Emerging viruses in Companion Animals. Outline of conversation. Viral evolution will happen. You are the most likely person to discover changes.

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Emerging viruses in Companion Animals Consider diagnostics, pathogens, and pathogenesis Patricia A. Pesavento papesavento@ucdavis.

disease,!and!!!! diagnostic!dilemmas!(circo,!boca,!astro,! Corona,!Giardia,!Campy!etc) Viral evolution will happen.

1 Emerging viruses in Companion Animals Consider diagnostics, pathogens, and pathogenesis Patricia A. Pesavento Outline of conversation 1.!Emergence!pathways!! Viral!evolution:!Parvovirus!! Ecosystem!impact! 2.!Canine!in9luenza! 3.!Diarrhea,!polymicrobial!disease,!and!!!! diagnostic!dilemmas!(circo,!boca,!astro,! Corona,!Giardia,!Campy!etc) Viral evolution will happen. You are the most likely person to discover changes. Our!pets!are!a!relatively!unguarded!interface! 15!million!dogs/cats!vs.!9!million!cows,!280!vs.!3000!veterinarians Polymicrobial!infections Impact!of!medical!intervention Stress

Mechanisms of Emergence!!!! Virus! changes in virulence, episodic epidemics, species-jumping Host! Breeds, medicine, and contact Environment! Anthropogenic Viral Discovery Why do diagnostics?

2 Mechanisms of Emergence!!!! Virus! changes in virulence, episodic epidemics, species-jumping Host! Breeds, medicine, and contact Environment! Anthropogenic Viral Discovery Why do diagnostics? Help the individual animal, help the herd, identify emergence, identify zoonoses Having a diagnosis will result in a better prognosis. REGARDLESS OF WHETHER OR NOT THERE IS A CURE pain& duration&of&disease& time&to&death& Viral& Discovery&

Method Detection Limitation PCR Microarray Metagenomics (massive sequencing) EM specific, sensitive, standard broad range of pathogens (family) almost unbiased unbiased Requires knowledge of target

3 Method Detection Limitation PCR Microarray Metagenomics (massive sequencing) EM specific, sensitive, standard broad range of pathogens (family) almost unbiased unbiased Requires knowledge of target pathogen not broadly available, cost depends on informatics, costly, slow not broadly available, not always specific Culture bacteria biased Serology broad range of systemic pathogens exposure only Viral!discovery!curve Estimate!that!mammals!alone!harbor!at!least!320,000!viruses!waiting!to!be!discovered Anthony S J et al. mbio 2013 Interpretation of results

quantitative PCR Based on the intact presence of genetic material Highly sensitive Highly specific Fast turn-around time for results Many different types of biologic samples can be interrogated

4 quantitative PCR Based on the intact presence of genetic material Highly sensitive Highly specific Fast turn-around time for results Many different types of biologic samples can be interrogated Organism Salmonella Giardia * Canine coronavirus Canine parvovirus 2 Canine distempervirus Campylobacter Clinical signs Fever, sepsis, anorexia, may or may not be hemorrhagic Acute/ chronic/ intermitt ent Acute diarrhea, with vomiting can have fever Acute, hemorrhagic Vomiting, diarrhea Prevalence Found at LOW rates in both nondiarrhetic and diarrhetic animals (<2%) Overall 8% 50% in puppies up to 100% in shelters 15-26% healthy 60% in nondiarrhea in a shelter 73% in diarrhea in a shelter High in identified cases (young, hemorrhagic diarrhea) Not done. GI can be presenting sign Clinical significance significant, zoonotic potential can treat, but don t retest NOT significant usually, but can be significant significant also.campylobacter coli, C.p A gene, C. p E gene, Cryptosporidium Diagnostics of microbes: Microbiology in the post-genomics era Campylobacter!spp!were!isolated!from!5%! dogs!with!diarrhea!and!28%!control!dogs... No!signi9icant!difference!(%!dogs)!Campylobacter! isolated!from!young!dogs!with!and!without! diarrhea.! 58%!of!healthy!dogs!and!97%!of!diarrheic! dogs!shed!detectable!levels!of!campylobacter! spp. Some spp. of Campylobacter are significantly associated with diarrhea, and polymicrobial infections can be important

