Order: Nidovirales & Family: Coronaviridae Flashcards
Where does the name Nidovirales come from?
nido = nest
What 3 families make up the order Nidovirales?
- Arteriviridae
- Coronaviridae
- Roniviridae
Morphology and structure of members of Nidovirales:
What is the characteristic appearance of Coronaviridae?
“halo” - surface proteins create an image reminiscent of the solar corona
What are the envelope and genetic structures of Coronaviridae?
enveloped + spike proteins
positive-strand RNA virus with cytoplasmic replication
How does Coronaviridae enter the host cell? What 2 characteristics is it notorious for?
- budding into ER and Golgi
- difficult to propagate in culture
- high frequency of recombination
What are the 2 major reservoirs for Coronaviridae? What are 3 special abilities of certain coronaviruses?
bats and birds
- change tissue tropism
- pass species barriers
- adapt to new ecological niches
What are the 3 major causes of Coronaviridae variation?
- accumulation of point mutations
- poor proofreading capability of RNA-dependent RNA polymerase gene
- possibility of recombination
Classification of Coronaviridae:
What is characteristic of Nidovirales RNA structure?
presence of nested sets of sub-genomic mRNAs
What is the order of the coronavirus genome?
5’-UTR-gene 1 (ORF-1a and 1b)-S (spike; binding)-E (virion assembly)-M (virion assembly, IFN antagonist)-N (virion assembly)-UTR-Poly(A) tail-3’
(conserved among all coronaviruses)
What is the pathogenesis of Coronaviruses?
outer membrane spike proteins arranged in a 6-helix bundle of receptors S1 and S2 are used to latch onto and enter host cells
What host receptors do the spikes of SARS-CoV, MERS-CoV, and IBV bind to?
- ACE2
- DPP4
- Neu5Ac
What is the lifecycle of Coronavirus like?
- attachment to spike protein
- entry via fusion with plasma membrane and endosomal formation
- uncoating
- translation of ORF1a and ORF1b from +RNA using RNA-dependent RNA polymerase
- transport from rER into Golgi
- vesicle formation
- viral release via exocytosis
What are the 8 human Coronaviruses currently known?
- HCoV-229E
- HCoV-OC43
- SARS-CoV
- HCoV-NL-63
- HCoV-HKU1
- MERS-CoV (beta)
- HCoV-44 (enteric)
- SARS-CoV-2 (beta)
How has human Coronaviruses been able to evolve and spread?
- the original Coronavirus present in bats mutated and made it able to spread to animals in close proximity, like camels (MERS-CoV), civet cats (SARS-CoV), and pangolins (SARS-CoV-2)
- further mutations allowed spread to humans and possibly other animals, like pets
What had the SARS-CoV outbreak in 2003 been found to originate from?
mongoose - most deaths in China and Hong Kong (10% case fatality)
(severe acute respiratory syndrome - Betacoronavirus)
What genus does Middle East Respiratory Syndrome Coronavirus (MERS-CoV) belong to? How does MERS-CoV spread?
Betacoronavirus (like SARS-CoV)
- first reported in 2012
from person to person
What is the most common symptom of MERS-CoV infection? What else is noted? What is the fatality rate?
- severe acute respiratory illness with fever, cough, and shortness of breath
- mild respiratory illness
50%
What is the global distribution of MERS-CoV cases like?
LOCAL INFECTION: Saudia Arabia, Qatar, Oman. France, UK
IMPORTED CASES: Spain, Italy, Germany, Tunisia
What lineage of Betacoronavirus does MERS-CoV belong to?
2c
MERS-CoV evolution theories:
MERS-CoV updated hypothesis of transmission:
What animals play a role in MERS-CoV transmission? How does this happen?
Dromedary camels
Dromedary camels are the only animals able to seroconvert to MERS-CoV, especially older individuals
- some can have high titers of MERS-CoV without BCoV reactivity
- some can be infected with BCoV and be identical to MERS-CoV
What are the 2 hypotheses of how SARS-CoV-2 enters host cells? What is able to block both of these pathways?
- endocytic pathway using ACE2 receptor - convalescent serum from SARS-CoV-2 patient
- membrane fusion pathway using TMPR552 and ACE2 - Amiodorone, Camostat mesylate (TMPR552)
What are the 8 most common signs of SARS-CoV-2?
MULTISYSTEM INFLAMMATION
1. bulbar conjunctivitis
2. red and cracked lips
3. cervical and mesenteric lymphadenitis
4. skin rash
5. neurological signs
6. respiratory signs
7. left ventricle dysfunction (100%) - shock, coronary dilatation, pericarditis
8. digestive involvement - nausea, diarrhea
What are the 3 SARS-CoV-2 (D614G, China) variants of concern? What are 3 possible functional changes? What causes these changes?
