Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus

Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain largely unknown. In this study, we identified 19 IBV strains from clinical samples from January 2021 to June 2022 in China, including 12 strains of GI-19, 3 strains of GI-7, and 1 strain each of GI-1, GI-9, GI-13, and GI-28. These results indicated that lineages GI-19 and GI-7 IBVs are still the most prevalent IBVs in China. Here, we investigated the evolution and transmission dynamics of lineage GI-7 IBVs. Our results revealed that the Taiwan province might be the origin of lineage GI-7 IBVs and that South China plays an important role in the spread of IBV. Furthermore, we found low codon usage bias of the S1 gene in lineage GI-7 IBVs. This allowed IBV to replicate in the host during evolution as a result of reduced competition, mainly driven by natural selection and mutational pressure, where the role of natural selection is more prominent. Collectively, our results reveal the genetic diversity and evolutionary dynamics of lineage GI-7 IBVs, which could assist in the prevention and control of viral infection.

Which strain of the avian coronavirus vaccine will become the prevalent one in China next?

Infectious bronchitis virus (IBV) is a vital pathogen in poultry farms, which can induce respiratory, nephropathogenic, oviduct, proventriculus, and intestinal diseases. Based on the phylogenetic classification of the full-length S1 gene, IBV isolates have been categorized into nine genotypes comprising 38 lineages. GI (GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, GI-7, GI-13, GI-16, GI-18, GI-19, GI-22, GI-28, and GI-29), GVI-1 and GVII-1 have been reported in China in the past 60 years. In this review, a brief history of IBV in China is described, and the current epidemic strains and licensed IBV vaccine strains, as well as IBV prevention and control strategies, are highlighted. In addition, this article presents unique viewpoints and recommendations for a more effective management of IBV. The recombinant Newcastle Disease virus (NDV) vector vaccine expressed S gene of IBV QX-like and 4/91 strains may be the dominant vaccine strains against NDV and IBV.

Construction and immunogenicity of recombinant rabies virus expressing S gene of SARS-CoV-2

[Background] The coronavirus disease 2019（COVID-19） pandemic has lasted for nearly three years in the globe, which has not only caused serious harm to humans but also affected companion animals. The COVID-19 vaccines for human have been used globally, while those for animals are rarely reported. [Objective] To develop a bivalent vaccine against both severe acute respiratory syndrome coronavirus 2（SARS-CoV-2） and rabies virus（RABV） for animal use. [Methods] We cloned the S and S1 genes of SARS-CoV-2 into the region between G and L genes of the attenuated RABV vaccine strain rHEP-Flury to construct the recombinant plasmids pHEP-nCOV-S and pHEP-nCOV-S1, respectively.The two plasmids were respectively co-transfected into BHK-21 cells with the helper plasmids and finally the recombinant viruses rHEP-nCOV-S and rHEP-nCOV-S1 were rescued. The recombinant viruses were confirmed by RT-PCR and direct fluorescent antibody staining against RABV N protein.Western blotting was employed to detect the expression of S and S1 proteins in the cells infected with the recombinant viruses. The growth curves, pathogenicity, and immunogenicity of recombinant viruses were confirmed in NA cells and mice. [Results] The rescued recombinant viruses rHEP-nCOV-S and rHEP-nCOV-S1 respectively carrying the S and S1 genes of SARS-CoV-2 were confirmed by direct fluorescent antibody assay based on the green fluorescence from the supernatants 7 days post infection.rHEP-nCOV-S1 rather than rHEP-nCOV-S showed stronger proliferation and diffusion abilities than the parental virus rHEP-Flury in NA cells. The specific bands at 72 kDa and 144 kDa in the Western blotting confirmed the efficient expression of S and S1 in the recombinant viruses, respectively. The mice vaccinated with the recombinant viruses did not show significant changes in the body weight compared with those vaccinated with rHEP-Flury, and the recombinant viruses induced the production of neutralizing antibody against RABV in mice. [Conclusion] The production of the recombinant RABV carrying the S/S1 gene of SARS-CoV-2 provides a foundation for the development of the bivalent vaccine against both SARS-CoV-2 and rabies virus for animal use.

