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Xu B, Xiong D, Zhang X, Wei H, Yu J. Development of an ARMS-Quadruplex-qPCR assay for the rapid identification of MPXV and the clades Ia, Ib, IIa and IIb. J Virol Methods 2025; 334:115125. [PMID: 39947350 DOI: 10.1016/j.jviromet.2025.115125] [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: 12/11/2024] [Revised: 02/04/2025] [Accepted: 02/08/2025] [Indexed: 02/16/2025]
Abstract
Monkeypox was re-emerging in 2022 and spread to more than 100 countries. Two clades of Monkeypox virus (MPXV) result in different lethality rates and varying transmission capabilities. Rapid identification of MPXV and differentiation of its clades and subclades are crucial for effective control of the disease. In this study, we developed an ARMS-Quadruplex-qPCR method to detect MPXV and distinguish clades (Ia, Ib, IIa and IIb). F3L gene was used to detect all clades of MPXV from other orthopoxviruses. A 1953 bp fragment containing the C3L gene was found to be completely absent in clade II. Additionally, a sequence spanning from the 177th to the 1318th position (1142 bp) within the 1953 bp fragment was missing in Ib. Therefore, the 1142 bp sequence was used to distinguish Ia from other subclades, and the sequence with the 1142 bp region missing in Ib was used to discriminate Ib from other subclades. Since subclades IIa and IIb are too close to have large deletions and insertions, a unique single nucleotide polymorphism (SNP) was used to design a primer/probe set for ARMS-qPCR to differentiate clade IIa from IIb. The ARMS-Quadruplex-qPCR system can detect down to 2 copies per reaction of MPXV and effectively differentiate all the four subclades. Altogether, four qPCR primer/probe sets in one tube were deployed to recognize MPXV and differentiate MPXV subclades. The high sensitivity, rapidity and specificity of the developed system make it a promising alternative for the diagnosis of MPXV and the determination of the subclades of the infected MPXV.
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Affiliation(s)
- Bohan Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhou H, Cui K, Su X, Zhang H, Xiao B, Li S, Yang B. Overview of Recent Advances in Canine Parvovirus Research: Current Status and Future Perspectives. Microorganisms 2024; 13:47. [PMID: 39858815 PMCID: PMC11767475 DOI: 10.3390/microorganisms13010047] [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: 11/30/2024] [Revised: 12/24/2024] [Accepted: 12/26/2024] [Indexed: 01/27/2025] Open
Abstract
Canine parvovirus (CPV-2) was first identified in the late 1970s and has since become one of the most significant infectious agents affecting dogs. CPV-2 causes severe diseases such as hemorrhagic gastroenteritis and myocarditis, posing a major threat to canine health, particularly with a high mortality rate in puppies. It is globally recognized as a highly contagious and lethal pathogen. CPV is prone to rapid mutation, leading to the emergence of new variants. Despite widespread vaccination efforts, CPV remains one of the primary causes of acute gastroenteritis and death in young and juvenile dogs. Furthermore, the detection of CPV in swine populations has introduced additional challenges to its control. This review summarizes the current epidemiological status of CPV, highlighting recent advancements in diagnostic techniques and vaccine development. Additionally, it discusses the latest research on the pathogenesis of the virus and the development of antiviral agent research and proposes prevention and control suggestions for CPV under the One Health concept. In particular, there is a need to enhance surveillance of viral dynamics, accelerate the development of novel vaccines, and deepen the exploration of the underlying pathogenic mechanisms. This review aims to provide a scientific foundation for effective control of CPV and to guide future research directions.
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Affiliation(s)
- Hongzhuan Zhou
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
| | - Kaidi Cui
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 117004, China
| | - Xia Su
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
| | - Huanhuan Zhang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 117004, China
| | - Bing Xiao
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
| | - Songping Li
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 117004, China
| | - Bing Yang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (H.Z.); (K.C.); (X.S.); (H.Z.); (B.X.)
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SALTIK HS, KOÇ BT. First identification of canine parvovirus -2a/2b variant in unvaccinated domestic dogs with gastrointestinal signs in Türkiye. Vet Med Sci 2024; 10:e1523. [PMID: 38958584 PMCID: PMC11221316 DOI: 10.1002/vms3.1523] [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: 01/05/2024] [Revised: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Canine parvovirus type 2 (CPV-2) is the most common enteric virus that infects canids. CPV is the causative agent of a contagious disease defined mostly by clinical gastrointestinal signs in dogs. During the late 1970s, CPV-2 emerged as a new virus capable of infecting domestic dogs and growing across the world. The VP2 gene stands out as a key determinant in the pathogenicity, antigenicity, and host interactions of CPV-2. AIMS The molecular characterization of the VP2 gene is crucial for understanding CPV evolution and epidemiology. MATERIALS & METHODS Genes encoding the VP2 protein were sequenced and compared to reference strains worldwide. The maximum likelihood method was used to build a phylogenetic tree using CPV VP2 gene nucleotide sequences. RESULTS Our phylogenetic analysis of the VP2 gene revealed that five strains were very similar and clustered together, and three strains were in the 2b clade, whereas the other two were in the 2a/2b clade. DISCUSSION This paper reports the molecular characterization of two novel CPV-2a/2b subtypes in dogs with gastrointestinal symptoms. Genetic analysis was conducted on a CPV genomic region encompassing one of the open reading frames (ORFs) encoding the structural protein VP2. Sequence analysis indicates new and unreported sequence changes, mainly affecting the VP2 gene, which includes the mutations Ser297Ala and Leu87Met. This study represents the first evidence of a new CPV-2a/2b subtype in Türkiye. Due to VP2's crucial role in encoding the capsid protein of CPV-2 and its significant involvement in the host-virus interaction, it is critical to closely monitor its evolutionary changes and be cautious while searching for novel or pre-existing subtypes. CONCLUSION This study highlights the significance of continuous molecular research for acquiring more insights on the circulation of novel CPV mutants.