B.1.1.7 (UK, alpha), B.1.351 (South Africa, beta), P.1 (Brazil, gamma)
- more efficient transmission
- reduced antibody binding and immune protection
- reduced vaccine efficacy against B.1.351 and P.1
- mutations in the S (spike) gene receptor binding domain
In what 2 ways are variants of SARS-CoV-2 labeled by WHO?
- variant of concern (VOC) - increase in transmissibility, change in clinical disease presentations, or decrease in effectiveness of public health and social measures, available diagnostics, vaccines, and therapeutics
- variant of interest (VOI) - community transmission or multiple cases/clusters detected in multiple countries (WHO SARS-CoV-2 Virus Evolution Working Group)
How are testing assay kits using the DIVA concept for SARS-CoV-2 infection?
3 wells containing a control, N protein, and S protein are present on the test
- NAIVE ONLY = lack of immunity, or immunologic memory, to a disease (true negative)
- VACCINATED = control well + S well
- INFECTED = all 3 wells colored
What are some strategies for preventing/treating Coronavirus infection?
- block attachment (anti-S1 antibodies, S2 fusion inhibitors, furin inhibitors, anti-hos cell receptor antibodies)
- block membrane fusion (TMPR522 inhibitors)
- block endosome formation (clathrin-mediated endocytosis inhibitors, cathepsin inhibitors)
- block translation (PLpro and 3CLpro inhibitors, helicase inhibitors)
- block transcription and replication (nucleic acid synthesis inhibitors)
- block rER delivery and Golgi packaging (ERK/MAPK and Pl3K/AKT/mTOR signaling inhibitors)
- target released virion (exogenous IFN-α and IFN-β)
Therapeutic trials of SARS-CoV-2:
What is the tropism of Bovine Coronavirus (BCoV)? When does shedding increase?
epithelial cells of the gut an respiratory tract
winter and at calving
What are the 3 clinical syndromes of Bovine Coronavirus (BCoV)?
- calf diarrhea - yellow liquid diarrhea with mucous and blood clots, dehydration, depression, fever, and recumbency
- winter dysentery - adults with watery and bloody diarrhea, dehydration/depression, fever, anemia, anorexia, drop in milk yield, and respiratory signs
- bovine respiratory disease complex (BRDC) - youngstock with nasal discharge, dyspnea, coughing, fever, and respiratory distress
How are the strains of Bovine Coronavirus (BCoV) causing enteric and respiratory signs different?
belong to the same serotype, but are 2 subtypes with point mutations in the S gene
How does the intensity of clinical signs compare to the kinetics of Bovine Coronavirus (BCoV)?
What was the first known Coronavirus?
Infectious Bronchitis Virus (IBV)
- 1930 in US
What is the tropism of Infectious Bronchitis Virus (IBV)? What 3 samples can be taken for detection?
upper respiratory tract (trachea/bronchi) and reproductive tract of chicken with disease most severe in chicks
- blood - viremia
- nasal secretions
- feces/urine
What are the 3 other secondary organs affected by Infectious Bronchitis Virus (IBV)?
- oviducts
- intestine
- kidney (nephropathogenic strains by serial passage in the cloaca)
- sites of IBV persistence with periodic nasal shedding
What leads to the differences in antigenic properties and virulence of the different strains of Infectious Bronchitis Virus (IBV)?
mutations and recombination
How are younger chicks protected from Infectious Bronchitis Virus( IBV)? What are the 5 most common clinical signs?
maternal antibodies control infection for 3 weeks
- suffocation
- cough
- sternutation
- formation of urate plug
- drop in egg laying
How long can Infectious Bronchitis Virus survive at 56 degrees Celcius? Room temperature? What is used for disinfection?
- 15 mins
- 2-3 days
common detergents
What are 6 common pathologies associated with Infectious Bronchitis Virus (IBV) infection?
- acute catarrhal tracheitis
- sinusitis/air sacculitis
- nephritis
- bronchitis
- local pneumonia
- salpingitis (eggs!)
What are 3 major economic impacts of Infectious Bronchitis Virus (IBV)?
- poor growth performance and mortality due to respiratory infection
- loss in egg production and low-quality egg production
- loss associated with renal damage in broilers and breeder chickens
What are the 3 most common macroscopic lesions associated with the respiratory disease caused by Infectious Bronchitis Virus (IBV)?
- mucus and redness of trachea
- froth in air sacs of older chickens
- yellow/cheesy plug at the tracheal bifurcation in young chicks
What are the 3 most common macroscopic lesions associated with the reproductive disease caused by Infectious Bronchitis Virus (IBV)?
- fluid yolk material in abdomen
- abnormal ovary with misshapen follicles
- production of eggs with ridges/concretions and watery albumen
What are the 2 most common macroscopic lesions associated with the renal disease caused by Infectious Bronchitis Virus (IBV)?