Adenovirus Vaccine Containing Truncated SARS-CoV-2 Spike Protein S1 Subunit Leads to a Specific Immune Response in Mice.

The development of an efficient and safe coronavirus disease 2019 (COVID-19) vaccine is a crucial approach for managing the severe acute respiratory disease coronavirus 2 (SARS-CoV-2) pandemic in light of current conditions. In this study, we produced a shortened segment of the optimized SARS-CoV-2 spike gene (2043 bp, termed S1) that was able to encode a truncated S1 protein. The protein was tested to determine if it could elicit efficient immunization in mice against SARS-CoV-2. The presence of the S1 protein was confirmed with immunofluorescence and Western blotting. An adenovirus vaccine bearing the S1 gene fragment (Ad-S1) was administered intramuscularly to mice four times over 4 weeks. SARS-CoV-2 S1 protein humoral immunity was demonstrated in all immunized mice. The serum from immunized mice demonstrated excellent anti-infection activity in vitro. A robust humoral immune response against SARS-CoV-2 was observed in the mice after vaccination with Ad-S1, suggesting that the adenovirus vaccine may aid the development of vaccines against SARS-CoV-2 and other genetically distinct viruses.

MOLECULAR SIMILARLY BETWEEN INFECTIOUS BRONCHITIS VIRUSES AND COMMON VACCINES

Infectious bronchitis is an acute extremely infectious respiratory illness caused by the avian gamma-corona virus. Infection with infectious bronchitis virus predisposes the bird to subsequent bacterial infection, worsening the situation. Infection causes severe morbidity and variable mortality in broilers, as well as a significant decrease in layer production of eggs. Samples were collected from clinical cases submitted for necropsy at local veterinary clinics.This study was conducted to detect the molecular similarity in S1 gene sequence between field viruses and commonly used vaccines. In order to compare the sequences of field viruses with vaccinal viruses, two vaccines are chosen based on their popularity in veterinary clinics. These are MA5 strain and H120 strain. Molecular identification was done by using polymerase chain reaction (PCR) which was employed using primers target the S1 gene. Four positive field cases and two vaccine samples were sent to sequencing. The results of sequence alignment showed that vaccine viruses differ by more than 30% when compared to sequences of all the field viruses. The difference between genetic sequence leads to vaccine failure due to difference in the antigenic molecules on the spike protein of IBV © 2022, Revista Iberoamericana de Psicologia del Ejercicio y el Deporte.All Rights Reserved.

MOLECULAR SIMILARLY BETWEEN INFECTIOUS BRONCHITIS VIRUSES AND COMMON VACCINES

Infectious bronchitis is an acute extremely infectious respiratory illness caused by the avian gamma-corona virus. Infection with infectious bronchitis virus predisposes the bird to subsequent bacterial infection, worsening the situation. Infection causes severe morbidity and variable mortality in broilers, as well as a significant decrease in layer production of eggs. Samples were collected from clinical cases submitted for necropsy at local veterinary clinics.This study was conducted to detect the molecular similarity in S1 gene sequence between field viruses and commonly used vaccines. In order to compare the sequences of field viruses with vaccinal viruses, two vaccines are chosen based on their popularity in veterinary clinics. These are MA5 strain and H120 strain. Molecular identification was done by using polymerase chain reaction (PCR) which was employed using primers target the S1 gene. Four positive field cases and two vaccine samples were sent to sequencing. The results of sequence alignment showed that vaccine viruses differ by more than 30% when compared to sequences of all the field viruses. The difference between genetic sequence leads to vaccine failure due to difference in the antigenic molecules on the spike protein of IBV © 2022, Revista Iberoamericana de Psicologia del Ejercicio y el Deporte.All Rights Reserved.

Genotyping and In Silico Analysis of Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Spike 1 (S1) Glycoprotein.

