WEEK 1: INFLUENZA VIRUSES

Question 1

Acute respiratory tract infection caused by influenza viruses can be:
Sporadic
Seasonal
Epidemic
Pandemic

Define the terms.

Answer 1

Sporadic: No regular or predictable pattern

Seasonal: Regularly at a certain time of the year

Epidemic: Epidemic diseases are diseases that affect a large number of people in a specific population or area in a short time, more than what is normally expected

Pandemic: A pandemic is an epidemic of an infectious disease that has spread across a large region, for instance multiple continents or worldwide, affecting a substantial number of individuals.

Question 2

What is an endemic?

Give examples of endemic diseases in Botswana.

Answer 2

An endemic disease is a disease that is always present in a particular population or region.

It often occurs in cycles and has a predictable rate of infection.

Some examples of endemic diseases are the flu, malaria, HIV, and syphilis.

Question 3

Illnesses range from mild to severe disease

According to WHO (Jan 2023) epidemics of seasonal influenza result in 3-5 million cases of severe disease and about 290 000 to 650 000 respiratory deaths.

In industrialized world’s most deaths occur in ____________VS in developing countries which accounts for an estimated 99% of influenza related deaths in __________.

Answer 3

In industrialized world’s most deaths occur in 65 years or older VS in developing countries which accounts for an estimated 99% of influenza related deaths in under 5.

Question 4

State and describe the 4 types of influenza viruses.

Answer 4

Type A – cause potentially most severe disease, epidemics and pandemics, cause infection in humans, birds and other mammals

Type B – less severe disease, can cause epidemics, almost exclusively human infection although more recently infection in seals and pigs (mostly experimentally) reported.

Type C – antigenically stable, mild to asymptomatic illness, minimal public health impact, also almost exclusively human infection but infection in pigs reported.

Type D – no epidemiological relevance to humans, found in cattle.

Question 5

No epidemiological relevance to humans, found in cattle.
Name the virus.

Answer 5

Type D

Question 6

cause potentially most severe disease, epidemics and pandemics.

Answer 6

Type A

Question 7

Which influenza affects humans only?

Answer 7

Type B

Question 8

How many gene segments and viral proteins are found in the following types of influenza viruses?
A
B
C

Answer 8

A: 8 gene segments, 10 viral proteins
B: 8 gene segments, 11 viral proteins
C: 7 gene segments, 9 viral proteins

Question 9

Influenza can be traced as far back as______.

Hippocrates described a cough outbreak in ______in present day ________at the turn of autumn.

Answer 9

Influenza can be traced as far back as 400 BC

Hippocrates described a cough outbreak in 412BC in present day Turkey at the turn of autumn.

Question 10

State the years for the occurrence of the following pandemics.

*Spanish FLU
*Asian FLU
*Hong Kong FLU
*H1N1

Answer 10

1918 – Spanish FLU
1957 – Asian FLU
1968 – Hong Kong FLU
2009 – H1N1

Question 11

What is the family of influenza viruses?
Describe their general structure and genome.

Answer 11

Family: Orthomyxoviridae – spherical/tubular

Enveloped (host derived lipid bilayer)
SEGMENTED negative-sense single-strand RNA segments with EIGHT SEGMENTS.

Question 12

State the functions of the following structural proteins and where they are found.

Hemagglutinin (HA)

Neuraminidase (NA)

M1 (matrix protein)
M2 (ion channel)

THREE polymerase proteins PB1, PB2, and PA

NEP (nonstructural protein 2)

Nucleoprotein (NP)

Answer 12

1. Hemagglutinin (HA): A glycoprotein on the surface of the virus that binds to sialic acid receptors on host cells and mediates viral entry. It also determines the subtype of influenza A virus12.
2. Neuraminidase (NA): A glycoprotein on the surface of the virus that cleaves sialic acid residues from host cell membranes and viral particles, facilitating viral release and spread. It also determines the subtype of influenza A virus12.

Neuraminidase is also known as sialidase because it breaks the linkages between sialic acid and cellular glycoproteins and glycolipids found in cell walls.

3. M1 (matrix protein): A protein that forms a layer under the viral envelope and maintains the shape and stability of the virus. It also interacts with viral RNAs and other proteins3.
4. M2 (ion channel): A protein that forms a proton channel on the viral envelope and allows protons to enter the virus, lowering the pH and triggering the fusion of HA with host cell membrane3.
5. PB1, PB2, and PA (polymerase proteins): Three proteins that form a complex with viral RNA and nucleoprotein (NP) and act as RNA-dependent RNA polymerase, synthesizing viral RNA from viral RNA template.
6. NEP (nonstructural protein 2): A protein that binds to viral RNPs and mediates their export from the nucleus to the cytoplasm.
7. NP (nucleoprotein): A protein that coats the viral RNA segments and forms the viral RNPs. It also interacts with polymerase proteins and M1 protein.

