Post on 25-Jul-2020
transcript
Bioinformaticsand
Comparative Genomics Applications
12OCT2016
Richard H. Scheuermann, Ph.D.Director of Informatics - JCVI
Outline
• Bioinformatics and the Big Data value proposition• Viral database resources
– Influenza Research Database (IRD)– Virus Pathogen Resource (ViPR)
• Comparative genomics applications– Identification of diagnostic regions of Zika and other
human flaviviruses– Identification of virulence determinants of enterovirus D68
What is Bioinformatics?
• And related terms – biomedical informatics, computational biology, systems biology
• Wikipedia– Bioinformatics: an interdisciplinary field that develops and improves on methods for
storing, retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to develop software tools to generate useful biological knowledge.
• NIH Biomedical Information Science and Technology Initiative Consortium (BISTIC)
– Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.
– Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.
Biological data types and analysis objectives
• Genomics– Nucleotide genome sequences, metagenomic sequences– Gene finding, functional annotation, homology determination, sequence alignment, comparative analysis, phylogenetic
inferencing, association analysis, mutation functional prediction, species distribution analysis• Transcriptomics
– RNA expression levels, transcription factor binding, chromatin structure information– Differential expression, clustering, functional enrichment, transcriptional regulation/causal reasoning
• Proteomics– Proteins levels, protein structures, protein interactions– Protein identification, protein functional predictions, structural predictions, structural comparison, molecular dynamic simulation,
mutation functional prediction, docking predictions, network analysis• Metabolomics
– Metabolite/small molecule levels– Pathway/network analysis
• Imaging– Microscopy images, MRI images, CT scans– Feature extraction, high content screening
• Cytometry– Cell levels, cell phenotypes– Cell population clustering, cell biomarker discovery
• Systems biology– All of the above– Network analysis, causal reasoning, reverse causal reasoning, drug target prediction, regulatory network analysis, information
flow, population dynamics, modeling and simulation
Big DataBIG DATA
Data Science at NIH
Big Data 3 V’s
Variety
No VarietyA/Boston/26/2008
A/Canada-M
B/RV2018/2009
A/Canada-S
K/RV1767/2009
A/Canada-M
B/RV1975/2009
A/Mexico/InD
RE13495/2009
A/Lyon/969/2009
A/M
ichigan/30/2009A/Kanagaw
a/140/2009A/Taiw
an/90262/2011A/England/328/2009
A/England/348/2009
A/England/345/2009
A/England/377/2009
A/England/360/2009
A/England/364/2009
A/England/349/2009
A/England/399/2009
A/England/342/2009
A/England/374/2009
A/England/350/2009
A/Beijing/16/2009
A/California/08/2009
A/California/07/2009
A/Helsinki/490/2013
A/Helsinki/753/2013
A/Helsinki/979/2013
A/California/07/2009
A/California/07/2009
A/California/07/2009
A/California/07/2009
A/England/201/2009
A/California/08/2009
A/California/08/2009
A/California/04/2009
A/Hangzhou/04/2009
A/Pennsylvania/09/2009
A/California/04/2009
A/California/04/2009
A/Hangzhou/06/2009
A/Hangzhou/10/2009
A/Fukuoka-C
/3/2009A/Fukuoka-C
/2/2009A/Fukuoka-C
/1/2009A/Kagoshim
a/1/2009A/California/04/2009
A/California/07/2009
0.01
Big Data
Volume + Variety = Value
Variety = Metadata
DMID Genomics
Courtesy of Alison Yao, DMID
www.viprbrc.org www.fludb.org
Bioinformatics Resource Centers (BRCs)
www.patricbrc.orgwww.eupathdb.org
www.vectorbase.org
IRD Data Summarywww.fludb.org
Virus Pathogen Resource
www.viprbrc.org
Database Query
Analysis Tools
Personal Workbench
Identification of diagnostic regions of Zika and other human flaviviruses
Alex Lee
Zika virus background
Motivation
• Current ELISA and neutralization assays are not conclusive for detecting antibodies against specific flaviviruses due to cross reactivity between related flaviviruses.
