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El-Ansary RE, Kasem S, El-Tabakh MAM, Badr Y, Abdel-Moneim AS. Isolation, molecular characterization, and genetic diversity of recently isolated foot-and-mouth disease virus serotype A in Egypt. PLoS One 2023; 18:e0295319. [PMID: 38051725 DOI: 10.1371/journal.pone.0295319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/19/2023] [Indexed: 12/07/2023] Open
Abstract
Foot-and-mouth Disease (FMD) is a highly contagious viral disease affecting all hoof-cloven animals. Serotypes A, O and SAT 2 of the foot-and-mouth disease virus (FMDV) are circulating in Egypt. The present study aimed to identify and molecularly characterize the FMDV strains circulating in Northern Egypt during an epidemic that struck the nation in 2022. RNA was extracted from the epithelial specimens, vesicular fluid from affected cattle. The samples were screened using real-time reverse-transcription polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene. Positive samples underwent individual serotype-specific amplification using primers designed for VP1 of O, A, and SAT 2 serotypes. Subsequently, direct sequencing was performed on the positive samples. The real-time RT-PCR detected positive samples from epithelial and vesicular fluid samples, but not in the blood of infected animals. Out of the 16 samples, seven tested positive for FMDV serotype A. Of these seven positive samples, six were categorized as serotype A-African topotype-G-IV, and these positive samples were isolated in BHK-21 cells, yielding an overt cytopathic effect caused by the virus. In conclusion, it is necessary to sustain continuous surveillance of the evolution of circulating FMDV strains to facilitate the assessment and aid in the selection of vaccine strains for the effective control of FMDV in Egypt.
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Affiliation(s)
- Ramy E El-Ansary
- Faculty of Science, Zoology and Entomology Department, Al-Azhar University, Cairo, Egypt
| | - Samy Kasem
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, El Geish Street, Kafrelsheikh, Egypt
| | - Mohamed A M El-Tabakh
- Faculty of Science, Zoology and Entomology Department, Al-Azhar University, Cairo, Egypt
| | - Yassien Badr
- Faculty of Veterinary Medicine, Department of Animal Medicine (Infectious Diseases Division), Damanhour University, Damanhour, El-Beheira, Egypt
| | - Ahmed S Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
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2
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Cui X, Xia D, Huang X, Sun Y, Shi M, Zhang J, Li G, Yang Y, Wang H, Cai X, An T. Analysis of Recombinant Characteristics Based on 949 PRRSV-2 Genomic Sequences Obtained from 1991 to 2021 Shows That Viral Multiplication Ability Contributes to Dominant Recombination. Microbiol Spectr 2022; 10:e0293422. [PMID: 36073823 PMCID: PMC9602502 DOI: 10.1128/spectrum.02934-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 01/04/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases affecting the pig-raising industry. The PRRS virus (PRRSV) has high genetic diversity, partly owing to viral recombination. Some individual recombinant type 2 PRRSV (PRRSV-2) strains have been detected; however, the sequence composition characteristics of recombination hot spots and potential driving forces for recombinant PRRSV-2 are still unreported. Therefore, all available genomic sequences of PRRSV-2 (n = 949, including 29 genomes sequenced in this study) from 11 countries from 1991 to 2021 were collected and analyzed. The results revealed that the dominant major recombinant parent has been converted from lineage 3 (L3) to L1 since 2012. The recombination hot spots were located at nucleotides (nt) 7900 to 8200 (in NSP9, encoding viral RNA-dependent RNA polymerase) and nt 12500 to nt 13300 (in ORF2-ORF4, mean ORF2 to ORF4); no AU-rich characteristics were found in the recombination hot spots. Based on infectious clones of L1 and L8 PRRSV-2, recombinant PRRSVs were generated by switching complete or partial NSP9 (harboring the recombination hot spot). The results showed that recombinant PRRSVs based on the L1 backbone, but not the L8 backbone, acquired a higher replication capacity in pig primary alveolar macrophages. These findings will help to understand the reason behind the dominance of L1-based recombination in PRRSV-2 strains and provide new clues for an in-depth study of the recombination mechanism of PRRSV-2. IMPORTANCE Recombination is an important driver of the genetic shifts that are tightly linked to the evolution of RNA viruses. Viral recombination contributes substantially to the emergence of new variants, alterations in virulence, and pathogenesis. PRRSV is genetically diverse, partly because of extensive recombination. In this study, we analyzed interlineage recombination based on available genomic sequences of PRRSV-2 from 1991 to 2021. The study revealed the temporal and geographical distribution of recombinant PRRSVs and the recombination hot spot's location and showed that artificially constructed recombinant PRRSVs (harboring a high-frequency region) had more viral genomic copies than their parental virus, indicating that dominant recombination was shaped by a tendency to benefit viral replication. This finding will enrich our understanding of PRRSV recombination and provide new clues for an in-depth study of the recombination mechanism.
