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Heli Siljander - One of the best experts on this subject based on the ideXlab platform.
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intestinal virome changes precede autoimmunity in type i diabetes susceptible children
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Guoyan Zhao, Aleksandar Kostic, Tiffany W Poon, Hera Vlamakis, Heli Siljander, Tommi Vatanen, Arnold Park, Lindsay DroitAbstract:Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of Circoviridae-related sequences in samples from controls in comparison with cases. Enterovirus, Kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.
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intestinal virome changes precede autoimmunity in type i diabetes susceptible children
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Guoyan Zhao, Aleksandar Kostic, Tiffany W Poon, Hera Vlamakis, Heli Siljander, Tommi Vatanen, Arnold Park, Lindsay DroitAbstract:Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of Circoviridae-related sequences in samples from controls in comparison with cases. Enterovirus, Kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.
Peter Pankovics - One of the best experts on this subject based on the ideXlab platform.
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genomic analysis of a novel picornavirus from a migratory waterfowl greater white fronted goose anser albifrons
Archives of Virology, 2018Co-Authors: Akos Boros, Tung Gia Phan, Peter Pankovics, Peter Simmonds, Eric Delwart, Tamas Kiss, Gabor ReuterAbstract:The complete genome of goose picornavirus 1 (GPV-1) strain goose/NLSZK2/HUN/2013 (MF358731) was determined by RT-PCR and next-generation sequencing from a cloacal sample of a migratory waterfowl, greater white-fronted goose (Anser albifrons) in Hungary. The genome of GPV-1 shows an L-3-3-4 organization pattern with a 5'-terminal origin of replication (ORI) region, a type-IV IRES, and an Hbox/NC-type 2A protein. This virus showed the highest overall sequence identity to the members of the genus Kobuvirus, although the phylogenetic position of GPV-1 is different in the analyzed P1, 2C and 3CD phylogenetic trees, which further increases the diversity of known avian picornaviruses.
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DISPATCHES Evolution of Porcine Kobuvirus
2013Co-Authors: Gabor Reuter, Peter Pankovics, Sándor Kecskeméti, Kobuvirus The Genus KobuvirusAbstract:Porcine Kobuvirus was fi rst identifi ed in early 2007 in Hungary. Originally thought to be confi ned to the intestine, almost 2 years later the virus was found in the blood of clinically healthy pigs on the same farm. Porcine Kobuvirus may be widely distributed on pig farms worldwide. Picornaviruses (family Picornaviridae) are small, nonenveloped viruses with single-stranded, positive-sense genomic RNA; they are divided into 12 genera: Aphthovirus
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Kobuvirus in domestic sheep hungary
Emerging Infectious Diseases, 2010Co-Authors: Gabor Reuter, Akos Boros, Peter Pankovics, László EgyedAbstract:To the Editor: Picornaviruses (family Picornaviridae) are small, nonenveloped viruses with single-stranded, positive-sense genomic RNA. They are divided into 12 genera: Enterovirus, Aphthovirus, Cardiovirus, Hepatovirus, Parechovirus, Erbovirus, Teschovirus, Sapelovirus, Senecavirus, Tremovirus, Avihepatovirus, and Kobuvirus. The genus Kobuvirus consists of 2 officially recognized species, Aichi virus (1) and Bovine Kobuvirus (2), and 1 candidate species, porcine Kobuvirus (3). The Kobuvirus genome is ≈8.2–8.4 kb long and has the typical picornavirus genome organization of leader (L) protein following the structural (viral protein [VP] 0, VP3, and VP1) and nonstructural (2A–2C and 3A–3D) regions (2,4). The genetic identity on the coding region between Aichi (strain A846/88), bovine (U-1), and porcine (S-1-HUN) viruses is between 35% (L protein) and 74% (3D region) (2,4). Aichi virus and bovine Kobuvirus were first detected in fecal samples from humans and cattle in Japan, in 1991 and 2003, respectively (1,2). Porcine Kobuvirus was identified from domestic pigs in Hungary in 2008 (3,4). Recent studies demonstrated that Aichi virus circulates in Asia (5), Europe (6,7) including Hungary (4), South America (6), and North Africa (8) and can cause gastroenteritis in humans. In addition, bovine and porcine Kobuviruses are detected among these farm animals in Europe (4) and