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4.1 Medical Microbiology > Respiratory Viruses - Sars CoV2 > Flashcards

Respiratory Viruses - Sars CoV2 Flashcards

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1
Q

What are the three Coronaviridiae viruses that we are most concerned with?

A

SARS outbreak 2002

MERS outbreak 2012

SARS-CoV-2 outbreak 2019

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2
Q

What was the SARS outbreak, when did it happen, how many cases etc?

A

In 2002 there was an outbreak of Severe acute Respiratory Syndrome (SARS) in China

It causes 8000 cases

There was 880 deaths (mortality of 11%(

It had a low transmission rate

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3
Q

What was the MERS outbreak, when did it happen, how many cases etc?

A

In 2012 there was MERS - Middle East Respiratory Syndrome

It caused 2500 cases across 20 countries

It caused 80 deaths (mortality of 34%)

It had a very low transmissibility rate

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4
Q

What was the SARS-CoV-2 outbreak, when did it happen, how many cases etc?

A

Severe acute resiratory syndrome coronavirus 2

It caused 750million cases worlwide

It caused 6.9 million deaths (mortality of approx 1%)

Transmission was way higher than past outbreaks

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5
Q

What are the two methods of surveillance?

A

Passive Surveillance

Active Surveillance

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6
Q

What is passive surveillance, give an example?

A

This is the notification of a disease/its symptoms or an agent to relative authorities

Since the SARS outbreak 2002 this has been carried out in China, they report any cases of pneumonia like symptoms for which they could not determine a cause

You are notifying the agent of a novel pneumonia like disease

For SARS CoV2 this was carried out, it allowed China to trace back any pneumonia like cases relating to the fish maket in Wuhan -> from this they began active surveillance but by then it was already too late and the pandemic had spread

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7
Q

What is active surveillance, give an example?

A

This is case finding, testing and contract tracing

i.e. chasing down any close contacts and testing to see if they are also positive etc

China did this in late December 2020 and the rest of the world was doing it by Januar 2020 as well

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8
Q

How did the timeline of the Covid-19 pandemic compare to the lives of the HIV pandemic?

A

Covid-19 happened very quickly, spread rapidly, but also ended quickly
- in only a few months we had designed a test for covid
- in less than a year we had a vaccine -> crazy fast

Compared to HIV where we still dont have a vaccine

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9
Q

What are the three strucutral components of the SARS-CoV-2 coronavirus?

A

Genetic material

Nucleocapsid

Envelope

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10
Q

What kind of genetic material does SARS-CoV-2 have?

A

It has a large genome

It consists of positive sense RNA

It is similar to different strains of CoV such as bat and pangolin

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11
Q

How similar was Sars-CoV-2 to CoV in bats, pangolins, SARS-CoV1, MERS and the common cold CoV, why is this significant?

A

96% similar to bats
91% similar to pangolin
80% similar to CoV-1
55% similar to MERS
50% similar to common cold

This let us know that the virus likely didnt originate from fish at the fish market but probably from bats or pangolin -> proves it wasnt made in a lab -> it was likely that human to human transmission occured at the market and not fish to human

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12
Q

How similar was Sars-CoV-2 to CoV in bats, pangolins, SARS-CoV1, MERS and the common cold CoV, why is this significant?

A

96% similar to bats
91% similar to pangolin
80% similar to CoV-1
55% similar to MERS
50% similar to common cold

This let us know that the virus likely didnt originate from fish at the fish market but probably from bats or pangolin -> proves it wasnt made in a lab -> it was likely that human to human transmission occured at the market and not fish to human

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13
Q

Talk about the Sars-CoV-2 envelope

A

Spike (S) glycoprotein

Envelope (E)

Membrane (M) protein

i.e. the Sars-CoV-2 envelope consisits of S, E and M proteins

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14
Q

What is the S protein of SarscoV2, functions etc?

A

S protein consists of S1 and S2 subunits

S protein is what gives covid its Crown shaped structure

Responsible for entry to cells through ACE 2 - S unit attaches to ACE-2 on surface human epithelial cells

Responsible for neutralising antibodies

S1 is responsible for host cell tropism i.e. SARS ability to invade specific cells

S2 is responsible for virus-cell membrane fusion

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15
Q

What is ACE2?

