Dr. Declan Schroeder - Molecular Diagnostics: Present and Future

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Information about Dr. Declan Schroeder - Molecular Diagnostics: Present and Future

Published on October 31, 2018

Author: trufflemedia

Source: slideshare.net

1. Molecular Diagnostics: Present and Future Declan Schroeder dcschroe@umn.edu Molecular Virologist Veterinary Population Medicine Leman conference St Paul, 17-18 September 2018

2. 1977 1986 1995 20051998 2007 bp Gbp THROUGHPUT 20152011 2010

3. Hassan Magboul - YouTube Yes Yes No No Can you Do something about it ? Do you have a problem? Then Why Worry?Sequence ! Then Why Worry

4. Sample Types Tissue, Tissue Homogenate, Blood/Serum, Feces, surface tissues Swabs, Oral Fluids, Processing fluids, Food/water/air & environment (abiotic/biotic) Sequencing Sanger, Illumina (Novaseq, HiSeq, MiSeq, iSeq, & Miniseq), PacBio & MinION Decision tree metagenomics Nucleic Acid Isolation DNA RNA Isolates (pathogen) genomics Library PrepPCRBarcoding Microbiome/ Pathogen discovery Transcriptomics (RNAseq) RT-PCR

5. Genome Assembly (reference or de novo) Comparative Genomics Bioinformatic Pipelines (Linux or off-the-shelf) Decision tree (continued)

6. www.mba.ac.uk

7. Infection Death (individual/population) Assymptomatic Infection Disease free (individual/population) Healthy (individual/population) The power of molecular diagnostics

8. Wilfert et al. 2016 59% ↓ 1947 2005 DWV

9. Infection Death (individual/population) Assymptomatic

10. Definition a virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche from Virus Taxnomy by 8th ICTV Report

11. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Lauring AS, Andino R (2010) Quasispecies Theory and the Behavior of RNA Viruses. PLoS Pathog 6(7): e1001005. doi:10.1371/journal.ppat.1001005 & master variants

12. Figure 1. RNA viruses exist as a quasispecies. Lauring AS, Andino R (2010) Quasispecies Theory and the Behavior of RNA Viruses. PLOS Pathogens 6(7): e1001005. doi:10.1371/journal.ppat.1001005 http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001005

13. Family Picornaviriales Genus Iflavirus Species Deformed Wing Virus Varroa destructor virus 1 Deformed Wing Virus Strains Deformed wing virus Varroa destructor virus 1 Kakugo virus Type A Type BVariants Type C

14. * * Type B Type A Type C 319 Years 181 Years

15. DWV strain diversity 1.E+11 1.E+08 1.E+10 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 NumberofDWVcopiesperbee * DWV strain diversity 1.E+11 1.E+08 1.E+10 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 1.E+11 1.E+08 1.E+10 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 NumberofDWVcopiesperbee * 0 0 0 <1 <2 >3Varroa exposure time (years) -- Location Year DWV prevalence DWV strain diversity 2009 2009 2009 2009 2010 2009 Kauai Maui Big Is. Big Is. Big Is. Oahu 0 0 0 <1 <2 >3Varroa exposure time (years) 0 0 0 <1 <2 >3Varroa exposure time (years) -- Location Year DWV prevalence DWV strain diversity 2009 2009 2009 2009 2010 2009 Kauai Maui Big Is. Big Is. Big Is. Oahu 0 0 0 <1 <2 >3Varroa exposure time (years) -- Location Year DWV prevalence DWV strain diversity 2009 2009 2009 2009 2010 2009 1.E+08 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 NumberofDWVcopiesperbe * Kauai Maui Big Is. Big Is. Big Is. Oahu 0 0 0 <1 <2 >3Varroa exposure time (years) 0 0 0 <1 <2 >3Varroa exposure time (years) -- Location Year DWV prevalence DWV strain diversity 2009 2009 2009 2009 2010 2009 1.E+08 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 1.E+08 1.E+09 1.E+07 1.E+06 1.E+05 1000 1.E+04 100 NumberofDWVcopiesperbe * Kauai Maui Big Is. Big Is. Big Is. Oahu Type A

16. Swindon Hawaii No DWV Type C

17. Kevill & Martin

18. Baltimore Classification BLV DWV & PPRSV EhV & LdV SIV

19. Acknowledgements • Agricultural Research, Education, Extension and Technology Transfer Program (AGREETT) • Minnesota Department of Agriculture

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