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A limited outbreak of nephropathogenic infectious bronchitis (NIB) occurred in three Delmarva (DMV) commercial broiler chicken flocks in 2011. Isolates of NIB virus (NIBV)—DMV/1639/11, DMV/3432/11, and DMV/3902/11—were characterized by sequence analysis of the N-terminal subunit (S1) of the spike (S) gene. Findings indicated that the isolates were identical to each other and to PA/9579A/10, a 2010 isolate from poultry in Pennsylvania. The 2010 and 2011 isolates appear to have originated from a 1997–2000 NIB outbreak in Pennsylvania. DMV/1639/11 and PA/9579A/10 were determined to be nephropathogenic in susceptible chickens, yielding virus reisolations from kidney and inducing characteristic interstitial nephritis microscopic lesions. In a controlled laboratory study, 40% of chickens vaccinated with a combination live vaccine containing infectious bronchitis virus (IBV) strains Massachusetts (Mass) + Connecticut (Conn) were positive on virus isolation attempts after challenge with DMV/1639/11, compared with only 13% of Mass + Arkansas (Ark) vaccinates. Both combination vaccines gave partial protection against the development of DMV/1639/11-induced renal lesions. Although numerically fewer chickens vaccinated with Mass + Conn had interstitial nephritis compared with those vaccinated with Mass + Ark, neither vaccine combination offered greater protection (P < 0.05) than observed in unvaccinated chickens challenged with DMV/1639/11. Mass + Ark vaccinations, applied under commercial conditions in the hatchery (spray) and on-farm (spray), did not protect the trachea or kidney from DMV/1639/11 challenge. Serologic testing of broiler flocks found <3% (2 of 69) tested to possess specific antibodies to DMV/1639/11, indicating the virus had not become established in the region. Caracterización del virus nefropatogénico de la bronquitis infecciosa DMV/1639/11 aislado de pollos de engorde en el área de Delmarva en el año 2011. Se presentó un brote limitado de bronquitis infecciosa nefropatogénica (NIB) en tres parvadas comerciales de pollos de engorde en el año 2011 en el área de Delmarva. Se caracterizaron los aislamientos de virus nefropatogénicos de bronquitis infecciosa DMV/1639/11, DMV/3432/11 y DMV/3902/11 se caracterizaron mediante el análisis de la secuencia del gene de la subunidad S1 de la espícula (S). Los resultados indicaron que los aislamientos eran idénticos entre sí y con el aislamiento PA/9579A/10, que es un aislamiento de aves comerciales en Pennsylvania del año 2010. Las cepas de los años 2010 y 2011 parecen haberse originado a partir de un brote de bronquitis infecciosa nefropatogénica que se presentó entre los años 1997 al 2000 en Pennsylvania. Se determinó que los aislamientos DMV/1639/11 y PA/9579A/10 eran nefropatogénicos en pollos susceptibles, que eran reaislados del riñón e inducían las lesiones de nefritis intersticial microscópica característica. En un estudio controlado de laboratorio, el 40% de los pollos vacunados con una vacuna viva que contenía la combinación cepas Massachussets (Mass) y Connecticut (Conn) fueron positivos a los intentos de aislamiento del virus después del desafío con el virus DMV/1639/11, en comparación con sólo el 13% de los pollos vacunados con la combinación Massachussets y Arkansas (Ark). Ambas combinaciones de vacunas confirieron una protección parcial contra el desarrollo de las lesiones renales inducidas por el virus DMV/1639/11. Aunque un número menor de los pollos vacunados con la combinación Massachussets y Connecticut mostraron nefritis intersticial en comparación con los pollos vacunados con Massachussets y Arkansas, ninguna combinación de vacunas ofreció una mayor protección (P < 0.05) que la observada en los pollos no vacunados y desafiados con el virus DMV/1639/11. Las vacunaciones con la combinación Massachussets y Arkansas, aplicadas en condiciones comerciales en la planta de incubación (aerosol) y en las explotaciones agrícolas (aerosol), no protegieron a la tráquea o a los riñones ante el desafío con el virus DMV/1639/11. Las pruebas serológicas demostraron que menos del 3% de las parvadas (2 de 69) poseían anticuerpos específicos contra el virus DMV/1639/11, lo que indica que el virus no se había establecido en la región.

Four infectious bronchitis virus (IBV) isolates were recovered from commercial broiler chicken flocks located on the Delmarva Peninsula (east coast of the United States) in the spring of 2006. Sequence analysis of the S1 subunit of the spike glycoprotein gene showed the four isolates were highly related to each other (≥99.6% nucleotide identity; ≥98.9% amino acid identity). Basic local alignment search tool analysis indicated the highest S1 amino acid identity of isolate DMV/5642/06, typical of the four Delmarva (DMV) isolates, was to CA/1737/04, an isolate obtained from broilers in California in 2004. A pathogenicity study conducted, using two-week-old commercial broilers, showed that DMV/5642/06 caused respiratory but not renal (kidney) disease. A vaccination–challenge study in three-week-old specific-pathogen-free leghorn chickens demonstrated that a commercial live attenuated IBV vaccine containing the Massachusetts strain conferred protection against challenge with DMV/5642/06 based on virus reisolation attempts and microscopic pathology.

