Lecture 29 Flashcards
(33 cards)
What are the three important coronaviruses that emerged in the past two decades and why?
- SARS-CoV-1 in 2002 (palm civet cat and raccoon dogs)
- MERS-CoV in 2012 (dromadary)
- SARS-CoV-2 in 2019 (unknown origin)
- generally zoonotic pathogens likely from bats, possibly through an intermediate host
Index case and initial spread of SARS-CoV-1?
- zoonotic disease
- 1st emerging in late 2002 BUT THEN 21 Feb 2003, Dr. Liz Jianlun stayed at the Metropol Hotel in Hong Kong and transmitted the infection to 16 others
- seeded outbreaks in Hong Kong, Toronto, Singapore and Vietnam (and eventually all over the world)
- within weeks, had spread to affect more than 8000 people in 25 countries across 5 continents
- authorities alerted by Vietnam healthcare workers
- Index case in metropole Hotel 9th floor, blue infections are secondary infections, and swabbed virus from the halls, stairwell, elevator lobby then index case was from Guangdong province and had gone to Hong Kong for a wedding and then went shopping and attend pre-wedding events, infected people at the hotel and healthcare workers and died at the hospital, all the people who had stayed at the hotel returned home and caused outbreak, then a healthcare worker in Vietnam alerted the authorities when a lot of health care workers in Vietnam were becoming sick quite quickly
Global spread?
- one hotel guest had come from Canada where 251 person outbreak occurred and led to 43 deaths
- total of 8096 infections and 774 deaths worldwide, 10% case fatality rate (9.6%)
- so many other countries infected though like Taiwan, Korea, China, India, Vietnam, Singapore, Europe, South Africa, USA
- Quickly progressing disease and not a lot of asymptomatic cases, also a lower respiratory tract infection, so controlled a bit more quickly
What are the clinical features of SARS-CoV-1?
Transmission: droplet infection, aerosolization, fomites, contaminated stool
Clinical symptoms: 2-10 day incubation period (is contagious), lower respiratory tract illness (viral pneumonitis) vs upper respiratory tract in SARS-CoV-2, fever , myalgia, malaise, chills, dry cough, shortness of breath, lymphopenia, decreased platelet counts, prolonged coagulation, elevated hepatic enzymes
10-20% require mechanical ventilation p, serious illness/difficult to breathe
More severe disease and mortality in the elderly (>65)
What was the zoonotic event that led to SARS-CoV-1?
- Probably first emerged in Guangdong (Nov 2002)
- many affected individuals in nov-dec 2002 that had contact with live-game trade (palm civet cat and raccoon dogs)
- Initially described as an “infectious atypical pneumonia”
- etiological agent was identified as a new coronavirus not previously endemic in humans
When is it a good idea to sequence for a novel pathogen?
Faster progression, an outbreak, different etiology
Index case and beginnings of MERS?
- index case, Saudi Arabia, sep 2012
- 60 yr old male patient, died of acute pneumonia and subsequent renal failure
- virus recovered, genome sequenced within weeks, novel coronavirus named MER-CoV vs hep c which took 10 years to sequence and sars cov2 which took a matter of days
MERS subsequent outbreak out of Middle East ?
- MERS-CoV outbreak in Korea in July 2015 after a businessman had traveled to the Middle East
All cases linked to single chain transmission (excluding the index case) - Associated with healthcare facilities
- Since 2012, WHO has been notified of 2468 confirmed cases and 851 related deaths
World MERS outbreaks?
- Index case from Bahrain and other people were infected in Saudi Arabia, Qatar, UAE and the Korean business man who returned from Qatar and infected his family, a bunch of other patients and healthcare workers which led to big outbreak
- A lot of transmission among camels, camels to humans (in Middle East and Africa)
- Human to human has happened in Middle East but largest outbreak out of Middle East was in Korea
- Ongoing cases throughout the years with a high case fatality rate of about 35%
What was the zoonotic event that led to MERS?
Circulating in dromedary (1 hump) camels as early as 1993 (intermediate host?), subsequently isolated from bats who were probably the reservoir with 10p% nucleotide identity
Primary cases more severe than secondary infections probably due to higher doses from camel to human than human to human, it is probably more readily transmissible from intermediate reservoir to humans than from human to human
What are super spreaders?
Super-spreader is a host, an organism infected with a disease that disproportionately infects more secondary contacts than other hosts who are also infected with the same disease
Important to avoid super-spreader events (concentrating lots of people in one place, more likely to host a super spreader event
- Scary cuz may not show any symptoms of the disease
- High concern in epidemiology (study of the spread of a disease)
- Some cases but not all conform to the 20/80 rule (80% of infections are caused by 20% of the infected) although super spreaders can account for a higher or lower % of infections
- Shaped by multiple factors: nosocomial infections in hospitals with immunocompromised sick patients, lots of susceptible hosts, viral load, virulence, airflow dynamics, misdiagnosis, immune suppression, co-infection, absence or decline in herd immunity, etc.
SARS-CoV-1 and MERS super spreaders and how they are worsened?
- lead to large amounts of healthcare workers who became infected and spread the infection to others
So early discovery, diagnosis, intervention and quarantine can limit pathogen spread - Failure of any one of these factors can lead to prolonged and sustained pathogen transmission
R not definition?