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Affiliation(s)
- Xingyang Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dasong Xia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyi Huang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mang Shi
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Yongbo Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Haiwei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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El Bagoury GF, Elhabashy R, Mahmoud AH, Hagag NM, El Zowalaty ME. Development and evaluation of one-step real-time RT-PCR assay for improved detection of foot-and-mouth-disease virus serotypes circulating in Egypt. J Virol Methods 2022; 306:114525. [PMID: 35337855 DOI: 10.1016/j.jviromet.2022.114525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease (FMD) is an extremely contagious and economically important viral disease affecting livestock. Rapid and precise diagnosis of FMD is critical for efficient control and surveillance strategies of the disease. In this study, one-step real-time reverse transcription-polymerase chain reaction (RT-qPCR) assays using newly designed primers/probe sets in the conserved regions within the VP1 coding sequence were developed for specific detection of FMDV serotypes SAT 2 and O with their different lineage circulating in Egypt. The assays were validated for the efficacy to detect different lineages of these endemic serotypes in Egypt; the detection limit was 10 genomic copies for serotype SAT 2 and one genomic copy for serotype O, with no cross-reactivity observed. These findings were confirmed by the specific and sensitive detection of FMDV in clinical samples obtained from different regions in Egypt and representing a range of subtypes within the SAT 2 and O serotypes. The results illustrate the potential of tailored RT-qPCR tools for the rapid detection and serotyping of FMDV belonging to different lineages of serotypes SAT 2 and O circulating in Egypt with high sensitivity and specificity. The developed assays could be easily deployed for routine surveillance and hence improving the disease control measures.
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Affiliation(s)
- Gabr F El Bagoury
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Rawan Elhabashy
- Biotechnology Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt.
| | - Ayman H Mahmoud
- Biotechnology Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt.
| | - Mohamed E El Zowalaty
- Department of Microbiology and Immunology, Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida, 44813, Ash Sharqia, Egypt; Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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Hassan AM, Zaher MR, Hassanien RT, Abd-El-Moniem MI, Habashi AR, Ibraheem EM, Shahein MA, El Zowalaty ME, Hagag NM. Molecular detection, phylogenetic analysis and genetic diversity of recently isolated foot-and-mouth disease virus serotype A African topotype, Genotype IV. Virol J 2022; 19:1. [PMID: 34980196 PMCID: PMC8722054 DOI: 10.1186/s12985-021-01693-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 11/04/2021] [Indexed: 01/06/2023] Open
Abstract
Background Surveillance for circulating emerging diseases of economic importance has a major role in the rapid response to major pathogen outbreaks. Foot-and-mouth disease virus (FMDV) is one of the significant endemic viruses in Egypt. FMDV is periodically investigated for monitoring evolution and emergence of new variants. The genetic characterization of foot-and-mouth disease (FMD) virus serotype A responsible for recent outbreaks of FMD in Egypt was determined. Methods Samples were collected from different locations and virus isolation was performed using BHK-21 cells. Viral RNA was extracted and samples were screened for FMDV using real-time RT-PCR. DNA sequence analysis was performed and computational and bioinformatics analyses were used to determine the substitution rates and phylogenetic relationship. Results Sequence and phylogenetic analyses of full-length 1D region of FMDV samples collected from different governorates in 2020 showed close similarity to Egyptian FMDV strains from serotype A-African topotype-G-IV with genetic variation of 6.5%. Recently isolated FMDV strains showed high genetic variations from locally used vaccine strains in the major antigenic sites of VP1 region. Conclusions Although, efforts made by the veterinary authorities to implement an effective mass vaccination plan, the recently detected FMDV strains in this study could not be subtyped using the FMDV primers routinely used for molecular serotyping. These dissimilarities raise the alarm for reconsideration of the FMDV isolates used in vaccine manufacture. Clearly close monitoring of FMD in Egypt is urgently required to define the risks of future outbreaks and to ensure appropriate control measures against FMD major outbreaks. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01693-y.
