faculty, staff, & students of isu vdl
DESCRIPTION
Emerging Coronaviruses in US Swine “Diagnostic Lab Update” RB Baker, R Main, & K Mueller Department of Veterinary Diagnostic and Production Animal Medicine , Veterinary Diagnostic Lab, Iowa State University, Ames, IA 50011. Faculty, Staff, & Students of ISU VDL. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/1.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Emerging Coronaviruses in US Swine“Diagnostic Lab Update”
RB Baker, R Main, & K Mueller
Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Lab, Iowa State University, Ames, IA 50011
![Page 2: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/2.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Faculty, Staff, & Students of ISU VDL
≈22 Faculty, 100 Technical Staff, & 20 Graduate Students/Residents
![Page 3: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/3.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Serving Food Animal Agriculture Comprehensive Diagnostic Service, Teaching, and Discovery
(Iowa’s only Full-Service & Fully Accredited Veterinary Diagnostic Laboratory)
Processing 55,000+ cases/year from livestock producersApplying world-class technology to real-world problems
![Page 4: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/4.jpg)
Veterinary Diagnostic LaboratoryIowa State University
≈ 75% Swine, 10% Bovine, 10% Poultry, + 5% Everything Else
![Page 5: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/5.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Where the Pigs Are Located in US
≈ 500,000 pigs/week imported to IA to be grown
![Page 6: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/6.jpg)
Total Positive PEDv Cases (NAHLN)Seems to very closely resemble the US pig density map reflecting PEDV’s broad dissemination across the US
![Page 7: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/7.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Porcine Coronaviruses in US Swine
TGE: Transmissible GastroenteritisPEDV: Porcine Endemic Diarrhea VirusPDCoV: Porcine Deltacoronavirus
* Field reports suggest it to be a pathogen* Koch’s postulates yet to be fulfilled
-----------------------------------------------------------------------------------------------------------------------------
PRCV = Porcine Respiratory Coronavirus* Seems to be more of a friend than a foe
Porcine enteric disease picture in the US has rapidly become more complex
![Page 8: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/8.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Porcine Coronavirus Diagnostic Specimens(TGE, PEDV, & most recently PDCoV)
• Intestine (Fresh & Fixed)• Feces• Fecal Swabs• Oral Fluids • Serum (Antibody)
Antemortem diagnostic tools are increasingly used (especially Oral fluids & Molecular Dx) to monitor the heath status of US swine in real-time.
![Page 9: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/9.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Porcine Coronavirus Serology (Antibody Testing)
• PEDV – IFA (labor intensive, subjective, but it has been fairly robust)
• PEDV-Elisa (only routine @ UMN that I’m aware)– Duration of detectable antibody response needs to be understood with PEDV
– Others In Development (ISU, SDSU, et al.) – Commercially Available PEDV Elisa’s → Very Poor
• TGE-PRCV Differential Elisa• PDCoV = No Assays Available
![Page 10: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/10.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PEDV IFAPrimary PEDV Antibody Detection Assay Used Today @ ISU VDL
In-House Experimental PEDV Elisa Coming Soon
• Indirect Fluorescence Antibody Test (IFA)– Serology / Antibody Based Assay– Screening assay for antibody at 1:40 dilution
(positive/negative)– 4-fold dilution (40, 80, 160, 320)– Limitations
• Limited correlation between IFA titer and protective immunity• IFA antibody duration is short• Difficult to correlate IFA titer with success of feedback
Dr. Kyoung-Jin Yoon, ISU-VDLDr. John Johnson, ISU-VDL
![Page 11: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/11.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Yoon, Madson, Magstad, Labois, et al – experimentally infected with PEDV.
![Page 12: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/12.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PEDV & TGEV Diagnostics• Immunohistochemistry (IHC)
– Valuable tool, but much less sensitive than PCR– Detection varies based on timing of infection
• Virus Isolation (VI)– Difficult and time consuming– Success rate very low
Late PEDv infection (~36 hrs PI): Severe villus atrophy & loss of
absorptive epithelium
(Source: Schwartz, Madson, Magstad et al.)(Source: Dr. Jianqiang Zhang, ISU-VDL)
Late PEDv infection (~36 hrs PI): Few infected cells remain (brown
stain) & absorptive cells destroyed PDCoV = Presently No IHC or Success with VI
![Page 13: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/13.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Porcine Coronavirus Molecular Diagnostic Assays @ ISU VDLRed = New Assays in Past 12-months
• TGE – PCR• PEDV – PCR• PEDV Differential – PCR
– Original US strain vs. more recently identified variant
• PDCoV – PCR• Pan-Corona – PCR (Discovery – Yoon et al)
• PEDV Sequencing– S1 Gene (Routine)– Whole Genome (Research)
• PDCoV Sequencing– (Research to date)
↑ Sensitive, Semi-quantitative, Same-day testing, Used Extensively
![Page 14: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/14.jpg)
Veterinary Diagnostic LaboratoryIowa State University
![Page 15: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/15.jpg)
15-A
pr29
-Apr
13-M
ay27
-May
10-Ju
n23
-Jun
7-Ju
l21
-Jul
4-Au
g18
-Aug
1-Se
p15
-Sep
29-S
ep13
-Oct
27-O
ct10
-Nov
24-N
ov8-
Dec
22-D
ec5-
Jan
19-Ja
n2-
Feb
16-F
eb2-
Mar
0
50
100
150
200
250
300
350
Positive PEDv Cases per Week by Farm Type(Data Collated by USDA NAHLN)
UnknownGrow-FinishSow
Date by Week
# PE
Dv
Posi
tive
Case
s
**black lines represent the total number of positive cases for that week
![Page 16: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/16.jpg)
15-A
pr29
-Apr
13-M
ay27
-May
10-Ju
n24
-Jun
8-Ju
l22
-Jul
5-Au
g19
-Aug
2-Se
p16
-Sep
30-S
ep14
-Oct
28-O
ct11
-Nov
24-N
ov8-
Dec
22-D
ec5-
Jan
19-Ja
n2-
Feb
16-F
eb2-
Mar
0
1000
2000
3000
4000
5000
6000
Cumulative Positive PEDv Cases by Farm Type
UnknownGrow-FinishSow
Date by Week
# PE
Dv
Posi
tive
Case
s
![Page 17: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/17.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PEDV: DiagnosticsPolymerase chain reaction (PCR)
• Target: Nucleoprotein (ISU) or Matrix– Targets the conserved portion of the genome
• PCR tests are very sensitive and specific– Detect small amounts of target (virus) in the sample– Does not require much fecal content for detection
• Same day testing• Sample types = Intestine, Feces, Fecal Swabs, Oral Fluids• Tests require interpretation
– Based on clinical presentation, sample type, location, etc.– Is the test outcome what you expected?
