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Malik YS, Ansari MI, Karikalan M, Sircar S, Selvaraj I, Ghosh S, Singh K. Molecular Characterization of Rotavirus C from Rescued Sloth Bears, India: Evidence of Zooanthroponotic Transmission. Pathogens 2023; 12:934. [PMID: 37513781 PMCID: PMC10384673 DOI: 10.3390/pathogens12070934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The present study reports the detection and molecular characterisation of rotavirus C (RVC) in sloth bears (Melursus ursinus) rescued from urban areas in India. Based on an RVC VP6 gene-targeted diagnostic RT-PCR assay, 48.3% (42/87) of sloth bears tested positive for RVC infection. The VP6, VP7, and NSP4 genes of three sloth bear RVC isolates (UP-SB19, 21, and 37) were further analysed. The VP6 genes of RVC UP-SB21 and 37 isolates were only 37% identical. The sequence identity, TM-score from structure alignment, and selection pressure (dN/dS) of VP6 UP-SB37 with pig and human RVCs isolates were (99.67%, 0.97, and 1.718) and (99.01%, 0.93, and 0.0340), respectively. However, VP6 UP-SB21 has an identity, TM-score, and dN/dS of (84.38%, 1.0, and 0.0648) and (99.63%, 1.0, and 3.7696) with human and pig RVC isolates, respectively. The VP7 genes from UP-SB19 and 37 RVC isolates were 79.98% identical and shared identity, TM-score, and dN/dS of 88.4%, 0.76, and 5.3210, along with 77.98%, 0.77, and 4.7483 with pig and human RVC isolates, respectively. The NSP4 gene of UP-SB37 RVC isolates has an identity, TM-score, and dN/dS of 98.95%, 0.76, and 0.2907, along with 83.12%, 0.34, and 0.2133 with pig and human RVC isolates, respectively. Phylogenetic analysis of the nucleotide sequences of the sloth bear RVC isolates assigned the isolate UP-SB37 to genotype G12, I2 for RVC structural genes VP7 and VP6, and E1 for NSP4 genes, respectively, while isolates UP-SB19 and UP-SB21 were classified as genotype G13 and GI7 based on the structural gene VP7, respectively. The study suggests that the RVCs circulating in the Indian sloth bear population are highly divergent and might have originated from pigs or humans, and further investigation focusing on the whole genome sequencing of the sloth bear RVC isolate may shed light on the virus origin and evolution.
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Affiliation(s)
- Yashpal Singh Malik
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India
| | - Mohd Ikram Ansari
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- Department of Biosciences, Integral University, Lucknow 226026, India
| | - Mathesh Karikalan
- Centre for Wildlife Conservation Management and Disease Surveillance, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Shubhankar Sircar
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kalpana Singh
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India
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Arakaki L, Tollefson D, Kharono B, Drain PK. Prevalence of rotavirus among older children and adults with diarrhea: A systematic review and meta-analysis. Vaccine 2021; 39:4577-4590. [PMID: 34244008 DOI: 10.1016/j.vaccine.2021.06.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/10/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Older children and adults are susceptible to rotavirus, but the extent to which rotavirus affects this population is not fully understood, hindering accuracy of global rotavirus estimations. OBJECTIVE To determine what proportion of diarrhea cases are due to rotavirus among persons ≥ 5 years old and to estimate this proportion by age strata. METHODS We conducted a systematic review and meta-analysis using the PRISMA guidelines. We included studies that reported on conditional rotavirus prevalence (i.e., percent of diarrhea due to rotavirus) in persons ≥ 5 years old who were symptomatic with diarrhea/gastroenteritis and had laboratory confirmation for rotavirus infection. Studies on nosocomial infections and outbreak investigations were excluded. We collected age group-specific conditional rotavirus prevalence and other variables, such as study geography, study setting, and study type. We calculated pooled conditional rotavirus prevalence, corresponding 95% confidence intervals (95% CI), heterogeneity (I2) estimates, and prediction intervals (PI). RESULTS Sixty-six studies from 32 countries met the inclusion criteria. Conditional rotavirus prevalence ranged from 0% to 30% across the studies. The total pooled prevalence of rotavirus among persons ≥ 5 years old with diarrhea was 7.6% (95% CI: 6.2-9.2%, I2 = 99.6%, PI: 0-24%). The pooled prevalence of rotavirus among older children and adolescents was 8.7% (95% CI: 6.2-11.7%, I2 = 96%, PI:0-27%), among younger adults was 5.4% (95% CI: 1.4-11.8%, I2 = 96%, PI:0-31%), and among older adults was 4.7% (95% CI: 2.8-7.0%, I2 = 96%, PI:0-16%). Pooled conditional rotavirus prevalences did not differ by other variables. CONCLUSION In this systematic review and meta-analysis of rotavirus among persons ≥ 5 years old with diarrhea, we found relatively low pooled conditional rotavirus prevalence compared to what is typically reported for children < 5 years; however, results should be interpreted with caution as the wide prediction intervals suggest large heterogeneity.
