1
|
Magouz A, El-Kon I, Raya-Álvarez E, Khaled E, Alkhalefa N, Alhegaili AS, El-khadragy MF, Agil A, Elmahallawy EK. Molecular typing of canine parvovirus type 2 by VP2 gene sequencing and restriction fragment length polymorphism in affected dogs from Egypt. Front Microbiol 2023; 14:1254060. [PMID: 38143867 PMCID: PMC10740174 DOI: 10.3389/fmicb.2023.1254060] [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: 07/06/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Canine parvovirus-2 (CPV-2) is one of the most common infectious diseases in dogs characterized by severe gastroenteritis, vomiting, and bloody diarrhea. Little information is available about this topic in Egypt, particularly in the Delta region. This study reports the prevalence and molecular analysis of CPV-2 variants collected from El-Gharbia and Kafrelsheikh governorates in the Delta of Egypt. Methods In this study, 320 rectal swabs were collected from infected domestic dogs from two districts in delta Egypt. The samples were investigated by rapid immunochromatographic test and polymerase chain reaction for detection the prevalence of CPV-2 variants. The genetic characterization was performed using restriction fragment length polymorphism (RFLP) analysis and partial VP2 gene sequence. Results and discussion The viral antigen was detected in (264/320, 82.5%) of samples by IC test, while PCR was found more sensitive by detecting (272/320, 85%) positive samples. The RFLP technique using MboII restriction enzyme was successfully used for the differentiation of CPV-2c antigenic variants from CPV-2a/2b strains. Interestingly, the molecular and phylogenetic analysis revealed that both CPV-2a and CPV-2c are circulating in the study area. Deduced amino acid sequence analysis showed changes at residue (N426E) and residue (T440A).: Our results indicated that CPV-2 is prevalent among dogs in Egypt, and therefore further molecular and epidemiological studies of CPV-2 are warranted.
Collapse
Affiliation(s)
- Asmaa Magouz
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ismail El-Kon
- Department of Gynaecology, Obstetrics and Artificial Insemination, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | | | - Enas Khaled
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Noura Alkhalefa
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Alaa S. Alhegaili
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Manal F. El-khadragy
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahmad Agil
- Department of Pharmacology, Biohealth Institute Granada (IBs Granada) and Neuroscience Institute, School of Medicine, University of Granada, Granada, Spain
| | - Ehab Kotb Elmahallawy
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
- Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| |
Collapse
|
2
|
Phongroop K, Rattanasrisomporn J, Tangtrongsup S, Rungsipipat A, Piewbang C, Techangamsuwan S. High-resolution melting analysis for simultaneous detection and discrimination between wild-type and vaccine strains of feline calicivirus. Vet Q 2023; 43:1-12. [PMID: 37851857 PMCID: PMC11003490 DOI: 10.1080/01652176.2023.2272188] [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: 04/10/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
High-resolution melting (HRM) analysis, a post-polymerase chain reaction (PCR) application in a single closed tube, is the straightforward method for simultaneous detection, genotyping, and mutation scanning, enabling more significant dynamic detection and sequencing-free turnaround time. This study aimed to establish a combined reverse-transcription quantitative PCR and HRM (RT-qPCR-HRM) assay for diagnosing and genotyping feline calicivirus (FCV). This developed method was validated with constructed FCV plasmids, clinical swab samples from living cats, fresh-frozen lung tissues from necropsied cats, and four available FCV vaccines. We performed RT-qPCR to amplify a 99-base pair sequence, targeting a segment between open reading frame (ORF) 1 and ORF2. Subsequently, the HRM assay was promptly applied using Rotor-Gene Q® Software. The results significantly revealed simultaneous detection and genetic discrimination between commercially available FCV vaccine strains, wild-type Thai FCV strains, and VS-FCV strains within a single PCR reaction. There was no cross-reactivity with other feline common viruses, including feline herpesvirus-1, feline coronavirus, feline leukemia virus, feline immunodeficiency virus, and feline morbillivirus. The detection limit of the assay was 6.18 × 101 copies/µl. This study, therefore, is the first demonstration of the uses and benefits of the RT-qPCR-HRM assay for FCV detection and strain differentiation in naturally infected cats.
