Hungary was characterized using viral metagenomics and RT-PCR. This sapelovirus strain showed only 64 % nucleotide identity in the VP1 region to its closest PSV-1 relative. Complete VP1 sequence-based epidemiological investigations of PSVs circulating in Hungary showed the presence of diverse strains found in high prevalence in enteric and respiratory samples collected from both asymptomatic and paraplegic pigs from 12 swine farms. Virus isolation attempts using PK-15 cell cultures were successful in 3/8 cases for the classic but not the novel PSV genotype. Sequence comparisons of faeces and isolate strains derived VP1 showed that cultured PSV strains not always represent the dominant PSVs found in vivo.

Detection and complete genome characterization of a novel RNA virus related to members of the Hepe-Virga clade in bird species, hoopoe (Upupa epops)

Using viral metagenomics, next-generation sequencing and RT-PCR techniques a genetically divergent hepevirus-like RNA virus was identified and characterized from a faecal sample of wild bird species, hoopoe (Upupa epops) in Hungary. The complete viral genome sequence of hoopoe/BBanka01/2015/HUN (GenBank accession number MN852439) is 7052 nt long including a 54-nt 5' and an 18-nt 3' non-coding region without poly(A)-tail. Sequence analysis indicated that the hoopoe/BBanka01/2015/HUN genome has potentially three overlapping open reading frames (ORFs). The ORF1 (6558 nt/2185aa) encodes a long, non-structural polyprotein (replicase) including putative functional domains and conserved aa motifs of methyltransferase with domain Y, RNA helicase and RdRp and has <33% aa identity to the known hepe- and hepe-like viruses. The ORF2 (1446 nt/481aa) encodes a putative structural (capsid) protein overlapping with ORF1 but translated in different coding frame. The functions of the short ORF3 (426 nt/141aa) were not predictable. Similar virus sequences were not detected from samples from 21 further bird species. The taxonomic position of this novel virus is presently unknown.

Characterization of an integrated, endogenous mouse mammary tumor virus-like (MMTV) betaretrovirus genome in a black Syrian hamster (Mesocricetus auratus)

Retroviruses (family Retroviridae) are important agents of humans and animals. This study reports the detection and complete genome characterization of a novel endogenous retrovirus from the black Syrian hamster (Mesocricetus auratus) with a squamous cell skin tumor. The proviral genome, tentatively named black Syrian hamster retrovirus (BSHRV/2013/HUN, MK304634), was 8784 nucleotide in length with typical full-length betaretrovirus genome organization of 5'LTR-gag-pro-pol-env-3'LTR and with a characteristic mouse mammary tumor virus-like (MMTV) betaretrovirus dUTPase domain but without a sag gene. The BSHRV gag (534aa), pro/pol (~1099aa) and env (672aa) proteins had 56%/63%/50% aa identity to the corresponding proteins of MMTV (AF228552). The proviral DNA is detectable in tumor as well as in tumor-free cells by conventional PCR and qPCR but only visible in the tumor cells by in situ hybridization. Low level retroviral RNA expression was found only in the DNase-treated RNA tumor samples using RT/nested PCR. BSHRV/2013/HUN-like betaretrovirus DNA was also identified from a faecal and tissue samples from 1 of the further 3 tested individuals by nested-PCR and qPCR. Further research is needed to investigate the distribution, activity and etiological role of this novel MMTV-like betaretrovirus species in hamster.

Analysis of a novel RNA virus in a wild northern white-breasted hedgehog (Erinaceus roumanicus)

Tombusviruses are generally considered plant viruses. A novel tombus-/carmotetravirus-like RNA virus was identified in a faecal sample and blood and muscle tissues from a wild northern white-breasted hedgehog (Erinaceus roumanicus). The complete genome of the virus, called H14-hedgehog/2015/HUN (GenBank accession number MN044446), is 4,118 nucleotides in length with a readthrough stop codon of type/group 1 in ORF1 and lacks a poly(A) tract at the 3' end. The predicted ORF1-RT (RdRp) and the capsid proteins had low (31-33%) amino acid sequence identity to unclassified tombus-/noda-like viruses (Hubei tombus-like virus 12 and Beihai noda-like virus 10), respectively, discovered recently in invertebrate animals. An in vivo experimental plant inoculation study showed that an in vitro-transcribed H14-hedgehog/2015/HUN viral RNA did not replicate in Nicotiana benthamiana, Chenopodium quinoa, or Chenopodium murale, the most susceptible hosts for plant-origin tombusviruses.