Question 13

Describe the viral replication of influenza virus.

Answer 13

1. the HA receptor-binding site attaches the virus to surface glycoconjugates that contain terminal SA residues.
2. Virus endocytosis, taken into the cell in an endosome.
3. Acidification of the endosome by proton entry via M2 ion channels allows for uncoating of the virus.
4. Nucleocapsid sent to the nucleus.
5. There is transcription and translation forming mRNA and -ssRNA
6. mRNA taken to the ER where it is used to form Hemagglutinin and neuraminidase.
7. The viral genome and HA, NA migrate to the surface where they bud off as a new virion.

Their release is highly dependent on the sialidase activity of NA.

Question 14

Where do Influenza viruses replicate within?

How is that an advantage and a disadvantage?

Answer 14

Influenza viruses replicate within the nucleus of the host cell.

This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication.

However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection.

Question 15

State the Influenza virus structural differences.

Answer 15

1. Unlike Type A, Type B have NB and BM2 structural proteins instead of the M2 ion channel, the latter which is said to have same functional activity as M2 protein.

*Increasing pH in endosome to facilitate uncoating
*Maintaining viral membrane PH during entry and trans Golgi apparatus transport

2. Type C has hemagglutinin-esterase-fusion (HEF) which corresponds to HA and NA, as well CM2 structural protein.

Question 16

Describe the simplified Influenza virus simplified pathway.

Answer 16

1. Virus
2. Superficial epithelium of respiratory tract
3. Inflammation
4. Necrosis

Question 17

Outline the differences between antigenic shift and drift.

Answer 17

DRIFT
*Minor changes
*Happens in Type A and B
*May result in epidemics
*Results from point mutations
*Lead to changes in the surface proteins called HA and NA
*Changes happen gradually

SHIFT
*Major changes
*Happens in Type A only
*May result in pandemics
*Result from exchanging of gene segments.
*Combine to form a new subtype with a mixture of surface antigens from the original viruses
*Changes occur abruptly.

Question 18

Describe the mode of transmission for Influenza viruses.

Answer 18

predominantly by aerosol infection, i.e. relatively large droplets (>5 μm) created particularly while talking, coughing, or sneezing.

transmission might occur by (droplet cores) which are smaller (<5 μm) and able to remain in the air for longer periods (aerogenic transmission).

transmission can occur by direct contact with virus-contaminated surfaces (fomites) (e.g. shaking hands) and subsequent mouth-nose contact.

After infection the viruses replicate in the nasal and laryngeal mucosae. This replication also affects the lower airways as the infection progresses.

Question 19

Avian influenza was transmitted form birds to humans.

State the modes of transmission.

Answer 19

Bird to human
Fecal-oral (poultry excreta)
Direct contact
Ingestion of undercooked food

Question 20

What is the difference between flu and cold?

Answer 20

Flu presents with the following which are rare in cold.

Fever, headache, body ache

Flu has gradual onset and can have severe symptoms and there is no sneezing.
Cold has gradual onset and presents with mild symptoms.

Question 21

What are the common symptoms in both flu and cold?

Answer 21

Runny nose, sore throat, cough

Question 22

How is COVID 19 different from flu and cold?

Answer 22

It has shortness of breath and stuffy nose does not present in the 2.

There is no sneezing in COVID 19 and FLU.

Question 23

Naming of the influenza viruses is made of 5 components. Name them.

Answer 23

Type / place virus isolated/ strain number/ year of isolation/ viral subtype.

A / Sydney / 05/ 95/ H3N2

Question 24

What are the 4 samples of influenza?

Answer 24

Nasal swab
Nasopharyngeal swab
Oropharyngeal swab
Bronchial aspirates

Question 25

How are the samples packaged?

Answer 25

Triple packaging system (primary, secondary outer container with labels)

Question 26

What are the diagnostic tests for influenza?

Answer 26

Viral culture in egg culture

RNA detection via RT PCR

Immunoassays
LFA (50-70% sensitivity for Type A and B)
ELISA

Question 27

What are the main vaccines for flu?

Answer 27

Quadrivalent vaccine – protects against 2 type A and 2 type B, given IM, annual dosing.

Live attenuated (weakened virus) – given as nasal spray.

Question 28

What is the vaccine efficacy according to CDC?

Answer 28

Vaccine efficacy according to CDC may range from 40-60%

Question 29

What are the ways of preventing influenza?

