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. 2022 Jun 25;14(7):1392.
doi: 10.3390/v14071392.

Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens

Alexandre Flageul  1 , Chantal Allée  1 , Céline Courtillon  1 , Véronique Béven  2 , Hélène Quenault  2 , Yannick Blanchard  2 , Michel Amelot  3 , David Courtois  3 , Sjaak De Wit  4 , Nicolas Eterradossi  1 , Béatrice Grasland  1 , Paul A Brown  1
Affiliations

Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens

Alexandre Flageul et al. Viruses. .

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.

Keywords: coronavirus; evolution; infectious bronchitis; vaccination; variants.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Comparison of relative mean of D388 viral RNA in both tracheas and kidneys of vaccinated and unvaccinated subjects. Statistical tests (comparison of mean of two independent samples) were performed using Wilcoxon test. ** p-value below 0.001; *** p-value below 0.0001.
Figure 2
Figure 2
Genetic variant map of the EggP1 D388 inoculum. EggP1 D388 inoculum was deep sequenced and NGS data were processed through VVV. The upper graphic shows genome coverage, While the middle graphic presents detected genetic variants over the viral genome; numbers = variants above the threshold. The table provides the details of the detected genetic variants (1–9).
Figure 3
Figure 3
D388 variants detected in tracheal and kidney tissues of VB and NVB in passage 1, 2, and 3. Variants are indicated by light blue squares when they were detected in less than 50% of the population and by dark blue squares when they were detected in 50% or above. Variants for each individual at each passage are presented by line. Genomic regions and with genome locations for the variants are indicated above the graphic. Percentages of Var1 to Var8 in the viral population of the inoculum are shown next to the genome location when detected.
See this image and copyright information in PMC

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