1
|
Fujii Y, Masatani T, Nishiyama S, Takahashi T, Okajima M, Izumi F, Sakoda Y, Takada A, Ozawa M, Sugiyama M, Ito N. Molecular characterization of an avian rotavirus a strain detected from a large-billed crow (Corvus macrorhynchos) in Japan. Virology 2024; 596:110114. [PMID: 38781709 DOI: 10.1016/j.virol.2024.110114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Avian rotaviruses A (RVAs) are occasionally transmitted to animals other than the original hosts across species barriers. Information on RVAs carried by various bird species is important for identifying the origin of such interspecies transmission. In this study, to facilitate an understanding of the ecology of RVAs from wild birds, we characterized all of the genes of an RVA strain, JC-105, that was detected in a fecal sample of a large-billed crow (Corvus macrorhynchos) in Japan. All of the genes of this strain except for the VP4 and VP7 genes, which were classified as novel genotypes (P[56] and G40, respectively), were closely related to those of the avian-like RVA strain detected from a raccoon, indicating the possibility that crows had been involved in the transmission of avian RVAs to raccoons. Our findings highlight the need for further viral investigations in wild birds and mammals to understand the mechanisms of avian-to-mammal RVA transmission.
Collapse
Affiliation(s)
- Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsunori Masatani
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsuki Takahashi
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Fumiki Izumi
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Makoto Ozawa
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| | - Naoto Ito
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| |
Collapse
|
2
|
Díaz Alarcón RG, Liotta DJ, Miño S. Zoonotic RVA: State of the Art and Distribution in the Animal World. Viruses 2022; 14:v14112554. [PMID: 36423163 PMCID: PMC9694813 DOI: 10.3390/v14112554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA genomic constellations described in animal hosts. This review included animal RVA strains in humans. We compiled detection methods, hosts, genotypes and complete genomes. RVA was described in 86 animal species, with 52% (45/86) described by serology, microscopy or the hybridization method; however, strain sequences were not described. All of these reports were carried out between 1980 and 1990. In 48% (41/86) of them, 9251 strain sequences were reported, with 28% being porcine, 27% bovine, 12% equine and 33% from several other animal species. Genomic constellations were performed in 80% (32/40) of hosts. Typical constellation patterns were observed in groups such as birds, domestic animals and artiodactyls. The analysis of the constellations showed RVA's capacity to infect a broad range of species, because there are RVA genotypes (even entire constellations) from animal species which were described in other studies. This suggests that this virus could generate highly virulent variants through gene reassortments and that these strains could be transmitted to humans as a zoonotic disease, making future surveillance necessary for the prevention of future outbreaks.
Collapse
Affiliation(s)
- Ricardo Gabriel Díaz Alarcón
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
| | - Domingo Javier Liotta
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
- National Institute of Tropical Medicine (INMeT)—ANLIS “Dr. Carlos Malbrán”, Puerto Iguazú 3370, Misiones, Argentina
| | - Samuel Miño
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
- National Institute of Agricultural Technology (INTA), EEA Cerro Azul, National Route 14, Km 836, Cerro Azul 3313, Misiones, Argentina
- Correspondence: ; Tel.: +54-376-449-4740 (ext. 120)
| |
Collapse
|
3
|
Fujii Y, Masatani T, Nishiyama S, Okajima M, Izumi F, Okazaki K, Sakoda Y, Takada A, Ozawa M, Sugiyama M, Ito N. Molecular characterisation of a novel avian rotavirus A strain detected from a gull species ( Larus sp.). J Gen Virol 2022; 103. [PMID: 36223171 DOI: 10.1099/jgv.0.001792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recent study demonstrated the possibility that migratory birds are responsible for the global spread of avian rotavirus A (RVA). However, little is known about what types of RVAs are retained in migratory birds. In this study, to obtain information on RVA strains in migratory birds, we characterised an RVA strain, Ho374, that was detected in a faecal sample from a gull species (Larus sp.). Genetic analysis revealed that all 11 genes of this strain were classified as new genotypes (G28-P[39]-I21-R14-C14-M13-A24-N14-T16-E21-H16). This clearly indicates that the genetic diversity of avian RVAs is greater than previously recognised. Our findings highlight the need for investigations of RVA strains retained in migratory birds, including gulls.