• In order to achieve better incidence and prevalence estimates for Zika and other flavivirus infection, can we identify peptide regions in flavivirus proteins that are sensitive and specific for each of the different species co-circulating in endemic areas for detection of serum antibodies?
Genome sequence selection
Mature peptide
prediction
Meta-CATS comparative
analysis
Sensitivity & specificity calculation
Diagnostic peptide region determination
Epitope and structure
prediction
Species X vs other species within the genusZIKV vs DENV1, 2, 3, 4, YFV, WNV, SLEV, JEV
Identification of diagnostic peptide regions
Flavivirus protein sequences
NS1 diagnostic sites
E diagnostic sites
Diagnostic peptide regions for ZIKV
Diagnostic peptide regions for all flaviviruses
Diagnostic peptide regions for all flaviviruses
Group 1 Count Group 2 CountNo. significant sites
(512 total sites)aNo. candidate
diagnostic sitesbNo. 15-mers with at least
3 diagnostic sites
No. 15-mers with at least 3 diagnostic residues and is
surface exposed
Dengue Virus 1(DENV1) 997 All Other 5305 381 34 55 45
Dengue Virus 2(DENV2) 1,000 All Other 5302 379 59 143 94
Dengue Virus 3(DENV3) 1,000 All Other 5302 378 41 87 55
Dengue Virus 4(DENV4) 897 All Other 5405 380 68 149 86
Ilheus Virus (ILHV) 4 All Other 6298 85 38 63 37
Japanese Enchephalitis Virus (JEV) 1,000 All Other 5302 391 48 79 57
St. Louis Encephalitis Virus (SLEV) 178 All Other 6124 355 60 152 93
West Nile Virus (WNV) 993 All Other 5309 379 46 100 59
Yellow Fever Virus (YFV) 162 All Other 6140 382 160 448 254
Zika Virus (ZIKV) 71 All Other 6231 303 82 217 129a Significant sites determined by Meta-CATS group comparison at a p value cutoff of 9.766e-5 (0.05/512)b Candidate diagnostics sites that were significant by Meta-CATS group comparison and showed average sensitivity/specificity above 98%
Summary statistics for E proteins
Group 1 Count Group 2 CountNo. significant sites
(353 total sites)aNo. candidate
diagnostic sitesbNo. 15-mers with at least
3 diagnostic sites
No. 15-mers with at least 3 diagnostic residues and is
surface exposed
Dengue Virus 1(DENV1) 1,000 All Other 3499 250 31 53 28
Dengue Virus 2(DENV2) 1,000 All Other 3499 249 26 51 35
Dengue Virus 3(DENV3) 951 All Other 3548 246 24 45 25
Dengue Virus 4(DENV4) 185 All Other 4314 213 35 63 53
Ilheus Virus (ILHV) 6 All Other 4493 24 23 63 45
Japanese Enchephalitis Virus (JEV) 227 All Other 4272 217 45 112 57
St. Louis Encephalitis Virus (SLEV) 36 All Other 4463 173 50 132 66
West Nile Virus (WNV) 988 All Other 3511 248 35 57 42
Yellow Fever Virus (YFV) 72 All Other 4427 239 115 302 169
Zika Virus (ZIKV) 34 All Other 4465 175 76 233 131a Significant sites determined by Meta-CATS group comparison at a p value cutoff of 1.416e-4 (0.05/353)b Candidate diagnostics sites that were significant by Meta-CATS group comparison and showed average sensitivity/specificity above 98%
Summary statistics for NS1 proteins
0
5
10
15
201 10 19 28 37 46 55 64 73 82 91 100
109
118
127
136
145
154
163
172
181
190
199
208
217
226
235
244
253
262
271
280
289
298
307
316
325
334
343
352
361
370
379
388
397
406
415
424
433
442
451
460
469
478
487
496
505
ZIKV E protein
ab c d
ef g
ab
c
d
e
f
g
Note: Highlighted bars correspond to 15-mers where ZIKV have at least 3 diagnostic residue and is surface exposed
Summary
• Using sequence data and comparative genomics analysis tools in ViPR, identified regions of the E and NS1 proteins that are sensitive and specific for each of the major human flavivirus species
• These regions are now being used to develop peptide arrays for the detection of serum antibodies against the different species for epidemiological analysis of disease outbreaks and spread
• Lee A, et al. (2016) “Identification of Diagnostic Peptide Regions that Distinguish Zika Virus from Related Mosquito-Borne Flaviviruses” PLOS One, submitted.
