IgM and IgY CDR3 sequences from naive, vaccinated and/or infected chickens

Avian influenza viruses (AIVs) are a major economic burden to the poultry industry, and pose serious zoonotic risk, with human infections being reported every year. To date, the vaccination of birds remains the most important method for the prevention and control of AIV outbreaks. Most national vaccination strategies against AIV infection use whole-virus inactivated vaccines, which predominantly trigger a systemic antibody-mediated immune response. There are currently no studies that have examined the antibody repertoire of birds that were infected with and/or vaccinated against AIV. To this end, we evaluate the changes in the H9N2-specific IgM and IgY repertoires in chickens subjected to vaccination(s) and/or infectious challenge. We show that a large proportion of the IgM and IgY clones were shared across multiple individuals, and these public clonal responses are dependent on both the immunisation status of the birds and the specific tissue that was examined. Furthermore, analysis re..., 1.1. Experimental design and tissue samples
White leghorn chickens (Valo breed, n=70) were hatched and reared in the poultry facility at the Pirbright Institute according to national and institute-specific regulations (licence number P68D44CF4). Birds were divided into 6 treatment groups (G1-6) and maintained together until infection, then transferred to isolators at day 21 post-hatching. Uninfected birds remained together for the duration of the experiment. Chickens from G1 (n=10), G2 (n=10), G4 (n=10), and G5 (n=10) received a single subcutaneous injection of 0.2ml of 1024 HAU/dose inactivated H9N2 vaccine immediately after hatching. Individuals from G2 and G5 received an additional dose of the vaccine at 14 days after hatching. Birds from G3 (n=15) and G6 (n=15) did not receive the vaccine. Weekly blood samples were collected from all birds immediately after the first intervention (i.e. infection or vaccination). At day 21 post-hatching, birds from G1-3 received a single intranasal i..., , # IgM and IgY CDR3 sequences from naive, vaccinated and/or infected white VALO chickens

[https://doi.org/10.5061/dryad.9cnp5hqtq](https://doi.org/10.5061/dryad.9cnp5hqtq)

## Description of the data and file structure

### Files and variables

#### File: IgY\_data\_submission.csv

**Description:** 

##### Variables

* bird: unique ID of individual bird from which the sequence was derived from
* status: immunisation group identifier
* tissue: tissue origin for the specific sequence
* CDR3nt: IgY CDR3 nucleotide sequence identified in the specific tissue of the specific bird
* CDR3aa: corresponding (translated) CDR3 amino acid sequence
* count: number of sequence reads identified in the tissue sample

#### File: IgM\_data\_submission.csv

**Description:** 

##### Variables

* bird: unique ID of individual bird from which the sequence was derived from
* status: immunisation group identifier
* tissue: tissue origin for the specific sequence
* CDR3nt: IgM CDR3 nucleotide sequence identified...