Diverse picornaviruses are prevalent among free-living and laboratory rats (Rattus norvegicus) in Hungary and can cause disseminated infections

In this study, the full length genomes of three phylogenetically distant picornaviruses (family Picornaviridae) belonging to the genus Rosavirus (rat08/rRoB/HUN, MN116648), Kobuvirus (rat08/rAiA/HUN, MN116647), and Cardiovirus (rat08/rCaB/HUN, MN116646) were obtained from a single faecal sample of a free-living Norway rat (Rattus norvegicus) in Hungary using viral metagenomics and RT-PCR/Sanger sequencing. The acquired complete genomes were in silico analyzed in detail revealing the presence of a second minor open reading frame encoding an alternative Leader peptide (L*) in rat08/rCaB/HUN and a ca. 222 nt-long sequence repeat with compact secondary RNA structure in the 3' UTR of rat08/rRoB/HUN. The studied rat picornaviruses were frequently detectable by RT-PCR with relatively high viral loads ranged between 8.99E+02 and 1.29E+06 copies/ml in rat faecal samples collected from five geographically distant locations throughout Hungary. The VP1 sequence-based phylogenetic analyses show the presence of multiple, mostly location-specific lineages for all three picornaviruses. Rat rosavirus and rat cardiovirus were identified in spleen while rat cardiovirus was also detected in liver, muscle and kidney samples with variable copy numbers (6.42E+01-1.90E+05 copies/μg total RNA) suggesting extra-intestinal dissemination. Both viruses were also prevalent (70.0% and 18.2%) among two populations of laboratory rats ("Wistar-type" and "hooded-type") held in different, isolated laboratory animal units.

Genetically highly divergent RNA virus with astrovirus-like (5'-end) and hepevirus-like (3'-end) genome organization in carnivorous birds, European roller (Coracias garrulus)

Astroviruses (family Astroviridae) and hepeviruses (family Hepeviridae) are small, non-enveloped viruses with genetically diverse +ssRNA genome thought to be enteric pathogens infecting vertebrates including humans. Recently, many novel astro- and hepatitis E virus-like +ssRNA viruses have been described from lower vertebrate species. The non-structural proteins of astro- and hepeviruses are highly diverse, but the structural/capsid proteins represent a common phylogenetic position shed the light of their common origin by inter-viral recombination. In this study, a novel astrovirus/hepevirus-like virus with +ssRNA genome (Er/SZAL5/HUN/2011, MK450332) was serendipitously identified and characterized from 3 (8.5%) out of 35 European roller (Coracias garrulus) faecal samples by RT-PCR in Hungary. The complete genome of Er/SZAL5/HUN/2011 (MK450332) is 8402 nt-long and potentially composed three non-overlapping open reading frames (ORFs): ORF1a (4449 nt/1482aa), ORF1b (1206 nt/401aa) and ORF2 (1491 nt/496aa). The ORF1ab has an astrovirus-like genome organization containing the non-structural conserved elements (TM, CC, NLS, VPg) and enzyme residues (trypsine-like protease, RNA-dependent RNA-polymerase) with low amino acid sequence identity, 15% (ORF1a) and 44% (ORF1b), to astroviruses. Supposedly the ORF2 is a capsid protein but neither the astrovirus-like subgenomic RNA promoter (sgRNA) nor the astrovirus-like capsid characteristics have been identifiable. However, the predicted capsid protein (ORF2) showed 26% identity to the corresponding protein of hepevirus-like novel Rana hepevirus (MH330682). This novel +ssRNA virus strain Er/SZAL5/HUN/2011 with astrovirus-like genome organization in the non-structural genome regions (ORF1a and ORF1b) and Rana hepevirus-related capsid (ORF2) protein represent a potentially recombinant virus species and supports the common origin hypothesis, although, the taxonomic position of the studied virus is still under discussion.