Asia (2,9). These data indicate that Kobuviruses are widely distributed geographically and raise the possibility of additional animal host species. We detected Kobuvirus in sheep. On March 17, 2009, a total of 8 fecal samples were collected from young, healthy, domestic sheep (Ovis aries) <3 weeks of age in a herd of 400 animals in central Hungary. At this farm, merino ewes from Hungary were mated with blackhead meat rams from Germany. At the time of sampling, no clinical signs of diarrhea were reported. Reverse transcription–PCR was performed by using generic Kobuvirus screening primers (UNIV-kobu-R/F) reported previously (4). These primers were designed for Aichi virus (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB040749","term_id":"15186718","term_text":"AB040749"}}AB040749), bovine ({"type":"entrez-nucleotide","attrs":{"text":"AB084788","term_id":"24817742","term_text":"AB084788"}}AB084788), and porcine Kobuvirus ({"type":"entrez-nucleotide","attrs":{"text":"EU787450","term_id":"219524015","term_text":"EU787450"}}EU787450) sequences and amplify a 216-nt region of 3D (RNA-dependent RNA polymerase region). The continuous 3D and 3′ untranslated regions (UTRs) of the Kobuvirus genome in sheep were determined by using the 5′/3′ RACE (rapid amplification of cDNA ends) kit, 2nd generation (Roche Diagnostics GmbH, Mannheim, Germany) and primers UNIV-kobu-F and S-1-F-7518/7540 (5′-CACTTCCATCATCAACACCATCA-3′ corresponding to nt 7518–7540 of bovine Kobuvirus) (4). PCR products were sequenced directly in both directions by using the BigDye Reaction Kit (Applied Biosystems, Warrington, UK) with the PCR primers and sequenced by an ABI PRISM 310 Genetic Analyzer (Applied Biosystems, Stafford, TX, USA). Phylogenetic analysis was conducted by using MEGA version 4.1 (www.megasoftware.net). The sequence for Kobuvirus/sheep/TB3-HUN/2009/Hungary was submitted to GenBank under accession no. {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693. Of the 8 sheep fecal samples, 5 (62.5%) were positive for Kobuvirus. The partial 3D region (216 nt) was genetically identical for all 5 strains. The 3′ continuous nucleotide sequence of the partial 3D (688 nt) and 3′ UTR (174 nt) regions of strain Kobuvirus/sheep/TB3-HUN/2009/Hungary (TB3-HUN; {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693) was determined. TB3-HUN had 59%–66% (862) nt and 77%–84% aa identities to Aichi and porcine Kobuviruses, respectively. Strain TB3-HUN had 89/97% nt/aa and 86% nt identities to bovine Kobuvirus in the 3D/3′ UTR (862 nt) and 3′ UTR (174 nt) regions, respectively. Phylogenetic analysis of the overlapping partial 3D/3′ UTR nucleotide sequence of TB3-HUN from sheep and of reference bovine, porcine, and human Kobuviruses confirmed that ovine Kobuvirus strain TB3-HUN is related to bovine Kobuviruses (Figure). Figure Phylogenetic analysis of Kobuvirus in sheep (Kobuvirus/sheep/TB3-HUN/2009/Hungary, {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693) and Kobuvirus lineages in humans, cattle, and swine, according ... The nucleotide sequence of the partial 3D/3′ UTR region of Kobuvirus in sheep has high nucleotide identity to bovine Kobuviruses and forms the same lineage (but a different sublineage) with the Kobuvirus strains in cattle. This result raised the following questions: can a highly similar Kobuvirus be present in (and pathogenic for) 2 animal species (cattle and sheep), or is this result a consequence of natural contamination? The concept of sheep as host is supported by the high prevalence of Kobuvirus in young healthy sheep; by the sublineage position of the sheep strain on the phylogenetic tree according to the most conserved genetic region; and by the genetic relation between the 2 potential ruminant hosts, cattle and sheep. The existence of 1 pathogen in 2 host species (cattle and sheep) is well known, e.g., for bluetongue virus, adenoviruses, ovine herpesvirus type 2, and foot-and-mouth disease picornaviruses (10). Alternatively, the possibility of natural contamination cannot be excluded. The possibility of passive virus shedding in sheep exists because a cattle farm was located next to the tested sheep herd and would enable fecal–oral transmission of Kobuvirus between these farm animals. Both possibilities (host and passive virus reservoir) are preliminary perceptions, regardless which is true. Further molecular and epidemiologic studies are required to determine the relevance, distribution, and diversity of Kobuvirus or Kobuviruses in sheep.