Answer 29

Ensure good ventilation.
Avoid overcrowding.
PPE
Hand hygiene

Question 30

What are the contraindication for flu vaccine.

Answer 30

Contraindication

1. Previous adverse effects

Anaphylaxis: A serious life-threatening allergic reaction which usually occurs within few seconds or minutes of exposure to allergic substances.

Guilian barre Syndrome: a rare disorder in which your body’s immune system attacks your nerves.

Moderate to severe fever

2. People who are immunosuppressed cannot be given life attenuated vaccines.

Question 31

Name the different types of seasonal influenza viruses. Which ones are RNA vs DNA viruses?

Answer 31

Influenza A, B

All -ssRNA viruses.

Question 32

Among the known influenza viruses, which one(s) are known to cause pandemics?

Answer 32

Type A

Question 33

Which influenza viruses are classified into lineages versus subtypes?

Answer 33

Influenza A viruses are classified into lineages based on the genetic and antigenic characteristics of their hemagglutinin (HA) and neuraminidase (NA) surface proteins.

Question 34

What are the 2 lineages of influenza A viruses?

Answer 34

Seasonal Lineages: These lineages include the influenza A (H1N1) and A (H3N2) viruses that circulate in the human population during seasonal flu outbreaks. These lineages can undergo genetic changes over time, leading to the need for updated vaccines.

Zoonotic Lineages: Influenza A viruses can also be found in animals, such as birds and swine.

Some of these zoonotic lineages have caused occasional outbreaks in humans, such as avian influenza viruses (e.g., H5N1, H7N9) and swine influenza viruses (e.g., H1N1pdm09).

Question 35

How are the subtypes of influenza A formed?

Answer 35

Influenza A viruses are further classified into subtypes based on the specific combinations of their HA and NA proteins.

For example, the subtype H1N1 represents an influenza A virus with an H1 hemagglutinin and an N1 neuraminidase.

Influenza A viruses can have various combinations of HA and NA subtypes, resulting in different subtypes such as H1N1, H3N2, H5N1, H7N9, and so on. These subtypes help to categorize and track the genetic diversity of influenza A viruses.

Question 36

Influenza B viruses are classified into two lineages based on the genetic characteristics of their HA protein. What are they?

Answer 36

Victoria Lineage
Yamagata Lineage

Question 37

Which influenza viruses mostly cause disease in cattle?

Answer 37

Type D

Question 38

How many people contract influenza annually?

Question 39

How many people die from influenza annually?

Question 40

Name the part of the part of the world with the highest estimated influenza fatalities

Question 41

What do national influenza centers do?

Why is their work important?

Answer 41

*National Influenza Centers (NICs) collect virus specimens in their country and perform preliminary analysis.

*They ship representative clinical specimens and isolated viruses to WHO CCs for advanced antigenic and genetic analysis.

*The results form the basis for WHO recommendations on the composition of influenza vaccine each year, as well as relevant risk assessment activities of WHO.

Question 42

How does influenza spread from person to person?

Answer 42

*Airborne / respiratory aerosols
*Respiratory droplets from coughing
*Fomites

Question 43

What is the difference between airborne/aerosol and droplet transmission? How can this be relevant for influenza?

Answer 43

Droplet Transmission:
Droplet transmission occurs when respiratory droplets containing infectious agents (such as viruses or bacteria) are produced when an infected person coughs, sneezes, talks, or even breathes.

These respiratory droplets are relatively large in size and tend to be heavy, so they don’t remain suspended in the air for long. Instead, they typically travel short distances, usually within about 3 to 6 feet from the infected person.

People nearby can become infected if they inhale these droplets or if the droplets land on their mucous membranes (eyes, nose, mouth).

Influenza is primarily transmitted through droplet transmission. This is why measures like wearing face masks, practicing good hand hygiene, and maintaining physical distance can be effective in reducing its spread.

Airborne (Aerosol) Transmission:

Airborne transmission, on the other hand, involves much smaller respiratory particles, known as aerosols, that can remain suspended in the air for extended periods.

These aerosols can be produced not only when someone coughs or sneezes but also when they talk, sing, or simply exhale.

Infectious aerosols can travel beyond 6 feet and linger in enclosed spaces, potentially infecting people even after the infected person has left the area.

Influenza can also be transmitted through aerosols, especially in crowded or poorly ventilated spaces, where the virus can build up in the air over time.

REVELANCE FOR INFLUENZA

Understanding the modes of transmission for influenza is crucial for implementing appropriate preventive measures:

Droplet Transmission:

In healthcare settings, where close contact with infected patients is common, healthcare workers are advised to wear masks, especially when within close proximity to patients with respiratory infections like influenza.