Basic reproduction number, Rnot
# of cases one case generates on average over the course of its infectious period, in an otherwise uninfected population (must be naive, hard to calculate today when people have been infected or are vaccinated)
When Rnot lower than 1, infection will die out in the long run but when Rnot higher than 1, the infection will be able to spread in a population
In general the larger the Rnot, the harder it is to control the epidemic
Affected by several factors: duration of infectivity, infectiousness, # of susceptible individuals in the population that come into contact
Herd immunity (through vaccination or natural infection) is important because if 1 infects 4, with herd immunity 1 will maybe only infect 1if 75% is immune, this drives down infection rates
Flu 1.3-4,5
COV2 similar
Measles and rubella much higher
If Rnot is 4, and vaccine is 100% effective, then you need at least 67% of the population in order to protect people
So Rnot is related to amount of herd immunity needed and vaccine effectiveness
Cornaviruses morphology and etymology?
Corona (latin = crown or halo) due to the appearance under EM of the viral spike peplomers (morphology)
Enveloped viruses, coiled helical capsid (120-160 nm in diameter) which causes the different shapes and not perfectly round, not icosahedral
Genome (+) ssRNA, monopartite, linear and largest RNA viruses known to infect humans, 27-32 kb in length
The coronaviridae family
Separated into alpha, beta and gamma coronaviruses.
Alpha: common cold coronaviruses like 229E, OC43 or NL63
Beta: SARS, bat cornaviruses and MERS
Gamma: veterinary coronaviruses that cause hepatitis or kidney infections
Diseases caused by coronaviruses?
First identified in the 1950s, huge campaigns to identify etiological agent of common colds
- Cause respiratory illnesses in humans and important veterinary diseases, 30% of common colds in humans, may cause gastroenteritis and encephalitis (rare)
SARS, MERS
- Veterinary diseases (peritonitis, pneumonia, gastroenteritis, hepatitis)
- SARS-CoV-2 (first CoV vaccine!), molnupiravir first drug (nucleoside analog)
The genome organization of coronaviruses?
- positive-sense RNA genome (27-32kb)
- contains a 5’ cap and an encoded poly A tail
- 5’ end 2/3rds of the genome encodes a large poly protein (ORF1a/b) which is proteolytically cleaved to generate 15-16 non-structural proteins (nsps)
- the 3’ end (1/3rd of the genome encoded four structural proteins which are conserved across all coronaviruses spike (S) membrane (M) envelope (E) and nucleocapsid (N)
Accessory proteins are also encoded but are unique to each virus species
Coronavirus structure?
- helical nucleocapsid, N protein wrapped around viral RNA, also an envelope protein E and membrane glycoprotein (M), and spike protein (S) or envelope glycoprotein which mediates interactions with host cell receptors and viral entry
How do coronaviruses bind to the cell and enter?
- different coronavirus spike proteins bind to a variety of different cellular receptors
- SARS binds to angiotensin converting enzyme 2 or ACE2 and L-SIGN ( a lectin)
- the virus envelope fuses with the plasma membrane on an endosymbiosis membrane which depends on the specific infecting coronavirus, some even use both pathways
- spike protein(s) mediate attachment and fusion
How does translation work?
RNA is uncoated and capped, so ribosome ready and can be translated into the first open reading Frame 1A and then 1ab. Replicase gene is large gene 1 is directly translated into the viral poly proteins pp1a (1-11) and pp1ab (1-16) through frameshifting when it bumps into a pseudo knot so ribosome bounces back and slips on the slippery sequence. This happens 40% of the time. The poly proteins are then processed by VIRAL proteases not cellular proteases (Nsp3 and Nsp5)
Coronavirus non structural protein functions?
- All made from ORF1A and ORF1AB and these are proteins involved in replication and mRNA synthesis.
Polyprotein processing by proteases to get mature viral proteins. For RNA replication, we have RdRp, RNA helicase to unwind genome for RNA synthesis. Proteins involved in making the replication organelle or replication complex (Replication complex formation). Has RNA cap formation, carries its own capping machinery and has RNA modifying enzymes which help that process to occur.
Cool protein from coronaviruses: nsp14 which is a 3’ to 5’ exoribonuclease, so proofreading; RNA cap formation (guanine N7) methyltramsferase, if mutated, virus becomes hypermutable cuz no more proofreading. Thanks to protein much less mutable than say HCV.
Where are the replication complexes of coronaviruses?
- replication complexes are made after replicase/nsps are made and are the sites of viral RNA synthesis (both mRNA and genome)
- altered membrane structures are virally-induced, there is a reticulovesicular network of modified membranes and modifications include double-membrane vesicles (DMVs), vesicle Packets (VPs) and convoluted membranes (CMs)
DMVs can associate to the ER - encapsidation (packaging also occurs at these sites)
What is the mechanism of viral RNA replication and transcription?
There is a leader sequence at the 5’ end and then there are TRS (transcriptional regulatory sequences) one right after leader and a bunch throughout body of viral genome. When RdRp and replicase proteins are there, mRNA is made from the 3’ end of the viral genome. Sometimes it will hit a TRS and stops and falls off and restarts synthesis at the first TRS of the genome and completes the leader sequence. This is an antisense nested negative strand RNA and can then be copied into a subgenomic mRNA. If no falling off at TRS, makes its way to the end of the genome and makes the negative sense antigenome and can then be used as template for the synthesis of the full length + sense genome like subgenomic mRNA synthesis. This is discontinuous transcription.
How does the little segment jump onto the TRS near the leader sequence of the genome?
The 3 step model for CoV transcription: complex formation between viral proteins at the 3’ end of the viral RNA and at complex at the leader TRS. So the polymerase is copying the RNA and holds onto the 5’ end of the RNA and when it hits the TRS junction, it can continue on, or it can transfer to the leader sequence to make the mRNA.