A

Angiotensin-converting enzyme 2

This is what Covid uses to get into cells

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16
Q

Talk about variation in Covid

A

There is a very high mutation rate in covid which has been responsible for the emergence of new variants

At first we kept detailed track on all of these variants and named them all etc but now there is so many and few are of any actual concern

alpha, beta, omicron etc etc

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17
Q

How does SARS invade host cells?

A

SARS binds to ACE-2 on human epithelial cells through the use of S1 and S2 subunits of S protein

Covid then releases its viral genome RNA into the cytoplasm of the cell

RNA replication occurs and encodes sub genomic RNA

Nucleocapsid proteins and envelope glycoproteins assemble in the ER and Golgi to produce viral buds

Viral buds fuse with cell membrane to release the virus

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18
Q

What happens when SARS-CoV-2 binds too ACE 2?

A

This induces active replication of viral RNA and thus the release of virus into tissue such as the lung

This is what causes non specific symptoms such as fever, headache etc etc

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19
Q

What cells in the body is ACE2 protein present on, why is this significant?

A

Lung alveolar epithelial cells

Enterocytes of small intestine

Endothelial cells of the kidney

Blood vessels

*protein displayed on many different cell types, this is how covid causes widespread symptoms

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20
Q

What are the sequelae of SARS

A

Loss of taste and smell due to damage to the cells in the olfactory epithelium

Lymphocytic endothelitis

Myocardial infarction

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21
Q

What is the usual course of infection in COVID
(3)

A

Viral entry resulting in T cell mediated inflammatory response

Eliminates infected cells before spread of virus

Recovery in most patients

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22
Q

What is the course of severe covid?

A

Bilateral diffuse alveolar damage (ARDS)

Hyaline-membrane formation

Interstital mononuclear inflammatroy infiltrates

Desquamation

Mucus plugs with fibrinous exudate - this damages the lung parenchyma

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23
Q

What are some risk factors for Covid severe disease?

A

Older age
Hypertension
Cardiovascular disease
Chronic obstructive pulmonary disease
Diabetes
Obesity
Malignancy

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24
Q

What are some lab markers for sever CoV2 disease?

A

Neutrophilia/lymphopenia
Raised lactate and lactate dehydrogenase
Raised CRP
Raised ferritin
Raised IL-6
Raised ACE2
D dimers >1

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25
Q

Why was transmission of SARS CoV2 so high?

A

The incubation period was long and people were often transmissible before they began having symptoms

Incubation period was between 5-8 days in most but could range from 1-3 to 11-3 with the medican being 5 days

98% of people showed symptoms within 11-5 days of infection -> it meant 5 days where you were spreading disease without knowing you had it

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26
Q

Compare the transmission of SARs Cov2 to that of SARS 1 and MERS

A

SARS CoV2 had a high transmission R0= 2-4
- ie one person infected between 2 and 4 others
SARS 1 and MERS had an R0 = 1.1
- i.e. one person infected 1

For SARS1 and MERS they also couldnt really spread disease when asymptomatic however SAR2 had a RO >1 even when presymptomatic

27
Q

Why was SARS2 transmissible in the presympthomatic phase?

A

This is because this was when viral load was at its highest i.e. week one of infection

28
Q

What percentage of severe covid needed hospitilsation?

A

20% of mild to severe disease requireed hospitilisation

About 1/16000 required ICU -> about 2/3%

29
Q

What put you at risk of picking up covid?

A

Contact pattern -> how many people were you in contact with, were any of these positive

Environment -> work environment, indoors vs outdoors etc

Host factors -> your immune system etc

Socioeconomic factors -> were you required to continue work -> access to PPE etc etc

30
Q

How many cases of COV2 were there in Ireland vs the world

A

1.7 million in Ireland

770 million in the world

31
Q

How many COV2 deaths were there in ireland vs the world?

A

8900 in ireland

6.9 million in the wold

32
Q

Initially how did we control the spread of SARS-CoV-2?

A

At first we had no pharmaceutical interventions -> no vaccine or monoclonals etc

We had to use non-pharma interventions such as track and trace, governmental policies, travel restricition, social distancing and hygiene measures etc etc - we shut the world down

33
Q

What were the two types of vaccines offered for COVID, which was more successful?

A

mRNA vaccines such as Moderna and Pfizer and BioNTech

Viral vectored such as Oxford and Johnson and Johnson

*mRNA had way higher efficacy (94% for moderna nad 95% for Pfizer) compared to only 60% in oxford and 67% in J&J

34
Q

What were the two types of vaccines offered for COVID, which was more successful?

