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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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Jampanil N, Kumthip K, Maneekarn N, Khamrin P. Genetic Diversity of Rotaviruses Circulating in Pediatric Patients and Domestic Animals in Thailand. Trop Med Infect Dis 2023; 8:347. [PMID: 37505643 PMCID: PMC10383398 DOI: 10.3390/tropicalmed8070347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Rotavirus A is a highly contagious virus that causes acute gastroenteritis in humans and a wide variety of animals. In this review, we summarized the information on rotavirus described in the studies in the last decade (2008 to 2021) in Thailand, including the prevalence, seasonality, genetic diversity, and interspecies transmission. The overall prevalence of rotavirus infection in humans ranged from 15-33%. Rotavirus infection was detected throughout the year and most frequently in the dry and cold months, typically in March. The diversity of rotavirus genotypes varied year to year and from region to region. From 2008 to 2016, rotavirus G1P[8] was detected as the most predominant genotype in Thailand. After 2016, G1P[8] decreased significantly and other genotypes including G3P[8], G8P[8], and G9P[8] were increasingly detected from 2016 to 2020. Several uncommon rotavirus strains such as G1P[6], G4P[6], and G3P[10] have also been occasionally detected. In addition, most studies on rotavirus A infection in animals in Thailand from 2011 to 2021 reported the detection of rotavirus A in piglets and canine species. It was reported that rotavirus could cross the host species barrier between humans and animals through interspecies transmission and genetic reassortment mechanisms. The surveillance of rotavirus infection is crucial to identify the trend of rotavirus infection and the emergence of novel rotavirus genotypes in this country. The data provide information on rotavirus infection and the diversity of rotavirus genotypes circulating in the pre-vaccination period, and the data will be useful for the evaluation of the effectiveness of rotavirus vaccine implementation in Thailand.
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Affiliation(s)
- Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
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Tran H, Friendship R, Ojkic D, Poljak Z. Assessment of seasonality of rotavirus PCR detection in swine from Ontario and Quebec between 2016-2020 using submissions to a diagnostic laboratory. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2022; 86:241-253. [PMID: 36211211 PMCID: PMC9536357 DOI: pmid/36211211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/14/2022] [Indexed: 04/03/2023]
Abstract
The goal of this study was to determine if seasonality of rotavirus A, B, and C infection is present in Ontario and Quebec swine herds by investigating submissions to a diagnostic laboratory. Samples (N = 1557) within 755 case submissions from Canadian swine herds between 2016 and 2020 were tested for rotaviruses A, B, and C using a real-time polymerase-chain reaction assay and described. Data from Ontario and Quebec were additionally analyzed using boxplots, 6-week rolling averages, time-series decomposition, and negative binomial regression models. Percentage positivity of submissions for rotaviruses A, B, and C were discovered to be highest in nursery/weaner (n = 100, 94.0%, 60.0%, 80.0%) and grower/finisher (n = 13, 84.6%, 46.2%, 61.5%) pigs and lowest in gilt/sow (n = 45, 68.9%, 20.0%, 40.0%) and suckling pigs (n = 102, 67.6%, 10.8%, 38.2%), respectively. The most common combination of rotavirus at the sample level was AC (n = 252, 17%) and ABC (n = 175, 23.2%) at the submission level. Percent positivity for rotavirus A, B, and C across all Canadian provinces included in the study were 69.9%, 32.6%, and 53.1%, respectively. Descriptive analysis suggested little to no evidence of seasonal patterns, although a spike in November was seen in the monthly total submissions and monthly total positive submissions. Statistically, the overall month effect could not be identified as statistically significant (P > 0.05) for any of the evaluated submission counts. Overall, there was no evidence supporting seasonality of rotavirus within Ontario and Quebec swine herds between 2016 and 2020.