Polymicrobial infections 10 10 cfu EPEC =

% mortality severe disease increased shedding =

Environmental interaction is unique for every

5 Polymicrobial infections cfu EPEC = inapparent-mild disease tcv 10 4 cfu 7 days EPEC 50 % mortality severe disease increased shedding = Pakpinyo et al, Avian Dis, 2003 Host susceptibility Environmental interaction is unique for every animal Anthropogenic challenges Movement (animals=mismatch.. and pathogens) Bottlenecks eg a simultaneous outbreak of MDR Salmonella Schwartzengrund in US, Denmark, Thailand

Animal-Human Interface KF Hurley 16 Is Vaccination Driving Emergence?

Weidt, et al J Virol. (1995 )November; 69(11): 7147 7151!

Ectodomain of Matrix Protein 2 Darya Zharikova et al J Virol, June (2005), p.

6 Animal-Human Interface KF Hurley 16 Is Vaccination Driving Emergence? Emergence of Virus Escape Mutants after Immunization with Epitope Vaccine G. Weidt, et al J Virol. (1995 )November; 69(11): ! Influenza Type A Virus Escape Mutants Emerge In Vivo in the Presence of Antibodies to the Ectodomain of Matrix Protein 2 Darya Zharikova et al J Virol, June (2005), p , Vol. 79, No. 11! Genogrouping of Vaccine Breakdown Strains of Feline Calicivirus in Japan Ohe et al Vet Res Comm, 31 (2007) ! Case: 1 year old Beagle-cross

C.S. Potten, 1998 1400 cells/villus per day 1400cells/villus/day VILLUS 3500 cells 0 300 cells /crypt/day/j M/J 2 x 10 8 cells shed per small intestine/day Tc»24h (P) Paneth cells Calicivirus,

7 C.S. Potten, cells/villus per day 1400cells/villus/day VILLUS 3500 cells cells /crypt/day/j M/J 2 x 10 8 cells shed per small intestine/day Tc»24h (P) Paneth cells Calicivirus, Coronavirus, Astrovirus, enteroviruses, E. coli, Cryptosporidium, Rotavirus polymicrobial problems Parvovirus detection test? Ag detection (fecal ELISA, aka SNAP) Diarrhea panel (real time quantitative PCR) CBC, Chemistry Antimicrobials Other supportive information Spike gene mutations & host range FPV has not undergone significant changes in antigenic and biological properties since 1920 CPV has undergone significant changes (1978): CPV-2a, CPV-2b, CPV-2c Host range determinant: spike gene (VP2) 6 AA changes differentiate FPV from CPV (80, 93, 103, 323, 564, and 568) 5 AA changes differentiate 2a, b and c from CPV-2 (87, 300, 305, 426, and 555) Host range determinants: AA 93, 375, and 426

8 1.Do newly recognized parvovirus strains have differences in virulence? Reconsidering dogma: What is virulence? CPV 2C Glu-426 mutation (VP2) = 2c Parvovirus Widespread in Europe (2000) and US Vaccine susceptible Ag test valid Decaro N, Desario C, Addie DD, Martella V, Vieira MJ, Elia G, et al. Molecular epidemiology of canine parvovirus, Europe. Emerg Infect Dis 2007 Aug. CPV$2c$in$California: Case Breed Age Type 1 Min pin 2c 2 pit 6 mo CPV310 3 chihuahua 3 mo 2c 4 pit 2 mo 2c 5 chihuahua 6 mo 6 mix 8mo CPV310 7 shepherd <2 mo 2c 8 maltese 6 mo 9 pit 6 mo 2c 10 pit 4 mo 2c 11 pit X 6 mo 2c 12 X 6 mo 2c 13 X 3 mo 2c 14 pitpit 4 mo 2c 15 adult 2c 16 2c 17 2a Dr. Jyothi Robertson, Koret Shelter Medicine Service

9 Mechanisms for rapid occupation by 2c Parvovirus higher virulence more severe? susceptibility in adults? vaccine resistance? lower virulence? shedding can be per gram feces In a day 2 x single dose is 10 5 viruses Endemic(pathogens(of(higher(or#lower#virulence(might(be(successful.