Collapse
Affiliation(s)
- Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsunori Masatani
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Fumiki Izumi
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Katsunori Okazaki
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Makoto Ozawa
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Naoto Ito
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| |
Collapse
|
4
|
Kanda M, Fukuda S, Hamada N, Nishiyama S, Masatani T, Fujii Y, Izumi F, Okajima M, Taniguchi K, Sugiyama M, Komoto S, Ito N. Establishment of a reverse genetics system for avian rotavirus A strain PO-13. J Gen Virol 2022; 103. [PMID: 35749287 DOI: 10.1099/jgv.0.001760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Avian rotavirus A (RVA) is one of major enteric pathogens that cause diarrhoea in young avian individuals. Importantly, some of the avian RVA strains of G18P[17] genotype are naturally transmitted to and cause clinical diseases in mammalian species, indicating their potential risks to animal health. Although molecular information on the pathogenesis by avian RVA strains will be useful for estimating their risks, the absence of a reverse genetics (RG) system for these strains has hindered the elucidation of their pathogenic mechanisms. In this study, we aimed to establish an RG system for the avian G18P[17] prototype strain PO-13, which was isolated from a pigeon in Japan in 1983 and was experimentally shown to be pathogenic in suckling mice. Transfection with plasmids expressing 11 genomic RNA segments of the strain resulted in rescue of the infectious virus with an artificially introduced genetic marker on its genome, indicating that an RG system for the PO-13 strain was successfully established. The rescued recombinant strain rPO-13 had biological properties almost identical to those of its wild-type strain (wtPO-13). Notably, both rPO-13 and wtPO-13 induced diarrhoea in suckling mice with similar efficiencies. It was thus demonstrated that the RG system will be useful for elucidating the pathogenic mechanisms of the PO-13 strain at the molecular level. This is the first report of the establishment of an RG system for an avian RVA strain.
Collapse
Affiliation(s)
- Marika Kanda
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Nanami Hamada
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Tatsunori Masatani
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Joint Graduate School of Veterinary Sciences, Gifu University, Japan
| | - Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, Japan
| | - Fumiki Izumi
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Sciences, Gifu University, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Joint Graduate School of Veterinary Sciences, Gifu University, Japan
| |
Collapse
|
5
|
Fujii Y, Hirayama M, Nishiyama S, Takahashi T, Okajima M, Izumi F, Takehara K, Masatani T, Sugiyama M, Ito N. Characterization of an avian rotavirus A strain isolated from a velvet scoter ( Melanitta fusca): implication for the role of migratory birds in global spread of avian rotaviruses. J Gen Virol 2022; 103. [PMID: 35175915 DOI: 10.1099/jgv.0.001722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Avian G18P[17] rotaviruses with similar complete genome constellation, including strains that showed pathogenicity in mammals, have been detected worldwide. However, it remains unclear how these strains spread geographically. In this study, to investigate the role of migratory birds in the dispersion of avian rotaviruses, we analysed whole genetic characters of the rotavirus strain RK1 that was isolated from a migratory species of birds [velvet scoter (Melanitta fusca)] in Japan in 1989. Genetic analyses revealed that the genotype constellation of the RK1 strain, G18-P[17]-I4-R4-C4-M4-A21-N4-T4-E4-H4, was highly consistent with those of other G18P[17] strains detected in various parts of the world, supporting the possibility that the G18P[17] strains spread via migratory birds that move over a wide area. Furthermore, the RK1 strain induced diarrhoea in suckling mice after oral gastric inoculation, indicating that at least some of the rotaviruses that originated from migratory birds are infectious to and pathogenic in mammals. In conclusion, it was demonstrated that migratory birds may contribute to the global spread of avian rotaviruses that are pathogenic in mammalian species.