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Affiliation(s)
- Hoc Tran
- Department of Population Medicine (Tran, Friendship, Poljak) and Animal Health Laboratory (Ojkic), Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1
| | - Robert Friendship
- Department of Population Medicine (Tran, Friendship, Poljak) and Animal Health Laboratory (Ojkic), Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1
| | - Davor Ojkic
- Department of Population Medicine (Tran, Friendship, Poljak) and Animal Health Laboratory (Ojkic), Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1
| | - Zvonimir Poljak
- Department of Population Medicine (Tran, Friendship, Poljak) and Animal Health Laboratory (Ojkic), Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1
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Assessing the Epidemiology of Rotavirus A, B, C and H in Diarrheic Pigs of Different Ages in Northern Italy. Pathogens 2022; 11:pathogens11040467. [PMID: 35456143 PMCID: PMC9025647 DOI: 10.3390/pathogens11040467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
Rotaviruses are classified in 10 groups (A to J), where rotavirus A (RVA) is the major cause of diarrhea in humans and animals. With some exceptions, there is scarce information on the epidemiology of non-A rotaviruses in human and animal hosts. Currently, five species (A, B, C, E and H) have been identified in pigs. In the present study we investigated the prevalence of RVA, RVB, RVC and RVH among diarrheic pigs of different ages, in different seasons and in the presence of co-infections. Two molecular assays were developed for the detection of porcine RVA, RVB, RVC and RVH and were used to screen 962 stool specimens from suckling, weaning and fattening pigs with acute enteritis. Overall, rotaviruses were detected in a high percentage of samples (78%), with RVA being predominant (53%), followed by RVC (45%), RVB (43%) and RVH (14%). RVA was more common in the suckling (58%) and weaning cohorts (64%), while RVB, RVC and RVH were also frequently detected in fattening pigs. Only RVA and RVB infections followed a seasonal trend and exhibited age-related differences. Rotavirus infections were frequently present in combination with other pathogens. The present study depicts a portrait of rich rotavirus diversity in porcine herds, identifying seasonal and age-related patterns of circulation of the different rotavirus species in the surveyed areas.
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Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Fukuda S, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Ruchusatsawast K, Kawamura Y, Sriwanthana B, Motomura K, Tatsumi M, Takeda N, Yoshikawa T, Murata T, Uppapong B, Taniguchi K, Komoto S. Full genome-based characterization of G4P[6] rotavirus strains from diarrheic patients in Thailand: Evidence for independent porcine-to-human interspecies transmission events. Virus Genes 2021; 57:338-357. [PMID: 34106412 DOI: 10.1007/s11262-021-01851-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/17/2021] [Indexed: 12/18/2022]
Abstract
The exact evolutionary patterns of human G4P[6] rotavirus strains remain to be elucidated. Such strains possess unique and strain-specific genotype constellations, raising the question of whether G4P[6] strains are primarily transmitted via independent interspecies transmission or human-to-human transmission after interspecies transmission. Two G4P[6] rotavirus strains were identified in fecal specimens from hospitalized patients with severe diarrhea in Thailand, namely, DU2014-259 (RVA/Human-wt/THA/DU2014-259/2014/G4P[6]) and PK2015-1-0001 (RVA/Human-wt/THA/PK2015-1-0001/2015/G4P[6]). Here, we analyzed the full genomes of the two human G4P[6] strains, which provided the opportunity to study and confirm their evolutionary origin. On whole genome analysis, both strains exhibited a unique Wa-like genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The NSP1 genotype A8 is commonly found in porcine rotavirus strains. Furthermore, on phylogenetic analysis, each of the 11 genes of strains DU2014-259 and PK2015-1-0001 appeared to be of porcine origin. On the other hand, the two study strains consistently formed distinct clusters for nine of the 11 gene segments (VP4, VP6, VP1-VP3, and NSP2-NSP5), strongly indicating the occurrence of independent porcine-to-human interspecies transmission events. Our observations provide important insights into the origin of zoonotic G4P[6] strains, and into the dynamic interaction between porcine and human rotavirus strains.