The cat-dog shuffle Cross-Species Transmission of Canine

Panleukopenia Syndrome Christian Leutenegger, DrMedVet, PhD,

, Sacramento, CA Hongwei Liu, MS, Niels C.

10 The cat-dog shuffle Cross-Species Transmission of Canine Parvovirus 2 to Healthy Shelter Kittens and Cats with Feline Panleukopenia Syndrome Christian Leutenegger, DrMedVet, PhD, IDEXX Laboratories, Inc., Sacramento, CA Hongwei Liu, MS, Niels C. Pedersen, DVM, PhD Center for Companion Animal Health, University of California, Davis, CA; 2. Do CPV strains cause disease in privately owned US cats? 3. Can we identify CPV strains in asymptomatic US shelter cats? 4. Does FPV expand its host range and infect US dogs?

FPV vs CPV Assay in Infected Cats Cats can be infected with CPV (2b, 2c) or FPV (CPV-like mutation) Cases: sick cats with clinical diarrhea FPV vs CPV Cust Shelter Universal Parvo # Panel Material

11 FPV vs CPV Assay in Infected Cats Cats can be infected with CPV (2b, 2c) or FPV (CPV-like mutation) Cases: sick cats with clinical diarrhea FPV vs CPV Cust Shelter Universal Parvo # Panel Material Num Desc FPV CPV Call Country Flag PCR Result* 1 JP N FELINE DIARRHEA PANEL COMP FPV / CPV 2 US N FELINE DIARRHEA PANEL COMP CPV 3 US N FELINE DIARRHEA PANEL COMP FPV 4 JP N FELINE DIARRHEA PANEL COMP FPV 5 JP N FELINE DIARRHEA PANEL COMP FPV 6 MX N FELINE DIARRHEA PANEL COMP FPV 7 US N FELINE DIARRHEA PANEL COMP FPV 8 US N FELINE DIARRHEA PANEL COMP FPV 9 KR N FELINE DIARRHEA PANEL COMP FPV 10 JP N FELINE DIARRHEA PANEL COMP FPV 11 US Y FELINE DIARRHEA PANEL COMP FPV 12 US N DIARRHEA PCR COMP PLUS FE FPV 13 JP N FELINE DIARRHEA PANEL COMP FPV 14 US N FELINE DIARRHEA PANEL COMP CPV 15 JP N FELINE DIARRHEA PANEL COMP FPV 16 KR N FELINE DIARRHEA PANEL COMP FPV / CPV 17 JP N FELINE DIARRHEA PANEL COMP FPV 18 US N FELINE DIARRHEA PANEL COMP FPV / CPV 19 US N FELINE DIARRHEA PANEL COMP FPV 20 JP N FELINE DIARRHEA PANEL COMP FPV * CP Value (Cycle point) Privately owned cats, sick Clear identification of canine parvovirus infections! Shelter kittens Clear identification of canine parvovirus 2a, b, and c CPV-2c cannot be explained by vaccine High Parvovirus load in sick and healthy kittens! Privately owned dogs, sick No dog has been identified with FPV infection Parvovirus Types in Shelter Kittens 367 fecal samples for Parvovirus typing (July 10, July 11, January 12) June 2010: 47 June 2011: 217 Janu 2012: 103 Two categories of parvovirus load Low viral load <1.2 million viral equivalents per gram of stool Environmental contamination Vaccine interference (MLV) Carrier with no clinical manifestations High viral load >1.2 million viral equivalents per gram of stool Normally associated with (some sort of) clinical signs Highest viral load detected: 2.38 x (2.38 Trillion)

12 Dora the Labrador 34 A"watermold"story A"watermold"story... help the individual animal help the herd identify emergence identify zoonoses 36

Clinical presentation in dogs herd individual

13 Rice, Golf, and Lawncare? 37 Canine Influenza Two distinct strains of IAV have emerged in domestic dogs, with each circulating widely for several years. Clinical presentation in dogs herd individual Diagnostics Exposure (serology) and viremia (shedding and circulation) Natural history of influenza, myths and predictability

*From where is the isolate? Co-pathogens?