Collapse
Affiliation(s)
- Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Mihoko Hirayama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsuki Takahashi
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Fumiki Izumi
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Kazuaki Takehara
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Tatsunori Masatani
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Naoto Ito
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Gifu Center for Highly Advanced Integration of Nanosciences and Life Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| |
Collapse
|
6
|
Falkenhagen A, Tausch SH, Labutin A, Grützke J, Heckel G, Ulrich RG, Johne R. OUP accepted manuscript. Virus Evol 2022; 8:veac004. [PMID: 35169491 PMCID: PMC8838746 DOI: 10.1093/ve/veac004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/16/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Species A rotaviruses (RVAs) are important aetiological agents of severe diarrhoea in young children. They are also widely distributed in mammals and birds, and increasing evidence indicates the possibility of zoonotic transmission of RVA strains between animals and humans. Moreover, reassortment of the eleven segments of the RVA genome can result in rapid biological changes and may influence pathogenic properties. Here, the nearly complete genome of an RVA strain from a common shrew (Sorex araneus) was sequenced, which showed high nucleotide sequence similarity to additionally determined partial sequences from common shrew RVAs but only very low identity (below 68 per cent) to RVAs from other animal species and humans. New genotypes were assigned to most genome segments of the novel common shrew RVA strain KS14/269, resulting in the genome constellation G39-P[55]-I27-R26-C22-M22-A37-N26-T26-E30-H26. Phylogenetic analyses clustered the common shrew RVAs as ancestral branches of other mammalian and avian RVAs for most of the genome segments, which is in contrast to the phylogeny of the hosts. Nevertheless, conserved sequences typical for all RVAs were identified at the 5ʹ- and 3ʹ- non-coding segment termini. To explore whether the common shrew RVA can exchange genetic material with other mammalian RVAs by reassortment, a reverse genetics system based on the simian RVA strain SA11 was used. However, no viable reassortants could be rescued by exchanging the VP4-, VP6-, or VP7-encoding genome segment alone or in combinations. It can be concluded that highly divergent RVAs are present in common shrews, indicating an evolution of these viruses largely separated from other mammalian and avian RVAs. The zoonotic potential of the virus seems to be low but needs to be further analysed in future.
Collapse
Affiliation(s)
- Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | | |
Collapse
|
7
|
Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
Collapse
Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
| |
Collapse
|
8
|
Čolić D, Krešić N, Mihaljević Ž, Andreanszky T, Balić D, Lolić M, Brnić D. A Remarkable Genetic Diversity of Rotavirus A Circulating in Red Fox Population in Croatia. Pathogens 2021; 10:pathogens10040485. [PMID: 33923799 PMCID: PMC8072941 DOI: 10.3390/pathogens10040485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022] Open
Abstract
Rotaviruses (RV), especially Rotavirus A (RVA), are globally recognized as pathogens causing neonatal diarrhea, but they also affect intensive animal farming. However, the knowledge on their significance in wildlife is rather limited. The aim of the study was to unveil the prevalence, molecular epidemiology, and genetic diversity of RVA strains circulating in the red fox (Vulpes vulpes) population in Croatia. From 2018 to 2019, 370 fecal samples from fox carcasses hunted for rabies monitoring were collected. All samples were first tested using a VP2 real-time RT-PCR; in the subsequent course, positives were subjected to VP7 and VP4 genotyping. The results revealed an RVA prevalence of 14.9%, while the circulating RVA strains showed a remarkable genetic diversity in terms of 11 G and nine P genotypes, among which one G and three P were tentatively identified as novel. In total, eight genotype combinations were detected: G8P[14], G9P[3], G9P[23], G10P[11], G10P[3], G11P[13], G15P[21], and G?P[?]. The results suggest a complex background of previous interspecies transmission events, shedding new light on the potential influence of foxes in RVA epidemiology. Their role as potential reservoirs of broad range of RVA genotypes, usually considered typical solely of domestic animals and humans, cannot be dismissed.
Collapse
Affiliation(s)
- Daniel Čolić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (D.Č.); (N.K.); (Ž.M.)
