COVID-19  The severity of COVID-19 symptoms can
- The COVID-19 pandemic, also known as
the coronavirus pandemic, is an ongoing
pandemic of coronavirus disease 2019
(COVID-19) caused by severe acute
respiratory syndrome coronavirus 2
(SARS-CoV-2). It was first identified in
December 2019 in Wuhan, China.
- Disease: Coronavirus disease 2019
(COVID-19) contagious disease
- Virus strain: Severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2)
- Date: December 2019 – present
- Index case: Wuhan, Hubei, China
- FAMILY: CORONAVIRIDAE (1st named as
novel coronavirus 2019 NCoV).
Symptoms:
- Symptoms may appear 2-14 days after
exposure to the virus. People with these
symptoms may have COVID-19: Cough,
shortness of breath or difficulty breathing,
fever, chills, muscle pain, sore throat, new
loss of taste or smell.
Incubation period:
- The median incubation period for COVID-
19 4-5 days. Most symptomatic people
experience symptoms within two to seven
days after exposure.
Mode of transmission:
- Human-to-human transmission via
respiratory droplets/aerosols
 This time after exposure and before
having symptoms is called the incubation
period. You can still spread COVID-
19 before you have symptoms
(presymptomatic transmission). Common
signs and symptoms can include:
 Fever,cough,tiredness
 Early symptoms of COVID-19 may include
a loss of taste or smell.
 Shortness of breath or difficulty breathing
 Muscle aches
 Chills
 Sore throat
 Runny nose
 Headache
 Chest pain
 Pink eye (conjunctivitis)
 Nausea
 Vomiting
 Diarrhea
 Rash
 Children have similar symptoms to adults
and generally have mild illness.
range from very mild to severe. Some
people may have only a few symptoms.
Some people may have no symptoms at
all, but can still spread it (asymptomatic
transmission). Some people may
experience worsened symptoms, such as
worsened shortness of breath and
pneumonia, about a week after symptoms
start.
 Some people experience COVID-
19 symptoms for more than four weeks
after they're diagnosed. These health
issues are sometimes called post-COVID-
19 conditions. Some children experience
multisystem inflammatory syndrome, a
syndrome that can affect some organs
and tissues, several weeks after
having COVID-19. Rarely, some adults
experience the syndrome too.
 People who are older have a higher risk of
serious illness from COVID-19, and the
risk increases with age. People who have
existing medical conditions also may have
a higher risk of serious illness. Certain
medical conditions that may increase the
risk of serious illness from COVID-
19 include:
 Serious heart diseases, such as
heart failure, coronary artery
disease or cardiomyopathy.
 Cancer
 Chronic obstructive pulmonary
disease (COPD)
 Type 1 or type 2 diabetes
 Overweight, obesity or severe
obesity
 High blood pressure
 Smoking
 Chronic kidney disease
 Sickle cell disease or thalassemia
 Weakened immune system from
solid organ transplants or bone
marrow transplants
 Pregnancy
 Asthma
 Chronic lung diseases such as
cystic fibrosis or pulmonary
hypertension
 Liver disease
 Dementia
 Down syndrome
 Weakened immune system from
bone marrow transplant, HIV or
some medications
 Brain and nervous system
conditions, such as strokes
 Substance use disorders
 COVID-19
FAMILY: CORONAVIRIDAE
- SARS‑CoV‑2 is a positive-sense single-
stranded RNA virus,enveloped
- Contagious to humans
- SARS‑CoV‑2 is a virus of the
species severe acute respiratory
syndrome–related
coronavirus (SARSr-CoV), related to
the SARS-CoV-1 virus that caused
the 2002–2004 SARS outbreak
- Zoonotic= similar genetic with bat
coronaviruses but research is still ongoing
(bats directly or indirectly intermediate
host)
- The virus shows little genetic diversity,
indicating that the spillover
event introducing SARS‑CoV‑2 to humans
is likely to have occurred in late 2019.
- It enters human cells by binding
to angiotensin-converting enzyme
2 (ACE2), a membrane protein that
regulates the renin–angiotensin system
(mechanism of cell entry)
- S protein is responsible for allowing the
virus to attach to and fuse with
the membrane of a host cell.