A humán parechovírusok klinikai jelentősége súlyos újszülött- és csecsemőkori fertőzésekben hazánkban

Abstract:

Introduction: Most human parechovirus (HPeV, family Picornaviridae) infections are asymptomatic but may cause gastroenteritis in children. New reports show that HPeVs can be associated with severe central nervous system symptoms and sepsis-like syndromes in infants. The clinical significance of HPeVs in Hungary has not been investigated before. Aim: The aim of this study was to detect genotype HPeV in faecal samples of children and analysis of the clinical symptoms. Method: For the detection and genotyping of HPeV strains, reverse transcription–polymerase chain reaction and sequencing methods were used from faecal samples of children with gastroenteritis divided into three groups: group A) hospitalised children younger than 10 years (n = 75); group B) 0–12 months infants (n = 237) and group C) children less than 18 years of age with sepsis-like/neurological symptoms (n = 105) were tested. Results: Three HPeV positive samples (3/75, 4%) were found in group A, two of them belong to the HPeV type 1, the third was non-typeable. All positive samples were from infants of 7 to 11 months of age. In group B, HPeV was detected in 6.8% (16/237) of the samples. Five were HPeV1, six were HPeV3 and five were non-typeable. While most of the infants with HPeV1 (4/5) did not require hospitalisation, 83% of the HPeV3 infected infants (5/6) did. Five (4.8%) HPeV strains detected from children less than 18 years of age with sepsis-like/neurological symptoms (group C) belonged to HPeV1 (three) and HPeV3 (two). All positive samples were from hospitalised infants less than 2 months of age. Conclusion: HPeV1 infections are less severe in infants than HPeV3 infections. The leading symptom of HPeV1 was diarrhoea, although in infants less than 1–2 months neurological symptoms (somnolence, lassitude) were also present. HPeV3 infections were more common among newborns. The main symptoms of severe HPeV3 infection are: gastroenteritis (7/8), fever ≥38 °C (6/7), loss of appetite (6/7), rash (4/7), somnolence/lassitude (3/7), sepsis-like syndrome (3/7) and respiratory symptoms (2/7). Orv Hetil. 2019; 160(10): 386–395.

Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals

Astroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms "astrovirus/encephalitis" and "astrovirus/meningitis" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.

Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken

Picobirnaviruses (PBVs) of family Picobirnaviridae have bisegmented (S1 and S2 segments), double-stranded RNA genomes. In this study a total of N = 12 complete chicken PBVs (ChPBV) segments (N = 5 of S1 and N = 7 of S2, Acc. Nos.: MH425579-90) were determined using viral metagenomic and RT-PCR techniques from a single cloacal sample of a diarrheic chicken. The identified ChPBV segments are unrelated to each other and distant from all of the currently known PBVs. In silico sequence analyses revealed the presence of conserved prokaryotic Shine-Dalgarno-like (SD-like) sequences upstream of the three presumed open reading frames (ORFs) of the S1 and a single presumed ORF of the S2 segments. According to the results of expression analyses in E. coli using 6xHis-tagged recombinant ChPBV segment 1 construct and Western blot these SD-like sequences are functional in vivo suggesting that S1 of study PBVs can contain three ORFs and supporting the bacteriophage-nature of PBVs.

Detection of a novel RNA virus with hepatitis E virus-like non-structural genome organization in amphibian, agile frog (Rana dalmatina) tadpoles

In recent years, relatives (bastrovirus, hepelivirus) of hepeviruses (family Hepeviridae) have been reported in a variety of vertebrate hosts. Preliminary studies indicated that inter-viral family recombination events at the junction of the genomes that encodes non-structural (ORF1) and structural protein (ORF2) were implicated in the genesis of hepeviruses. Using viral metagenomics, next generation sequencing and RT-PCR techniques a genetically divergent hepevirus-like RNA virus was identified and characterized from agile frog (Rana dalmatina) tadpoles living in aquatic environment in three natural ponds (Mélymocsár, Lake Ilona and Lake Katlan) in the Pilis Mountains, in Hungary. The complete genome of the viral strain agile frog/RD6/2015/HUN (MH330682) is 7188 nt long including a 48-nt 5' and a 122-nt 3' non-coding region. Sequence analysis indicated that the agile frog/RD6/2015/HUN genome has potentially three non-overlapping ORFs. ORF1 (4740 nt/1579aa) has a hepevirus-like non-structural genome organization and encodes several hepevirus-like amino acid sequence motifs. The ORF2 is a potential capsid protein. The functions of the ORF3 were not predictable. The study virus was present in 18 (46%) of the 39 faecal specimen pools from agile frog tadpoles. The taxonomic position of this novel virus is presently unknown.