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Affiliation(s)
- Ratana Tacharoenmuang
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Tipsuda Luechakham
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Busarawan Sriwanthana
- Medical Sciences Technical Office, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
- Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan.
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Nan P, Wen D, Opriessnig T, Zhang Q, Yu X, Jiang Y. Novel universal primer-pentaplex PCR assay based on chimeric primers for simultaneous detection of five common pig viruses associated with diarrhea. Mol Cell Probes 2021; 58:101747. [PMID: 34116142 DOI: 10.1016/j.mcp.2021.101747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/18/2022]
Abstract
Viral pathogens associated with diarrhea in pigs include porcine circovirus 2 (PCV2), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus A (RVA) and C (RVC) among others. In this study, a novel universal primer-based pentaplex PCR (UP-M-PCR) assay was developed for simultaneous detection and differentiation of these five viruses. The assay uses a short-cycle multiplex amplification by chimeric primers (CP), which are virus specific, with a tail added at the 5' end of the universal primer (UP), followed by universal amplification using UPs and a regular cycle amplification. Five universal primers with CPs (UP1-5) were designed and evaluated in an UP-based single PCR (UP-S-PCR). All five UPs were found to work efficiently and UP2 exhibited the best performance. After system optimizations, the analytical sensitivity of the UP-M-PCR, using plasmids containing the specific viral target fragments, was 5 copies/reaction for each of the five viruses irrespective of presence of a single or multiple viruses in the reaction. No cross-reaction was observed with other non-target viruses. When 273 fecal samples from clinically healthy pigs were tested, the assay sensitivity was 90.9-100%, the specificity was 98.0-100%, and the agreement rate with the UP-S-PCR was 98.5-99.6% with a Kappa value being 0.95-0.98. In summary, the UP-M-PCR developed here is a rapid and highly sensitive and specific detection method that can be used to demonstrate mixed infections in pigs with diarrhea.
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Affiliation(s)
- Pei Nan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Dan Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Qiuya Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xiaoya Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
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Shi Y, Li B, Tao J, Cheng J, Liu H. The Complex Co-infections of Multiple Porcine Diarrhea Viruses in Local Area Based on the Luminex xTAG Multiplex Detection Method. Front Vet Sci 2021; 8:602866. [PMID: 33585617 PMCID: PMC7876553 DOI: 10.3389/fvets.2021.602866] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/05/2021] [Indexed: 01/17/2023] Open
Abstract
The large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since 2010, resulting in great damage to the pig industry. However, multiple infections have contributed to the outbreak of the disease and also resulted in great difficulties in diagnosis and control of the disease. Thus, a Luminex xTAG multiplex detection method, which was more sensitive and specific than general multiplex PCR method, was developed for the detection of 11 viral diarrhea pathogens, including PKoV, PAstV, PEDV, PSaV, PSV, PTV, PDCoV, TGEV, BVDV, PoRV, and PToV. To investigate the prevalence of diarrhea-associated viruses responsible for the outbreaks, a total of 753 porcine stool specimens collected from 9 pig farms in Shanghai during 2015-2018 were tested and the pathogen spectrums and co-infections were analyzed. As a result, PKoV, PAstV and PEDV were most commonly detected viruses in diarrheal pigs with the rate of 38.65% (291/753), 20.32% (153/753), and 15.54% (117/753), respectively. Furthermore, multiple infections were commonly seen, with positive rate of 28.42%. Infection pattern of the viral diarrhea pathogens in a specific farm was changing, and different farms had the various diarrhea infection patterns. A longitudinal investigation showed that PEDV was the key pathogen which was closely related to the death of diarrhea piglets. Other pathogens might play synergistic roles in the pathogenesis of diarrhea disease. Furthermore, the surveillance confirmed that variant enteropathogenic viruses were leading etiologic agents of porcine diarrhea, either mono-infection or co-infections of PKoV were common in pigs in Shanghai, but PEDV was still the key pathogen and multiple pathogens synergistically complicated the infection status, suggesting that controlling porcine diarrhea might be more complex than previously thought. The study provides a better understanding of diarrhea viruses in piglets, which will aid in better preventing and controlling epidemics of viral porcine diarrhea.
