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Virology & Molecular Diagnostics – List of Tests and Preferred

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Virology & Molecular Diagnostics – List of Tests and Preferred Virology & Molecular Diagnostics – List of Tests and Preferred Specimens July 2021 The following tables show recommended specimen(s) and procedures used for pathogen detection or serological analysis in the Virology, Molecular Diagnostics and Serology sections of the Animal Health Centre. If you are unsure of the suitability of a specimen for a particular disease or pathogen, please contact the Animal Health Centre Laboratory at 604-556-3003 or email [email protected]. Follow guidelines for Submission of Specimens for Virology and Molecular Diagnostics for proper collection and submission of specimens. ABBREVIATIONS: AGID Agar Gel Immunodiffusion ELISA Enzyme Linked Immunosorbent Assay EM Electron Microscopy HI Hemagglutination Inhibition PCR Polymerase Chain Reaction VI Virus Isolation VN Virus Neutralization 1 Virus AVIAN Serology Virology/Molecular Disease/Pathogen Specimen [Volume of serum Diagnostics Methods needed = 0.5ml/bird] Avian Adenovirus (Inclusion Body Hepatitis, Liver, spleen AGID (Adenovirus PCR, VI, EM Hemorrhagic Enteritis) group-1) ELISA (HEV) Avian Astrovirus (Chicken astrovirus) Kidney, liver, proventriculus, intestine/cecum PCR Avian Bornavirus (Proventricular Dilatation Crop, proventriculus, brain PCR Disease) Avian Encephalomyelitis virus (AE) Brain, pancreas, gizzard PCR, VI, EM ELISA Avian Infectious Bronchitis virus (IBV) Trachea/bronchus, tracheal swab, lungs, kidney, fecal swab, cecal PCR, VI, EM ELISA tonsil Avian Infectious Laryngotracheitis virus (ILT) Trachea, tracheal swab, lungs, eyelid PCR, VI, EM ELISA Avian Influenza (AI) virus Oropharyngeal swab, cloacal swab, trachea, spleen, PCR, VI, EM ELISA, AGID lungs, kidney, brain, cecal tonsil Avian Nephritis virus Kidney PCR Avian Paramyxovirus (APMV)- 1 (Newcastle Trachea, Oropharyngeal swab, lungs, brain, proventriculus, PCR, VI, EM ELISA Disease) cecal tonsil, cloacal swab, spleen, kidney Avian Pneumovirus Trachea, lung PCR Avian Polyoma virus Feather pulp, skin, lung, liver, kidney, whole blood, feces, PCR, EM cloacal swab Avian Reovirus (Enteric and Respiratory) Intestine, pancreas, feces, trachea, lung PCR, VI, EM ELISA Avian Reovirus (Viral arthritis) Joint swab, tendons, heart (chicks) PCR, VI, EM ELISA Chicken Anemia virus Bursa, thymus, bone marrrow, feces PCR ELISA Duck Viral Enteritis Liver, spleen, intestine, cecal tonsil PCR, VI Fowl Pox virus Skin lesions PCR, EM, VI Hemorrhagic Enteritis See Avian Adenovirus Infectious Bursal Disease virus Bursa PCR, VI ELISA Pigeon Circovirus Feces, bursa PCR Proventricular Dilatation Disease (avian Crop, proventriculus, brain PCR bornavirus) Psittacine Beak & Feather virus Feather pulp, skin, bursa, thymus, feces, whole blood PCR 2 Psittacine Herpes virus (Pacheco’s Disease) Lung, liver, spleen, feces, whole blood PCR, VI Reticuloendotheliosis virus Buffy coat (whole blood), tumor tissues, spleen PCR Turkey Coronavirus Feces, intestine, bursa PCR, EM West Nile Virus Brain, cloacal swab, choanal swab, liver, kidney, spleen PCR BOVINE Nasal swabs, lesions, whole blood, spleen, lymphnodes