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Evolution of Porcine Kobuvirus Infection, Hungary
'Centers for Disease Control and Prevention (CDC)', 2010Co-Authors: Gabor Reuter, Sándor Kecskeméti, Peter PankovicsAbstract:Porcine Kobuvirus was first identified in early 2007 in Hungary. Originally thought to be confined to the intestine, almost 2 years later the virus was found in the blood of clinically healthy pigs on the same farm. Porcine Kobuvirus may be widely distributed on pig farms worldwide
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Detection of Aichi virus shedding in a child with enteric and extraintestinal symptoms in Hungary
Archives of virology, 2009Co-Authors: Gabor Reuter, Akos Boldizsar, Gábor Papp, Peter PankovicsAbstract:Aichi virus, genus Kobuvirus, family Picornaviridae, has been proposed as a causative agent of gastroenteritis in human. Although high seroprevalence has been detected, it has been identified in only a few cases. We report detection of Aichi virus in Hungary. A total of 65 stool samples were tested retrospectively, collected from children with diarrhea, by reverse transcription-polymerase chain reaction. One (1.5%) sample from a 3-year-old girl was positive. Besides diarrhea, fever, purulent conjunctivitis and respiratory symptoms were also present at the same time with virus shedding. The genotype A virus, Kobuvirus/human/Szigetvar-HUN298/2000/Hungary (FJ225407), has 96% nucleotide identity to Aichi virus.
Gabor Reuter - One of the best experts on this subject based on the ideXlab platform.
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genomic analysis of a novel picornavirus from a migratory waterfowl greater white fronted goose anser albifrons
Archives of Virology, 2018Co-Authors: Akos Boros, Tung Gia Phan, Peter Pankovics, Peter Simmonds, Eric Delwart, Tamas Kiss, Gabor ReuterAbstract:The complete genome of goose picornavirus 1 (GPV-1) strain goose/NLSZK2/HUN/2013 (MF358731) was determined by RT-PCR and next-generation sequencing from a cloacal sample of a migratory waterfowl, greater white-fronted goose (Anser albifrons) in Hungary. The genome of GPV-1 shows an L-3-3-4 organization pattern with a 5'-terminal origin of replication (ORI) region, a type-IV IRES, and an Hbox/NC-type 2A protein. This virus showed the highest overall sequence identity to the members of the genus Kobuvirus, although the phylogenetic position of GPV-1 is different in the analyzed P1, 2C and 3CD phylogenetic trees, which further increases the diversity of known avian picornaviruses.
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DISPATCHES Evolution of Porcine Kobuvirus
2013Co-Authors: Gabor Reuter, Peter Pankovics, Sándor Kecskeméti, Kobuvirus The Genus KobuvirusAbstract:Porcine Kobuvirus was fi rst identifi ed in early 2007 in Hungary. Originally thought to be confi ned to the intestine, almost 2 years later the virus was found in the blood of clinically healthy pigs on the same farm. Porcine Kobuvirus may be widely distributed on pig farms worldwide. Picornaviruses (family Picornaviridae) are small, nonenveloped viruses with single-stranded, positive-sense genomic RNA; they are divided into 12 genera: Aphthovirus
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Kobuvirus in domestic sheep hungary
Emerging Infectious Diseases, 2010Co-Authors: Gabor Reuter, Akos Boros, Peter Pankovics, László EgyedAbstract:To the Editor: Picornaviruses (family Picornaviridae) are small, nonenveloped viruses with single-stranded, positive-sense genomic RNA. They are divided into 12 genera: Enterovirus, Aphthovirus, Cardiovirus, Hepatovirus, Parechovirus, Erbovirus, Teschovirus, Sapelovirus, Senecavirus, Tremovirus, Avihepatovirus, and Kobuvirus. The genus Kobuvirus consists of 2 officially recognized species, Aichi virus (1) and Bovine Kobuvirus (2), and 1 candidate species, porcine Kobuvirus (3). The Kobuvirus genome is ≈8.2–8.4 kb long and has the typical picornavirus genome organization of leader (L) protein following the structural (viral protein [VP] 0, VP3, and VP1) and nonstructural (2A–2C and 3A–3D) regions (2,4). The