In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.

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.

This study focuses on virus isolation of avian reoviruses from a tenosynovitis outbreak between September 2015 and June 2018, the molecular characterization of selected isolates based on partial S1 gene sequences, and the full genome characterization of seven isolates. A total of 265 reoviruses were detected and isolated, 83.3% from tendons and joints, 12.3% from the heart and 3.7% from intestines. Eighty five out of the 150 (56.6%) selected viruses for sequencing and characterization were successfully detected, amplified and sequenced. The characterized reoviruses grouped in six distinct genotypic clusters (GC1 to GC6). The most represented clusters were GC1 (51.8%) and GC6 (24.7%), followed by GC2 (12.9%) and GC4 (7.2%), and less frequent GC5 (2.4%) and GC3 (1.2%). A shift on cluster representation throughout time occurred. A reduction of GC1 and an increase of GC6 classified strains was noticed. The highest homologies to S1133 reovirus strain were detected in GC1 (~77%) while GC2 to GC6 homologies ranged between 58.5 and 54.1%. Over time these homologies have been maintained. Seven selected isolates were full genome sequenced. Results indicated that the L3, S1 and M2 genes, coding for proteins located in the virus capsid accounted for most of the variability of these viruses. The information generated in the present study helps the understanding of the epidemiology of reoviruses in California. In addition, provides insights on how other genes that are not commonly studied add variability to the reovirus genome.

The variant porcine epidemic diarrhea virus (PEDV) has caused considerable economic losses to the global pig industry since 2010. In this study, a total of 5859 diarrhea samples were collected from different pig farms in China’s Guangxi province during January 2020 and March 2024 and tested for PEDV using RT-qPCR. The positivity rate of PEDV was 11.90% (697/5859). Ninety-two PEDV-positive samples were selected based on sampling time, and the sampling region for amplification, sequencing, and analysis of the S1, M, and N genes. Phylogenetic analysis of the S1 gene revealed that all strains from Guangxi province were distributed in three subgroups, i.e., 81.5% (75/92) in the G2a subgroup, 4.3% (4/92) in the G2b subgroup, and 14.1% (13/92) in the G2c subgroup. The sequence analysis revealed that the S1 gene sequences from Guangxi province had higher homology with the variant strains than with the classical strains, showing as high as 99.2% with the variant strain AJ1102 and only 94.3% with the classical strain CV777. Recombination analysis revealed that the GX-BS08-2023 strain (G2c) from Guangxi province originated from inter-lineage recombination between the GX-BS09-2023 (G2a) and CH-JN547228-2011 (G1a) strains. In addition, the S1 gene of the G2a and G2b subgroup strains shared many mutations and insertions. There were common mutations of N143D and P235L in the G2a subgroup. Evolutionary analysis revealed that all Guangxi strains belonged to the G2 genotype. These strains have spread rapidly since the PEDV variant strains that emerged in 2010, weakened until 2021, and then remained stable. In conclusion, the results revealed the latest genetic evolution of circulating PEDV strains in Guangxi province in recent years, providing important information for preventing and controlling PEDV infection. Currently, the G2a subgroup strains are the predominant strains circulating in pig herds in Guangxi province, southern China.

The release and outgrowth of axillary buds are essential parts of the process of shoot branching in plants, but knowledge of the underlying regulatory mechanisms remains limited. Analysis of mab1‐D, a tobacco mutant with a greater number of axillary branches, showed that the mutant phenotype resulted from positive modulation of axillary buds release and outgrowth. TAIL‐PCR and co‐separation analyses suggested that NtMAB1‐S1, a member of the Related to ABI3/VP1 (RAV) subfamily that was highly expressed in the base of axillary buds, was associated with the mutant phenotype. Phenotypic analyses of mab1‐D overexpression, knockdown, knockout and complementation lines demonstrated that NtMAB1‐S1 was a positive regulator of axillary buds release and outgrowth. NtMAB1‐S1 accelerated these processes through transcriptional repression via the B3 repression domain. RNA‐sequencing analysis revealed that NtMAB1‐S1 was involved in the trehalose‐6‐phosphate and gibberellin metabolism pathways. Moreover, NtMAB1‐S1 enhanced the release and outgrowth of axillary buds by directly repressing transcription of NtTPPF, a trehalose‐6‐phosphate phosphatase, and NtGA2ox8, a gibberellin oxidase. NtMAB1‐S1 thus plays a pivotal role in regulating the release and outgrowth of axillary buds and is a potential target for genetic interventions aimed at shaping ideal plant architecture.