14 Streptococcus, isolation in normal dogs skin conjunctiva oropharynx genital gastrointestinal urinary When is isolation significant? *From where is the isolate? Co-pathogens? Herd Health (Shelter perspective) References: Chalker et al, 2003 Kim et al, 2007 Pesavento et al, 2008 Byun et al 2009 Britton et al, 2010

Frequency has declined over the past 4 years!

15 Canine Influenza Virus H3N8! Data range 2007 April 2015! CRD panel includes 11 infectious agents & 7 quality controls! Frequency has declined over the past 4 years! Chicago CIV H3N8 cluster detected in 2008, single positives in the past 6 years! Other active clusters in Southern California, Texas and New York Establishment"of"influenza"in"new"hosts Parrish"et"al,"

H3N2 Influenza Virus Submissions across the US from March to May 2015 were re-tested with H3N2 real-time PCR in a

5% tested positive April: 871 swabs were tested of which 173 or 19.9% were positive.

New Jersey, n=1 Texas, n=1 Virginia, n=1 Wisconsin, n=3 Data source: unpublished data, IDEXX Laboratories, Inc.

16 H3N2 Influenza Virus Submissions across the US from March to May 2015 were re-tested with H3N2 real-time PCR in a retrospective study March: 949 swabs were tested of which 89 or 9.5% tested positive April: 871 swabs were tested of which 173 or 19.9% were positive. Positive cases: (March 1st May 5th): Alabama, n=2 California, n=1 Illinois, n=222 Indiana, n=2 Michigan, n=3 Minnesota, n=6 New Jersey, n=1 Texas, n=1 Virginia, n=1 Wisconsin, n=3 Data source: unpublished data, IDEXX Laboratories, Inc. Version Canine&Circo*,&Boca*,&and&Kobuviruses Virus&:&Host&Interaction Vasculitis? Diarrhea Pathogen&discovery Kobuvirus Sapovirus Circovirus Bocavirus Amdovirus Discovery*vs.*research*that*determines*causality*and*pathogenesis

17 Vasculitis,&histiocytic&disease Normal"artery Case"1:arteriAs virus 89 FiCV Cap DogCV 2063 bp Rep StCV RaCV CaCV CoCV GuCV BFDV SwCV ORF3 100 GoCV DuCV 100 PCV1 PCV DogCV-UCD3 Blood Canine CV isolate 214 DogCV-UCD2 Feces DogCV-UCD1 Tissue Barbel CV 68 CyCV NG13 Catfish CV CyCV TN CyCV PK5034 CyCV PK5006 CyCV NG chicken 8 CAV Cap PCV bp 0.1 ORF3 Rep

&perfringens&alpha&toxin,&giardia&spp.,&salmonella&spp.,&campylobacter&& jejuni,&and&campylobacter&coli In*blood: Dogs&with&thrombocytopenia& & 16/480&& & & 3.

18 Frequency&of&dogCV&detected&by&real&time&PCR In*feces: healthy&dogs:&&& & & & & & 14/204&& & & 6.9&% diarrheic&dogs&& & & & & & 19/168& & & 11.3&%& & Thirteen&of&19&positives&dogs&(68%)&were&co*infected&with&one&or&multiple&& other&pathogens,&including&canine&enteric&coronavirus,& Cryptosporidium& & spp.&,&c.&perfringens&alpha&toxin,&giardia&spp.,&salmonella&spp.,&campylobacter&& jejuni,&and&campylobacter&coli In*blood: Dogs&with&thrombocytopenia& & 16/480&& & & 3.3% or&neutropenia& (similar&to&that&reported&previously&in&canine&serum&samples&(2.9%,&6/205) One*amplicon*from*blood*samples*had*>10%*nucleotide*distance*to*DogCVAUCD1&2.& Frequency&of&dogCV&detected&by&real&time&PCR Frequency&of&dogCV&detected&by&serology? Bernice Barbour Foundation

Important Tools for Disease Outbreak Investigation and Control

Important Tools for Disease Outbreak Investigation and Control Cracking the Infection Control Code: Using and Interpreting Diagnostic Tests to Control Infectious Diseases in Shelters Dr. Ronald D. Schultz, Professor and Chair Department of Pathobiological Sciences