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Nina Krešić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (D.Č.); (N.K.); (Ž.M.)
| | - Željko Mihaljević
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (D.Č.); (N.K.); (Ž.M.)
| | - Tibor Andreanszky
- Veterinary Department, Croatian Veterinary Institute, Podmurvice 29, 51000 Rijeka, Croatia;
| | - Davor Balić
- Veterinary Department, Croatian Veterinary Institute, Josipa Kozarca 24, 32100 Vinkovci, Croatia; (D.B.); (M.L.)
| | - Marica Lolić
- Veterinary Department, Croatian Veterinary Institute, Josipa Kozarca 24, 32100 Vinkovci, Croatia; (D.B.); (M.L.)
| | - Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (D.Č.); (N.K.); (Ž.M.)
- Correspondence: ; Tel.: +385-1-6123-650
| |
Collapse
|
9
|
Group A Rotavirus VP1 Polymerase and VP2 Core Shell Proteins: Intergenotypic Sequence Variation and In Vitro Functional Compatibility. J Virol 2019; 93:JVI.01642-18. [PMID: 30355692 DOI: 10.1128/jvi.01642-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Group A rotaviruses (RVAs) are classified according to a nucleotide sequence-based system that assigns a genotype to each of the 11 double-stranded RNA (dsRNA) genome segments. For the segment encoding the VP1 polymerase, 22 genotypes (R1 to R22) are defined with an 83% nucleotide identity cutoff value. For the segment encoding the VP2 core shell protein, which is a functional VP1-binding partner, 20 genotypes (C1 to C20) are defined with an 84% nucleotide identity cutoff value. However, the extent to which the VP1 and VP2 proteins encoded by these genotypes differ in their sequences or interactions has not been described. Here, we sought to (i) delineate the relationships and sites of variation for VP1 and VP2 proteins belonging to the known RVA genotypes and (ii) correlate intergenotypic sequence diversity with functional VP1-VP2 interaction(s) during dsRNA synthesis. Using bioinformatic approaches, we revealed which VP1 and VP2 genotypes encode divergent proteins and identified the positional locations of amino acid changes in the context of known structural domains/subdomains. We then employed an in vitro dsRNA synthesis assay to test whether genotype R1, R2, R4, and R7 VP1 polymerases could be enzymatically activated by genotype C1, C2, C4, C5, and C7 VP2 core shell proteins. Genotype combinations that were incompatible informed the rational design and in vitro testing of chimeric mutant VP1 and VP2 proteins. The results of this study connect VP1 and VP2 nucleotide-level diversity to protein-level diversity for the first time, and they provide new insights into regions/residues critical for VP1-VP2 interaction(s) during viral genome replication.IMPORTANCE Group A rotaviruses (RVAs) are widespread in nature, infecting numerous mammalian and avian hosts and causing severe gastroenteritis in human children. RVAs are classified using a system that assigns a genotype to each viral gene according to its nucleotide sequence. To date, 22 genotypes have been described for the gene encoding the viral polymerase (VP1), and 20 genotypes have been described for the gene encoding the core shell protein (VP2). Here, we analyzed if/how the VP1 and VP2 proteins encoded by the known RVA genotypes differ from each other in their sequences. We also used a biochemical approach to test whether the intergenotypic sequence differences influenced how VP1 and VP2 functionally engage each other to mediate RNA synthesis in a test tube. This work is important because it increases our understanding of RVA protein-level diversity and raises new ideas about the VP1-VP2 binding interface(s) that is important for viral replication.
