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Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens. Viruses 2022; 14:v14071392. [PMID: 35891373 PMCID: PMC9319055 DOI: 10.3390/v14071392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.
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Flageul A, Courtillon C, Allée C, Leroux A, Blanchard Y, Deleforterie Y, Grasland B, Brown PA. Extracting Turkey Coronaviruses from the intestinal lumen of infected turkey embryos yields full genome data with good coverage by NGS. Avian Pathol 2022; 51:291-294. [PMID: 35201915 DOI: 10.1080/03079457.2022.2046701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Currently, turkey coronaviruses (TCoV) are isolated from homogenized intestines of experimentally infected embryos to ensure a maximum recovery of viral particles from all components of the intestines. However, the process of homogenization also ensures a release of an important amount of cellular RNAs into the sample that hinders downstream viral genome sequencing. This is especially the case for next generation sequencing (NGS) that sequences molecules at random. This characteristic means that the heavily abundant cellular RNA in the sample drowns out the minority viral RNA during the sequencing process and consequently very little to no viral genome data is obtained.To address this problem, a method was developed, in which ten descendent isolates of the European strain of TCoV were recovered uniquely from the intestinal lumen without homogenization of the tissue. For nine out of ten samples, NGS produced viral RNA reads with good coverage depth over the entire TCoV genomes. This is a much-needed new, simple and cost effective method of isolating TCoV that facilitates downstream NGS of viral RNA and should be considered as an alternative method for isolating other avian enteric coronaviruses in the interest of obtaining full-length genome sequences.
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Affiliation(s)
- Alexandre Flageul
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) laboratory of Ploufragan-Plouzané-Niort, Virology, immunology and parasitology in poultry and rabbit (VIPAC) Unit, Université de Rennes 1
| | - Céline Courtillon
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) laboratory of Ploufragan-Plouzané-Niort, Virology, immunology and parasitology in poultry and rabbit (VIPAC) Unit, Université de Rennes 1
| | - Chantal Allée
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) laboratory of Ploufragan-Plouzané-Niort, Virology, immunology and parasitology in poultry and rabbit (VIPAC) Unit, Université de Rennes 1
| | - Aurélie Leroux
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, Université de Rennes 1
| | - Yannick Blanchard
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, Université de Rennes 1
| | | | - Béatrice Grasland
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) laboratory of Ploufragan-Plouzané-Niort, Virology, immunology and parasitology in poultry and rabbit (VIPAC) Unit, Université de Rennes 1
| | - Paul Alun Brown
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) laboratory of Ploufragan-Plouzané-Niort, Virology, immunology and parasitology in poultry and rabbit (VIPAC) Unit, Université de Rennes 1
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Cubas-Gaona LL, Flageul A, Courtillon C, Briand FX, Contrant M, Bougeard S, Lucas P, Quenault H, Leroux A, Keita A, Amelot M, Grasland B, Blanchard Y, Eterradossi N, Brown PA, Soubies SM. Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages in vitro and ex vivo in the Presence of a Mutagenic Nucleoside Analog. Front Microbiol 2021; 12:678563. [PMID: 34177862 PMCID: PMC8226269 DOI: 10.3389/fmicb.2021.678563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2'-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens.
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Affiliation(s)
- Liliana L Cubas-Gaona
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alexandre Flageul
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Céline Courtillon
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Francois-Xavier Briand
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Maud Contrant
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Stephanie Bougeard
- Epidemiology, Animal Health and Welfare Unit (EPISABE), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Pierrick Lucas
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Hélène Quenault
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Aurélie Leroux
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alassane Keita
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Michel Amelot
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Béatrice Grasland
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Yannick Blanchard
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Nicolas Eterradossi
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Paul Alun Brown
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Sébastien Mathieu Soubies
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
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