Identification of virulence determinants of Enterovirus D68 (EV-D68)
Yun Zhang
Enterovirus D68 2014 Outbreak
Mid-August 2014 – mid-January 2015: • 1,153 confirmed cases including 14 deaths in
the US; likely many more cases of mild EV-D68 infections (CDC)
• 103 paralysis cases of unknown etiology in the USo 4/10 paralyzed children in CO were EV-D68
positiveo 2/23 Acute Flaccid Paralysis (AFP) cases in CA
(June 2012 – June 2014) were EV-D68 positive
• EV-D68 positive AFP cases Canada, France, Norway, and Australia
http://media.healthday.com/images/editorial/girlhospital_40286.jpg
http://www.cdc.gov/amd/images/aia-girl-breathing.jpg
Enterovirus D68 in 2016
• On October 3, 2016 the US CDC reported that as of August 2016 there have been 50 cases of confirmed AFM across 24 states
• More than double the 21 cases reported in all of 2015
US AFM cases
• Source - http://www.cdc.gov/acute-flaccid-myelitis/afm-surveillance.html
Enterovirus clinical symptoms
Most infections are asymptomatic
Polioviruses, types 1-3Paralysis (complete to slight muscle weakness)Aseptic meningitisUndifferentiated febrile illness, particularly during the summer
Coxsackieviruses, group A, types 1-24HerpanginaAcute lymphatic or nodular pharyngitisAseptic meningitisParalysisExanthemaHand-foot-and-mouth disease (A10, A16)Pneumonitis of infants"Common cold"HepatitisInfantile diarrheaAcute hemorrhagic conjunctivitis (type A24 variant)
Coxsackieviruses, group BPleurodyniaAseptic meningitisParalysis (infrequently)Severe systemic infection in infants, meningoencephalitis, and myocarditisPericarditis, myocarditisUpper respiratory illness and pneumoniaRashHepatitisUndifferentiated febrile illness
Echoviruses, types 1-33Aseptic meningintisParalysisEncephalitis, ataxia, or Guillain-Barre syndromeExanthemaRespiratory diseaseOthers: DiarrheaPericarditis and myocarditisHepatic disturbance
Enterovirus, types 68-71Pneumonia and bronchiolitisAcute hemorrhagic conjunctivitis (type 70)Paralysis (types 70, 71)Meningoencephalitis(types 70, 71)Hand-foot-and-mouth disease (type 71 )
Fields Virology, 2007
Enterovirus Genome
Non-enveloped+ssRNA
Goal & Analysis Workflow
Are genetic changes in recent D68 outbreak isolates responsible for the increased disease severity and severe neurologic symptoms?
Select all D68 nucleotide and protein sequences
Mature peptide
prediction
Phylogeny-trait
association with BaTS
Meta-CATS, sensitivity & specificity calculation
Comparison with other paralysis-causing
enteroviruses
Functional prediction
EV-D68VP1
Nucleotide Tree
Phylogeny-trait correlation
Objective: Test for phylogeny-trait correlations
Given a discrete trait for each tip in the phylogenetic tree, are more closely related taxa more likely to share the same trait values than we would expect by chance?