or bone Blue Tongue virus PCR ELISA marrow Bovine Adenovirus Type 1,2,3,4-8 Nasal swab, feces PCR, VI, EM Bovine Coronavirus Nasal swab, lung, trachea, feces PCR, EM VN Nasal swab, conjunctival swab vaginal swab, trachea Bovine Herpesvirus 1 (BHV-1, IBR, IPV) Fetus: lung, liver, kidney, adrenal gland, placenta PCR, VI, EM VN Lesions (scrapings, scabs), respiratory tissues, nasal swabs, PCR, VI, EM Bovine Herpesvirus 4 secretions, whole blood Bovine Papillomavirus Lesions PCR, EM Bovine Parainfluenza 3 Virus Nasal swab, lung PCR, VI VN Bovine Parvovirus Feces, intestine PCR, EM Bovine Respiratory Syncytial Virus (BRSV) Nasal-pharyngeal washings, deep nasal swab, lung PCR, VI, EM VN Bovine Rotavirus Feces, small intestine PCR, EM Buffy coat (10 ml whole blood), serum, feces, intestine, Peyer’s Bovine Viral Diarrhea Virus (BVDV) Types 1 & 2 patches, spleen, mesenteric lymph node, lung, milk; Fetus: lung, PCR, VI, EM VN liver, spleen, thymus, thyroid, placenta, fetal fluids Infectious Bovine Rhinotracheitis (IBR) see Bovine Herpesvirus 1 Malignant Catarrhal Fever (MCF) Wildebeest Buffy coat, tonsil, lymph node, kidney, liver, brain PCR Parapoxvirus Lesions PCR, EM Bovine Torovirus Feces PCR, EM Bovine IgG/ IgM Neonates: Serum RID OVINE & CAPRINE Nasal swabs, lesions, whole blood, spleen, lymphnodes or bone PCR ELISA Blue Tongue virus marrow Border Disease virus Buffy coat (whole blood), lymphoid tissue, brain PCR Caprine Arthritis Encephalitis (CAE) Joint swab, buffy coat (whole blood), brain PCR ELISA 3 Caprine Herpesvirus 2 Buffy coat (whole blood), tonsil, lymph node PCR Ovine Herpes 2 virus (Malignant Catarrhal Fever) Buffy coat (whole blood), tonsil, lymph node PCR (MCF - Sheep) Ovine Progressive Pneumonia virus (OPP) Buffy coat (whole blood) PCR ELISA Ovine Respiratory Syncytial Virus Nasal swab, lung PCR Parapoxvirus (ORF virus, Contagious Ecthyema) Lesions PCR, EM EQUINE Equine Adenovirus pneumonia Nasal swab, lung VI Equine Coronavirus, Rotavirus Feces EM Adult: Deep nasal swabs, conjunctival swab, whole blood (buffy Equine Herpes Virus 1 coat), lung, spinal cord, brain PCR, VI VN Fetus: Liver , lung Equine Herpes Virus 2 Nasal swabs, buffy coat (whole blood) PCR Equine Herpes Virus 3 Swabs from genital/oral lesions PCR Equine Herpes Virus 4 Nasal swabs, conjunctival swab PCR Equine Influenza virus Nasal swab, tracheal wash, lung PCR, VI, EM Equine infectious anemia (EIA) ELISA Equine rhinitis A virus (Equine Rhinovirus 1) Nasal swab, tracheal wash, lung PCR Adult: lung, thymus, whole blood (buffy coat), Equine Viral Arteritis (EVA) mesentery lymph node, liver, spleen PCR, VI VN Fetus: lung, spleen, thymus, placenta, liver Whole blood, cerebrospinal fluid, cerebrum, brain stem, lung, Western Equine Encephalomyelitis (WEE) PCR liver, kidney, spleen, visceral lymph nodes Brain, spinal cord, cerebrospinal fluid for horse, other species West Nile Virus have different site predilection for virus accumulation, kidney, PCR liver, heart, etc. Equine IgG/ IgM Serum, Fetus: heart blood RID PORCINE African swine fever virus Spleen, tonsils, lymph nodes, kidney, liver PCR Hemagglutinating Encephalomyelitis Brain, upper spinal Cord VI Porcine Circovirus 1 & 2 a, b Feces, nasal secretions, lung, oropharyngeal swab, buffy coat PCR Porcine