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Xin Z, Li S, Lu X, Liu L, Gao Y, Hu F, Yu K, Ma X, Li Y, Huang B, Wu J, Guo X. Development and Clinical Application of a Molecular Assay for Four Common Porcine Enteroviruses. Vet Sci 2024; 11:305. [PMID: 39057989 PMCID: PMC11281614 DOI: 10.3390/vetsci11070305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine rotavirus-A (PoRVA) are the four main pathogens that cause viral diarrhea in pigs, and they often occur in mixed infections, which are difficult to distinguish only according to clinical symptoms. Here, we developed a multiplex TaqMan-probe-based real-time RT-PCR method for the simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA for the first time. The specific primers and probes were designed for the M protein gene of PEDV, N protein gene of TGEV, N protein gene of PDCoV, and VP7 protein gene of PoRVA, and corresponding recombinant plasmids were constructed. The method showed extreme specificity, high sensitivity, and excellent repeatability; the limit of detection (LOD) can reach as low as 2.18 × 102 copies/μL in multiplex real-time RT-PCR assay. A total of 97 clinical samples were used to compare the results of the conventional reverse transcription PCR (RT-PCR) and this multiplex real-time RT-PCR for PEDV, TGEV, PDCoV, and PoRVA detection, and the results were 100% consistent. Subsequently, five randomly selected clinical samples that tested positive were sent for DNA sequencing verification, and the sequencing results showed consistency with the detection results of the conventional RT-PCR and our developed method in this study. In summary, this study developed a multiplex real-time RT-PCR method for simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA, and the results of this study can provide technical means for the differential diagnosis and epidemiological investigation of these four porcine viral diarrheic diseases.
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Affiliation(s)
- Zhonghao Xin
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Shiheng Li
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Xiao Lu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Liping Liu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Yuehua Gao
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Feng Hu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Kexiang Yu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Xiuli Ma
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Yufeng Li
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Bing Huang
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Jiaqiang Wu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Science, Jinan 250100, China;
| | - Xiaozhen Guo
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
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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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Joshi MS, Walimbe AM, Arya SA, Gopalkrishna V. Evolutionary analysis of all eleven genes of species C rotaviruses circulating in humans and domestic animals. Mol Phylogenet Evol 2023:107854. [PMID: 37302675 DOI: 10.1016/j.ympev.2023.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Species C rotaviruses (RVC) are the second most common rotavirus species known to cause gastroenteritis in humans and pigs and with occurrence documented in cattle, dogs, ferrets, and sloth bears. Despite the host-specific nature of RVC genotypes, cross-species transmission, reassortment, and recombination events are also documented. In the present study, we inferred the evolutionary history of globally circulating RVC strains, including time scale stasis, the most probable ancestral country, and the most probable source host using Bayesian methods implemented in BEAST v.1.8.4. The human-derived RVC strains were majorly monophyletic and further grouped into two lineages. The RVC strains derived from pigs were monophyletic for the VP1 and the remaining genes were classified into 2 to 4 groups based on the high posterior support. The root mean age for all the genes indicated the circulation of RVC for over 800 years. Overall, the time to Most Recent Common Ancestor of human RVC strains dated back to the beginning of the 20th century. The VP7 and NSP2 genes had the lowest rates of evolution compared to other genes. The majority of the genes of RVC showed their origin in Japan except for VP7 and VP4 genes in South Korea. The phylogeographic analysis with the country as a trait showed the role of Japan, China, and India in the dispersion of the virus. In the current study, significant transmission links between different hosts were analyzed for the first time using the host as a trait. Significant transmission links between pigs and other animal species as well as humans indicate possible transmission from the pig as a source host and suggest monitoring of proximity with animals.
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Affiliation(s)
- Madhuri S Joshi
- Enteric Viruses Group, ICMR- National Institute of Virology, Pune, India.
| | - Atul M Walimbe
- Bioinformatics Group, ICMR- National Institute of Virology, Pune, India.
| | - Shalu A Arya
- Enteric Viruses Group, ICMR- National Institute of Virology, Pune, India
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Global Infection Rate of Rotavirus C during 1980-2022 and Analysis of Critical Factors in the Host Range Restriction of Virus VP4. Viruses 2022; 14:v14122826. [PMID: 36560830 PMCID: PMC9781963 DOI: 10.3390/v14122826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Information on rotavirus C (RVC) infection is lacking, partly because the prevalence of RVC among humans and animals worldwide is undefined. Data on the characteristics of the P genotype among RVC strains are also required. We performed systematic searches on the infection rates of RVC since 1980 based on the literature and gene sequences of the PubMed and GenBank databases. A phylogenetic tree of VP4 genes was constructed to evaluate the distribution of the P genotype of RVC from various hosts. The specific mutation motifs in VP8* with P [2]/P [4]/P [5] specificity were analyzed to elucidate their roles in host range restriction. The rate of RVC infection in humans has fallen from 3% before 2009 to 1%, whereas in animals it has risen from 10% to 25%. The P genotype of RVC showed strict host species specificity, and current human RVC infections are exclusively caused by genotype P [2]. In the VP8* hemagglutinin domain of the P [4]/P [5] genotype of swine RVC, specific insertion or deletion were found relative to the human P [2] genotype, and these motifs are a possible critical factor for host range restriction. Our findings highlight the need for further epidemiological surveillance, preventive strategies, and elucidation of the factors involved in the specific host range restriction of RVC-circulating strains.