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Affiliation(s)
- Ying Shi
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Benqiang Li
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jie Tao
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huili Liu
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
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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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Chepngeno J, Diaz A, Paim FC, Saif LJ, Vlasova AN. Rotavirus C: prevalence in suckling piglets and development of virus-like particles to assess the influence of maternal immunity on the disease development. Vet Res 2019; 50:84. [PMID: 31640807 PMCID: PMC6805359 DOI: 10.1186/s13567-019-0705-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 01/05/2023] Open
Abstract
Rotavirus C (RVC) has been detected increasingly in humans and swine in different countries, including the US. It is associated with significant economic losses due to diarrheal disease in nursing piglets. In this study we aimed: (1) to determine the prevalence of RVC in healthy and diarrheic suckling piglets on US farms; and (2) to evaluate if maternal antibody (Ab) levels were associated with protection of newborn suckling piglets against RVC. There was a significantly higher prevalence (p = 0.0002) of litters with diarrhea born to gilts compared with those born to multiparous sows. Of 113 nursing piglet fecal samples tested, 76.1% were RVC RNA positive. Fecal RVC RNA was detected in significantly (p = 0.0419) higher quantities and more frequently in piglets with diarrhea compared with healthy ones (82.5 vs. 69.9%). With the exception of the historic strain Cowden (G1 genotype), field RVC strains do not replicate in cell culture, which is a major impediment for studying RVC pathogenesis and immunity. To circumvent this, we generated RVC virus-like particles (VLPs) for Cowden (G1), RV0104 (G3) and RV0143 (G6) and used them as antigens in ELISA to detect swine RVC Abs in serum and milk from the sows. Using RVC-VLP Ab ELISA we demonstrated that sows with diarrheic litters had significantly lower RVC IgA and IgG Ab titers in milk compared to those with healthy litters. Thus, our data suggest that insufficient lactogenic protection provided by gilts plays a key role in the development of and the increased prevalence of clinical RVC disease.
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Affiliation(s)
- Juliet Chepngeno
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH USA
| | - Annika Diaz
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH USA
- Present Address: College of Food, Agricultural and Environmental Sciences, The Ohio State University, Agricultural Administration Building, Columbus, OH 43210 USA
| | - Francine C. Paim
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH USA
| | - Linda J. Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH USA
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH USA
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10
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Jia S, Feng B, Wang Z, Ma Y, Gao X, Jiang Y, Cui W, Qiao X, Tang L, Li Y, Wang L, Xu Y. Dual priming oligonucleotide (DPO)-based real-time RT-PCR assay for accurate differentiation of four major viruses causing porcine viral diarrhea. Mol Cell Probes 2019; 47:101435. [PMID: 31415867 PMCID: PMC7127266 DOI: 10.1016/j.mcp.2019.101435] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/28/2019] [Accepted: 08/12/2019] [Indexed: 01/25/2023]
Abstract
Currently in China, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus (PoRV), and porcine deltacoronavirus (PDCoV) are the major causes of porcine viral diarrhea, and mixed infections in clinics are common, resulting in significant economic losses in pig industry. Here, a dual priming oligonucleotide (DPO)-based multiplex real-time SYBR Green RT-PCR assay were developed for accurately differentiating PEDV, TGEV, PoRV, and PDCoV in clinical specimens targeting the N gene of TGEV, PEDV, and PDCoV, and the VP7 gene of PoRV. Results showed that the DPO primer allowed a wider annealing temperature range (40–65 °C) and had a higher priming specificity compared to conventional primer, in which more than 3 nucleotides in the 3′- or 5′-segment of DPO primer mismatched with DNA template, PCR amplification efficiency would decrease substantially or extension would not proceed. DPO-based multiplex real-time RT-PCR method had analytical detection limit of 8.63 × 102 copies/μL, 1.92 × 102 copies/μL, 1.74 × 102 copies/μL, and 1.76 × 102 copies/μL for PEDV, TGEV, PoRV, and