3’ORF1a
ORF1bS ORF3 M
N
frameshift
E
L AAA
Dr. Jianqiang Zhang, ISU-VDL
Cycle threshold values: Range: 8-12 in acutely
affected, neonatal pigletsLots of PEDV!
![Page 18: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/18.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PEDV: DiagnosticsPEDV Sequencing• Spike protein sequence
– Variable portion of genome– Determine genetic relatedness of PED viruses– Evaluate genetic evolution
• Sequencing at ISU-VDL– S1 gene: 2.2 kb
• Highly variable portion of spike gene being used for routine sequencing for epidemiological purposes.
![Page 19: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/19.jpg)
Dr. Jianqiang Zhang, ISU-VDL
Two Distinctly Different Groups of PEDVs Circulating in US
• January 2014 – ISU VDL S1 Sequencing– 15 PEDV positive cases– 10 cases shared 99.1-100% nucleotide
identities to PEDV strains identified in US swine since April 2013
– 5 cases shared 99.6-100% nucleotide identities to each other but only 93.4-94.6% nucleotide identities to the originally identified US strain
![Page 20: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/20.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PEDV Variant: Epidemiology• January 2014 – ISU VDL retrospective testing
– 183 random PEDV PCR positive fecal samples from ISU VDL cases submitted May to September 2013
– 6 of 183 cases were positive “PEDV variant” – Five of the 6 PEDV variant positive cases were submitted in May 2013
and the other in early June
• In retrospect, both PEDV strains have been present and circulating in US since April/May 2013.– Earliest PEDV positive case identified in the US was submitted to the
ISU VDL on April 15, 2013.
![Page 21: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/21.jpg)
Veterinary Diagnostic LaboratoryIowa State University
PDCoV• PDCoV not PEDV or TGEV or PRCV
– Delta vs. Alpha Coronaviruses– Doesn’t appear to be any cross-protection
• Vomiting and diarrhea (Field/Diagnostic Reports)
– Similar clinical signs and lesions to PEDV/TGE– Reportedly more transient &/or less severe – Koch’s postulates yet to be fulfilled
• ISU-VDL Available Assays– PDCV PCR is currently offered– PDCV sequencing becoming available
• Limited retrospective testing on PDCoV completed to date
Alphacoronavirus: PEDV
Deltacoronavirus: PDCV
![Page 22: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/22.jpg)
Veterinary Diagnostic LaboratoryIowa State University
0
2
4
6
8
10
12
14
16
18
Positive PDCoV Cases @ ISU VDL per Week by Farm Type
Unknown
Grow-Finish
Sow
Date by Week
# PD
CoV
Posi
tive
Case
s
2-17-14Began PDCV PCR
Testing at ISU VDL
![Page 23: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/23.jpg)
Veterinary Diagnostic LaboratoryIowa State University
22-D
ec
29-D
ec
5-Ja
n
12-Ja
n
19-Ja
n
26-Ja
n
2-Fe
b
9-Fe
b
16-F
eb
23-F
eb
2-M
ar
9-M
ar
16-M
ar
0
10
20
30
40
50
60
70
80Cumulative Positive PDCoV Cases by Farm Type
UnknownGrow-FinishSow
Date by Week
# PD
CoV
Posi
tive
Case
s
2-17-14Began PDCV PCR
Testing at ISU VDL
![Page 24: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/24.jpg)
Veterinary Diagnostic LaboratoryIowa State University
ISU VDL PDCoV Positive Swine CasesWeek Received
@ VDL Total # PCR
Positive Cases
Farm State
IA IL IN MI MN MO NC NE OH OK PA ? 12/22/13 1 1
12/29/13
1/5/14
1/12/14
1/19/14 2 1 1
1/26/14
2/2/14 2 1 1
2/9/14 6 4 1 1
2/16/14 10 6 1 1 1 1
2/23/14 12 2 1 5 1 1 1 1
3/2/14 14 1 5 1 3 1 1 1
3/9/14 17 8 1 1 1 3 1 1 1
3/16/14 8 3 1 3 1
Total 71 26 10 7 1 3 9 4 3 3 1 3 1
**totals include biological samples only--no environmental or feed samples are included in the this data
![Page 25: Faculty, Staff, & Students of ISU VDL](https://reader033.vdocuments.mx/reader033/viewer/2022061616/568130a1550346895d969e89/html5/thumbnails/25.jpg)
Veterinary Diagnostic LaboratoryIowa State University
Emerging Coronaviruses in US Swine“Diagnostic Lab Update”
Lots New, Lots Going On!
Thank YouQuestions ?