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Chacón RD, Sánchez-Llatas CJ, L Pajuelo S, Diaz Forero AJ, Jimenez-Vasquez V, Médico JA, Soto-Ugaldi LF, Astolfi-Ferreira CS, Piantino Ferreira AJ. Molecular characterization of the meq oncogene of Marek's disease virus in vaccinated Brazilian poultry farms reveals selective pressure on prevalent strains. Vet Q 2024; 44:1-13. [PMID: 38465827 DOI: 10.1080/01652176.2024.2318198] [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: 06/07/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Marek's disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek's disease (MD) outbreaks in recent years. Our study aimed to analyze the complete meq gene sequences to understand the molecular epidemiological basis of MD outbreaks in Brazilian vaccinated layer farms. We detected a high incidence rate of visceral MD (67.74%) and multiple circulating MDV strains. The most prevalent and geographically widespread genotype presented several clinical and molecular characteristics of a highly virulent strain and evolving under positive selective pressure. Phylogenetic and phylogeographic analysis revealed a closer relationship with strains from the USA and Japan. This study sheds light on the circulation of MDV strains capable of infecting vaccinated birds. We emphasize the urgency of adopting preventive measures to manage MDV outbreaks threatening the poultry farming industry.
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Affiliation(s)
- Ruy D Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | | | - Andrea J Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Jack A Médico
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
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Chacón RD, Sánchez-Llatas CJ, Diaz Forero AJ, Guimarães MB, Pajuelo SL, Astolfi-Ferreira CS, Ferreira AJP. Evolutionary Analysis of a Parrot Bornavirus 2 Detected in a Sulphur-Crested Cockatoo ( Cacatua galerita) Suggests a South American Ancestor. Animals (Basel) 2023; 14:47. [PMID: 38200778 PMCID: PMC10778322 DOI: 10.3390/ani14010047] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Parrot bornavirus (PaBV) is an RNA virus that causes Proventricular Dilatation Disease (PDD), neurological disorders, and death in Psittaciformes. Its diversity in South America is poorly known. We examined a Cacatua galerita presenting neuropathies, PDD, and oculopathies as the main signs. We detected PaBV through reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of the nucleoprotein (N) and matrix (M) genes. Maximum likelihood and Bayesian phylogenetic inferences classified it as PaBV-2. The nucleotide identity of the sequenced strain ranged from 88.3% to 90.3% against genotype PaBV-2 and from 80.2% to 84.4% against other genotypes. Selective pressure analysis detected signs of episodic diversifying selection in both the N and M genes. No recombination events were detected. Phylodynamic analysis estimated the time to the most recent common ancestor (TMRCA) as the year 1758 for genotype PaBV-2 and the year 1049 for the Orthobornavirus alphapsittaciforme species. Substitution rates were estimated at 2.73 × 10-4 and 4.08 × 10-4 substitutions per year per site for N and M, respectively. The analysis of population dynamics showed a progressive decline in the effective population size during the last century. Timescale phylogeographic analysis revealed a potential South American ancestor as the origin of genotypes 1, 2, and 8. These results contribute to our knowledge of the evolutionary origin, diversity, and dynamics of PaBVs in South America and the world. Additionally, it highlights the importance of further studies in captive Psittaciformes and the potential impact on endangered wild birds.
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Affiliation(s)
- Ruy D. Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid (UCM), 28040 Madrid, Spain;
| | - Andrea J. Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Marta B. Guimarães
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Sarah L. Pajuelo
- Faculty of Biological Sciences, National University of Trujillo, Trujillo 13001, La Libertad, Peru;
| | - Claudete S. Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Antonio J. Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
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Marín-Sánchez O, Pesantes-Grados P, Pérez-Timaná L, Marín-Machuca O, Sánchez-Llatas CJ, Chacón RD. Comparative Epidemiological Assessment of Monkeypox Infections on a Global and Continental Scale Using Logistic and Gompertz Mathematical Models. Vaccines (Basel) 2023; 11:1765. [PMID: 38140170 PMCID: PMC10747842 DOI: 10.3390/vaccines11121765] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
The monkeypox virus (MPXV) has caused an unusual epidemiological scenario-an epidemic within a pandemic (COVID-19). Despite the inherent evolutionary and adaptive capacity of poxviruses, one of the potential triggers for the emergence of this epidemic was the change in the status of orthopoxvirus vaccination and eradication programs. This epidemic outbreak of HMPX spread worldwide, with a notable frequency in Europe, North America, and South America. Due to these particularities, the objective of the present study was to assess and compare cases of HMPX in these geographical regions through logistic and Gompertz mathematical modeling over one year since its inception. We estimated the highest contagion rates (people per day) of 690, 230, 278, and 206 for the world, Europe, North America, and South America, respectively, in the logistic model. The equivalent values for the Gompertz model were 696, 268, 308, and 202 for the highest contagion rates. The Kruskal-Wallis Test indicated different means among the geographical regions affected by HMPX regarding case velocity, and the Wilcoxon pairwise test indicated the absence of significant differences between the case velocity means between Europe and South America. The coefficient of determination (R2) values in the logistic model varied from 0.8720 to 0.9023, and in the Gompertz model, they ranged from 0.9881 to 0.9988, indicating a better fit to the actual data when using the Gompertz model. The estimated basic reproduction numbers (R0) were more consistent in the logistic model, varying from 1.71 to 1.94 in the graphical method and from 1.75 to 1.95 in the analytical method. The comparative assessment of these mathematical modeling approaches permitted the establishment of the Gompertz model as the better-fitting model for the data and the logistic model for the R0. However, both models successfully represented the actual HMPX case data. The present study estimated relevant epidemiological data to understand better the geographic similarities and differences in the dynamics of HMPX.
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Affiliation(s)
- Obert Marín-Sánchez
- Departamento Académico de Microbiología Médica, Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru;
| | - Pedro Pesantes-Grados
- Unidad de Posgrado, Facultad de Ciencias Matemáticas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru;
| | - Luis Pérez-Timaná
- Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru;
| | - Olegario Marín-Machuca
- Departamento Académico de Ciencias Alimentarias, Facultad de Oceanografía, Pesquería, Ciencias Alimentarias y Acuicultura, Universidad Nacional Federico Villarreal, Calle Roma 350, Miraflores 15074, Peru;
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (U.C.M.), C. de José Antonio Nováis, 12, 28040 Madrid, Spain;
| | - Ruy D. Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando M. Paiva, 87, São Paulo 05508-270, Brazil
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Chacón JL, Chacón RD, Sánchez-Llatas CJ, Morín JG, Astolfi-Ferreira CS, Piantino Ferreira AJ. Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype. Avian Pathol 2023; 52:323-338. [PMID: 37477586 DOI: 10.1080/03079457.2023.2228725] [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: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.
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Affiliation(s)
- Jorge L Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Ruy D Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Jaime G Morín
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Claudete S Astolfi-Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Antonio J Piantino Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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