A

mRNA vaccines such as Moderna and Pfizer and BioNTech

Viral vectored such as Oxford and Johnson and Johnson

*mRNA had way higher efficacy (94% for moderna nad 95% for Pfizer) compared to only 60% in oxford and 67% in J&J

35
Q

How do the mRNA vaccines work?

A

These vaccines dont actually include a part of the virus instead they make use of the voral mRNA

This was the first time these kinds of vaccines were used -> advancement in technology (mRNA)

Moderna -> mRNA induced CD4 T cell response against virus

Pfizer used mRNA to induce long lastin IgG against virus as well as T cell response (hence considered the best vaccine)

36
Q

How do the viral vectored vaccines work?

A

Oxford made use of nonreplicating chimpanzee adenovirus vaccine vector to deliver the RNA into the cells -> this induced anti-spike igG responses and spike-speicifc T cell responses

J&J made use of nonreplicating adenovirus type 5 viral vector expressing SARS-CoV-2 spike protein to induce anti-spike IgG responses and spike-specific T cell responses

37
Q

What is the gold standard clinical sample for Covid?

A

Nasopharyngeal swab
Best on day 5-6 -> detection rate of 100%

Nasal or oropharyngeal samples collected alone or in combination are ideal

38
Q

What other sample types other than nasopharyngeal were used for Covid testing?

A

We tried absolutely everything
- BALS, tracheal aspirates, pleural fluids,urine, blood and even faeces
- Saliva was also used in non clinical diagnostics i.e. for at home

39
Q

How sensitive was blood for the detection of Covid?

A

Blood was 88% sensitive -> this is good but nasopharyngeal still best at 100%

40
Q

Talk about the use of saliva to detect covid

A

Saliva should only ever be used in NON-clinical diagnostics

It was used in at home tests

Sensitivity of 78% but otherwise not suitable for diagnostics

41
Q

What molecular method do we use to detect covid, what are the targets

A

We use Revere transcriptase PCR

Target:
- RdRp gene
- E gene (envelope protein)
- S gene
- M gene
- N2 gene

42
Q

What are the benefits of molecular methods of detecting covid

A

turn around time of only 3-4 hours from receipt in lab compared to days in nvrl etc

commercial kits for covid are now widely available -> covid is included in multiplex biofire panel now

exceptional sensitivity and specificity

The GeneXpert is readily used ad this only takes 20 mins to give a result

43
Q

Talk about the use of the biofire to dect covid, targets, runtime, cost etc

A

Covid is included on the respiratory panels (RP and RP2)

It detects the S and M gene

It runs for 45 mins

Increased cost - between 100 and 150 euros

Sens of 93% and spec of 100%

44
Q

Talk about the use of the gene xpert to dect covid, targets, runtime, cost etc

A

Has a specific SARS-CoV-2 test -> multiplex PCR

Targets E gene and N2 gene

Run time of about 20 minutes

45
Q

What are some drawbacks of PCR?

A

Poorly timed specimen collection- high viral load

Poor quality specimen collection- high viral load required

Trained staff -> debate into if this is actually an issue

Longer TAT but rapidly falling

Reagent shortages -> especially during pandemic

Either detected or detected does not identify strain or variants

If there are mutations in the primer binding site this may hinder assay sensitivity -> amplification wont occur

No influenza testing originally included

46
Q

why was there a lot of debate surrounding who should run covid PCR samples

A

Is there a need for highly trained staff -> who understand the PCR etc

Or can lab aides run samples etc etc

Medical scientists want to keep standard high but there was a huge work load etc etc

47
Q

Why was there a need to include influenza testing in covid PCR?

A

Patients were coming up as covid negative but we werent actually diagnosing them with anything
-> opening up a can of worms
-> it was meaning we were having to run the same again on another assay etc

With the inclusion of the influenza for common cold it meant a lot of these patients were actually getting a diagnosis

48
Q

Talk about the use of antigen tests for SARS Cov, what were the pros and cons

A

Good sensitivity in high load cases only

Rapid drop of in sensitivity after the infectious period

Companies claim 91-100% sensitivity but this was only when highly infection, Ct was found to be 28-31 ie. only about 76% sensitive -> this gave a false sense of security

They were great for pandemic control though -> great for contact tracing and isolation etc -> really reduced numbers etc etc

49
Q

How did the covid antibody tests work, when were they used?

