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Chen Y, He Z, Luo Y, Su Q, Wang Q, Wang J, He J, Yu M, You H, Chen H. Tris stabilized AuNPs based lateral flow immunochromatography for the simultaneous detection of porcine epidemic diarrhea virus and rotavirus on-site. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124670. [PMID: 38908108 DOI: 10.1016/j.saa.2024.124670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV) and rotavirus has posed a significant threat to the pig industry annually across different nations, resulting in huge economic losses. The frequent co-infection of these two viruses in clinical settings complicates the process of differential diagnoses. Rapid and accurate detection of PEDV and rotavirus is in great demand for timely diarrhea disease prevention and control. In this study, tris stabilized AuNPs were prepared and a sensitive lateral flow immunoassay (LFIA) sensor was developed for the simultaneous and rapid detection of PEDV and rotavirus on site. After the system optimization, the established LFIA can simultaneously identify PEDV and rotavirus with limits of detection (LOD) of 1.25 × 103 TCID50 mL-1 and 3.13 × 102 pg mL-1, respectively. When applying for clinical samples, the LFIA show a concordance of 95 % and 100 % to reverse transcript polymerase chain reaction (RT-PCR) for PEDV and rotavirus respectively. Therefore, this LFIA can qualitatively detect PEDV and rotavirus in 18 min with high sensitivity and accuracy without any sophisticated equipment and operation, making it a promising candidate for the early diagnosis of PEDV or/and rotavirus diarrhea on site.
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Affiliation(s)
- Yingkai Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Zhaoyuan He
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yaxiang Luo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Qianlian Su
- Guangxi Agricultureal Engineering Vocational Technical College, Nanning 532100, Guangxi, China
| | - Qiuhua Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Jinzi Wang
- School of Marine Science and Biotechnology, Guangxi Minzu University, Nanning 530006, Guangxi, China
| | - Jiakang He
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, Guangxi, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, Guangxi, China
| | - Meiling Yu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, Guangxi, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, Guangxi, China.
| | - Hui You
- School of Mechanical Engineering, Guangxi University, Nanning 530004, Guangxi, China.
| | - Hailan Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, Guangxi, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, Guangxi, China.
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Wu Q, Liu X, Wang J, Xu S, Zeng F, Chen L, Zhang G, Wang H. An isothermal nucleic acid amplification-based enzymatic recombinase amplification method for dual detection of porcine epidemic diarrhea virus and porcine rotavirus A. Virology 2024; 594:110062. [PMID: 38522136 DOI: 10.1016/j.virol.2024.110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
Viral diarrhea is the predominant digestive tract sickness in piglings, resulting in substantial profit losses in the porcine industry. Porcine rotavirus A (PoRVA) and porcine epidemic diarrhea virus (PEDV) are the main causes of grave gastroenteritis and massive dysentery, especially in piglets. PoRVA and PEDV have high transmissibility, exhibit similar clinical symptoms, and frequently co-occur. Therefore, to avoid financial losses, a quick, highly efficient, objective diagnostic test for the prevention and detection of these diseases is required. Enzymatic recombinase amplification (ERA) is a novel technology based on isothermal nucleic acid amplification. It demonstrates high sensitivity and excellent specificity, with a short processing time and easy operability, compared with other in vitro nucleic acid amplification technologies. In this study, a dual ERA method to detect and distinguish between PEDV and PoRVA nucleic acids was established. The method shows high sensitivity, as the detection limits were 101 copies/μL for both viruses. To test the usefulness of this method in clinical settings, we tested 64 swine clinical samples. Our results were 100% matched with those acquired using a commercially available kit. Therefore, we have successfully developed a dual diagnostic ERA nucleic acids method for detecting and distinguishing between PEDV and PoRVA.