genetic identity on the coding region between Aichi (strain A846/88), bovine (U-1), and porcine (S-1-HUN) viruses is between 35% (L protein) and 74% (3D region) (2,4). Aichi virus and bovine Kobuvirus were first detected in fecal samples from humans and cattle in Japan, in 1991 and 2003, respectively (1,2). Porcine Kobuvirus was identified from domestic pigs in Hungary in 2008 (3,4). Recent studies demonstrated that Aichi virus circulates in Asia (5), Europe (6,7) including Hungary (4), South America (6), and North Africa (8) and can cause gastroenteritis in humans. In addition, bovine and porcine Kobuviruses are detected among these farm animals in Europe (4) and Asia (2,9). These data indicate that Kobuviruses are widely distributed geographically and raise the possibility of additional animal host species. We detected Kobuvirus in sheep. On March 17, 2009, a total of 8 fecal samples were collected from young, healthy, domestic sheep (Ovis aries) <3 weeks of age in a herd of 400 animals in central Hungary. At this farm, merino ewes from Hungary were mated with blackhead meat rams from Germany. At the time of sampling, no clinical signs of diarrhea were reported. Reverse transcription–PCR was performed by using generic Kobuvirus screening primers (UNIV-kobu-R/F) reported previously (4). These primers were designed for Aichi virus (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB040749","term_id":"15186718","term_text":"AB040749"}}AB040749), bovine ({"type":"entrez-nucleotide","attrs":{"text":"AB084788","term_id":"24817742","term_text":"AB084788"}}AB084788), and porcine Kobuvirus ({"type":"entrez-nucleotide","attrs":{"text":"EU787450","term_id":"219524015","term_text":"EU787450"}}EU787450) sequences and amplify a 216-nt region of 3D (RNA-dependent RNA polymerase region). The continuous 3D and 3′ untranslated regions (UTRs) of the Kobuvirus genome in sheep were determined by using the 5′/3′ RACE (rapid amplification of cDNA ends) kit, 2nd generation (Roche Diagnostics GmbH, Mannheim, Germany) and primers UNIV-kobu-F and S-1-F-7518/7540 (5′-CACTTCCATCATCAACACCATCA-3′ corresponding to nt 7518–7540 of bovine Kobuvirus) (4). PCR products were sequenced directly in both directions by using the BigDye Reaction Kit (Applied Biosystems, Warrington, UK) with the PCR primers and sequenced by an ABI PRISM 310 Genetic Analyzer (Applied Biosystems, Stafford, TX, USA). Phylogenetic analysis was conducted by using MEGA version 4.1 (www.megasoftware.net). The sequence for Kobuvirus/sheep/TB3-HUN/2009/Hungary was submitted to GenBank under accession no. {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693. Of the 8 sheep fecal samples, 5 (62.5%) were positive for Kobuvirus. The partial 3D region (216 nt) was genetically identical for all 5 strains. The 3′ continuous nucleotide sequence of the partial 3D (688 nt) and 3′ UTR (174 nt) regions of strain Kobuvirus/sheep/TB3-HUN/2009/Hungary (TB3-HUN; {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693) was determined. TB3-HUN had 59%–66% (862) nt and 77%–84% aa identities to Aichi and porcine Kobuviruses, respectively. Strain TB3-HUN had 89/97% nt/aa and 86% nt identities to bovine Kobuvirus in the 3D/3′ UTR (862 nt) and 3′ UTR (174 nt) regions, respectively. Phylogenetic analysis of the overlapping partial 3D/3′ UTR nucleotide sequence of TB3-HUN from sheep and of reference bovine, porcine, and human Kobuviruses confirmed that ovine Kobuvirus strain TB3-HUN is related to bovine Kobuviruses (Figure). Figure Phylogenetic analysis of Kobuvirus in sheep (Kobuvirus/sheep/TB3-HUN/2009/Hungary, {"type":"entrez-nucleotide","attrs":{"text":"GU245693","term_id":"342240198","term_text":"GU245693"}}GU245693) and Kobuvirus lineages in humans, cattle, and swine, according ... The nucleotide sequence of the partial 3D/3′ UTR region of Kobuvirus in sheep has high nucleotide identity to bovine Kobuviruses and forms the same lineage (but a different sublineage) with the Kobuvirus strains in cattle. This result raised the following questions: can a highly similar Kobuvirus be present in (and pathogenic for) 2 animal species (cattle