- swollen, pale kidneys with tubules and ureters distended with urate
- urolithiasis
What group is Infectious Bronchitis Virus (IBV) a member of? What is it the main cause of?
group 3 Coronavirus
economic loss in US poultry farms (young chicks and broilers)
Infectious Bronchitis Virus (IBV) clinical presentation:
CHICKENS
How can the laboratory diagnose Infectious Bronchitis Virus (IBV) infection?
- sample collection: nasal swab/secretions, urine, egg, biopsy
- detection of virus by EM
- detection of viral antigens by immunofluorescence, hemagglutinin inhibition test, serum neutralization test
- detection of viral antibodies by ELISA, fluorescent antibody test
- detection of viral RNA by rtPCR
- sequencing of viral genome
What 3 vaccines are available for Infectious Bronchitis Virus (IBV)?
- live attenuated vaccine
- killed vaccine vaccine
- recombination strain
(coccidiosis + IBV combined gel vaccine)
Limitations of IBV vaccines:
What are the most common signs of vaccine reactions to the IBV vaccine?
mildly infected eyes with slightly high temperatures withing ~ 2 days post-vaccination
What is another name for turkey transmissible enteritis? What is its etiology?
Bluecomb Disease
Turkey Coronavirus (TCoV)
What are the 5 characteristics of bluecomb disease?
- catarrhal enteritis
- head cyanosis
- sudden onset
- low mortality
- non-transmissible in nature
(transmissible enteritis - Turkey Coronavirus)
What are the 2 variants of pantropic Canine Coronavirus (CCoV)? What are 5 common pathologies?
CCoV-I and CCoV-II
- extensive lobar pneumonia
- bowel discoloration
- enlargement of the spleen
- necrosis and hemorrhage of liver
- severe atrophy of intestinal villi
How can pantropic Canine Coronavirus (CCoV) infection be diagnosed?
- virus detection in feces by EM
- antigen detections via ELISA and rapid tests
- lateral flow immunoassay
- rtPCR
How is pantropic Canine Coronavirus (CCoV) infection prevented?
vaccines available to protect puppies and adults
- should start at about 6 weeks of age
What are the 2 biotypes of Feline Coronavirus (FCoV)?
- Feline enteric Coronavirus (FECoV) - ubiquitous (domestic and large cats)
- Feline infectious Peritonitis Virus (FIPV) - virulent
How is Feline Coronavirus (FCoV) transmitted? What tropism does it have?
fecal-oral route: cats become persistently infected and continuously/intermittently shed in feces
- litter trays
- fomites
enterocytes - FeCoV
monocytes - FIPV
What plays a key role in the epidemiology of Feline infectious Peritonitis Virus (FIPV)?
healthy carriers able to remain healthy despite systemic infection
What is the most useful diagnostic of Feline infectious Peritonitis Virus (FIPV)? What is the gold standard of FCoV diagnosis?
sampling the effusion, when present
FCoV antigen immunostaining
How is fecal rtPCR used in Feline Coronavirus (FCoV) diagnosis? Antibody tests?
not useful for FIP diagnosis, but can identify FCoV shedders in a cat colony
positive FCoV tests are not confirmatory of FIPV, but absence of FCoV antibodies makes FIPV less likely
How do titers of Feline Coronavirus I and Feline Coronavirus II compare?
type I induces a higher antibody titer with a greater association of clinical signs and/or FIP
What are vaccines against Feline Coronavirus (FCoV) based on?
FCoV type I related antigens
What is the origin of Feline Coronavirus type II?
recombination between FCoV type I and CCoV
What is the pathogenesis of Feline Infectious Peritonitis?
- ingestion of FeCoV with replication in the intestinal epithelium, upper respiratory tract, and resional lymph nodes
- virus is shed and is able to disseminated/replicate in macrophages
- HUMORAL RESPONSE ONLY = not protective; FIP develops, resulting in anorexia, ascites, and fibrinous peritonitis)
- HUMORAL + CELLULAR RESPONSE = partial protection with excretion or complete protection
What are the 2 forms of Feline Infectious Peritonitis?
- WET - effusive; classical form with inflammation of the visceral peritoneum, pleura, and omentum caused by Ag-Ab-complement complex deposition, leading to fluid accumulation (ascites)
- DRY - granulomatous lesions in internal organs, CNS, and eyes (uveitis) —> mesenteric LN, kidneys, meninges with little to no accumulation of fluids in body cavities
What is the characteristic necropsy and cytology findings in the effusive (wet) form of Feline Infectious Peritonitis? What causes the appearance of the effusion?
- fine, granular appearance to the abdominal viscera due to fibrin deposition
- neutrophils, macrophages, lymphocytes
yellow and frothy = high concentration of fibrin in fluid
Dry form Feline Infectious Peritonitis:
What are 4 common clinical signs associated with Feline Infectious Peritonitis?
