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Lachheb J, Bouslama Z, Nsiri J, Badr C, Al Gallas N, Souissi N, Khazri I, Larbi I, Kaboudi K, Ghram A. Phylogenetic and phylodynamic analyses of subtype-B metapneumovirus from chickens in Tunisia. Poult Sci 2022; 102:102253. [PMID: 36455491 PMCID: PMC9712995 DOI: 10.1016/j.psj.2022.102253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/01/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Swollen Head Syndrome (SHS) is an economically important viral disease of chickens caused by avian metapneumovirus (aMPV). The virus comprises 6 different subtypes (A,B,C,D, New-1 and New-2). To date, no information was available on the presence of the virus in Tunisian poultry. The present work aims to detect the presence of (aMPV) in broiler chicken in Tunisia, then to characterise the isolates in order to determine their subtype and to estimate their geographic origin of introduction. A total of 289 samples were collected, aMPV detection was detected by real time RT-PCR and molecular characterization was warried out by Sanger sequencing on the glycoprotein (G) gene. Phylogenetic analysis was carried out using Beast 2 software. Out of the 289 samples, 21 were revealed positive to aMPV. Only 2 isolates have been confirmed by sequencing analysis ; one isolate sampled in 2015 and another in 2019. Based on the partial G gene sequence, analysis of these 2 Tunisian isolates showed that they belong to subtype B. The isolate sampled in 2015, appeared to be phylogenetically related to derived vaccine strain. However, the one sampled in 2019 appeared to be a field strain. Phylodynamic analysis provided evidence that this field strain derived from a Spanish strain and probably the virus has been introduced from Spain to North Africa back in 2016. This study is the first that highlighted the circulation of (aMPV) in Tunisia. It is possible that aMPV has been circulating in Tunisia and neighboring countries without being detected. Also, multiple strains could be present and therefore multiple introductions have happened. Through this study, we shed the light on the importance of reinforcing farms biosecurity as well as virological surveillance.
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Affiliation(s)
- Jihene Lachheb
- Laboratory of Epidemiology and Veterinary Microbiology, LR 11 IPT 03, Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia.
| | - Zied Bouslama
- Laboratory of Viruses, Vectors and Hosts, LR20 IPT 02 Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology, LR 11 IPT 03, Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia
| | - Chaima Badr
- Laboratory of Epidemiology and Veterinary Microbiology, LR 11 IPT 03, Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia
| | - Nazek Al Gallas
- Food and Water Control Laboratory, National Center for Salmonella, Shigella, and Vibriospp. Institut Pasteur de Tunis, Tunisia
| | - Nada Souissi
- Veterinary Research Institute of Tunis (IRVT), Tunisia
| | - Imed Khazri
- Veterinary Research Institute of Tunis (IRVT), Tunisia
| | - Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology, LR 11 IPT 03, Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia
| | - Khaled Kaboudi
- Department of Poultry Farming and Pathology, National Veterinary Medicine School, Sidi Thabet, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR 11 IPT 03, Institut Pasteur de Tunis, Université de Tunis El Manar (UTM), Tunisia
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Bouslama Z, Kharmachi H, Basdouri N, Ben Salem J, Ben Maiez S, Handous M, Saadi M, Ghram A, Turki I. Molecular Epidemiology of Rabies in Wild Canidae in Tunisia. Viruses 2021; 13:v13122473. [PMID: 34960742 PMCID: PMC8703460 DOI: 10.3390/v13122473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/25/2022] Open
Abstract
Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.
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Affiliation(s)
- Zied Bouslama
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
- Faculty of Sciences, Université Tunis El Manar, Tunis 2092, Tunisia
- Correspondence:
| | - Habib Kharmachi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Nourhene Basdouri
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Jihen Ben Salem
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Samia Ben Maiez
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mariem Handous
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mohamed Saadi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Abdeljalil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR 16 IPT 03, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 2092, Tunisia;
| | - Imed Turki
- Service des Maladies Contagieuses, Ecole Nationale de Médecine Vétérinaire-Sidi Thabet, Université Manouba, Sidi Thabet 2020, Tunisia;
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Othman H, Bouslama Z, Brandenburg JT, da Rocha J, Hamdi Y, Ghedira K, Srairi-Abid N, Hazelhurst S. Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochem Biophys Res Commun 2020; 527:702-708. [PMID: 32410735 PMCID: PMC7221370 DOI: 10.1016/j.bbrc.2020.05.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 11/23/2022]
Abstract
The spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2.
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Affiliation(s)
- Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Zied Bouslama
- Laboratory of Veterinary Epidemiology and Microbiology LR16IPT03, Institut Pasteur of Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Najet Srairi-Abid
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT08 Venins et Biomolécules Thérapeutiques, 1002, Tunis, Tunisia
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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Picot V, Rasuli A, Abella-Rider A, Saadatian-Elahi M, Aikimbayev A, Barkia A, Benmaiz S, Bouslama Z, De Balogh K, Dehove A, Davlyatov F, Farahtaj F, Gongal G, Gholami A, Imnadze P, Issad M, Khoufi S, Nedosekov V, Rafila A, Rich H, Soufi A, Tuychiev J, Vranjes N, Vodopija R, Zaouia I, Nel L. The Middle East and Eastern Europe rabies Expert Bureau (MEEREB) third meeting: Lyon-France (7–8 April, 2015). J Infect Public Health 2017; 10:695-701. [DOI: 10.1016/j.jiph.2017.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/20/2017] [Accepted: 03/26/2017] [Indexed: 10/19/2022] Open
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