Collapse
Affiliation(s)
- Kannika Phongroop
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Companion Animal and Wildlife Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Thailand
| | - Jatuporn Rattanasrisomporn
- Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Sahatchai Tangtrongsup
- Department of Companion Animal and Wildlife Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Thailand
- Research Center of Producing and Development of Products and Innovations for Animal Health and Production, Chiang Mai University, Thailand
| | - Anudep Rungsipipat
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
3
|
Ferreira BIDS, da Silva-Gomes NL, Coelho WLDCNP, da Costa VD, Carneiro VCDS, Kader RL, Amaro MP, Villar LM, Miyajima F, Alves-Leon SV, de Paula VS, Leon LAA, Moreira OC. Validation of a novel molecular assay to the diagnostic of COVID-19 based on real time PCR with high resolution melting. PLoS One 2021; 16:e0260087. [PMID: 34807915 PMCID: PMC8608302 DOI: 10.1371/journal.pone.0260087] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/03/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of the COVID-19 pandemic resulted in an unprecedented need for RT-qPCR-based molecular diagnostic testing, placing a strain on the supply chain and the availability of commercially available PCR testing kits and reagents. The effect of limited molecular diagnostics-related supplies has been felt across the globe, disproportionally impacting molecular diagnostic testing in developing countries where acquisition of supplies is limited due to availability. The increasing global demand for commercial molecular diagnostic testing kits and reagents has made standard PCR assays cost prohibitive, resulting in the development of alternative approaches to detect SARS-CoV-2 in clinical specimens, circumventing the need for commercial diagnostic testing kits while mitigating the high-demand for molecular diagnostics testing. The timely availability of the complete SARS-CoV-2 genome in the beginning of the COVID-19 pandemic facilitated the rapid development and deployment of specific primers and standardized laboratory protocols for the molecular diagnosis of COVID-19. An alternative method offering a highly specific manner of detecting and genotyping pathogens within clinical specimens is based on the melting temperature differences of PCR products. This method is based on the melting temperature differences between purine and pyrimidine bases. Here, RT-qPCR assays coupled with a High Resolution Melting analysis (HRM-RTqPCR) were developed to target different regions of the SARS-CoV-2 genome (RdRp, E and N) and an internal control (human RNAse P gene). The assays were validated using synthetic sequences from the viral genome and clinical specimens (nasopharyngeal swabs, serum and saliva) of sixty-five patients with severe or moderate COVID-19 from different states within Brazil; a larger validation group than that used in the development to the commercially available TaqMan RT-qPCR assay which is considered the gold standard for COVID-19 testing. The sensitivity of the HRM-RTqPCR assays targeting the viral N, RdRp and E genes were 94.12, 98.04 and 92.16%, with 100% specificity to the 3 SARS-CoV-2 genome targets, and a diagnostic accuracy of 95.38, 98.46 and 93.85%, respectively. Thus, HRM-RTqPCR emerges as an attractive alternative and low-cost methodology for the molecular diagnosis of COVID-19 in restricted-budget laboratories.
Collapse
Affiliation(s)
- Beatriz Iandra da Silva Ferreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Natália Lins da Silva-Gomes
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | - Rafael Lopes Kader
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa Pimentel Amaro
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lívia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Fábio Miyajima
- Oswaldo Cruz Foundation (Fiocruz), Branch Ceará, Eusebio, Brazil
| | - Soniza Vieira Alves-Leon
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Luciane Almeida Amado Leon
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Otacilio Cruz Moreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| |
Collapse
|
4
|
Simultaneous detection of feline parvovirus and feline bocavirus using SYBR Green I-based duplex real-time polymerase chain reaction. 3 Biotech 2021; 11:400. [PMID: 34377624 PMCID: PMC8343365 DOI: 10.1007/s13205-021-02947-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022] Open
Abstract
Since both feline parvovirus (FPV) and feline bocavirus (FBoV) can cause diarrhea in cats, it is difficult to distinguish them clinically. This study aimed to develop a SYBR Green I-based duplex real-time polymerase chain reaction (PCR) assay for distinguishing FPV and FBoV-1 on the basis of the melting temperature of the PCR product. A total of 132 fecal samples from different domestic and feral cats were collected, and the results of SYBR Green I-based duplex real-time PCR assay were compared with those of the traditional PCR assay for a comprehensive evaluation. The melting temperatures were found to be 86 °C and 77.5 °C for FBoV-1 and FPV, respectively, and no specific melting peaks for other non-targeted feline viruses were observed. The data obtained from this assay had a good linear relationship; the detection limits of FPV and FBoV-1 were 2.907 × 101 copies/μL and 3.836 × 101 copies/μL, respectively. In addition, the experiment exhibited high reproducibility. The positive detection rates of the SYBR Green I-based duplex real-time PCR assay for FPV and FBoV-1 were 16.67% (22/132) and 6.82% (9/132), respectively, and the positive detection rate for co-infection with FPV and FBoV-1 was 3.03% (4/132). This result was much more sensitive than that of the traditional PCR method. Thus, the developed SYBR Green I-based assay is a sensitive, rapid, specific, and reliable method for the clinical diagnosis of FPV and FBoV-1 and can provide technical support for the simultaneous detection of co-infection with these viruses in the future.