In the community, during flu season, it is recommended for individuals to practice respiratory hygiene (covering the mouth and nose when coughing or sneezing) to reduce the spread of respiratory droplets.

Airborne Transmission:

Although influenza is primarily transmitted through droplets, there can be situations, such as in crowded indoor settings, where airborne transmission becomes more relevant.

Adequate ventilation, air filtration, and air exchange in enclosed spaces can help reduce the concentration of infectious aerosols and lower the risk of airborne transmission.

In summary, while influenza is mainly transmitted through droplet transmission, it’s essential to be aware of the potential for airborne transmission in specific circumstances.

Effective prevention measures include vaccination, wearing masks, practicing good hand hygiene, and maintaining proper ventilation in enclosed spaces to mitigate both droplet and airborne transmission of influenza.

Question 44

What are fomites?

In relation to influenza transmission, what is the role of contaminated fomites?

How can influenza transmission vis fomites be prevented.

Answer 44

Influenza transmission can also occur through contaminated fomites, which are inanimate objects or surfaces that become contaminated with influenza virus and can serve as a vehicle for the virus to be transmitted to other people.

The role of contaminated fomites in influenza transmission is as follows:

Virus Survival on Surfaces: Influenza viruses can survive for varying lengths of time on surfaces, depending on factors like temperature and humidity. Studies have shown that influenza viruses can remain infectious on surfaces for hours to days. When an infected person coughs, sneezes, or touches their face and then touches a surface, they can deposit influenza virus particles on that surface.

Indirect Transmission: When a person touches a contaminated surface, such as a doorknob, elevator button, or shared computer keyboard, and then touches their face, especially the eyes, nose, or mouth, they can introduce the virus into their own respiratory system. This can lead to infection.

Potential for Outbreaks: Contaminated fomites can be a significant concern in settings where people are in close contact, such as schools, offices, public transportation, and healthcare facilities. If one person with influenza touches a surface in such an environment, the virus can quickly spread to multiple individuals who touch the same surface.

Prevention: To reduce the risk of influenza transmission via contaminated fomites, it’s essential to practice good hand hygiene.

*Regularly washing hands with soap and water, using hand sanitizer, and

*Avoiding touching the face with unwashed hands can help prevent infection.

*Additionally, routine cleaning and disinfection of frequently touched surfaces can reduce the presence of the virus on these surfaces.

In summary, while influenza is primarily transmitted through respiratory droplets and, to some extent, through airborne transmission, contaminated fomites can play a role in its spread, especially in high-traffic areas and close-contact settings. Proper hygiene and cleaning practices are important measures to minimize the risk of influenza transmission via contaminated surfaces.

Question 45

Name at least 3 complications of severe influenza infection.

Answer 45

*Viral pneumonia
*Sinitis
*Myocarditis
*Pericarditis
*Guillan barre Syndrome: a rare disorder in which your body’s immune system attacks your nerves.

Question 46

Case fatality is higher for avian influenza as compared to seasonal influenza viruses. True/False

Answer 46

True. Case fatality rates for avian influenza (bird flu) are generally higher when compared to seasonal influenza viruses.

Avian influenza viruses, particularly subtypes like H5N1 and H7N9, have been associated with more severe illness in humans. These viruses can lead to a higher mortality rate, meaning that a larger proportion of individuals infected with avian influenza may die as a result of the infection compared to seasonal influenza.

Seasonal influenza, which circulates in human populations every year, typically has a lower case fatality rate. However, it can still lead to significant morbidity and mortality, especially among vulnerable populations like the very young, the elderly, and individuals with underlying health conditions.

It’s important to note that while avian influenza has a higher case fatality rate, it is less efficient in human-to-human transmission compared to seasonal influenza, which is why it has not caused large-scale pandemics in the same way that certain strains of seasonal influenza have. Nevertheless, avian influenza remains a concern due to its potential for genetic mutations and the risk of sparking a pandemic if it were to acquire the ability to spread easily among humans. Public health measures and surveillance are in place to monitor and respond to these threats.

Question 46

What is zoonotic influenza?

Answer 46

Zoonotic influenza, also known as avian influenza or bird flu, is a type of influenza virus that can be transmitted from animals to humans. These viruses primarily circulate among birds, particularly wild aquatic birds, but they can also infect domestic poultry and, on occasion, jump to humans.

Zoonotic influenza viruses are of concern because they have the potential to cause outbreaks and, in some cases, lead to pandemics if they acquire the ability to efficiently transmit from person to person.