- ataxia (dry - meninges affected)
- ascites with yellow, frothy effusion
- anterior uveitis with keratic precipitate (dry - eyes affected)
- icterus (wet)
What are the main 3 ways that Feline Infectious Peritonitis if diagnosed?
- detection of viral nucleic RNA by rtPCR - blood, effusion, tissue (liver, spleen), CSF, aqueous humor
- indirect detection of virus - antibody testing on blood, effusion, and CSF
- IHC - FIPR antigen presence in macrophages in effusion
What is Rivalta’s (point-of-care) test? What is a limitation? What was it originally used for?
test tube is filled with distilled water, acetic acid, and a drop of the effusion colored with methylene blue to be tested is added
- dissipation = negative (transudate)
- precipitation = positive (exudate, inflammation)
- positive result is not specific for FIPV, but negative results is useful to rule out FIPV at the point-of-care
originally developed for humans to differentiate transudate from exudate
What vaccine is used for Feline Infectious Peritonitis (and FCoV)?
intranasal vaccine that is a temperature-sensitive mutant of the type II FCoV strain DF2 aimed to induce local mucosal immune response (IgA) at the portal of entry and cell-mediated immunity
- systemic antibody production
In which cats can the Feline Infectious Peritonitis (and FCoV) vaccine be used on?
Ab positive and negative, especially if they are entering an FCoV-endemic environment and are at high risk
- first dose given after 16 weeks of age
- second dose given 3 weeks later
What are the 2 main groups of Coronaviruses affected swine?
- ALPHA - porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine respiratory coronavirus (PRCoV)
- DELTA - porcine deltacoronavirus (PDCoV)
When is mortality highest with transmissible gastroenteritis virus (TGEV) infection? What is its tropism and what does it cause?
100% in piglets less than one week
villous enterocytes of the small intestine - distends intestine with fuid in a thin transleucent intestinal wall
Transmissible gastroenteritis virus (TGEV) on villi:
What is the pathogenesis of transmissible gastroenteritis virus (TGEV) in pigs? How does it affect different parts of the small intestine?
- ingestion of TGEV
- virus is resistant to the low pH of the stomach and trypsin digestion in the intestine, allowing it to pass through
- viral replication takes place in villous epithelium of the jejunum and ileum following ingestion and 6-12 hours in the stomach
walls of jejunum and ileum are affected while the duodenum is left alone
What aspects of the immune system offers the best protection against transmissible gastroenteritis virus (TGEV)? How does the type of vaccine affect immune response?
- secretory IgA (immunity + clearance)
- protective IgA in colostrum
- cell-mediated immunity
IM immunization = humoral IgG = no protection
oral immunization = IgA protection
What is the origin of Porcine Respiratory Coronavirus (PRCoV)? What tropism does it have?
evolved from enteric transmissible gastroenteritis virus (TGEV) with a small mutation in the S gene responsible for tropism
respiratory epithelium and alveolar macrophages + limited GIT
Why is diagnosis of Porcine Respiratory Coronavirus (PRCoV) a challenge? What is a major advantage?
- both share many antigenic sites, so routine serology cannot distinguish between 2 viruses
- PRCV infection could be based on the absence of enteric disease, but this is not definitive
PRCV vaccination/infection induces cross-protection against TGEV
What are 3 important characteristics of Porcine Epidemic Diarrhea virus (PEDV)?
- NOT zoonotic
- NOT a food safety concern
- NOT a new disease, but is new to North America
- 39 states have reported cases as of 2017 since the first outbreak in 2013
What are 3 characteristics of Porcine Epidemic Diarrhea virus (PEDV) infection?
- mortality rate can reach 100% in 3-5 weeks
- affects pigs of all ages, but is most severe in the young
- transmission through fecal-oral route
What is the pathogenesis of Porcine Epidemic Diarrhea virus (PEDV)?
- ingestion of PEDV
- PEDV infects and replicated within enterocytes of the small intestine and cecum, causing enterocyte destruction and atrophy (thin-walled intestine)
- loss of enterocytes destroys the absorptive capability of the small and large intestines, making pigs unable to extract energy from their feed or milk and likely to develop severe malabsorptive osmotic diarrhea
How can Porcine Epidemic Diarrhea virus (PEDV) infection be diagnosed?
- rtPCR to detect the presence of viral RNA in feces and oral fluids
- IHC to detect virus association with lesions in the small intestine
- IFT to detect viral antibodies in the sera
- EM to detect viral particles
- virus isolation
- viral genome sequencing to determine the genetic signature of the virus
What is Equine Coronavirus (ECoV)? How is it transmitted? What does it cause?
highly contagious virus of foals and horses through exposure to contaminated fecal materials
- high morbidity with low mortality
- diarrhea
- colic
- fever
- respiratory disease
- rapid progression can lead to death