and sheep), or is this result a consequence of natural contamination? The concept of sheep as host is supported by the high prevalence of Kobuvirus in young healthy sheep; by the sublineage position of the sheep strain on the phylogenetic tree according to the most conserved genetic region; and by the genetic relation between the 2 potential ruminant hosts, cattle and sheep. The existence of 1 pathogen in 2 host species (cattle and sheep) is well known, e.g., for bluetongue virus, adenoviruses, ovine herpesvirus type 2, and foot-and-mouth disease picornaviruses (10). Alternatively, the possibility of natural contamination cannot be excluded. The possibility of passive virus shedding in sheep exists because a cattle farm was located next to the tested sheep herd and would enable fecal–oral transmission of Kobuvirus between these farm animals. Both possibilities (host and passive virus reservoir) are preliminary perceptions, regardless which is true. Further molecular and epidemiologic studies are required to determine the relevance, distribution, and diversity of Kobuvirus or Kobuviruses in sheep.
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Evolution of Porcine Kobuvirus Infection, Hungary
'Centers for Disease Control and Prevention (CDC)', 2010Co-Authors: Gabor Reuter, Sándor Kecskeméti, Peter PankovicsAbstract:Porcine Kobuvirus was first identified in early 2007 in Hungary. Originally thought to be confined to the intestine, almost 2 years later the virus was found in the blood of clinically healthy pigs on the same farm. Porcine Kobuvirus may be widely distributed on pig farms worldwide
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Detection of Aichi virus shedding in a child with enteric and extraintestinal symptoms in Hungary
Archives of virology, 2009Co-Authors: Gabor Reuter, Akos Boldizsar, Gábor Papp, Peter PankovicsAbstract:Aichi virus, genus Kobuvirus, family Picornaviridae, has been proposed as a causative agent of gastroenteritis in human. Although high seroprevalence has been detected, it has been identified in only a few cases. We report detection of Aichi virus in Hungary. A total of 65 stool samples were tested retrospectively, collected from children with diarrhea, by reverse transcription-polymerase chain reaction. One (1.5%) sample from a 3-year-old girl was positive. Besides diarrhea, fever, purulent conjunctivitis and respiratory symptoms were also present at the same time with virus shedding. The genotype A virus, Kobuvirus/human/Szigetvar-HUN298/2000/Hungary (FJ225407), has 96% nucleotide identity to Aichi virus.
Beatrix Kapusinszky - One of the best experts on this subject based on the ideXlab platform.
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porcine Kobuvirus in wild boars sus scrofa
Archives of Virology, 2013Co-Authors: Csaba Nemes, Beatrix KapusinszkyAbstract:Fecal samples (N = 10) from 6- to 8-week-old wild boar piglets (Sus scrofa), collected from an animal park in Hungary in April 2011, were analyzed using viral metagenomics and complete genome sequencing. Kobuvirus (genus Kobuvirus, family Picornaviridae) was detected in all (100 %) specimens, with the closest nucleotide (89 %) and amino acid (94 %) sequence identity of the strain wild boar/WB1-HUN/2011/HUN (JX177612) to the prototype porcine Kobuvirus S-1-HUN (EU787450). This study suggests that genetically highly similar (practically the same geno-/serotype) porcine Kobuvirus circulate in wild boars, the wildlife counterparts of domestic pigs. Wild boars could be an important host and reservoir for Kobuvirus.
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High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage
Journal of virology, 2012Co-Authors: Rachel L. Marine, Beatrix Kapusinszky, Chunlin Wang, Peter Simmonds, Ladaporn Bodhidatta, Bamidele Soji Oderinde, K. E. WommackAbstract:Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, 90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel Kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.
Akos Boldizsar - One of the best experts on this subject based on the ideXlab platform.