- Initial spike protein priming
by transmembrane protease, serine
2 (TMPRSS2) is essential for entry of
SARS‑CoV‑2.[The host protein neuropilin
1 (NRP1) may aid the virus in host cell
entry using ACE2.After a SARS‑CoV‑2
virion attaches to a target cell, the cell's
TMPRSS2 cuts open the spike protein of
the virus, exposing a fusion peptide in the
S2 subunit, and the host receptor
ACE2. After fusion, an endosome forms
around the virion, separating it from the
rest of the host cell. The virion escapes
when the pH of the endosome drops or
when cathepsin, a
host cysteine protease, cleaves it.The
virion then releases RNA into the cell and
forces the cell to produce and
disseminate copies of the virus, which
infect more cells
- Asymptomatic and symptomatic
transmission
- Re-infection
- No natural reservoir, bats most likely
- Two previous zoonosis-based coronavirus
epidemics, those caused by SARS-CoV-
1 and MERS-CoV
- 5 variants of concern: alpha, beta,
gamma, delta, omicron
- 60-40 nanometers
- 4 structural proteins: S(spike),
E(envelope), M (membrane),N
(nucleocapsid) proteins
- COVID-19
- RAT’s Rapid Antigen tests
- POC point of care test kits
- determines active virus in the body,less
reliable so follow-up rRT-PCR.
- NAAT’s or NAT’s
- Nucleic Acid Amplification tests
- PCR based: molecular biology
- rRT-PCR or real time reverse transcription
polymerase chain reaction(gold
standard,most often
performed,reliable,detect viral genetic
material even upto 90 days)
- Layman’s term: swab test (OPS/NPS
swab)
TREATMENT
 Supportive treatment, anti-fever
medications,anti-viral
 Only one anti-viral:Remdesivir currently
approved to treat
 Researchers are currently evaluating
drugs & treatment.Some drugs may help
reduce the severity of the disease
 PREVENTION: VACCINES (fully
vaccinated)
Prevention tips: Avoiding close contact with
sick individuals; frequently washing hands with
soap and water; not touching the eyes, nose, or
mouth with unwashed hands; and practicing good
respiratory hygiene
INFLUENZA OR FLU/GRIPPE
- Commonly known as “the flu”, infectious
disease caused by influenza viruses that
infects the nose, throat and sometimes
the lungs
Symptoms:
- fever, runny nose, sore throat, muscle
pain, headache, coughing, fatigue
 - Mild to severe illness that may lead to
death
- 1-4 days after exposure, duration 2-8
days
Mode of transmission:
- respiratory droplets (coughing &
sneezing), aerosols and intermediate
objects and surfaces contaminated by the
virus
- In healthy individuals, typically self-
limiting and rarely fatal but can be deadly
in high-risk groups
 Influenza may progress to pneumonia,
which can be caused by the virus or by a
subsequent bacterial infection. Other
complications of infection include acute
respiratory distress
syndrome, meningitis, encephalitis,
and worsening of pre-existing health
problems such
as asthma and cardiovascular disease.
 In humans, influenza viruses first cause
infection by infecting epithelial cells in the
respiratory tract. Illness during infection is
primarily the result of
lung inflammation and compromise
caused by epithelial cell infection and
death, combined with inflammation
caused by the immune system's response
to infection.
 Severe respiratory illness can be caused
by multiple, non-exclusive mechanisms,
including obstruction of the airways, loss
of alveolar structure, loss of lung epithelial
integrity due to epithelial cell infection and
death, and degradation of the
extracellular matrix that maintains lung
structure. In particular, alveolar cell
infection appears to drive severe
symptoms since this results in impaired
gas exchange and enables viruses to
infect endothelial cells, which produce
large quantities of pro-
inflammatory cytokines.
 Pneumonia caused by influenza viruses
is characterized by high levels of viral
replication in the lower respiratory tract,
accompanied by a strong pro-
inflammatory response called a cytokine
storm.
 Infection with H5N1 or H7N9 especially
produces high levels of pro-inflammatory
cytokines.
 In bacterial infections, early depletion
of macrophages during influenza creates
a favorable environment in the lungs for
bacterial growth since these white blood
cells are important in responding to
bacterial infection. Host mechanisms to
encourage tissue repair may inadvertently
allow bacterial infection. Infection also
induces production of
systemic glucocorticoids that can reduce
inflammation to preserve tissue integrity
but allow increased bacterial growth.
Pathophysiology of influenza
- is significantly influenced by which
receptors influenza viruses bind to during
entry into cells.
- Mammalian influenza viruses preferentially
bind to sialic acids.
- FAMILY: ORTHOMYXOVIRIDAE
- INFLUENZA VIRUS: ENVELOPED,
HELICAL NUCLEOCAPSID,
SEGMENTED, SS –NEGATIVE RNA
- 4 SPECIES; EACH IS A MEMBER OF IT’S
OWN GENUS:
 Influenza A virus (IAV),
genus Alphainfluenzavirus (aquatic
birds,humans,pigs)
 Influenza B virus (IBV),
genus Betainfluenzavirus (humans)
 Influenza C virus (ICV),
genus Gammainfluenzavirus(huma
ns)
 Influenza D virus (IDV),
genus Deltainfluenzavirus (cattle
and pigs)
- Influenza A &B: circulate in humans
and cause seasonal epidemics.