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Affiliation(s)
- Qianwen Wu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Jingyu Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Sijia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Fanliang Zeng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Ling Chen
- Ganzhou Quannan County Agriculture and Rural Bureau, Ganzhou, 341800, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
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Qiao M, Li M, Li Y, Wang Z, Hu Z, Qing J, Huang J, Jiang J, Jiang Y, Zhang J, Gao C, Yang C, Li X, Zhou B. Recent Molecular Characterization of Porcine Rotaviruses Detected in China and Their Phylogenetic Relationships with Human Rotaviruses. Viruses 2024; 16:453. [PMID: 38543818 PMCID: PMC10975774 DOI: 10.3390/v16030453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 05/23/2024] Open
Abstract
Porcine rotavirus A (PoRVA) is an enteric pathogen capable of causing severe diarrhea in suckling piglets. Investigating the prevalence and molecular characteristics of PoRVA in the world, including China, is of significance for disease prevention. In 2022, a total of 25,768 samples were collected from 230 farms across China, undergoing porcine RVA positivity testing. The results showed that 86.52% of the pig farms tested positive for porcine RVA, with an overall positive rate of 51.15%. Through the genetic evolution analysis of VP7, VP4 and VP6 genes, it was revealed that G9 is the predominant genotype within the VP7 segment, constituting 56.55%. VP4 genotypes were identified as P[13] (42.22%), P[23] (25.56%) and P[7] (22.22%). VP6 exhibited only two genotypes, namely I5 (88.81%) and I1 (11.19%). The prevailing genotype combination for RVA was determined as G9P[23]I5. Additionally, some RVA strains demonstrated significant homology between VP7, VP4 and VP6 genes and human RV strains, indicating the potential for human RV infection in pigs. Based on complete genome sequencing analysis, a special PoRVA strain, CHN/SD/LYXH2/2022/G4P[6]I1, had high homology with human RV strains, revealing genetic reassortment between human and porcine RV strains in vivo. Our data indicate the high prevalence, major genotypes, and cross-species transmission of porcine RVA in China. Therefore, the continuous monitoring of porcine RVA prevalence is essential, providing valuable insights for virus prevention and control, and supporting the development of candidate vaccines against porcine RVA.
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Affiliation(s)
- Mengli Qiao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (M.Q.); (M.L.)
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Meizhen Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (M.Q.); (M.L.)
| | - Yang Li
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Zewei Wang
- Beef Cattle Industry Development Center, Fangshan 033100, China;
| | - Zhiqiang Hu
- College of Animal Science, Xichang University, Xichang 615012, China;
| | - Jie Qing
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Jiapei Huang
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Junping Jiang
- China Agriculture Research System-Yangling Comprehensive Test Station, Xianyang 712100, China; (J.J.); (Y.J.)
| | - Yaqin Jiang
- China Agriculture Research System-Yangling Comprehensive Test Station, Xianyang 712100, China; (J.J.); (Y.J.)
| | - Jinyong Zhang
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Chunliu Gao
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Chen Yang
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
| | - Xiaowen Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (M.Q.); (M.L.)
- Shandong Engineering Research Center of Pig and Poultry Health Breeding and Important Disease Purification, Shandong New Hope Liuhe Co., Ltd., Qingdao 266000, China; (Y.L.); (J.Q.); (J.H.); (J.Z.); (C.G.); (C.Y.)
- China Agriculture Research System-Yangling Comprehensive Test Station, Xianyang 712100, China; (J.J.); (Y.J.)
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (M.Q.); (M.L.)