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Affiliation(s)
- Lola Arakaki
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Epidemiology, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Deanna Tollefson
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Brenda Kharono
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Paul K Drain
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Medicine, 1959 NE Pacific St, Seattle, WA 98195, United States.
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Hull JJA, Qi M, Montmayeur AM, Kumar D, Velasquez DE, Moon SS, Magaña LC, Betrapally N, Ng TFF, Jiang B, Marthaler D. Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States. PLoS One 2020; 15:e0244498. [PMID: 33373390 PMCID: PMC7771860 DOI: 10.1371/journal.pone.0244498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.
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Affiliation(s)
- Jennifer J. A. Hull
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Anna M. Montmayeur
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Deepak Kumar
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Daniel E. Velasquez
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sung-Sil Moon
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Laura Cristal Magaña
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Naga Betrapally
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Terry Fei Fan Ng
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Baoming Jiang
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Douglas Marthaler
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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Alsova OK, Loktev VB, Naumova EN. Rotavirus Seasonality: An Application of Singular Spectrum Analysis and Polyharmonic Modeling. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E4309. [PMID: 31698706 PMCID: PMC6888479 DOI: 10.3390/ijerph16224309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/23/2022]
Abstract
The dynamics of many viral infections, including rotaviral infections (RIs), are known to have a complex non-linear, non-stationary structure with strong seasonality indicative of virus and host sensitivity to environmental conditions. However, analytical tools suitable for the identification of seasonal peaks are limited. We introduced a two-step procedure to determine seasonal patterns in RI and examined the relationship between daily rates of rotaviral infection and ambient temperature in cold climates in three Russian cities: Chelyabinsk, Yekaterinburg, and Barnaul from 2005 to 2011. We described the structure of temporal variations using a new class of singular spectral analysis (SSA) models based on the "Caterpillar" algorithm. We then fitted Poisson polyharmonic regression (PPHR) models and examined the relationship between daily RI rates and ambient temperature. In SSA models, RI rates reached their seasonal peaks around 24 February, 5 March, and 12 March (i.e., the 55.17 ± 3.21, 64.17 ± 5.12, and 71.11 ± 7.48 day of the year) in Chelyabinsk, Yekaterinburg, and Barnaul, respectively. Yet, in all three cities, the minimum temperature was observed, on average, to be on 15 January, which translates to a lag between the peak in disease incidence and time of temperature minimum of 38-40 days for Chelyabinsk, 45-49 days in Yekaterinburg, and 56-59 days in Barnaul. The proposed approach takes advantage of an accurate description of the time series data offered by the SSA-model coupled with a straightforward interpretation of the PPHR model. By better tailoring analytical methodology to estimate seasonal features and understand the relationships between infection and environmental conditions, regional and global disease forecasting can be further improved.
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Affiliation(s)
- Olga K. Alsova
- Novosibirsk State Technical University, Novosibirsk 630073, Russia;
| | - Valery B. Loktev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia;
- State Research Center for Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk Region 630559, Russia
| | - Elena N. Naumova
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA
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Rudakov N, Samoylenko I, Shtrek S, Igolkina Y, Rar V, Zhirakovskaia E, Tkachev S, Kostrykina T, Blokhina I, Lentz P, Tikunova N. A fatal case of tick-borne rickettsiosis caused by mixed Rickettsia sibirica subsp. sibirica and "Candidatus Rickettsia tarasevichiae" infection in Russia. Ticks Tick Borne Dis 2019; 10:101278. [PMID: 31477530 DOI: 10.1016/j.ttbdis.2019.101278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 07/08/2019] [Accepted: 08/23/2019] [Indexed: 10/26/2022]
Abstract
North Asian tick-typhus (NATT), also known as Siberian tick typhus, is the main tick-borne rickettsiosis in Siberia, Russia. Recently, a fatal infection in a four-year-old girl with typical tick-borne rickettsiosis symptoms (fever, rash, eschar at the site of the tick bite, myalgia) and meningeal syndrome was registered. In order to identify the etiology of this infection, blood and brain samples from the patient were examined for the presence of a wide range of tick-transmitted agents and enteric viruses by polymerase chain reaction with subsequent sequencing. Rickettsia sibirica subsp. sibirica and "Candidatus Rickettsia tarasevichiae" DNA was identified in both blood and brain samples. Rickettsia sibirica was characterized by the gltA, ompA and ompB genes, and "Candidatus R. tarasevichiae" was characterized by the gltA and ompB genes. We report the first case of mixed R. sibirica and "Candidatus R. tarasevichiae" human infection with a fatal outcome in Russia.