Collapse
|
5
|
Xu S, Qiu X, Hou X, Zhou H, Chen D, Wang X, Han L, Li D, Sun L, Ji X, Li M, Zhang J, Li M, Li Z. Direct detection of Corynebacterium striatum, Corynebacterium propinquum, and Corynebacterium simulans in sputum samples by high-resolution melt curve analysis. BMC Infect Dis 2021; 21:21. [PMID: 33413116 PMCID: PMC7788810 DOI: 10.1186/s12879-020-05633-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pulmonary infections caused by non-diphtheriae corynebacteria are increasing. However, rapid identification of Corynebacterium species poses a challenge due to the low genetic variation within the genus. METHODS Three reference strains and 99 clinical isolates were used in this study. A qPCR followed by high-resolution melting (HRM) targeting ssrA was performed to simultaneously identify C. striatum, C. propinquum and C. simulans. To further evaluate this assay's performance, 88 clinical sputum samples were tested by HRM and the detection results were compared with those of the traditional culture method and multiple cross-displacement amplification (MCDA) assay. RESULTS The melting curve produced by a pair of universal primers generated species-specific HRM curve profiles and could distinguish the three target species from other related bacteria. The limit of detection of HRM assay for DNA from the three purified Corynebacterium species was 100 fg. Compared with the culture method, HRM detected 22 additional positive specimens, representing a 23.9% relative increase in detection rate. The HRM assay had 98.4% (95% confidence interval [CI], 90.5-99.9%) sensitivity and 100% (95% CI, 82.8-100%) specificity. Additionally, 95.5% concordance between HRM and MCDA (κ = 0.89 [95% CI, 0.79-0.99]) was noted. CONCLUSIONS The HRM assay was a simple, rapid, sensitive, and specific diagnostic tool for detecting C. striatum, C. propinquum, and C. simulans, with the potential to contribute to early diagnosis, epidemiological surveillance, and rapid response to outbreak.
Collapse
Affiliation(s)
- Shuai Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaotong Qiu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuexin Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongke Chen
- Department, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Xuebing Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lichao Han
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lina Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xingzhao Ji
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingshan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengtong Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
6
|
Hou J, Li Y, Ma C, Shi C. Accelerated denaturation bubble-mediated strand exchange amplification for rapid and accurate detection of canine parvovirus. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5514-5522. [PMID: 33164005 DOI: 10.1039/d0ay01751e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Canine parvovirus (CPV), a strong infectious canine pathogen, has been recognized as a threat to canine health worldwide since the 1970s. Although convenient detection methods have been developed, such as the colloidal gold test strip, most of these methods are based on antibody detection, which is relatively ineffective for detecting pathogens during the incubation period. For institutions and businesses with many dogs, e.g., dog training centers and kennels, more sensitive detection methods are required to prevent the swift spread of CPV. Thus, we developed accelerated denaturation bubble-mediated strand exchange amplification (ASEA) for CPV detection, and it is a rapid, convenient, and cost-effective method. ASEA was able to distinguish CPV genomic DNA in a mixture that included canine genomic DNA as well as nucleic acids sourced from nine other common pathogens, with detection of target DNA as low as 8.0 × 10-18 M within 16.6 min. Coupled with the thermal lysis method modified by us that only requires 3 min to perform, the entire detection procedure can be completed within approximately 20 min and only requires a simple heating block and an ordinary fluorescence PCR instrument. Moreover, ASEA exhibited greater sensitivity than colloidal gold test strips in actual specimen detection. This technique is rapid, easy to perform, and highly sensitive, and therefore, this approach has the potential to rapidly detect CPV in institutions with large populations of dogs.
Collapse
Affiliation(s)
- Jie Hou
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China.
| | | | | | | |
Collapse
|