This study analyzed 9,090 nasal swabs from piglets on 52 farms in 7 states to determine the impact of influenza vaccination on genetic diversity. Whole genome sequencing was performed on 391 samples. Multiple subtypes were found circulating within herds. Analysis of molecular variance showed that vaccination does not appear to be a major driver of influenza variability in these herds. Instead, diversity seems influenced by other unknown factors like co-circulation of different virus strains through new introductions. The findings imply that efforts should focus on decreasing new virus introductions to reduce pig influenza diversity.

1. Is Influenza vaccination a key
driver of influenza genetic
diversity in piglets?
Jayaveeramuthu Nirmala, Andres Perez, Marie Culhane, Matt
Allerson, Srinand Sreevatsan, Mitchell Kinney, Alicia Mohr and
Montse Torremorell
University of Minnesota

2. Influenza control
* Vaccination:
- Reduces lesions
- Reduces transmission rates
* Vaccination is thus the cornerstone of influenza control
* Influenza evolves constantly, warranting new vaccines

3. *9,090 nasal swabs from piglets-seven states
*52 Farms
*Sampled over a period of 6 months
Materials

4. * No vaccination
* Mass vaccination
* Pre-farrow vaccination
* Both commercial and autogenous vaccine use
Treatments

5. Whole Genome Sequencing-391 samples from 23 farms
* 8 samples/farm/month (If < 10, all the samples were sequenced)
* Samples chosen randomly within a farm (Ct Values 16.04-35.57)
*Whole genome amplified-from the total RNA of nasal swabs directly
*250 bp PE run-HiSeq 2500 rapid chemistry
*De novo assembly & reference genome alignment/FLAN Annotation tool
*AMOVA (ANALYSIS OF MOLECULAR VARIANCE)

6. Multiple subtypes encountered in the samples
101
101
95
35
28
17
12

7. Analysis of Molecular Variance (AMOVA)
* Statistical model for the assessing molecular variation in
a single species, typically biological (Excoffier, et al.,1992)
* Estimates population differentiation directly from molecular
data by testing hypotheses about such differentiation
*Elucidated from sequence data or phylogenetic trees
*(POPPR) (Kamvar et al., 2014)

8. * Vaccination does not appear to drive IAV diversity and variability
in the herds studied
* Instead, IAV diversity in piglets appears to be influenced by other
unknown factors and cannot be explained by the use of vaccination
alone
* There was tremendous influenza genetic variability with multiple
strains co-circulating within the herds studied
Conclusions

9. Implications
•In this study, vaccine use is unlikely to be a major driver of
influenza virus change
• most diversity appears to be due to co-circulation of different
viruses (new introductions?)
•Efforts should be made to decrease the introduction of new flu viruses in
pigs

10. Acknowledgements
Dr. Fabian Chamba
Dr. Todd Knutson
Dr. Andres Diaz
Samuel Hong
My Yang
This project was supported by Agriculture and Food Research Initiative
Competitive Grant # 2015-67015-23274 from the USDA National Institute of
Food and Agriculture
Dr. Montse Torremorell
Dr. Andres Perez
Dr. Marie Culhane
Dr. Srinand Sreevatsan
Dr. Matt Allerson
Dr. Alicia Mohr
Mitchell Kinney