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Affiliation(s)
- Ayah M Hassan
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Mostafa R Zaher
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Rabab T Hassanien
- Virology Research Department, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Mervat I Abd-El-Moniem
- Virology Research Department, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Ahmed R Habashi
- Virology Research Department, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Essam M Ibraheem
- Pathology Research Department, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Momtaz A Shahein
- Virology Research Department, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt
| | - Mohamed E El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75 123, Uppsala, Sweden.
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Center (ARC), Dokki, Giza, 12618, Egypt.
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Hassan AM, El-Mayet FS, El-Habbaa AS, Shahein MA, Zowalaty MEE, Hagag NM, Sharawi SSA. Molecular Characterization of newly emerging Foot-and-Mouth Disease Virus Serotype SAT2 of Lib-12 Lineage Isolated from Egypt. Virus Res 2021; 311:198651. [PMID: 34879242 DOI: 10.1016/j.virusres.2021.198651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/03/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
An outbreak of foot-and-mouth disease virus (FMDV) serotype SAT2 occurred in Egypt in 2018, which affected cattle and water buffalo. Previous phylogenetic studies on FMDV circulating in Egypt have mainly focused on genomic regions encoding structural proteins that determine the FMDV serotype. Still, none of them have analyzed the open reading frame (ORF) sequence of the Egyptian SAT2/Lib-12 lineage. The present study aimed to analyze and identify the ORF genome sequence of Lib-12 lineage that belongs to FMDV SAT2 topotype VII in Egypt. The protocol workflow was optimized and tested using a representative field isolate of FMDV/SAT2/Lib-12 from a bovine tongue sample collected in 2018 from Ismailia governorate (SAT2/EGY/Ismailia/2018). The protocol was based on reverse transcription polymerase chain reaction with multiple overlapping primers, amplicons sequencing, and assembly to complete the ORF consensus sequence. Alignments of the sequence fragments formed consensus genome sequence of 7219 nucleotides in length. The complete nucleotide sequence of the Egyptian isolate was related to Ethiopian, Nigerian, and Ghanaian strains, with identity not exceeding 95%. The divergence in the genetic identity of the Egyptian SAT2/Lib-12 lineage from other Egyptian strains and the neighboring Libyan isolates reached 7%, and this may be attributed to the absence of the Lib-12 lineage ORF sequence from Egypt and Libya in the database. The present study significantly advances the knowledge of the molecular analysis of FMDV SAT2 and the design of vaccine selection for FMDV SAT2 in Egypt. The study protocol could be applied to other FMDV serotypes.
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Affiliation(s)
- Ayah M Hassan
- Genome Research Unit, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Fouad S El-Mayet
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
| | - Ayman S El-Habbaa
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
| | - Momtaz A Shahein
- Virology Research Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Mohamed E El Zowalaty
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-75 123 Uppsala, Sweden
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Saad S A Sharawi
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
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Field Observations and Genetic Characterization of Sheep-Associated Malignant Catarrhal Fever in Egypt, 2018. Vet Sci 2020; 7:vetsci7040201. [PMID: 33322397 PMCID: PMC7768452 DOI: 10.3390/vetsci7040201] [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: 11/05/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 11/29/2022] Open
Abstract
Ovine gammaherpesvirus-2 (OvHV-2) causes a lethal disease in cattle and some wild ruminants called malignant catarrhal fever (MCF), which affects the epithelial and lymphoid tissues of the respiratory and digestive tracts and has an important impact on the livestock industry. In this study, MCF was diagnosed in 18 of 427 cattle from different sites in Egypt by its typical clinical signs, found in all 18 animals: corneal opacity, fever, erosions in the buccal cavity, lymphadenitis, and purulent nasal discharge. All affected cattle had been reared in contact with clinically inconspicuous sheep. Of the 18 clinically ill cattle, 13 succumbed to the disease, resulting in estimated morbidity and case fatality rates of 4.2% and 72.2%, respectively. Five samples collected from the affected cattle were positive for OvHV-2 by real-time PCR and were used for sequencing of an 832-bp fragment of the ORF27/gp48 gene. The ORF27 nucleotide sequence of all Egyptian samples was identical, but distinct from viruses found in other parts of Africa and the Mediterranean.
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