- ICV causes a mild infection, primarily in
children.
- IDV can infect humans but is not known
to cause illness.
  Antigenic drift and shift
2 key processes that influenza evolved:
- Antigenic drift is when an influenza
virus's antigens change due to the gradual
accumulation of mutations in the
antigen's (HA or NA) gene (minor
changes, slow, progressive) EPIDEMICS.
- Antigenic shift, antigenically different
strains that infect the same cell
can reassort genome segments with each
other, producing hybrid progeny (major
changes, sudden, drastic, occurs in same
genus) PANDEMICS/NEW EPIDEMICS.
Diagnostic methods:
INFLUENZA
- INFLUENZA A (H1N1 SUBTYPE)
- The structure of influenza A virus. IAV is a
negative-stranded RNA virus belonging to
the Orthomyxoviridae family.
- The IAV genome is divided into eight
segments that encode 11 viral proteins in
total (HA, NA, M1, M2, NP, NS1, NS2, PA,
PB1, PB2, and PB1-F2).
- The viral envelope of IAV contains the
transmembrane proteins HA, NA, and M2.
- Variants and subtypes: INFLUENZA A
- categorized into subtypes based on the
type of two proteins on the surface of the
viral envelope:
 (H/HA) Hemagglutinin- protein causes
rbc’s to agglutinate
 (N/NA) Neuraminidase-(neuraminic
acid) an enzyme that cleaves
the glycosidic bonds of
the monosaccharide sialic acid
- The hemagglutinin is central to the virus's
recognizing and binding to target cells,
and also to its then infecting the cell with
its RNA.
- The neuraminidase, on the other hand, is
critical for the subsequent release of the
daughter virus particles created within the
infected cell so they can spread to other
cells
- Different influenza viruses encode for
different hemagglutinin and
neuraminidase proteins. For example,
the H5N1 virus designates an influenza A
subtype that has a type 5 hemagglutinin
(H) protein and a type 1 neuraminidase
(N) protein.
- There are 18 known types of
hemagglutinin.
- 11 known types of neuraminidase.
- in theory, 198 different combinations of
these proteins are possible.
- include viral cultures, antibody- and
antigen-detecting tests,
immunofluorescent assays and nucleic
acid-based tests.
- Viruses can be grown in a culture of
mammalian cells or embryonated eggs for
3–10 days to monitor cytopathic effect.
Final confirmation can then be done via
antibody staining, hemadsorption
using red blood cells,
or immunofluorescence microscopy. Shell
vial cultures, which can identify infection
via immunostaining before a cytopathic
effect appears, are more sensitive than
traditional cultures with results in 1–3
days.
- relatively slow and require specialized
skills and equipment.
- A number of tests are available to detect
flu viruses in respiratory specimens. The
most common are called “rapid
influenza diagnostic tests (RIDTs).”
RIDTs work by detecting the parts of the
virus (antigens) that stimulate an immune
response. These tests can provide results
within approximately 10-15 minutes but
may not be as accurate as other flu tests.
Therefore, you could still have flu, even
though your rapid test result is negative.
- are a simple way of obtaining assay
results, are low cost, and produce results
quickly.
- can't distinguish between IAV and IBV or
between IAV subtypes and are not as
sensitive as nucleic-acid based tests.
- Other flu tests called “rapid molecular
assays” detect genetic material of the flu
virus. Rapid molecular assays produce
results in 15-20 minutes and are more
accurate than RIDTs.
- In addition to RIDTs and rapid molecular
assays, there are several more accurate
flu tests available that must be performed
in specialized laboratories, such as
hospital and public health laboratories.
 These tests include reverse transcription
polymerase chain reaction (RT-PCR), viral
culture, and immunofluorescence assays.
All of these tests require that a health
care provider swipe the inside of your
nose or the back of your throat with a
swab and then send the swab for testing.
Results may take one to several hours.
: two IBV lineages.
- can be used to detect an antibody
response to influenza after natural
infection or vaccination.
- Hemagglutination Inhibition assays that
detect HA-specific antibodies.
- Virus Neutralization assays that check
whether antibodies have neutralized the
virus.
- Enzyme-Linked Immunoabsorbant
Assays/ELISA
- relatively inexpensive and fast but are less
reliable than nucleic-acid based tests.
Immunofluorescence Assays
- Direct fluorescent or immunofluorescent
antibody (DFA/IFA) tests involve staining
respiratory epithelial cells in samples with
fluorescently-labeled influenza-specific
antibodies, followed by examination under
a fluorescent microscope. They can
differentiate between IAV and IBV but
can't subtype IAV.
Nucleic acid-based tests (NATs)
- amplify and detect viral nucleic acids
- RT-PCR reverse transcription polymerase
chain reaction
- most traditional, gold standard, fast, can
subtype IBV
- is relatively expensive and more prone to
false-positives than cultures.