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Affiliation(s)
- Nikolay Rudakov
- Omsk Research Institute of Natural Focal Infections, Omsk, Russia; Omsk State Medical University, Omsk, Russia.
| | - Irina Samoylenko
- Omsk Research Institute of Natural Focal Infections, Omsk, Russia.
| | - Sergey Shtrek
- Omsk Research Institute of Natural Focal Infections, Omsk, Russia; Omsk State Medical University, Omsk, Russia.
| | - Yana Igolkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia.
| | - Vera Rar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia.
| | - Elena Zhirakovskaia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia.
| | - Sergey Tkachev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia.
| | - Tatiana Kostrykina
- The Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Regional Department in Krasnoyarsk Province, Krasnoyarsk, Russia.
| | - Inga Blokhina
- Center of Hygiene and Epidemiology in Krasnoyarsk Region, Krasnoyarsk, Russia.
| | - Petr Lentz
- Kuraginsky District Hospital, Krasnoyarsk region, Kuragino, Russia.
| | - Nina Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia.
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6
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Trovão NS, Shepherd FK, Herzberg K, Jarvis MC, Lam HC, Rovira A, Culhane MR, Nelson MI, Marthaler DG. Evolution of rotavirus C in humans and several domestic animal species. Zoonoses Public Health 2019; 66:546-557. [PMID: 30848076 DOI: 10.1111/zph.12575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/21/2018] [Accepted: 02/10/2019] [Indexed: 12/19/2022]
Abstract
Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.
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Affiliation(s)
- Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Frances K Shepherd
- Comparative and Molecular Biosciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Katerina Herzberg
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Matthew C Jarvis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Ham C Lam
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, Minnesota
| | - Albert Rovira
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Marie R Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
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7
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Alekseev KP, Penin AA, Mukhin AN, Khametova KM, Grebennikova TV, Yuzhakov AG, Moskvina AS, Musienko MI, Raev SA, Mishin AM, Kotelnikov AP, Verkhovsky OA, Aliper TI, Nepoklonov EA, Herrera-Ibata DM, Shepherd FK, Marthaler DG. Genome Characterization of a Pathogenic Porcine Rotavirus B Strain Identified in Buryat Republic, Russia in 2015. Pathogens 2018; 7:pathogens7020046. [PMID: 29677111 PMCID: PMC6027140 DOI: 10.3390/pathogens7020046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 01/18/2023] Open
Abstract
An outbreak of enteric disease of unknown etiology with 60% morbidity and 8% mortality in weaning piglets occurred in November 2015 on a farm in Buryat Republic, Russia. Metagenomic sequencing revealed the presence of rotavirus B in feces from diseased piglets while no other pathogens were identified. Clinical disease was reproduced in experimentally infected piglets, yielding the 11 RVB gene segments for strain Buryat15, with an RVB genotype constellation of G12-P[4]-I13-R4-C4-M4-A8-N10-T4-E4-H7. This genotype constellation has also been identified in the United States. While the Buryat15 VP7 protein lacked unique amino acid differences in the predicted neutralizing epitopes compared to the previously published swine RVB G12 strains, this report of RVB in Russian swine increases our epidemiological knowledge on the global prevalence and genetic diversity of RVB.
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Affiliation(s)
- Konstantin P Alekseev
- N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia.
- Federal State Budget Scientific Institution "Federal Scientific Centre VIEV", Moscow 109428, Russia.
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow 127051, Russia.
- Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan 420021, Russia.
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexey N Mukhin
- N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia.
| | - Kizkhalum M Khametova
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Tatyana V Grebennikova
- N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia.
| | - Anton G Yuzhakov
- N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia.
- Federal State Budget Scientific Institution "Federal Scientific Centre VIEV", Moscow 109428, Russia.
| | - Anna S Moskvina
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Maria I Musienko
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Sergey A Raev
- Federal State Budget Scientific Institution "Federal Scientific Centre VIEV", Moscow 109428, Russia.
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Alexandr M Mishin
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Alexandr P Kotelnikov
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Oleg A Verkhovsky
- Independent Non-Profit Organization "Diagnostic and Prevention Research Institute for Human and Animal Diseases", Moscow 123098, Russia.
| | - Taras I Aliper
- N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia.