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Song W, Feng Y, Zhang J, Kong D, Fan J, Zhao M, Hua L, Xiang J, Tang X, Xiao S, Peng Z, Wu B. Development of a multiplex reverse transcription-quantitative PCR (qPCR) method for detecting common causative agents of swine viral diarrhea in China. Porcine Health Manag 2024; 10:12. [PMID: 38444040 PMCID: PMC10916220 DOI: 10.1186/s40813-024-00364-y] [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: 12/13/2023] [Accepted: 02/25/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Diarrheal diseases caused by viral agents have led to a great morbidity, mortality, and economic loss in global pig industry. Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and group A porcine rotavirus (RVA) are main causative agents of swine viral diarrhea with similar clinical signs on Chinese farms and their co-infection is also common. However, it is still lack of a convenient method to detect these four agents. METHODS A TaqMan multiplex qPCR method was developed to detect PEDV, TGEV, PDCoV, and RVA, simultaneously. This method was then applied to investigate 7,342 swine fecal samples or rectal swabs, as well as 1,246 swine intestinal samples collected from 2075 farms in China in 2022. RESULTS Minimum detection limits of this method were 3 copies/µL for PEDV, 4 copies/µL for TGEV, 8 copies/µL for RVA, and 8 copies/µL for PDCoV, suggesting a good sensitivity. No signals were observed by using this method detecting other viral agents commonly prevalent in pigs, which is suggestive of a good specificity. Application of this method on investigating clinical samples demonstrated a relatively high positive rate for PEDV (22.21%, 1907/8588) and RVA (44.00%, 3779/8588). In addition, co-infection between PEDV and RVA was observed on 360 investigated farms, accounting for 17.35% (360/2075) of the farms where co-infection events were screened. CONCLUSIONS A TaqMan multiplex qPCR method targeting PEDV, TGEV, PDCoV, and RVA was developed in this study. This method demonstrated a good specificity and sensitivity on investigating these four common viruses responsible for viral diarrhea on Chinese pig farms, which represents a convenient method for the monitoring and differential diagnosis of swine viral diarrhea.
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Affiliation(s)
- Wenbo Song
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China
| | - Yixue Feng
- Animal Disease Diagnosis Center of Wuhan Keqian Biology Co., Ltd, 430070, Wuhan, China
| | - Jiali Zhang
- Animal Disease Diagnosis Center of Wuhan Keqian Biology Co., Ltd, 430070, Wuhan, China
| | - Danni Kong
- Animal Disease Diagnosis Center of Wuhan Keqian Biology Co., Ltd, 430070, Wuhan, China
| | - Jie Fan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China
| | - Mengfei Zhao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China
| | - Lin Hua
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China
| | - Jinmei Xiang
- Hubei Vocational College of Bio-Technology, 430070, Wuhan, China
| | - Xibiao Tang
- Animal Disease Diagnosis Center of Wuhan Keqian Biology Co., Ltd, 430070, Wuhan, China
- Hubei Vocational College of Bio-Technology, 430070, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China.
- Hubei Hongshan Laboratory, 430070, Wuhan, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China.
| | - Bin Wu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China.
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Carossino M, Vissani MA, Barrandeguy ME, Balasuriya UBR, Parreño V. Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health. Viruses 2024; 16:130. [PMID: 38257830 PMCID: PMC10819593 DOI: 10.3390/v16010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
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Srivastava P, Prasad D. Human Norovirus Detection: How Much Are We Prepared? Foodborne Pathog Dis 2023; 20:531-544. [PMID: 37792418 DOI: 10.1089/fpd.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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Shi K, Zhou H, Feng S, He J, Li B, Long F, Shi Y, Yin Y, Li Z. Development of a Quadruplex RT-qPCR for the Detection of Porcine Rotaviruses and the Phylogenetic Analysis of Porcine RVH in China. Pathogens 2023; 12:1091. [PMID: 37764899 PMCID: PMC10538229 DOI: 10.3390/pathogens12091091] [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: 07/19/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Rotavirus A species (RVA), RVB, RVC, and RVH are four species of rotaviruses (RVs) that are prevalent in pig herds, and co-infections occur frequently. In this study, a quadruplex real-time quantitative RT-PCR (RT-qPCR) for the simultaneous detection of four porcine RVs was developed by designing specific primers and probes based on the VP6 gene of RVA, RVB, RVC, and RVH, respectively. The method showed high specificity and could only detect RVA, RVB, RVC, and RVH, without cross-reaction with other porcine viruses; showed excellent sensitivity, with a limit of detection (LOD) of 1.5 copies/µL for each virus; showed good repeatability, with intra-assay coefficients of variation (CVs) of 0.15-1.14% and inter-assay CVs of 0.07-0.96%. A total of 1447 clinical fecal samples from Guangxi province in China were tested using the developed quadruplex RT-qPCR. The results showed that RVA (42.71%, 618/1447), RVB (26.95%, 390/1447), RVC (42.92%, 621/1447), and RVH (13.68%, 198/1447) were simultaneously circulating in the pig herds, and the co-infection rate of different species of rotaviruses was found to be up to 44.01% (579/1447). The clinical samples were also detected using one previously reported method, and the coincidence rate of the detection results using two methods was more than 99.65%. The phylogenetic tree based on the VP6 gene sequences of RVH revealed that the porcine RVH strains from Guangxi province belonged to the genotype I5, which was closely related to Japanese and Vietnamese strains. In summary, an efficient, sensitive, and accurate method for the detection and differentiation of RVA, RVB, RVC, and RVH was developed and applied to investigate the prevalence of porcine RVs in Guangxi province, China. This study is the first to report the prevalence of porcine RVH in China.