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Detection of Aichi virus shedding in a child with enteric and extraintestinal symptoms in Hungary
Archives of virology, 2009Co-Authors: Gabor Reuter, Akos Boldizsar, Gábor Papp, Peter PankovicsAbstract:Aichi virus, genus Kobuvirus, family Picornaviridae, has been proposed as a causative agent of gastroenteritis in human. Although high seroprevalence has been detected, it has been identified in only a few cases. We report detection of Aichi virus in Hungary. A total of 65 stool samples were tested retrospectively, collected from children with diarrhea, by reverse transcription-polymerase chain reaction. One (1.5%) sample from a 3-year-old girl was positive. Besides diarrhea, fever, purulent conjunctivitis and respiratory symptoms were also present at the same time with virus shedding. The genotype A virus, Kobuvirus/human/Szigetvar-HUN298/2000/Hungary (FJ225407), has 96% nucleotide identity to Aichi virus.
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complete nucleotide and amino acid sequences and genetic organization of porcine Kobuvirus a member of a new species in the genus Kobuvirus family picornaviridae
Archives of Virology, 2009Co-Authors: Akos BoldizsarAbstract:Kobuvirus is a new genus in the family Picornaviridae. Two species are currently known: Aichi virus (human Kobuvirus) and Bovine Kobuvirus (U-1). In this study, the complete nucleotide and amino acid sequences and genetic organization of porcine Kobuvirus (Kobuvirus/swine/S-1-HUN/2007/Hungary, EU787450) were determined. The structure of the S-1-HUN genome, VPg–5′UTR–leader protein–structural proteins (VP0, VP3, VP1)–non-structural proteins (2A–2C, 3A–3D)–3′UTR–poly(A) tail, was found to be typical of picornavirus. The 8210-nucleotide (nt)-long RNA genome contains a large open reading frame (7467 nt) encoding a potential polyprotein precursor of 2488 amino acids (aa) that has 57/56% and 63/64% nt/aa identity with Aichi virus and U-1, respectively. The 5′UTR contains a hepacivirus/pestivirus-like internal ribosomal entry site (IRES type IV group-B-like) with conserved pseudoknot, II and IIIa–f domains. A tandem repeat (a 30-amino-acid-long motif) was detected in 2B. Thirty-nine (65%) of the 60 fecal samples from pigs under the age of 6 months at the tested farm were positive (the incidence was 90% under the age of 3 weeks). Porcine Kobuvirus belongs to a potential new species—the third—in the genus Kobuvirus.
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candidate new species of Kobuvirus in porcine hosts
Emerging Infectious Diseases, 2008Co-Authors: Gabor Reuter, Akos Boldizsar, Istvan Kiss, Peter PankovicsAbstract:To the Editor: Picornaviruses (family Picornaviridae) are small, nonenveloped viruses with single-stranded, positive-sense genomic RNA, currently divided into 8 genera: Enterovirus, Aphthovirus, Cardiovirus, Hepatovirus, Parechovirus, Erbovirus, Teschovirus, and Kobuvirus (1). To date, the genus Kobuvirus consists of 2 species, Aichi virus and Bovine Kobuvirus, each possessing 1 serotype. Aichi virus (strain A846/88) was first isolated from a stool sample obtained from a person with acute gastroenteritis in 1991 (2). Bovine Kobuvirus (strain U-1) was detected in bovine sera and in feces samples from clinically healthy cattle in 2003 (3). Human and bovine Kobuviruses were first isolated in Japan. Recently, Kobuviruses have also been detected in humans in other countries in Asia (4), Europe (5,6), and South America (5) and in calves with diarrhea in Thailand (7). The Aichi virus and bovine Kobuvirus genomes are approximately 8.2–8.3 kb, respectively, and both have a typical picornavirus genome organization, including the L protein following structural (VP0, VP3, and VP1) and nonstructural (2A–2C and 3A–3D) regions (1,3). Genetic identity between Aichi and U-1 viruses ranges from 47.7% (3′ untranslated region) through 70.8% (3D region) (3). In this study, we report a new candidate species of Kobuvirus. Porcine Kobuvirus was serendipitously detected in fecal samples from domestic pigs in Hungary. Fecal samples were collected in February 2007 from 15 healthy piglets (Sus scrofa domestica) <10 days of age