- Federal State Budget Scientific Institution "Federal Scientific Centre VIEV", Moscow 109428, Russia.
| | - Eugeny A Nepoklonov
- The Ministry of Agriculture of the Russian Federation, Orlikov Pereulok 1/11, Moscow 107139, Russia.
| | - Diana M Herrera-Ibata
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Ave, Manhattan, KS 66502, USA.
| | - Frances K Shepherd
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Ave, Manhattan, KS 66502, USA.
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8
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Bhat S, Kattoor JJ, Malik YS, Sircar S, Deol P, Rawat V, Rakholia R, Ghosh S, Vlasova AN, Nadia T, Dhama K, Kobayashi N. Species C Rotaviruses in Children with Diarrhea in India, 2010-2013: A Potentially Neglected Cause of Acute Gastroenteritis. Pathogens 2018; 7:E23. [PMID: 29462971 PMCID: PMC5874749 DOI: 10.3390/pathogens7010023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 11/16/2022] Open
Abstract
All over the world, children and adults are severely affected by acute gastroenteritis, caused by one of the emerging enteric pathogens, rotavirus C (RVC). At present, no extensive surveillance program is running for RVC in India, and its prevalence is largely unknown except cases of local outbreaks. Here, we intended to detect the presence of RVC in diarrheic children visiting or admitted to hospitals in Haldwani (state of Uttarakhand, India), a city located in the foothills of the Himalayas. During 2010-2013, we screened 119 samples for RVC by an RVC VP6 gene-specific RT-PCR. Of these, 38 (31.93%) were found positive, which is higher than the incidence rates reported so far from India. The phylogenetic analysis of the derived nucleotide sequences from one of the human RVC (HuRVC) isolates, designated as HuRVC/H28/2013/India, showed that the study isolate belongs to genotype I2, P2 and E2 for RVC structural genes 6 and 4 (VP6, and VP4) and non-structural gene 4 (NSP4), respectively. Furthermore, the VP6 gene of HuRVC/H28/2013/India shows the highest similarity to a recently-reported human-like porcine RVC (PoRVC/ASM140/2013/India, KT932963) from India suggesting zoonotic transmission. We also report a full-length NSP4 gene sequence of human RVC from India. Under the One-health platforms there is a need to launch combined human and animal RVC surveillance programs for a better understanding of the epidemiology of RVC infections and for implementing control strategies.Reoviridae, possess 11 double-stranded segments of RNA that encode six structural viral proteins (VP1, VP2, VP3, VP4, VP6, VP7) and five/six non-structural proteins (NSP1-NSP5/6) [7]. Based on the antigenic properties of the major inner capsid protein (VP6), RVs are subdivided into eight well-characterized species (A-H) and two putative species viz. I and J [8-10]. Humans and other mammalian species are affected by species A, B, C and H rotaviruses and birds by species D, F and G, and species E has been reported exclusively in pigs [7,8,11-17]. The newly-proposed species I is reported in dogs [18] and cats [19], whereas species J is found in bats [10].
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Affiliation(s)
- Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Pallavi Deol
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Vinita Rawat
- Department of Microbiology, Government Medical College, Haldwani, Nainital, Uttarakhand 263 139, India.
| | - Ritu Rakholia
- Department of Pediatrics, Government Medical College, Haldwani, Nainital, Uttarakhand 263 139, India.
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, St. Kitts, West Indies.
| | - Anastasia N Vlasova
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Touil Nadia
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d'Instruction Med V de Rabat; 110 000 Morocco.
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India.
| | - Nobumichi Kobayashi
- Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo 060-8556, Japan.
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9
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Kattoor JJ, Saurabh S, Malik YS, Sircar S, Dhama K, Ghosh S, Bányai K, Kobayashi N, Singh RK. Unexpected detection of porcine rotavirus C strains carrying human origin VP6 gene. Vet Q 2017. [DOI: 10.1080/01652176.2017.1346849] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Sharad Saurabh
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, West Indies
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Nobumichi Kobayashi
- School of Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
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10
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Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G, Woolhouse M, Kellam P, Rabaa MA, Cotten M. Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evol 2016; 2:vew027. [PMID: 28748110 PMCID: PMC5522372 DOI: 10.1093/ve/vew027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.
