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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.

Additional file 1. List of primers used to amplify and/or to sequence the GI.1d/00–21 complete coding sequence.

This work is part of a project validated by the “Pôle de Compétitivité Valorial”(programme 214) and was funded by the Conseil Régional de Bretagne, Conseil Départemental des Côtes d’Armor, Conseil Régional des Pays de la Loire, and Saint Brieuc Agglomération. We thank Zoopole Développement, Ploufragan (France) for their help in preparation of the project,and we acknowledge partners involved in the global project: CIDEF-CIPC, CECAB, Deltavit (groupe CCPA), Techna France Nutrition, Terrena, Triskalia, Sanders, Coopérative Le Gouessant, MG2Mix, and Selvet Conseil.; International audience; The sporulation of oocysts of Eimeria that infect poultry is known to be under the influence of environmental conditions, including temperature, oxygen supply, and moisture. However, even when these conditions are optimal, the level of sporulation can remain low. The effect of oocyst maturity on their ability to sporulate was investigated for two species of Eimeria : E. acervulina of chickens, and E. meleagrimitis of turkeys. After oral infection of birds, oocysts were collected at their production site in the intestine at different times around the prepatent period. The percentage of sporulation was determined by observation of 100 oocysts for each sample. With E. acervulina , it was observed that sporulation depended on the time of collection of the oocysts in the intestine, and that it increased with aging oocysts (from 5% to 40% globally in 8 h). With E. meleagrimitis , sporulation remained low with oocysts collected in the duodenum (below 20%), but oocysts collected in the midgut and in the lower intestine sporulated more efficiently (around 80%) than oocysts collected in the duodenum at the same time. One explanation for these results is the assumption that oocysts may be produced before fertilization, and that microgametes have not yet fertilized the newly produced oocysts. As time goes on, more oocysts would be fertilized, locally in the duodenum for E. acervulina , and descending along the gut for E. meleagrimitis . This hypothesis needs to be investigated further, but it could lead to new approaches to control these parasites by targeting the microgametes.; La sporulation des oocystes chez les Eimeria qui infectent la volaille est connue pour être influencée par les conditions environnementales (température, apport d’oxygène et humidité). Cependant, même lorsque ces conditions sont optimales, le niveau de sporulation peut rester faible. L’effet de la maturité des oocystes sur leur capacité à sporuler a été étudié pour deux espèces d’ Eimeria : E. acervulina du poulet et E. meleagrimitis de la dinde. Après infection orale des oiseaux, les oocystes ont été collectés sur leur site de production dans l’intestin à différents moments autour de la période prépatente. Le pourcentage de sporulation a été déterminé en observant 100 oocystes pour chaque échantillon. Avec E. acervulina , il a été observé que le pourcentage de sporulation dépendait du moment de la collecte des oocystes dans l’intestin, et qu’il augmentait avec des oocystes vieillissants (globalement de 5 % à 40 % en 8 heures). Avec E. meleagrimitis , le pourcentage de sporulation restait faible avec les oocystes collectés dans le duodénum (inférieur à 20 %), mais les oocystes collectés dans l’intestin moyen et dans l’intestin inférieur ont sporulé plus efficacement (environ 80 %) que les oocystes recueillis dans le duodénum en même temps. Une explication de ces résultats repose sur l’hypothèse que les oocystes peuvent être produits avant la fécondation et que les microgamètes n’ont pas encore fécondé les oocystes nouvellement produits. Avec le temps, davantage d’oocystes seraient fécondés, localement dans le duodénum pour E. acervulina , et descendant le long de l’intestin pour E. meleagrimitis . Cette hypothèse doit être approfondie, mais elle peut conduire à de nouvelles approches pour contrôler ces parasites en ciblant les microgamètes.