Parker J, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics & Evolution8:239-46 BaTS
Bayesian Tip Significance (BaTS)
• Sample posterior distribution of phylogenies produced by BEAST, with the more likely phylogenies sampled more frequently
• For every tree in the sample, calculate the PS, AI, MC statistics forming the posterior distribution of the statistics
• Generate n random trait-taxon association sets - null distribution
• If the median of the null distribution is more extreme than the median of the posterior distribution of the statistics observed, then the p-value is significant
BaTS Algorithm
BaTS results
Candidate genetic determinants
Multiple sequence alignments
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
5’UTR/127T 5’UTR/188A 5’UTR/262C 5’UTR/280C 5’UTR/339T 5’UTR/496G 5’UTR/669C
2C/1G 2C/102V 3D/135S 3D/274K2C/273G 3D/345Q2C/34T
VP2/222T VP3/24A VP1/98A VP1/290S VP1/308N 2A/66N5’UTR/697C
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
5’UTR/127T 5’UTR/188A 5’UTR/262C 5’UTR/280C 5’UTR/339T 5’UTR/496G 5’UTR/669C
2C/1G 2C/102V 3D/135S 3D/274K2C/273G 3D/345Q2C/34T
VP2/222T VP3/24A VP1/98A VP1/290S VP1/308N 2A/66N5’UTR/697C
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
5’UTR/127T 5’UTR/188A 5’UTR/262C 5’UTR/280C 5’UTR/339T 5’UTR/496G 5’UTR/669C
2C/1G 2C/102V 3D/135S 3D/274K2C/273G 3D/345Q2C/34T
VP2/222T VP3/24A VP1/98A VP1/290S VP1/308N 2A/66N5’UTR/697C
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
D68 Fermon
D68:A CA/RESP/10_786 US/KY/14_18953 EVD68/Homo_sapiens/USA/N0051U5/2012
D68:C JPOC10_290 JPOC10_378
D68:B1 CA/AFP/v12T00346 * US/CA/14_6092 * US/CA/14_6100 * US/CO/13_60 * US/CO/14_93 * US/CO/14_94 * EV68/Ontario/C818712/2014 US/MO/14_18947 US/MO/14_18950
D68:B2 US/IL/14_18952 NY73
D70 J670/71
PV Human_poliovirus_1_Mahoney * PV2/Bel_2 * P3/Leon/37 *
A71 AFP2001064/EV71/GX/CHN/2001_71 * AFP2001071/EV71/GX/CHN/2001_71 *
Capsid heterotrimer structure
IRES structure
Coding region
I II III
IV
V
VI
88 124 162 186 220 234 440
448 556
561 625
Variable region
743
Pyrimidine- rich region
GNRA sequence
IRES
262C 280C 339T
188A (185)
127U (123)
496G
CA/AFP/11-1767|2013|USA
CHN/CQ2860/2012|NA|China
2011-21186|11/15/2011|China
2013-0720-6|07/20/2013|China
2011-21282|12/19/2011|China
CA/AFP/v12T04950|2013|USA
CA/AFP/v12T00346|2013|USA
US/CO/13-60-EV-D68|11/2013|USA
EVD68/Homo sapiens/USA/MO41/2014-D68|2014|USA
EV68_Alberta4693_2014-D68|08/31/2014|Canada
EVD68/Homo sapiens/USA/MO12/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO19/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO51/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO8/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO35/2014-D68|2014|USAITA/25702/14|10/27/2014|Italy
BRE1466-FRA14|11/27/2014|France
ITA/25700/14|10/27/2014|Italy
CAE1133-FRA14|10/20/2014|France
ITA/25686/14|10/26/2014|Italy
ITA/25663/14|10/25/2014|Italy
ITA/25185/14|10/20/2014|Italy
ITA/25861/14|10/28/2014|Italy
ITA/23987/14|10/04/2014|Italy
ITA/25571/14|10/24/2014|Italy
NY160|10/05/2014|USA
US/CO/14-86|08/2014|USA
NY329|09/26/2014|USA
EV68/Ontario/C818712/2014|09/15/2014|Canada
CAE1103-FRA14|09/11/2014|France
CF298032_FRA14|10/2014|France
VERS342154_FRA14-nterovirus D68|11/2014|France
VALE2314_FRA14|10/23/2014|France
VALE2315_FRA14|10/23/2014|France
CAE1283-FRA14|10/27/2014|France
EVD68/Homo sapiens/USA/MO33/2014-D68|2014|USA
CAE1428-FRA14|11/25/2014|France
