Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015
Fanos Woldemariyam,1,2 Jan Paeshuyse1 1Laboratory of Host-Pathogen Interaction, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Leuven, Belgium; 2Department of Biomedical Sciences, College of Veterinary Medicine, Addis Ababa University, Bishoftu, EthiopiaCorresp...
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Dove Medical Press
2023-05-01
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| Series: | Veterinary Medicine: Research and Reports |
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| Online Access: | https://www.dovepress.com/viral-protein-1-vp1-sequence-based-genetic-diversity-of-sat-2-fmdv-cir-peer-reviewed-fulltext-article-VMRR |
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| author | Woldemariyam F Paeshuyse J |
| author_facet | Woldemariyam F Paeshuyse J |
| author_sort | Woldemariyam F |
| collection | DOAJ |
| description | Fanos Woldemariyam,1,2 Jan Paeshuyse1 1Laboratory of Host-Pathogen Interaction, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Leuven, Belgium; 2Department of Biomedical Sciences, College of Veterinary Medicine, Addis Ababa University, Bishoftu, EthiopiaCorrespondence: Jan Paeshuyse; Fanos Woldemariyam, Email jan.paeshuyse@kuleuven.be; fanos.tadesse@aau.edu.etIntroduction: Pathogen molecular epidemiology determines the origin of specific outbreaks locality of foot-and-mouth disease virus serotype South African Territories-2 sequence-based analysis of highly variable Viral Protein 1 (VP1), which helps to identify the evolution of this virus through time and space. The objective of this study was to compare the differences between SAT-2 VP1 sequences of FMDV circulated in Ethiopia from 1990 to 2015 at the genetic level.Methods: The nucleotide and amino acid sequences were analyzed using Basic Local Alignment Search Tools (BLAST), Multiple sequence alignment and sequence editing and Phylogenetic tree reconstruction. The nucleotide and amino acid sequences alignment, distance matrix, and phylogenetic tree constructions were done using the MEGA 6.0 software package.Result and Discussion: In this analysis, we found 76% nucleotide identities and amino acid similarities among the sequences. The overall group mean distance at nucleotide level was 19% with a mean intra-population diversity of 2%. The lowest sequence variation was observed among sequences obtained from the years 2007/09/10, 2014/15, and 1990/91 which was less than 5% among them. This analysis revealed that in the last 25 years, four different topotypes of the FMDV SAT-2 were circulating in Ethiopia. The Arg-Gly-Asp (RGD) amino acid (AA) motif at AA position 144– 146 within the G-H loop of the VP1 protein of FMDV is conserved, but up- and downstream hyper-variable AA sequences are identified. In this study, it was observed that four topotypes (IV, XIV, XIII, and VII) were circulating in Ethiopia for 25 years. Further, compared with sequences from neighboring countries (Sudan, Kenya) confirmed the presence of these topotypes.Conclusion: Pertinent to this genetic diversity control strategies in Ethiopia should be based on having regular antigenic and genetic vaccine matching tests with the circulating strain within a defined period, space, transboundary nature of the disease and applying biosecurity measures.Keywords: amino acid, Ethiopia, FMDV, genetic diversity, nucleotide, SAT-2, viral protein |
| first_indexed | 2024-03-13T09:33:35Z |
| format | Article |
| id | doaj.art-9773ac59a2394835b2a095865dde5cc7 |
| institution | Directory Open Access Journal |
| issn | 2230-2034 |
| language | English |
| last_indexed | 2024-03-13T09:33:35Z |
| publishDate | 2023-05-01 |
| publisher | Dove Medical Press |
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| series | Veterinary Medicine: Research and Reports |
| spelling | doaj.art-9773ac59a2394835b2a095865dde5cc72023-05-25T18:06:00ZengDove Medical PressVeterinary Medicine: Research and Reports2230-20342023-05-01Volume 149110183979Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015Woldemariyam FPaeshuyse JFanos Woldemariyam,1,2 Jan Paeshuyse1 1Laboratory of Host-Pathogen Interaction, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Leuven, Belgium; 2Department of Biomedical Sciences, College of Veterinary Medicine, Addis Ababa University, Bishoftu, EthiopiaCorrespondence: Jan Paeshuyse; Fanos Woldemariyam, Email jan.paeshuyse@kuleuven.be; fanos.tadesse@aau.edu.etIntroduction: Pathogen molecular epidemiology determines the origin of specific outbreaks locality of foot-and-mouth disease virus serotype South African Territories-2 sequence-based analysis of highly variable Viral Protein 1 (VP1), which helps to identify the evolution of this virus through time and space. The objective of this study was to compare the differences between SAT-2 VP1 sequences of FMDV circulated in Ethiopia from 1990 to 2015 at the genetic level.Methods: The nucleotide and amino acid sequences were analyzed using Basic Local Alignment Search Tools (BLAST), Multiple sequence alignment and sequence editing and Phylogenetic tree reconstruction. The nucleotide and amino acid sequences alignment, distance matrix, and phylogenetic tree constructions were done using the MEGA 6.0 software package.Result and Discussion: In this analysis, we found 76% nucleotide identities and amino acid similarities among the sequences. The overall group mean distance at nucleotide level was 19% with a mean intra-population diversity of 2%. The lowest sequence variation was observed among sequences obtained from the years 2007/09/10, 2014/15, and 1990/91 which was less than 5% among them. This analysis revealed that in the last 25 years, four different topotypes of the FMDV SAT-2 were circulating in Ethiopia. The Arg-Gly-Asp (RGD) amino acid (AA) motif at AA position 144– 146 within the G-H loop of the VP1 protein of FMDV is conserved, but up- and downstream hyper-variable AA sequences are identified. In this study, it was observed that four topotypes (IV, XIV, XIII, and VII) were circulating in Ethiopia for 25 years. Further, compared with sequences from neighboring countries (Sudan, Kenya) confirmed the presence of these topotypes.Conclusion: Pertinent to this genetic diversity control strategies in Ethiopia should be based on having regular antigenic and genetic vaccine matching tests with the circulating strain within a defined period, space, transboundary nature of the disease and applying biosecurity measures.Keywords: amino acid, Ethiopia, FMDV, genetic diversity, nucleotide, SAT-2, viral proteinhttps://www.dovepress.com/viral-protein-1-vp1-sequence-based-genetic-diversity-of-sat-2-fmdv-cir-peer-reviewed-fulltext-article-VMRRamino acidethiopiafmdvgenetic diversitynucleotidesat-2viral protein |
| spellingShingle | Woldemariyam F Paeshuyse J Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 Veterinary Medicine: Research and Reports amino acid ethiopia fmdv genetic diversity nucleotide sat-2 viral protein |
| title | Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 |
| title_full | Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 |
| title_fullStr | Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 |
| title_full_unstemmed | Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 |
| title_short | Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015 |
| title_sort | viral protein 1 vp1 sequence based genetic diversity of sat 2 fmdv circulating in ethiopia from 1990 to 2015 |
| topic | amino acid ethiopia fmdv genetic diversity nucleotide sat-2 viral protein |
| url | https://www.dovepress.com/viral-protein-1-vp1-sequence-based-genetic-diversity-of-sat-2-fmdv-cir-peer-reviewed-fulltext-article-VMRR |
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