Genetic diversity and evolution of infectious bronchitis virus (IBV) are mainly impacted by mutations in the spike 1 (S1) gene. This study focused on whole genome sequencing of an IBV isolate (IBV/Ck/Can/2558004), which represents strains highly prevalent in Canadian commercial poultry, especially concerning features related to its S1 gene and protein sequences. Based on the phylogeny of the S1 gene, IBV/Ck/Can/2558004 belongs to the GI-17 lineage. According to S1 gene and protein pairwise alignment, IBV/Ck/Can/2558004 had 99.44-99.63% and 98.88-99.25% nucleotide (nt) and deduced amino acid (aa) identities, respectively, with five Canadian Delmarva (DMV/1639) IBVs isolated in 2019, and it also shared 96.63-97.69% and 94.78-97.20% nt and aa similarities with US DMV/1639 IBVs isolated in 2011 and 2019, respectively. Further homology analysis of aa sequences showed the existence of some aa substitutions in the hypervariable regions (HVRs) of the S1 protein of IBV/Ck/Can/2558004 compared to US DMV/1639 isolates; most of these variant aa residues have been subjected to positive selection pressure. Predictive analysis of potential N-glycosylation and phosphorylation motifs showed either loss or acquisition in the S1 glycoprotein of IBV/Ck/Can/2558004 compared to S1 of US DMV/1639 IBV. Furthermore, bioinformatic analysis showed some of the aa changes within the S1 protein of IBV/Ck/Can/2558004 have been predicted to impact the function and structure of the S1 protein, potentially leading to a lower binding affinity of the S1 protein to its relevant ligand (sialic acid). In conclusion, these findings revealed that the DMV/1639 IBV isolates are under continuous evolution among Canadian poultry.

Molecular Characterization Analysis of Prevalent Infectious Bronchitis Virus and Pathogenicity Assessment of Recombination Strain in China.

Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.

Detection and genetic characterization of novel infectious bronchitis viruses from recent outbreaks in broiler and layer chicken flocks in southern China, 2021.

Avian infectious bronchitis virus (IBV) is a prevalent RNA virus that causes respiratory distress, nephritis, salpingitis, and egg production decline in chickens, resulting in significant economic loss. IBV is composed of complex genotypes and serotypes, which poses a great challenge for disease control. The current study reports 2 IBV outbreaks which were characterized by respiratory symptoms in IBV vaccinated commercial broilers and layers in Guangdong, China, in 2021. Two IBV strains, ZH01 and HH09, were identified via a RT-PCR assay through targeting the N gene and further characterization through full-length spike (S) gene sequence analysis. Phylogenetic analysis of S1 gene revealed that both ZH01 and HH09 belonged to the GI-19 lineage but contained a certain genetic distance from the GI-19 strain. Of note, the ZH01 and HH09 strains share a low homology of 70 and 86%, respectively, with common vaccine strains (H120), resulting in low vaccine protection. Further recombination analysis based on the S1 sequence suggested the newly identified IBV strains emerged through an intragroup recombination events between CK/CH/SCDY2003-2 and I0305/19 from G1-19 lineage. In addition, a number of novel mutations such as T273I, T292A, and S331K were found in the emerging IBV strains. Taken together, this study reports the genetic characteristics of 2 recent IBV outbreaks in southern China and emphasizes the urgent need for enhanced surveillance and development of novel vaccines for the control of IBV.

Genetic Analysis of the Complete S1 Gene in Japanese Infectious Bronchitis Virus Strains.

The complete nucleotide sequence of the S1 glycoprotein gene of the Japanese infectious bronchitis virus (IBV) strains was determined and genetically analyzed. A total of 61 Japanese IBV strains were classified into seven genotypes, namely GI-1, 3, 7, 13, 18, 19, and GVI-1 using the classification scheme that was proposed by Valastro et al, with three exceptions. These genotypes practically corresponded to those defined in Japan, namely Mass, Gray, JP-II, 4/91, JP-I, JP-III, and JP-IV, which have been identified through their partial nucleotide sequences containing hypervariable regions 1 and 2. In addition, three exceptive strains were considered to be derived from recombination within the S1 gene of IBV strains G1-13 and GI-19. By analyzing the amino acid polymorphism of the S1 glycoprotein among Japanese genotypes, a diversity was observed based on the genotype-specific amino acid residue, the proteolytic cleavage motif at the S1/S2 cleavage site, and the position of the potential N-glycosylation sites.