Question 46

There is well established human to human transmission of zoonotic influenza. True/false

Answer 46

False

Question 47

What is the gold standard for testing for influenza?

Describe how the test works.

Answer 47

The gold standard for testing for influenza is a laboratory-based diagnostic test known as Reverse Transcription Polymerase Chain Reaction (RT-PCR).

This test is highly sensitive and specific for detecting the presence of influenza virus in respiratory specimens, making it the most accurate method for diagnosing influenza.

Here’s how RT-PCR testing for influenza works:

Sample Collection: A respiratory specimen, typically obtained from a nasal or throat swab, is collected from the patient. This sample contains respiratory secretions that may contain the influenza virus.

RNA Extraction: The RNA (genetic material) of the influenza virus is extracted from the collected specimen. Influenza viruses contain RNA, and this test is designed to detect specific sequences of influenza RNA.

Reverse Transcription: The extracted RNA is then converted into complementary DNA (cDNA) using an enzyme called reverse transcriptase. This step is necessary because PCR works with DNA, not RNA.

Polymerase Chain Reaction (PCR): The cDNA is then subjected to a series of PCR cycles, which amplify specific sequences of influenza genes if the virus is present in the sample. This amplification process makes it easier to detect the virus.

Detection: The amplified DNA sequences are then analyzed using specific probes or primers that can identify the presence of influenza virus. If the virus is present, the test will produce a positive result.

RT-PCR is highly sensitive and can detect influenza virus even in the early stages of infection. It can also differentiate between different influenza virus subtypes (e.g., influenza A and B) and provide information on the specific strain of influenza. This information can be important for tracking and responding to influenza outbreaks.

While RT-PCR is the gold standard for influenza testing, there are also rapid influenza diagnostic tests (RIDTs) available. These tests provide results more quickly but are generally less sensitive and specific than RT-PCR. RIDTs can be useful for rapid diagnosis, especially in clinical settings, but may yield false-negative results and are not as accurate as RT-PCR. In cases where the diagnosis is critical or the patient’s condition is severe, RT-PCR is often used to confirm the results of a rapid test.

Question 48

What are the other test for testing for influenza?

Answer 48

Rapid Influenza Diagnostic Tests (RIDTs): RIDTs are point-of-care tests that provide relatively quick results, usually within 15-30 minutes. They are based on detecting viral antigens (proteins) present in respiratory specimens, such as nasal swabs. RIDTs are less sensitive than RT-PCR and may yield false-negative results, particularly later in the course of the illness.

Nucleic Acid Amplification Tests (NAATs): NAATs are molecular tests similar to RT-PCR but may have different methodologies. They are highly sensitive and specific for influenza detection and can provide results in a few hours. These tests are typically performed in a laboratory setting.

Viral Culture: This method involves growing the influenza virus in a laboratory setting, which can take several days to provide results. Viral culture is not commonly used for routine clinical diagnosis but is valuable for strain identification and research purposes.

Serological Tests: Serological tests, such as enzyme-linked immunosorbent assays (ELISAs), detect antibodies produced by the patient’s immune system in response to the influenza virus. They are useful for retrospectively confirming a recent influenza infection but are not suitable for diagnosing active infections.

Molecular Point-of-Care Tests: Some molecular tests, similar to RT-PCR, have been adapted for use at the point of care, providing relatively quick results with high sensitivity and specificity. These may be used in clinical settings for faster diagnosis.

Next-Generation Sequencing (NGS): NGS technologies can sequence the entire genetic material of a virus, providing a comprehensive analysis of the virus and its variants. NGS is not typically used for routine clinical diagnosis but is crucial for research and surveillance.

The choice of test depends on various factors, including the clinical setting, the need for rapid results, and the specific requirements of the patient. In many clinical settings, RIDTs or molecular point-of-care tests may be used to quickly identify potential influenza cases. If more accurate or confirmatory testing is needed, RT-PCR or NAATs are performed in a laboratory setting. It’s essential to select the most appropriate test based on the clinical context and the patient’s condition.

Question 49

Serology plays a central role in the diagnosis of influenza. True/False

Answer 49

False

Serology, which involves testing for antibodies (e.g., IgM and IgG) produced by the patient’s immune system in response to the influenza virus, is not typically used for the primary diagnosis of an acute influenza infection. Serological tests are more commonly used for research, epidemiological studies, and retrospective diagnosis to confirm past influenza infections or to determine the prevalence of influenza in a population.

In summary, while serology is a valuable tool in influenza research and surveillance, it is not the primary method for diagnosing an acute, ongoing influenza infection. Direct detection of the virus or its genetic material through methods like RT-PCR and RIDTs plays a central role in diagnosing influenza.