Avian disease studies are critical not only to keep healthy poultry productions but also to ensure constant soybean consumptions to promote healthy soybean industry.

Avian coronavirus, commonly named as infectious bronchitis virus (IBV) in poultry diseases, is one of the most important and highly contagious viral pathogens in chickens. It causes severe respiratory disease, kidney failure, decreased growth and deaths in young birds and economic losses in egg production and quality in egg-laying hens. Chickens of all ages, breeds and sex are susceptible to IBV infections. Commercial IBV vaccines have limitations in preventing IBV infection due to antigenic differences among numerous known and unknown serotypes of IBV. Continual variation in its antigenic composition occurs geographically and makes IBV a difficult poultry disease to prevent and control. The IBV variants pose a serious threat to poultry flocks because immunity to IBV is serotype specific and vaccination with known serotypes often confers little or no cross protection against these new variants.

This research project is to use the most advanced whole genome sequencing technique to conduct genome characterizations for the large accumulations of more than 1,000 IBV field variants we have isolated from PA poultry from 1990 – 2020. The genome sequencing characterizations would reveal new findings of how the revolutionary mutations of avian coronaviruses occurred in chickens during the last 30 years. Thus we would be able to better predict and prevent emerging new variants in the future.

During the last 30 years from 1990 – 2020, we have accumulated more than 1,000 avian coronavirus (or Infectious Bronchitis Virus, IBV, in poultry diseases) field variants isolated from PA poultry, and we have saved (-80 freezers) these IBV variants for further studies when new technologies become available, such as the most recent advanced whole genome sequencing technique, next generation sequencing (NGS). Therefore, we propose two major objectives in this research as the following:

1) to conduct full genome sequencing on these unique accumulations of avian coronavirus variants obtained during the past 30-years.

2) to conduct genomic characterization analysis to obtain much valuable scientific data of their revolutionary mutations occurred during the past 30 years.

3) to use the new findings of how the revolutionary mutations of avian coronaviruses occurred during the past, and to predict emerging new variants in the future.

Methods to achieve objective, working plans are as the follows.

1) Virus propagation. We will retrieve IBV field variants isolated from PA poultry during the last 30 years, 1990 - 2020, select about 10 IBV variants each year to be a total of approximately 300 variant strains, inoculate each strain into SPF embryonating chicken eggs (ECE) for virus propagation. Chorioallantoic fluids (CAF) will be harvested at 72 hours post inoculation for IBV confirmation test by RT-PCR.

2) Full genomic sequencing. We will extract IBV viral RNAs for full genomic sequencing analysis by using the Illumina MiSeq system, conduct assembling full genome sequences, complete sequencing data analysis and document the full genomic data to Genbank.

3) Expected results. It is expected that the outcome of this research would enable the poultry industry to apply vaccines appropriately to control IBV outbreaks. It would also provide evidence to encourage the continuing development of new vaccines against important emerging serotypes of IBV that are not adequately controlled by current commercially available vaccines.

4) Furthermore, research findings from this avian coronavirus project would be greatly benefits for better understanding of the ongoing COVID-19 pandemic outbreaks and providing scientific information and data for appropriate control measures and strategies.

Updated August 22, 2022:
During this research period, we retrieved 264 IBV field isolates (Table-1) from PA poultry during the last 30 years (1990 – 2020) and conducted both get RT-PCR and real-time RT-PCR tests to confirm positive for IBV. Of 264 isolates, 154 isolates were selected (yielded clear PCR bands and ct-values <35) and processed for S1 gene sequencing analysis.
The IBV S1-gene sequencing results shows that all the 154 IBV isolates fall into GI lineage among the five group lineages of IBV sequencing results. Within G-I lineage, there are further 27 sub-lineages. The 154 isolates belonged to six sub-lineages of 1, 3, 9, 17, 25 and 27. Distribution of the 154 IBV isolates to the IBV sub-lineages are as 121 for GI-1, 3 for GI-3, 5 for GI-9; 19 for GI-17, 1 for GI-25, and 5 for GI-27 (Fig. 1).
For the next research period, we will conduct full genomic sequencing test. We will extract IBV viral RNAs for full genomic sequencing analysis by using the Illumina MiSeq system, conduct assembling full genome sequences, complete sequencing data analysis and document the full genomic data to Genbank.

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Avian disease studies are critical not only to keep healthy poultry productions but also to ensure constant soybean consumptions to promote healthy soybean industry.

As the USDA annual statistic reports on poultry productions, Pennsylvania has continuously ranked the 4th largest egg-layer state in the US with 30,545,000 head in 2020 (28,235,000 in 2018; and 27,214,000 head in 2016). On average, 16.5 % of soybeans are the major protein component in laying hens’ feed, the over 30,545,000 head layers consume about 216,033 tons of soybeans annually (9 kg of soybeans/bird/year).

For broiler chickens, PA has 221,100,000 head in 2020 (200,100,000 in 2018). On average, Soybean in broiler feed: 1.27kg/head, (1.27kg x 221,000,000 = 280,670,000kg), so the 221 million head consume 280,670 tons of soybeans annually.

Therefore, healthy poultry productions are important in keeping constant soybean consumptions to promote healthy soybean industry.