NY210|10/14/2014|USAEVD68/Homo sapiens/USA/MO58/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO38/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO39/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO21/2014-D68|2014|USA
BRE1464-FRA14|10/21/2014|France
BRE1460-FRA14|10/31/2014|France
NY77|09/28/2014|USA
NY278|09/19/2014|USA
CAE1108-FRA14|09/25/2014|France
NY305|09/22/2014|USA
EVD68/Homo sapiens/USA/MO49/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO6/2014-D68|2014|USA
EV-D68/Haiti/1/2014|12/01/2014|Haiti
NY153|10/02/2014|USA
CAE1125-FRA14|10/16/2014|France
LYO1245353-FRA14|11/20/2014|France
LYO014118426101_FRA14|11/12/2014|France
LYO118426101-FRA14|11/12/2014|France
EV-D68/environment/Gainesville/1/2015|09/08/2015|USA
NY316|09/24/2014|USA
NY328|09/26/2014|USA
CA/AFP/v14T04344|2014|USA
EVD68/Homo sapiens/USA/MO18/2014-D68|2014|USAEVD68/Homo sapiens/USA/MO3/2014-D68|2014|USA
US/CA/14-R1|09/2014|USA
EVD68/Homo sapiens/USA/MO30/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO53/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO5/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO44/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO37/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO23/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO25/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO50/2014-D68|2014|USA
NY309|09/23/2014|USA
US/CA/14-6089|08/2014|USA
US/CA/14-6092-EV-D68|08/2014|USA
US/MO/14-18949-EV-D68|08/2014|USA
EVD68/Homo sapiens/USA/MO32/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO27/2014-D68|2014|USA
AMI030176_FRA14-nterovirus D68|10/2014|France
EVD68/Homo sapiens/USA/MO14/2014-D68|2014|USA
US/CO/14-94-EV-D68|09/2014|USA
EVD68/Homo sapiens/USA/MO31/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO2/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO1/2014-D68|2014|USAEVD68/Homo sapiens/USA/MO17/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO48/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO4/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO20/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO56/2014-D68|2014|USA
AMI030123_FRA14-nterovirus D68|09/2014|France
AMI030164_FRA14-nterovirus D68|10/2014|France
VERS339130_FRA14-nterovirus D68|10/2014|France
EVD68/Homo sapiens/USA/MO46/2014-D68|2014|USA
US/CO/14-93|09/2014|USA
EVD68/Homo sapiens/USA/MO57/2014-D68|2014|USA
US/CA/14-6100-EV-D68|10/2014|USA
US/CA/14-6103SIB-EV-D68|10/2014|USA
EVD68/Homo sapiens/USA/MO42/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO26/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO13/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO40/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO10/2014-D68|2014|USA
US/MO/14-18950-EV-D68|08/2014|USA
EVD68/Homo sapiens/USA/MO7/2014-D68|2014|USA
LYO1415548-FRA14|12/12/2014|France
NY275|09/19/2014|USA
NY126|09/28/2014|USAEVD68/Homo sapiens/USA/MO11/2014-D68|2014|USA
EV-D68_STL_2014_12|2014|USA
US/MO/14-18947-EV-D68|08/2014|USA
EVD68/Homo sapiens/USA/MO47/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO24/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO28/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO16/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO15/2014-D68|2014|USA
CF311065_FRA14|11/2014|France
CF287062_FRA14|10/2014|France
US/CA/14-6067|08/2014|USA
EVD68/Homo sapiens/USA/MO60/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO22/2014-D68|2014|USA
NY130|09/30/2014|USA
NY120|09/28/2014|USA
MEX/DGO/2014-InDRE2271|10/16/2014|Mexico
