Assessment of molecular and genetic evolution, antigenicity and virulence properties during the persistence of the infectious bronchitis virus in broiler breeders

Fernando, Filipe Santos; Kasmanas, Thaiane Coelho; Lopes, Priscila Diniz; Montassier, Maria de Fátima da Silva; Morés, M. A. Z.; Mariguela, Viviane Casagrande; Pavani, Caren; Santos, R. M.; Assayag, Mário Sérgio; Montassier, Hélio José

doi:10.1099/jgv.0.000893

Cited by 19 publications

(13 citation statements)

References 54 publications

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“…Although not longitudinally sampled, MERS-CoV was detected at frequencies of Ͼ40% in several groups of dromedary camels, similarly indicative of persistence (47) despite its more frequent clearance in infected humans (48). Other coronaviruses showing long-term persistence include mouse hepatitis virus, feline calicivirus (49), and infectious bronchitis virus in birds (50,51). Pigs are infected with a range of different coronaviruses of variable propensities to establish persistent infections (52)(53)(54)(55).…”

Section: Discussionmentioning

confidence: 99%

Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses

Simmonds

2020

mBio

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The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses—even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility. IMPORTANCE The detection and characterization of large-scale RNA secondary structure in the genome of SARS-CoV-2 indicate an extraordinary and unsuspected degree of genome structural organization; this could be effectively visualized through a newly developed contour plotting method that displays positions, structural features, and conservation of RNA secondary structure between related viruses. Such RNA structure imposes a substantial evolutionary cost; paired sites showed greater restriction in diversity and represent a substantial additional constraint in reconstructing its molecular epidemiology. Its biological relevance arises from previously documented associations between possession of structured genomes and persistence, as documented for HCV and several other RNA viruses infecting humans and mammals. Shared properties potentially conferred by large-scale structure in SARS-CoV-2 include increasing evidence for prolonged infections and induced immune dysfunction that prevents development of protective immunity. The findings provide an additional element to cellular interactions that potentially influences the natural history of SARS-CoV-2, its pathogenicity, and its transmission.

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Section: Discussionmentioning

confidence: 99%

Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses

Simmonds

2020

mBio

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“…Recently, protectotype analysis of some nephropathogenic BR-I IBV strains demonstrated that Massachusetts live attenuated vaccines conferred only partial protection to tracheal and kidney tissues [12, 14], although the combination of Massachusetts and 793B live attenuated vaccines improved protection against these BR-I nephropathogenic strains [12]. Additionally, virus neutralization tests (VNT) showed that some BR-I genotype strains do not belong to the Massachusetts serotype [5, 34].…”

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confidence: 99%

Memory immune responses and protection of chickens against a nephropathogenic infectious bronchitis virus strain by combining live heterologous and inactivated homologous vaccines

Santos

Fernando

Montassier

et al. 2019

The Journal of Veterinary Medical Science

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In this study, we evaluated antibody and cell-mediated immune (CMI) responses in the mucosal and systemic compartments and protection against challenge with a nephropathogenic Brazilian (BR-I) strain of infectious bronchitis virus (IBV) in chickens submitted to a vaccination regime comprising a priming dose of heterologous live attenuated Massachusetts vaccine followed by a booster dose of an experimental homologous inactivated vaccine two weeks later. This immunization protocol elicited significant increases in serum and lachrymal levels of anti-IBV IgG antibodies and upregulated the expression of CMI response genes, such as those encoding CD8β chain and Granzyme homolog A in tracheal and kidney tissues at 3, 7, and 11 days post-infection in the vaccinated chickens. Additionally, vaccinated and challenged chickens showed reduced viral loads and microscopic lesion counts in tracheal and kidney tissues, and their antibody and CMI responses were negatively correlated with viral loads in the trachea and kidney. In conclusion, the combination of live attenuated vaccine containing the Massachusetts strain with a booster dose of an inactivated vaccine, containing a BR-I IBV strain, confers effective protection against infection with nephropathogenic homologous IBV strain because of the induction of consistent memory immune responses mediated by IgG antibodies and TCD8 cells in the mucosal and systemic compartments of chickens submitted to this vaccination regime.

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“…The Mass IBV strain can persist in the cecal tonsils, spleen and kidney for about a month [ 78 ]. Although the period of IBV persistence is influenced by the age at infection [ 42 ], the length of persistence does not depend on the systemic anti-IBV antibody concentration [ 4 ]. The implications of IBV persistence in chickens are twofold.…”

Section: Ibv Persistencementioning

confidence: 99%

“…The implications of IBV persistence in chickens are twofold. First, persistently infected chickens are a source of infection for naïve chickens [ 4 ]. Second, persistent IBV infection promotes viral evolution [ 4 ].…”

Section: Ibv Persistencementioning

confidence: 99%

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Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression

et al. 2020

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In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host.

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Assessment of molecular and genetic evolution, antigenicity and virulence properties during the persistence of the infectious bronchitis virus in broiler breeders

Cited by 19 publications

References 54 publications

Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses

Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses

Memory immune responses and protection of chickens against a nephropathogenic infectious bronchitis virus strain by combining live heterologous and inactivated homologous vaccines

Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression

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