from a farm in Ebes located in eastern Hungary. The aim of the study was to detect porcine calicivirus (norovirus and sapovirus) in domestic pigs by using reverse transcription–PCR (RT-PCR), using the generic primer pairs p289/p290 designed for the calicivirus RNA-dependent RNA polymerase gene (319 nt for norovirus or 331 nt for sapovirus) (8). RNA isolation and RT-PCR were performed as described previously (9). PCR products were sequenced directly in both directions with the BigDye Terminator Cycle Sequencing Ready Reaction Kit (PE Applied Biosystems, Warrington, UK) by using the PCR primers and run on an automated sequencer (ABI PRISM 310 Genetic Analyzer; Applied Biosystems, Stafford, TX, USA). Phylogenetic analysis was conducted by using MEGA software version 4.0 (10). Complete nucleotide sequence of porcine Kobuvirus (strain Kobuvirus/swine/S-1-HUN/2007/Hungary) was submitted to GenBank under accession no. {"type":"entrez-nucleotide","attrs":{"text":"EU787450","term_id":"219524015","term_text":"EU787450"}}EU787450. Two (13.3%) of 15 samples were positive for porcine sapoviruses; however, a consequent nonspecific, ≈1,100-nt, strong, and single PCR product was found in all samples by agarose gel electrophoresis (data not shown). The nucleotide sequence of the 1,065-nt nonspecific PCR product was determined. Genetic and amino acid similarity was found to be bovine (U-1) and human Aichi Kobuvirus 3C (87 nt) and 3D (978 nt) regions in GenBank database by using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Nucleotide and amino acid identity of the 3C–3D regions were 73%–79% and 69%–70% to U-1 strain and Aichi virus, respectively. The phylogenetic tree confirmed that S-1-HUN belonged to Kobuviruses and formed a distinct lineage (Figure). Cleavage sites for 3C and 3D was Q/S. Highly conserved amino acid motif KDELR in 3D (RNA-dependent RNA polymerase) region and high rate of cytidine (29%) and uracil (26%) nucleoside composition were seen in the 3C and 3D parts of the genome of strain S-1-HUN; both are suspected to be a typical skew of Kobuviruses (3). Figure Phylogenetic tree of porcine Kobuvirus (Kobuvirus/swine/S-1-HUN/2007/Hungary, GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"EU787450","term_id":"219524015","term_text":"EU787450"}}EU787450), based upon the 1,065-nt fragment of the ... Most picornavirus genera consist of >2 species (1). Our study reports detection of Kobuvirus in domestic pigs. Serendipitously, the generic calicivirus primers p289 and p290, designed for a calicivirus RNA-dependent RNA polymerase region, amplified a Kobuvirus 3C/3D region when specimens were tested for porcine caliciviruses by RT-PCR. Comparison of the primers p289 and p290 and the S-1-HUN sequence showed that there are 12- and 11-bp homologous regions between the Kobuvirus and the 3′ end of the primer sequences, respectively. Reverse primer p289 designed for calicivirus (norovirus and sapovirus) conserved amino acid 3D motif YGDD, which is also present in Kobuviruses. All apparently healthy animals <10 days of age carried the Kobuvirus, which was excreted in the feces. These results indicate a general circulation and endemic infection of Kobuvirus on the tested farm. In addition, because of its analogy to other picornaviruses and because bovine Kobuvirus was first detected in culture medium that originated from cattle sera (1,3), we cannot exclude the possibility that the S-1-HUN–like Kobuvirus can cause viremia (and generalized infection) in swine. S-1-HUN–like virus may typically cause asymptomatic infections in swine. However, epidemiologic and molecular studies are required regarding the importance of this virus as a causative agent of some diseases of domestic pigs and related animals. Sequence analysis of the complete nucleotide and amino acid sequences of coding (L, P1, P2, and P3: 7,467 nt) and noncoding regions and the genetic organization strain indicate that S-1-HUN is a typical Kobuvirus. Phylogenetic analysis shows that S-1-HUN strain is genetically included in the genus Kobuvirus but is distinct from Aichi and bovine Kobuviruses. Porcine Kobuvirus strain S-1-HUN is a candidate for a new, third species of the genus Kobuvirus.
