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Larbi I, Arbi M, Souiai O, Tougorti H, Butcher GD, Nsiri J, Badr C, Behi IE, Lachhab J, Ghram A. Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia. Virus Res 2024; 344:199348. [PMID: 38467378 PMCID: PMC10995884 DOI: 10.1016/j.virusres.2024.199348] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections. The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.
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Affiliation(s)
- Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia.
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Halima Tougorti
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Gary David Butcher
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Chaima Badr
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Jihene Lachhab
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
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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: 2] [Impact Index Per Article: 1.0] [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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Badr C, Souiai O, Arbi M, El Behi I, Essaied MS, Khosrof I, Benkahla A, Chabchoub A, Ghram A. Epidemiological and Phylogeographic Study of Equid Herpesviruses in Tunisia. Pathogens 2022; 11:pathogens11091016. [PMID: 36145448 PMCID: PMC9504996 DOI: 10.3390/pathogens11091016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/27/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incidence of EHVs, the genetic characterization of Tunisian isolates and a spatiotemporal study, using 298 collected samples from diseased and clinically healthy horses. The global incidence of EHV infection was found to be about 71.81%. EHV2 and EHV5 were detected in 146 (48.99%) and 159 (53.35%) sampled horses, respectively. EHV1 was detected in 11 samples (3.69%); EHV4 was not detected. Co-infections with EHV1-EHV2, EHV1-EHV5 and EHV2-EHV5 were observed in 0.33%, 1.34% and 31.54% of tested horses, respectively. Phylogenetic analyses showed that gB of EHV2 and EHV5 displays high genetic diversity with a nucleotide sequence identity ranging from 88 to 100% for EHV2 and 97.5 to 100% for EHV5. Phylogeography suggested Iceland and USA as the most likely countries of origin of the Tunisian EHV2 and EHV5 isolates. These viruses detected in Tunisia seemed to be introduced in the 2000s. This first epidemiological and phylogeographic study is important for better knowledge of the evolution of equid herpesvirus infections in Tunisia.
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Affiliation(s)
- Chaima Badr
- Laboratory of Epidemiology and Microbiology Veterinary (LR19IPT03), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
- Correspondence:
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Microbiology Veterinary (LR19IPT03), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed S. Essaied
- National School of Veterinary Medicine, Sidi Thabet, University of Manouba, La Manouba 2010, Tunisia
| | - Ines Khosrof
- National School of Veterinary Medicine, Sidi Thabet, University of Manouba, La Manouba 2010, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Ahmed Chabchoub
- National School of Veterinary Medicine, Sidi Thabet, University of Manouba, La Manouba 2010, Tunisia
- Laboratory of Viruses, Vectors and Hosts (LR20IPT10), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Microbiology Veterinary (LR19IPT03), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
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Schemoul J, Belkacem A, Medina F, Chahour A, Diallo K, Jaafar D, Badr C, Émilie S, Caraux-Paz P, Raffetin A. Les polyarthromyalgies chez les patients consultant pour suspicion de borréliose de Lyme sont évocatrices de pathologies organiques ? Med Mal Infect 2020. [DOI: 10.1016/j.medmal.2020.06.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Diallo K, Medina F, Belkacem A, Jaafar D, Badr C, Raffetin A, Patey O, Matin C, Toure G, Caraux-Paz P. Impact d’une intervention par une équipe transversale d’infectiologie en chirurgie maxillo-faciale. Med Mal Infect 2020. [DOI: 10.1016/j.medmal.2020.06.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sammarco A, Hashemiaghdam A, Zappulli V, Badr C. An in-vivo mouse model to study drivers of metastases in mammary cancer. J Comp Pathol 2019. [DOI: 10.1016/j.jcpa.2018.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Davido B, Badr C, Lagrange A, Makhloufi S, De Truchis P, Perronne C, Salomon J, Dinh A. Serum protein electrophoresis: an interesting diagnosis tool to distinguish viral from bacterial community-acquired pneumonia. Eur J Clin Microbiol Infect Dis 2016; 35:899-902. [PMID: 26936614 DOI: 10.1007/s10096-016-2613-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/16/2016] [Indexed: 11/26/2022]
Abstract
29-69 % of pneumonias are microbiologically documented because it can be considered as an invasive procedure with variable test sensitivity. However, it drastically impacts therapeutic strategy in particular the use of antibiotics. Serum protein electrophoresis (SPEP) is a routine and non-invasive test commonly used to identify serum protein disorders. As virus and bacteria may induce different globulins production, we hypothesize that SPEP can be used as an etiological diagnosis test. Retrospective study conducted from 1/1/13 until 5/1/15 among patient hospitalized for an acute community-acquired pneumonia based on fever, crackles and radiological abnormalities. α/β, α/γ, β/γ globulins and albumin/globulin (A/G) ratio were calculated from SPEP. Data were analyzed in 3 groups: documented viral (DVP) or bacterial pneumonia (DBP) and supposedly bacterial pneumonia (SBP). We used ANOVA statistic test with multiple comparisons using CI95 and ROC curve to compare them. 109 patients included divided into DBP (n = 16), DVP (n = 26) and SBP (n = 67). Mean age was 62 ± 18 year-old with a sex ratio M/F of 1.3. Underlying conditions (e.g. COPD, diabetes) were comparable between groups in multivariate analysis. Means of A/G ratio were 0.80 [0.76-0.84], 0.96 [0.91-1.01], 1.08 [0.99-1.16] respectively for DBP, SBP and DVP (p = 0.0002). A/G ratio cut-off value of 0.845 has a sensitivity of 87.5 % and a specificity of 73.1 %. A/G ratio seems to be an easy diagnostic tool to differentiate bacterial from viral pneumonia. A/G ratio cut-off value below 0.845 seems to be predictable of a bacterial origin and support the use of antibiotics.
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Affiliation(s)
- B Davido
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France.
- Infectious Diseases Department, Raymond Poincaré Teaching Hospital, Garches, 92380, France.
| | - C Badr
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - A Lagrange
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - S Makhloufi
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - P De Truchis
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - C Perronne
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - J Salomon
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
| | - A Dinh
- Maladies Infectieuses, Hôpital Universitaire Raymond-Poincaré, AP-HP, Garches, France
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