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Affiliation(s)
- Hasbi Sait SALTIK
- Department of VirologyFaculty of Veterinary MedicineBurdur Mehmet Akif Ersoy UniversityBurdurTürkiye
| | - B Taylan KOÇ
- Department of VirologyFaculty of Veterinary MedicineAydın Adnan Menderes UniversityAydınTürkiye
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Hussain M, Khan HN, Abbas S, Ali A, Aslam MN, Awan FR. Tetra-ARMS-PCR assay development for genotyping of AGT rs699 T/C polymorphism, its comparison with PCR-RFLP and application in a case-control association study of cardiovascular disease patients. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-16. [PMID: 36815563 DOI: 10.1080/15257770.2023.2181972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Genetic variations in the AGT gene play a significant role in controlling the plasma concentration of angiotensinogen (precursor protein of bioactive octapeptide angiotensin II) and the efficacy of antihypertensive drugs. In the current study, Tetra-Amplification Refractory Mutation System-Polymerase Chain Reaction (T-ARMS-PCR) was developed for genotyping of AGT rs699 T/C polymorphism and validated through Sanger DNA sequencing. Its efficiency was also tested using 474 human DNA samples [control, n = 181; cardiovascular disease (CVD) patients, n = 293]. Results showed that T-ARMS-PCR is superior to the commonly used PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). Statistical analysis revealed that the AGT rs699 CC genotype is more prevalent in the CVD patient group (37% vs. 28%) and AGT rs699 C allele and CC genotype increased the risk of CVD by 1.4 and 1.9 fold, respectively. In summary, T-ARMS-PCR is the most suitable approach for quick and efficient genotyping of AGT rs699 T/C polymorphism in a large population in resource-limited countries, Furthermore, AGT rs699 T/C polymorphism is associated with the risk of CVD in the Punjabi Pakistani population.
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Affiliation(s)
- Misbah Hussain
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Department of Biotechnology, University of Sargodha, Sargodha, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan
| | - Haq Nawaz Khan
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan.,Department of Biological & Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Ansar Ali
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Fazli Rabbi Awan
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan
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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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Dema A, Tallapally MR, Ganji VK, Buddala B, Kodi H, Ramidi A, Yella NR, Putty K. A comprehensive molecular survey of viral pathogens associated with canine gastroenteritis. Arch Virol 2023; 168:36. [PMID: 36609588 PMCID: PMC9825073 DOI: 10.1007/s00705-022-05674-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/17/2022] [Indexed: 01/09/2023]
Abstract
Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been conducted. In this study, 475 rectal swabs collected over three years (2018-2021) from clinical canine gastroenteritis cases were screened for the presence of six major enteric viruses - canine parvovirus 2 (CPV-2), canine distemper virus (CDV), canine adenovirus 2 (CAdV-2), canine coronavirus (CCoV), canine astrovirus (CaAstV), and canine rotavirus (CRV) - by real-time PCR. The most frequently detected virus was CPV-2, which was present in 64.8% of the samples (subtype 2a, 21.1%; 2b, 77.4%; 2c, 1.5%), followed by CDV (8%), CaAstV (7.2%), CCoV (5.9%), and CAdV-2 (4.6%). Two to four of these viruses in different combinations were found in 16.8% of the samples, and CRV was not detected. The complete genome sequences of Indian isolates of CDV, CCoV, and CaAstV were determined for the first time, and phylogenetic analysis was performed. This study highlights the need for routine prophylactic vaccination with the appropriate vaccines. Notably, 70.3% of animals vaccinated with DHPPiL were found to be positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial for addressing vaccination failures.
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Affiliation(s)
- Anusha Dema
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Mounika Reddy Tallapally
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Vishweshwar Kumar Ganji
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Bhagyalakshmi Buddala
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Haritha Kodi
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Ashwini Ramidi
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Narasimha Reddy Yella
- grid.506065.0Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030 India
| | - Kalyani Putty
- Department of Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendranagar, Hyderabad, 500030, India.
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