A

These were N based or S based
They were used in epidemiological typing

Detected IgM, IgA or IgG

Used in studies done in Cork and in Sligo

50
Q

When is anti covid IgM, IgA and IgG detectable?

A

IgM is detectable between 7 and 14 days

IgA is deteectable between 4 and 10 days

IgG is detectabe between 7 and 48 days

51
Q

When were the antibody tests used?

A

They were used in localised seroprevalence studies e.g. in Cork

They are not a replacement for virology testing

52
Q

What were the antibody tests not suitabe for detecting presence of covid i.e. why are they not considered diagnostic

A

Antibody waning was seen in patients - reduced sensitivity of antibody assay

There was interference with some of the vaccines:
- Antibody tests targetting the S protein -> this resulted in false positives as the test could not distinguish between what was a anti-virus positive and what was an anti-vaccine antibody positive
-> ie antibodies produced against vaccine and against virus were too similar and could not be distinguished from each other

NB: use of antibody testing to detect anti-N protein worked a lot better than anti-S as no interference from vaccines

53
Q

How do we decide which test to use: a rapid antigen test, a serological antibody test or PCR/virology?

A

PCR:
- Diagnose sick patients of 1-3 weeks
- Contact tracing testing

Serology:
- Surveillance Tool
- Study of population transmission
- Ongoing investigation 2 weeks to months

Antigen test:
- Underresourceed countries
- areas of overcrowding

54
Q

If antigen test are not the gold standard why were we using these to diagnose people during the pandemic?

A

Antigen tests are suitable to use in underressourced countries and all countries were considered underrressourced during the pandemic as nobody was prepared for this or the level of testing required

=> the need to diagnose outweighed the lack of sensitivty of these assays

55
Q

Talk about whole genome sequencing for covid, when and where did we do it?
(3)

A

WGS allows us to identify strains based on sequencing each base pair of the virus genome

We sequenced approximately 20% of PCR positive cases

It was done in the NVRL using the minION and the GridION

56
Q

Compare the minION vs GridION whole genome sequencers?

A

MinION: fast, relatively cheap and available in labs across the countrie, shared data, good for small sequences of virus

GridION: scaled up larger version with higher throughput

57
Q

What are some applications of whole genome sequencing?

A

National surveillance of all variants (community & hospital)
Early detection of variants of concern which have originated from other countries
Monitoring emerging lineages in animals
Complex outbreak investigation
Vaccine escape/ reinfection investigation
Unexpected change in transmissibility/ virulence investigation
Antiviral resistance investigation
animal to human transmission investigation
Testing immunocompromised patients undergoing antibody therapy
Unexpected change in diagnostic performance investigation

58
Q

What are two additional methods of detecting covid that are rarely used

A

RT loop-mediated isothermal amplification (RT-LAMP)

Nanomaterials

59
Q

What were the main concerns with diagnostics in the Covid-19 era?

A

Which test to perform and when?
Assay performance?
Who is selling the test - strange that you could get an antigen test in lidl?
What does CE approved mean?
Who is performing the test, a lab or a normal member of public etc

60
Q

What three factors made SARS-CoV2 the perfect storm?
(3)

A

Pathogenicity and effcient transmission -> highly transmissible

Unlimited efficient and sustained transmission essential for Pandemic

Viral mutation promoted where humans birds and animals exist in close contact

61
Q

Talk about the possibility of a SARS CoV3/4/5 etc etc

A

Cov2 was a highly transmissible coronavirus but it didnt have the mortality associated with MERS or even SARS1
Cov2 is not in the repertoir of viruses that can infect humans
There is the possibility that Cov2 will combine with these other strains and cause another pandemic
If Cov2 was to combine with MERS it would be the end of humanity probably

62
Q

How did the covid pandemic affect other viruses

A

movement restriction and lack of contact virtually wiped out other viruses such as influenza and RSV

We no longer have seasonal patterns in these viruses because of this

Since the re-emergence of these other viruses weve seen a non-season, year round pattern

63
Q

How are we preventing another covid pandemic
(3)

A

Serological monitoring is ongoing in Harvard

Serological surveys are being carried out to predict a viral forecast

i.e. trying to predict which respiratory pathogens could be coming so we can begin producing vaccines against them

4.1 Medical Microbiology (30 decks)

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