PDCoV in clinical specimens, respectively. A total of 672 clinical specimens of piglets with diarrheal symptoms were collected in Northeastern China from 2017 to 2018 followed by analysis using the assay, and epidemiological investigation results showed that PEDV, TGEV, PoRV, and PDCoV prevalence was 19.05%, 5.21%, 4.32%, and 3.87%, respectively. The assay developed in this study showed higher detection accuracy than conventional RT-PCR method, suggesting a useful tool for the accurate differentiation of the four major viruses causing porcine viral diarrhea in practice. DPO-based real-time RT-PCR assay for differentiating PEDV, TGEV, PoRV, and PDCoV was developed. The assay has strong specificity and high sensitivity. The test of clinical specimens showed that accuracy of the assay was higher than traditional RT-PCR. The assay is useful tool for epidemiological investigation of the four viruses.
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Affiliation(s)
- Shuo Jia
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Baohua Feng
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Zhuo Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Yingying Ma
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Xuwen Gao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Yanping Jiang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Wen Cui
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Xinyuan Qiao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Lijie Tang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China
| | - Yijing Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China
| | - Li Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China.
| | - Yigang Xu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China.
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11
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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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12
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Tuanthap S, Vongpunsawad S, Luengyosluechakul S, Sakkaew P, Theamboonlers A, Amonsin A, Poovorawan Y. Genome constellations of 24 porcine rotavirus group A strains circulating on commercial Thai swine farms between 2011 and 2016. PLoS One 2019; 14:e0211002. [PMID: 30673764 PMCID: PMC6343967 DOI: 10.1371/journal.pone.0211002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 12/27/2022] Open
Abstract
Rotavirus A (RVA) infection is a major cause of diarrhea-related illness in young children. RVA is also one of the most common enteric viruses detected on pig farms and contributes to substantial morbidity and mortality in piglets. Long-term multi-site surveillance of RVA on Thai swine farms to determine the diversity of RVA strains in circulation is currently lacking. In this study, we characterized the 11 segments of the RVA genome from 24 Thai porcine RVA strains circulating between 2011 and 2016. We identified G9 (15/24) and P[13] (12/24) as the dominant genotypes. The dominant G and P combinations were G9P[13] (n = 6), G9P[23] (n = 6), G3P[13] (n = 5), G9P[19] (n = 3), G4P[6] (n = 2), G4P[19] (n = 1), and G5P[13] (n = 1). Genome constellation of the Thai strains showed the predominance of Wa-like genotype (Gx-P[x]-I1/I5-R1-C1-M1-A8-N1-T1/T7-E1/E9-H1) with evidence of reassortment between the porcine and human RVA strains (e.g., G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[19]-I5-R1-C1-M1-A8-N1-T7-E9-H1). To assess the potential effectiveness of rotavirus vaccination, the Thai RVA strains were compared to the RVA strains represented in the swine rotavirus vaccine, which showed residue variations in the antigenic epitope on VP7 and shared amino acid identity below 90% for G4 and G5 strain. Several previous studies suggested these variations might effect on virus neutralization specificity and vaccine efficacy. Our study illustrates the importance of RVA surveillance beyond the G/P genotyping on commercial swine farms, which is crucial for controlling viral transmission.
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Affiliation(s)
- Supansa Tuanthap
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supol Luengyosluechakul
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Phanlert Sakkaew
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Apiradee Theamboonlers
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alongkorn Amonsin
- Center of Excellence for Emerging and Reemerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (YP); (AA)
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (YP); (AA)
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