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Affiliation(s)
- Kaichuang Shi
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Hongjin Zhou
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Junxian He
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Biao Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Yanwen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
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8
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Yang W, Tao D, Xu B, Zheng Y, Zhao S. Detecting Melanocortin 1 Receptor Gene's SNPs by CRISPR/enAsCas12a. Genes (Basel) 2023; 14:genes14020394. [PMID: 36833321 PMCID: PMC9957350 DOI: 10.3390/genes14020394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, while the application of single nucleotide polymorphism (SNP) detection is limited. The MC1R SNPs were investigated by CRISPR/enAsCas12a and are not limited to the protospacer adjacent motif (PAM) sequence in vitro. Specifically, we optimized the reaction conditions, which proved that the enAsCas12a has a preference for divalent magnesium ion (Mg2+) and can effectively distinguish the genes with a single base difference in the presence of Mg2+, and the Melanocortin l receptor (MC1R) gene with three kinds of SNP sites (T305C, T363C, and G727A) was quantitatively detected. Since the enAsCas12a is not limited by PAM sequence in vitro, the method shown here can extend this extraordinary CRISPR/enAsCas12a detection system to other SNP targets, thus providing a general SNP detection toolbox.
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Affiliation(s)
- Wei Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yueting Zheng
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs and Key Laboratory of Animal Growth and Development of Henan Province, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (Y.Z.); (S.Z.)
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.Z.); (S.Z.)
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9
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Special Issue "State-of-the-Art Porcine Virus Research in China". Viruses 2023; 15:v15020412. [PMID: 36851626 PMCID: PMC9964372 DOI: 10.3390/v15020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
China is one of the major countries involved in pig production and pork consumption [...].
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10
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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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Jiao R, Ji Z, Zhu X, Shi H, Chen J, Shi D, Liu J, Jing Z, Zhang J, Zhang L, Feng S, Zhang X, Feng L. Genome Analysis of the G6P6 Genotype of Porcine Group C Rotavirus in China. Animals (Basel) 2022; 12:2951. [PMID: 36359075 PMCID: PMC9657714 DOI: 10.3390/ani12212951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 09/29/2023] Open
Abstract
Swine enteric disease is the predominant cause of morbidity and mortality, and viral species involved in swine enteric disease include rotaviruses and coronaviruses, among others. Awareness of the circulating porcine rotavirus group C (PoRVC) in pig herds is critical to evaluate the potential impact of infection. At present, due to the lack of disease awareness and molecular diagnostic means, the research on RVC infection in China is not well-studied. In this study, diarrhea samples collected from pig farms were detected positive for RVC by PCR, and the full-length RVC was not previously reported for Chinese pig farms. This rotavirus strain was designated as RVC/Pig/CHN/JS02/2018/G6P6. A natural recombination event was observed with breakpoints at nucleotides (nt) 2509 to 2748 of the VP2 gene. Phylogenetic analysis based on nsp1 revealed that a new branch A10 formed. Collectively, our data suggest a potentially novel gene recombination event of RVC in the VP2 gene. These findings provide a new insight into the evolution of the rotavirus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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