EVD68/Homo sapiens/USA/MO9/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO43/2014-D68|2014|USA
AMI030174_FRA14-nterovirus D68|10/2014|France
EVD68/Homo sapiens/USA/MO54/2014-D68|2014|USA
EV68_Alberta17390_2014-D68|08/18/2014|Canada
EVD68/Homo sapiens/USA/MO45/2014-D68|2014|USA
EVD68/Homo sapiens/USA/MO34/2014-D68|2014|USAUS/MO/14-18948-EV-D68|08/2014|USA
EVD68/Homo sapiens/USA/MO59/2014-D68|2014|USA
EV68/Ontario/C818710/2014|09/15/2014|Canada
NY326|09/25/2014|USA
NY263|09/18/2014|USA
US/CA/14-R2|09/2014|USA
MEX/DF/2014-InDRE2351|10/23/2014|Mexico
NY124|09/29/2014|USA
NY314|09/24/2014|USA
CHN/CQ7170/2014|09/18/2014|China
CHN/CQ5571/2013|10/16/2013|China
CHN/CQ7208/2014|09/22/2014|China
CHN/CQ7280/2014|10/13/2014|China
CHN/CQ7233/2014|09/30/2014|China
2014-R970|10/15/2014|China
CHN/CQ7349/2014|10/22/2014|China
CHN/CQ7174/2014|09/18/2014|China
2014-R0672|09/20/2014|China
CHN/CQ7188/2014|09/11/2014|China
2014-R1011|10/20/2014|China
2014-R1153|10/20/2014|China
EV68_Alberta2985_2014-D68|09/02/2014|CanadaCHN/CQ7214/2014|09/23/2014|China
CHN/CQ7226/2014|09/26/2014|China
CHN/CQ7225/2014|09/27/2014|China
2014-R1357|11/19/2014|China
Beijing-R0132|2014|China
CHN/CQ7283/2014|09/30/2014|China
CHN/CQ7307/2014|10/07/2014|China
CHN/CQ7360/2014|10/25/2014|China0.01
100
100
97
98
61
57
55
LEGENDYear- 2012
201320142015
* AFM + Encephalitis
*
*
**
*
*
*
*
+
***
0.01
Fermon|USA
Clade A
Clade C
Clade B
100
100
100
100
100
100
100
100B1
B2
US/KY/14-18953|08/2014|USA
CA/RESP/10-786|2013|USA
CA/RESP/09-817|2013|USA
EV-D68VP1
Nucleotide Tree
Hypothetical severity distribution
Paralysis in symptomatic:PV - ~3.6%D68 B1 - ~6.9%
Conclusions
• 3 distinct clades of EV-D68 are co-circulating during the recent outbreak• Unique amino acid and nucleotide substitutions were identified in the
recent EV-D68 isolates• Several of the EV-D68 unique substitutions are also found in the equivalent
positions of paralysis-associated poliovirus, EV-D70, and/or EV-A71 isolates
• These substitutions may be responsible for the apparent change in symptomatology associated with the new D68 outbreak
• Zhang Y, et al. (2016) “Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak” Virus Evolution, 2(1):vew015. doi: 10.1093/ve/vew015.
• RPRC Innovation Project - Test affects of these substitutions on IRES function, replication efficiency, and receptor binding using synthetic genomics
Summary
• Brief overview of IRD and ViPR resources• Identification of diagnostic regions of Zika and
other human flaviviruses• Identification of virulence determinants of
enterovirus D68
Team
NIAIDHHSN272201400028C
J. Craig Venter InstituteRichard Scheuermann (PI)Brian AevermannDouglas GreerAlexander LeeLucy StewartYun ZhangBrian Reardon
Northrop GrummanMary Shaffran, Program ManagerEd Klem, Project ManagerZhiping GuSherry HeSanjeev KumarXiaomei LiJason LucasTom SmithBryan WaltersSam ZarembaHongtao Zhao
Univ. AucklandCatherine Macken, Co-PI
Univ. Calif. DavisNicole Baumgarth, Co-PI
Harvard Medical SchoolDavid Knipe, Co-PI
Univ. Texas Medical BranchSlobodan Paessler, Co-PI
Univ. GeorgiaDaniel Perez, Co-PI
Purdue Univ.Richard Kuhn, Co-PI
VecnaChris LarsenAl RamseyGuangyu Sun
Scientific Working GroupGillian Air, Univ. OklahomaRalph Baric, Univ. North CarolinaRuben Donis, CDCNaomi Forrester, UTMBAdolfo Garcia-Sastre, Mt SinaiElodie Ghedin, Univ. PittsburghElliot Lefkowitz, Univ. AlabamaPhil Pellett, Wayne State Univ.David Topham, Univ. RochesterRichard Webby, St Jude
NIAID / DMIDAlison Yao
Data providers