- Other NATs
- loop-mediated isothermal amplification-
based assays
- simple amplification-based assays, and
- nucleic acid sequence-based amplification
(can identify infection by obtaining the
nucleic acid sequence of viral samples to
identify the virus and antiviral drug
resistance).
TREATMENT
- Anti-viral drugs, anti-fever, rest ,fluid
intake to avoid dehydration,cough
drops,throat sprays
PREVENTION
- (aside proper hand hygiene and infection
control)
- Annual vaccination (Influenza A&B)
- primary and most effective way to prevent
influenza and influenza-associated
complications, especially for high-risk
groups.
- Vaccines against the flu are trivalent or
quadrivalent, providing protection against
an H1N1 strain, an H3N2 strain, and one
or two IBV strains corresponding to the
MUMPS
- Mumps is best known for the puffy cheeks
and tender, swollen jaw that it causes.
- This is a result of a swollen salivary glands
under the ears on one or both sides, often
referred to as parotitis.
- Other symptoms that might begin a few
days before parotitis include:
- Fever, headache, muscle aches, tiredness,
loss of appetite
- Contagious disease that can also cause an
outbreak
- Outbreaks have most commonly occurred
among groups of people who have
prolonged, close contact, such as sharing
water bottles or cups, kissing, practicing
sports together, or living in close quarters,
with a person who has mumps. Some
vaccinated people may still get mumps if
they are exposed to the virus. However,
disease symptoms are milder in
vaccinated people.
- Some people who get mumps have very
mild symptoms (like a cold), or no
symptoms at all and may not know that
they have the disease
- Transmission: respiratory
droplets/aerosols/saliva
- Symptoms appear 16-18 days after
infection but this period can range from
12-25 days after infection
- Most people with mumps recover
completely within two weeks
- In rare cases, mumps can cause more
severe complications
- URT then spreads through blood and
infects the:
 Parotid gland-Parotitis (increases pain
when drinking citrus juices, salivary
gland)
 Testes- Orchitis (inflammation of
testicles)
 Ovaries-Oophoritis (inflammation of
ovary)
 Breast tissues-Mastitis (inflammation of
breast tissues)
 Meninges- aseptic Meningitis
(inflammation of the tissue covering the
brain and spinal cord) Encephalitis/brain
inflammation (CNS)
 Pancreas- Pancreatitis (inflammation of
pancreas)
 hearing loss/deafness
- FAMILY: PARAMYXOVIRIDAE
- GENUS: Orthorubulavirus
- Viral Characteristics: enveloped,helical
symmetry,ss -RNA non-segmented
- Mumps virus binds to sialic acid to enter
the polarized epithelial cells in the upper
respiratory tract from both sides
- Spreads to local lymph nodes then distant
lymph nodes and spleen
- Apical entries facilitate transmission to
neighboring cells
- Infection from basolateral side is probably
important for secondary infection via
bloodstream
- Apical sides of epithelial cells
(predominantly released), replicates in
glandular epithelium and mumps virus
shedding in saliva
- V, HN and F proteins
- Viremia: dissemination of the virus to
other organs including testes and kidney.
- Affinity to T cells and efficiently replicates
in these cells
- Virus-infected T cells: spread respiratory
tract to other sites of the body
- Generalized spread to salivary and other
glands, and to other body sites
- viral isolates can be collected: testes,
semen, urine.
- In general, mainly contains 7 structural
proteins: fusion protein, hemagglutinin-
neuraminidase protein,
phosphoprotein/V/I protein, matrix
protein, small hydrophobic protein, a
high-molecular-weight protein (L protein)
which combines with P protein to form
RdRp, and nucleocapsid protein.
- Mumps virus replicates by binding to
surface of cells, merges envelope with
host cell membrane to release capsid
inside the cell.
- Once inside the viral RdRp transcribes
mRNA from genome and later replicates
genome.
- Translation of viral proteins
- Virions are formed adjacent to the cell
membrane.
- Leave by budding from its surface using
the cell membrane as the envelope.
Laboratory Diagnosis:
- Buccal swab NAT’s: real-time RT-PCR
- Serologic Assay: Serum specimen for IgM
detection not IgG (since IgG is typically
present at symptom onset, previous
subclinical infection and those previously
vaccinated) or EIA (non-quantitative) or
IFA.
- Mumps is confirmed by detecting mumps
IgM antibody in serum collected as soon
as possible after onset. A positive IgM test
result indicates current, very recent
infection or reinfection.
TREATMENT: relieve symptoms/supportive in
nature.
- Rest, painkillers, anti-fever
PREVENTION:
- (aside from proper hygiene)
- MMR vaccine/Mumps Measles and Rubella
vaccine
- Infants and booster dose for adults