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Affiliation(s)
- My V T Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bas B Oude Munnink
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Phuc Tran My
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tue Ngo Tri
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,London School of Tropical Medicine and Hygiene, London, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark Woolhouse
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Kymab Inc., Cambridge, UK.,Imperial College, London, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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11
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Niira K, Ito M, Masuda T, Saitou T, Abe T, Komoto S, Sato M, Yamasato H, Kishimoto M, Naoi Y, Sano K, Tuchiaka S, Okada T, Omatsu T, Furuya T, Aoki H, Katayama Y, Oba M, Shirai J, Taniguchi K, Mizutani T, Nagai M. Whole genome sequences of Japanese porcine species C rotaviruses reveal a high diversity of genotypes of individual genes and will contribute to a comprehensive, generally accepted classification system. INFECTION GENETICS AND EVOLUTION 2016; 44:106-113. [PMID: 27353186 DOI: 10.1016/j.meegid.2016.06.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/16/2022]
Abstract
Porcine rotavirus C (RVC) is distributed throughout the world and is thought to be a pathogenic agent of diarrhea in piglets. Although, the VP7, VP4, and VP6 gene sequences of Japanese porcine RVCs are currently available, there is no whole-genome sequence data of Japanese RVC. Furthermore, only one to three sequences are available for porcine RVC VP1-VP3 and NSP1-NSP3 genes. Therefore, we determined nearly full-length whole-genome sequences of nine Japanese porcine RVCs from seven piglets with diarrhea and two healthy pigs and compared them with published RVC sequences from a database. The VP7 genes of two Japanese RVCs from healthy pigs were highly divergent from other known RVC strains and were provisionally classified as G12 and G13 based on the 86% nucleotide identity cut-off value. Pairwise sequence identity calculations and phylogenetic analyses revealed that candidate novel genotypes of porcine Japanese RVC were identified in the NSP1, NSP2 and NSP3 encoding genes, respectively. Furthermore, VP3 of Japanese porcine RVCs was shown to be closely related to human RVCs, suggesting a gene reassortment event between porcine and human RVCs and past interspecies transmission. The present study demonstrated that porcine RVCs show greater genetic diversity among strains than human and bovine RVCs.
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Affiliation(s)
- Kazutaka Niira
- Tochigi Prefectural South District Animal Hygiene Service Center, Tochigi, Tochigi 328-0002, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 682-0017, Japan
| | - Toshiya Saitou
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Tadatsugu Abe
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Mitsuo Sato
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 682-0017, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Shinobu Tuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Takashi Okada
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Furuya
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
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12
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Medici MC, Tummolo F, Martella V, Arcangeletti MC, De Conto F, Chezzi C, Fehér E, Marton S, Calderaro A, Bányai K. Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment. J Gen Virol 2016; 97:1888-1898. [PMID: 27154899 DOI: 10.1099/jgv.0.000497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Group C rotaviruses (RVC) are enteric pathogens of humans and animals. Whole-genome sequences are available only for few RVCs, leaving gaps in our knowledge about their genetic diversity. We determined the full-length genome sequence of two human RVCs (PR2593/2004 and PR713/2012), detected in Italy from hospital-based surveillance for rotavirus infection in 2004 and 2012. In the 11 RNA genomic segments, the two Italian RVCs segregated within separate intra-genotypic lineages showed variation ranging from 1.9 % (VP6) to 15.9 % (VP3) at the nucleotide level. Comprehensive analysis of human RVC sequences available in the databases allowed us to reveal the existence of at least two major genome configurations, defined as type I and type II. Human RVCs of type I were all associated with the M3 VP3 genotype, including the Italian strain PR2593/2004. Conversely, human RVCs of type II were all associated with the M2 VP3 genotype, including the Italian strain PR713/2012. Reassortant RVC strains between these major genome configurations were identified. Although only a few full-genome sequences of human RVCs, mostly of Asian origin, are available, the analysis of human RVC sequences retrieved from the databases indicates that at least two intra-genotypic RVC lineages circulate in European countries. Gathering more sequence data is necessary to develop a standardized genotype and intra-genotypic lineage classification system useful for epidemiological investigations and avoiding confusion in the literature.
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Affiliation(s)
- Maria Cristina Medici
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Fabio Tummolo
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Maria Cristina Arcangeletti
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Flora De Conto
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Carlo Chezzi
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Adriana Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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13
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Doan YH, Haga K, Fujimoto A, Fujii Y, Takai-Todaka R, Oka T, Kimura H, Yoshizumi S, Shigemoto N, Okamoto-Nakagawa R, Shirabe K, Shinomiya H, Sakon N, Katayama K. Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries. INFECTION GENETICS AND EVOLUTION 2016; 41:160-173. [PMID: 27071530 DOI: 10.1016/j.meegid.2016.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
Abstract
Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Fujimoto
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | | | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Ehime, Japan
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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