Epidemic Diarrhea Virus (PEDV) Feces, intestinal contents, intestine PCR 4 Porcine Delta Coronavirus Feces, intestinal contents, intestine PCR Porcine Parvovirus Fetus: lung. Liver, kidney, spleen, placenta PCR, EM Porcine Reproductive & Respiratory Syndrome Adult: Serum, blood swab in saline, lung, tonsil PCR (PRRSV) Fetus: lung, spleen, thymus, thoracic fluid Intact vesicles, Vesicular fluid, scrapings of vesicular lesions, Seneca Valley Virus (SVV) PCR serum Swine Influenza virus Nasal swab, trachea, lung PCR, VI, EM HI, VN Torovirus-Porcine Feces PCR Transmissible Gastroenteritis Virus (TGE) Feces, small intestine (Jejunum) PCR, EM VN CANINE & FELINE Canine Adenovirus Type 1 (Infectious Canine Liver, feces PCR, VI, EM Hepatitis) Canine Adenovirus Type 2 (Canine Respiratory Nasal swab, conjunctival or pharyngeal swab PCR, VI adenovirus) Canine Coronavirus Feces, fecal swab PCR, EM Buffy coat (whole blood), lung, kidney, liver, nasopharyngeal Canine Distemper virus swab, conjunctival swab PCR, VI, EM VN Canine Herpes virus Lung, liver PCR Canine Influenza virus Nasal swab, lung PCR Canine Parainfluenza Virus (Kennel Cough) Nasal swab, tracheal swab, trachea PCR Canine Parvovirus 2 a,b,c Fecal swab, feces, intestine PCR Feline Calicivirus Nasal swab, pharyngeal swab, lung PCR Feline Coronavirus Peritoneal fluid spleen, kidney, lung, feces PCR, EM Feline Herpesvirus-1 Pharyngeal swab, nasal swab, lung, conjunctival swab PCR, EM Feline Immunodeficiency virus Whole blood PCR Feline Leukemia Virus Whole blood (1 ml) PCR Feline parvovirus (Feline Panleukopenia virus) Small intestine, kidney, liver PCR FISH & AQUATIC ANIMALS Acipenserid herpesvirus 1 (AciHV-1) (White Skin lesions PCR Sturgeon Herpesvirus-1) Acipenserid herpesvirus 2 (AciHV-2) (White Skin lesions PCR Sturgeon Herpesvirus-2) 5 Betanodavirus Heart, kidney, spleen PCR Cyprinid herpesvirus 3 (CyHV-3) Gill, kidney PCR Epizootic Haematopoietic Necrosis virus (EHNV) Kidney, spleen, liver PCR, VI, EM Infectious Hematopoietic Necrosis Virus (IHNV) Kidney, spleen, liver, gills, mucus, whole fish PCR, VI, EM Infectious Pancreatic Necrosis virus (IPNV) Pyloric caecum, spleen, kidney, brain PCR, VI, EM Infectious Salmon Anemia virus (ISAV) Gills, heart, liver, kidney, spleen PCR Koi Herpes virus (KHV) Gill, kidney PCR Whole blood, nasal, pharyngeal or ocular swabs, trachea- Phocine Distemper virus PCR bronchial lymph nodes, spleen, liver, kidney, lung and brain Piscine myocarditis virus (PMCV) Heart PCR Piscine Orthoreovirus (PRV) Heart, kidney, liver, spleen, gills PCR Salmon Alphavirus (SAV) Organs, viremic serum PCR Salmonid Herpes virus-1 (SalHV-1) Liver, kidney, spleen PCR, VI, EM Whole blood, nasal, pharyngeal or ocular swabs, trachea- Seal Herpes virus PCR bronchial lymph nodes, spleen, liver, kidney, lung and brain Whole fish (small fish - less than 4 cm), viscera including the Spring Viremia of Carp virus (SVCV) kidney and encephalon from fish 4 to 6 cm long, kidney, PCR spleen, liver, gills and encephalon from larger fish Taura Syndrome Virus (TSV) Haemolymph, pleopods, whole small shrimp PCR Viral Hemorraghic Septicemia Virus (VHSV) Kidney, spleen, liver, brain, whole fish PCR, VI, EM Samples of or from the pleopods, gills,
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