Despite long‐term vaccination and control efforts, infectious bronchitis virus (IBV) remains a major threat to the global poultry industry, largely due to its high prevalence and extensive genetic diversity. This study aimed to characterize two novel GI‐13 (4/91‐like) IBV field strains, CK/CH/JS/2302 and CK/CH/AH/2307, isolated from H120‐vaccinated broiler flocks in China, in order to elucidate their pathogenicity, genomic characteristics, and evolutionary relationships. Although both isolates belonged to the GI‐13 genotype but exhibited divergent pathogenic profiles and evolutionary patterns. CK/CH/JS/2302 exhibited higher virulence, severe respiratory symptoms, tracheal hemorrhage, kidney lesions, and 10% mortality, while CK/CH/AH/2307 induced only mild respiratory signs and slight renal swelling. Phylogenetic analysis revealed that CK/CH/JS/2302 displayed a recombinant genome involving GX‐YL5 and IBV/India/ck/01/23, in which the S1 gene was clustered within GI‐13 genotype, whereas other genes showed high similarity to domestic GI‐7, GI‐19, and GI‐22 genotypes. In contrast, CK/CH/AH/2307 showed high genomic similarity to the 4/91 vaccine strain without evidence of recombination but still impaired tracheal ciliary activity. Sequence and structural modeling of the S1 protein revealed that amino acid substitutions within hypervariable regions (HVRs) may affect receptor binding and antigenicity, potentially reducing cross‐protection from current vaccines. These findings demonstrate the coexistence of a virulent recombinant strain (CK/CH/JS/2302) and a low‐pathogenic variant (CK/CH/AH/2307) within the same lineage in China, underscoring the role of recombination and immune selection in IBV evolution. Overall, these findings emphasize the necessity for continuous molecular surveillance and genotype‐specific vaccine development to improve protection against emerging 4/91‐like IBV variants and reduce the economic losses caused by infectious bronchitis in poultry production.

Background Infectious bronchitis virus (IBV) is a highly contagious evolving pathogen that causes respiratory, urinary and reproductive symptoms; threatening the poultry industry globally. Methods During this study, 90 tissue specimens were collected from various poultry flocks of seven Upper Egypt governorates from 2023 to 2024 for genetic characterization. Result Typical IBV lesions of the inoculated embryos in the specific-pathogen-free-embryonated chicken eggs (SPF-ECE) were observed. Using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay targeting the conserved N gene, only 60 samples were considered positive with 66.6%. Collectively, 23 tissue specimens were examined through a one-step PCR assay. Sequencing is targeting the S1 gene, and the phylogenetic analysis was conducted based on partial sequencing showed that Avian coronavirus (ACoV) isolates belong to GI-23 (n = 18), GI-12 (n = 2), GI-1 (n = 1), and GI-19 (n = 2). Genotyping of the S1 gene indicates that GI-23 shows a genetic similarity to Egyptian isolates, and Israeli variants with nucleotide identity percentages (95–97%) and, (88–92%); respectively. Concerning full sequencing, five ACoV isolates were clustered as GI-23 (n = 3), and GI-19 (n = 2). Currently, QX-strains showed low genomic relatedness with Egyptian strains, and vaccinal strains with nucleotide (78–79%), and amino acid (77–80%), and (75–77%) identities, respectively. This is the first detailed study that recorded various IBV isolates, especially the novel emerged QX strain circulating in chicken flocks in Egypt. The recombination event within the Assuit-1-QX-EGYIBV-2024 isolate was detected as a result of recombination between the major (GI-19) and minor (GI-22) putative parents. Importantly, the G1-19 and G1-23 shared multiple amino acids mutations at S1 gene. Conclusions This study provides empirical evidence for the ACoV circulating in Egypt in vaccinated and non-vaccinated poultry flocks despite the excessive vaccination schemes.

The QX-type avian infectious bronchitis virus (IBV) is still a prevalent genotype in Southwestern China. To analyze the antigenicity and pathogenicity characteristics of the dominant genotype strains (QX-type), S1 gene sequence analysis, virus cross-neutralization tests, and pathogenicity test of eight QX-type IBV isolates were conducted. Sequence analysis showed that the nucleotide homology between the eight strains was high, but distantly related to H120 and 4/91 vaccine strains. Cross-neutralization tests showed that all eight strains isolated from 2015 and 2017 belonged to the same serotype, but exhibited antigenic variations over time. The pathogenicity test of the five QX-type IBV isolates showed that only three strains, CK/CH/SC/DYW/16, CK/CH/SC/MS/17, and CK/CH/SC/GH/15, had a high mortality rate with strong respiratory and renal pathogenicity, whereas CK/CH/SC/PZ/17 and CK/CH/SC/DYYJ/17 caused only mild clinical symptoms and tissue lesions. Our results indicate that the prevalent QX-type IBVs displayed antigenic variations and pathogenicity difference. These findings may provide reference for research on the evolution of IBV and vaccine preparation of infectious bronchitis (IB).