Collapse
|
10
|
Rubbenstroth D, Peus E, Schramm E, Kottmann D, Bartels H, McCowan C, Schulze C, Akimkin V, Fischer N, Wylezich C, Hlinak A, Spadinger A, Großmann E, Petersen H, Grundhoff A, Rautenschlein S, Teske L. Identification of a novel clade of group A rotaviruses in fatally diseased domestic pigeons in Europe. Transbound Emerg Dis 2018; 66:552-561. [DOI: 10.1111/tbed.13065] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Dennis Rubbenstroth
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
- Institute of Diagnostic Virology Friedrich‐Loeffler‐Institut Greifswald – Insel Riems Germany
| | - Elisabeth Peus
- Clinic for Pigeons of the German Pigeon‐Breeders Association Essen Germany
| | - Eva Schramm
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
| | - Daniel Kottmann
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
| | - Hilke Bartels
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
| | - Christina McCowan
- Agriculture Victoria, Veterinary Diagnostics Bundoora Victoria Australia
| | | | - Valerij Akimkin
- Chemical and Veterinary Investigations Office Stuttgart Fellbach Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene University Medical Center Hamburg‐Eppendorf Hamburg Germany
- German Center for Research on Infection (DZIF) Partner Site Hamburg‐Borstel‐Lübeck‐Riems Hamburg Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology Friedrich‐Loeffler‐Institut Greifswald – Insel Riems Germany
| | - Andreas Hlinak
- Berlin‐Brandenburg State Laboratory Frankfurt (Oder) Germany
| | - Anja Spadinger
- Aulendorf state veterinary diagnostic centre Aulendorf Germany
| | - Ernst Großmann
- Aulendorf state veterinary diagnostic centre Aulendorf Germany
| | - Henning Petersen
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
- Chemical and Veterinary Investigations Office Ostwestfalen‐Lippe DetmoldGermany
| | - Adam Grundhoff
- German Center for Research on Infection (DZIF) Partner Site Hamburg‐Borstel‐Lübeck‐Riems Hamburg Germany
- Heinrich‐Pette Institute Leibniz Institute for Experimental Virology Hamburg Germany
| | - Silke Rautenschlein
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
| | - Lydia Teske
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
| |
Collapse
|
11
|
McCowan C, Crameri S, Kocak A, Shan S, Fegan M, Forshaw D, Rubbenstroth D, Chen H, Holmes C, Harper J, Dearnley M, Batovska J, Bergfeld J, Walker C, Wang J. A novel group A rotavirus associated with acute illness and hepatic necrosis in pigeons (Columba livia), in Australia. PLoS One 2018; 13:e0203853. [PMID: 30204797 PMCID: PMC6133385 DOI: 10.1371/journal.pone.0203853] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022] Open
Abstract
Cases of vomiting and diarrhoea were reported in racing pigeons in Western Australia in May, 2016. Morbidity and mortality rates were high. Similar clinical disease was seen in Victoria in December and by early 2017 had been reported in all states except the Northern Territory, in different classes of domestic pigeon–racing, fancy and meat bird–and in a flock of feral pigeons. Autopsy findings were frequently unremarkable; histological examination demonstrated significant hepatic necrosis as the major and consistent lesion, often with minimal inflammatory infiltration. Negative contrast tissue suspension and thin section transmission electron microscopy of liver demonstrated virus particles consistent with a member of the Reoviridae. Inoculation of trypsin-treated Vero, MDBK and MA-104 cell lines resulted in cytopathic changes at two days after infection. Next generation sequencing was undertaken using fresh liver samples and a previously undescribed group A rotavirus (genotype G18P[17]) of avian origin was identified and the virus was isolated in several cell lines. A q-RT-PCR assay was developed and used to screen a wider range of samples, including recovered birds. Episodes of disease have continued to occur and to reoccur in previously recovered lofts, with variable virulence reported. This is the first report of a rotavirus associated with hepatic necrosis in any avian species.
Collapse
Affiliation(s)
| | - Sandra Crameri
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Ayfer Kocak
- Agriculture Victoria, Bundoora, Victoria, Australia
| | - Songhua Shan
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Mark Fegan
- Agriculture Victoria, Bundoora, Victoria, Australia
| | - David Forshaw
- Department of Primary Industries and Regional Development, Albany, Western Australia, Australia
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Center–University of Freiburg, Freiburg, Germany
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald–Insel Riems, Germany
| | - Honglei Chen
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Clare Holmes
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Jenni Harper
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Megan Dearnley
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Jana Batovska
- Agriculture Victoria, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Jemma Bergfeld
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Colin Walker
- Melbourne Bird Veterinary Clinic, Scoresby, Melbourne, Australia
| | - Jianning Wang
- Australian Animal Health Laboratory, Geelong, Victoria, Australia
| |
Collapse
|