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Zhang L, Jiang Z, Zhou Z, Sun J, Yan S, Gao W, Shao Y, Bai Y, Wu Y, Yan Z, Sheng S, Lai A, Su S. A TaqMan Probe-Based Multiplex Real-Time PCR for Simultaneous Detection of Porcine Epidemic Diarrhea Virus Subtypes G1 and G2, and Porcine Rotavirus Groups A and C. Viruses 2022; 14:v14081819. [PMID: 36016441 PMCID: PMC9413770 DOI: 10.3390/v14081819] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022] Open
Abstract
Porcine viral diarrhea diseases affect the swine industry, resulting in significant economic losses. Porcine epidemic diarrhea virus (PEDV) genotypes G1 and G2, and groups A and C of the porcine rotavirus, are major etiological agents of severe gastroenteritis and profuse diarrhea, particularly among piglets, with mortality rates of up to 100%. Based on the high prevalence rate and frequent co-infection of PEDV, RVA, and RVC, close monitoring is necessary to avoid greater economic losses. We have developed a multiplex TaqMan probe-based real-time PCR for the rapid simultaneous detection and differentiation of PEDV subtypes G1 and G2, RVA, and RVC. This test is highly sensitive, as the detection limits were 20 and 100 copies/μL for the G1 and G2 subtypes of PEDV, respectively, and 50 copies/μL for RVA and RVC, respectively. Eighty-eight swine clinical samples were used to evaluate this new test. The results were 100% in concordance with the standard methods. Since reassortment between porcine and human rotaviruses has been reported, this multiplex test not only provides a basis for the management of swine diarrheal viruses, but also has the potential to impact public health as well.
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Affiliation(s)
- Letian Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zitong Zhou
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Shiyu Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenting Gao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuekun Shao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhe Bai
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Wu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zefei Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouzhi Sheng
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, Frankfort, KY 40601, USA
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Wang Y, Porter EP, Lu N, Zhu C, Noll LW, Hamill V, Brown SJ, Palinski RM, Bai J. Whole-genome classification of rotavirus C and genetic diversity of porcine strains in the USA. J Gen Virol 2021; 102. [PMID: 33950806 DOI: 10.1099/jgv.0.001598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus C (RVC) is associated with acute diarrhoea in both children and young animals. Because of its frequent occurrence, additional sequences have recently been generated. In this study, we sequenced 21 complete genomes from porcine diarrhoea samples and analysed them together with all available reference sequences collected from the GenBank database [National Center for Biotechnology Information (NCBI)]. Based on phylogenetic analysis and genetic distance calculation, the number of each segment was identified as 31G, 26P, 13I, 5R, 5C, 5M, 12A, 10 N, 9T, 8E and 4 H for genotypes encoding VP7, VP4, VP6, VP1, VP2, VP3 and NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. From the analysis, genotypes G19-G31, P[22]-P[26], R5, A9-A12, N9-N10, T7-T9 and E6-E8 were defined as newly identified genotypes, and genotype C6 was combined with C5, and M6 was combined with M1, due to their closely related nature. Estimated with the identity frequency ratio between the intergenotype and intragenotype, the nucleotide identity cutoff values for different genotypes were determined as 85, 85, 86, 84, 83, 84, 82, 87, 84, 81 and 79 % for VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Genotyping of the 49 US strains indicated possible segment reassortment in 9 of the 11 segments, with the exceptions being VP1 and NSP5, and the most prevalent genotypes for each segment genes in the USA were G6/G5/G21/G9-P5/P4-I6/I5-R1-C5-M1-A8-N1/N10-T1-E1-H1. Our study updated the genotypes of RVC strains and provided more evidence of RVC strain diversity that may be relevant to better understand genetic diversity, and the distribution and evolution of RVC strains.
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Affiliation(s)
- Yin Wang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Elizabeth P Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Nanyan Lu
- Bioinformatics Center, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Cong Zhu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Lance W Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Susan J Brown
- Bioinformatics Center, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M Palinski
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
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