Genetic analysis of infectious bronchitis virus (IBV) in vaccinated poultry populations over a period of 10 years.

Infectious bronchitis virus (IBV) is an avian pathogen from the Coronavirus family causing major health issues in poultry flocks worldwide. Because of its negative impact on health, performance, and bird welfare, commercial poultry are routinely vaccinated by administering live attenuated virus. However, field strains are capable of rapid adaptation and may evade vaccine-induced immunity. We set out to describe dynamics within and between lineages and assess potential escape from vaccine-induced immunity. We investigated a large nucleotide sequence database of over 1700 partial sequences of the S1 spike protein gene collected from clinical samples of Dutch chickens submitted to the laboratory of Royal GD between 2011 and 2020. Relative frequencies of the two major lineages GI-13 (793B) and GI-19 (QX) did not change in the investigated period, but we found a succession of distinct GI-19 sublineages. Analysis of dN/dS ratio over all sequences demonstrated episodic diversifying selection acting on multiple sites, some of which overlap predicted N-glycosylation motifs. We assessed several measures that would indicate divergence from vaccine strains, both in the overall database and in the two major lineages. However, the frequency of vaccine-homologous lineages did not decrease, no increase in genetic variation with time was detected, and the sequences did not grow more divergent from vaccine sequences in the examined time window. Concluding, our results show sublineage turnover within the GI-19 lineage and we demonstrate episodic diversifying selection acting on the partial sequence, but we cannot confirm nor rule out escape from vaccine-induced immunity.RESEARCH HIGHLIGHTSSuccession of GI-19 IBV variants in broiler populations.IBV lineages overrepresented in either broiler, or layer production chickens.Ongoing episodic selection at the IBV S1 spike protein gene sequence.Several positively selected codons coincident with N-glycosylation motifs.

The inactivated infectious bronchitis virus (IBV) vaccine used as booster in layer hens influences the breadth of protection against challenge with IBV variants.

To achieve long term protection of laying and breeding hens against aberrant egg production caused by infectious bronchitis virus (IBV), a vaccination programme incorporating both live-attenuated and inactivated IBV vaccines is required. High quality IBV vaccines of both types are widely available, but the number of IBV variants of global importance continues to increase and it is not possible to develop vaccines against each one of them. Therefore, it is desirable to perform studies under controlled conditions to determine which IBV vaccine(s) provide the best protection for laying hens against different IBV challenges. Previous vaccination and challenge studies have shown that it is possible to obtain relevant data in a small number of laying hens housed under conditions of strict isolation. The present work extends this finding by investigating the efficacy, against challenge with five IBV strains of global importance, of an IBV vaccination programme including two live-attenuated IBV vaccines (Massachusetts and 793B types) and three different commercially available inactivated vaccines each containing antigen against at least one IBV strain. The results reported here confirm the importance of IBV vaccination for laying hens, show that efficient live priming makes a beneficial contribution to this protection and confirm that inactivated IBV vaccines contribute significantly to effective protection against at least the five IBV challenge strains used here. Furthermore, we provide data to support the "protectotype concept", long-established using different live-attenuated IBV vaccines in young chickens, is valid in broadening protection against IBV challenges in laying birds.RESEARCH HIGHLIGHTSIBV vaccination is essential as an aid in protecting laying hens against IBV infection.Live priming is a beneficial part of the IBV vaccination programme.IBV inactivated vaccine improves IBV protection.Heterologous IBV protection is confirmed in laying hens.

Spotlight on avian coronaviruses.

Coronaviruses (CoVs) mainly cause enteric and/or respiratory signs. Mammalian CoVs including COVID-19 (now officially named SARS-CoV-2) belong to either the Alphacoronavirus or Betacoronavirus genera. In birds, the majority of the known CoVs belong to the Gammacoronavirus genus, whilst a small number are classified as Deltacoronaviruses. Gammacoronaviruses continue to be reported in an increasing number of avian species, generally by detection of viral RNA. Apart from infectious bronchitis virus in chickens, the only avian species in which CoV has been definitively associated with disease are the turkey, pheasant and guinea fowl. Whilst there is strong evidence for recombination between gammacoronaviruses of different avian species, and between betacoronaviruses in different mammals, evidence of recombination between coronaviruses of different genera is lacking. Furthermore, the recombination of an alpha or betacoronavirus with a gammacoronavirus is extremely unlikely. For recombination to happen, the two viruses would need to be present in the same cell of the same animal at the same time, a highly unlikely scenario as they cannot replicate in the same host!