VIRUSES OF PUBLIC HEALTH IMPORTANCE > After fusion, the viral genome is released to the

cytoplasm where it undergoes reverse transcription

> The viral capsid disassembles, and the DNA is
transported to the nucleus
> Viral DNA is integrated into the host chromatin (this
HUMAN IMMUNODEFICIENCY VIRUS / AIDS
step is what makes HIV a chronic infection)
> RNA products are transported to the cytoplasm
> Increasing in prevalence because HIV does not have a
> Viral protein synthesis occurs
cure
> The virus assembles on the surface of the cell
> Number of incidence (new infections) have been
> Further maturation occurs after budding from the host
decreasing globally since around 1900s when the
membrane
antiretroviral medications became available
> However, in the Philippines, the number of incidence
Viral Latency
(newly diagnosed) has been increasing
> A fraction of infected cells do not die but survives and
- 2010 - 1 case per day
reverts to a resting memory state
- 2012 - 9 cases per day
> There is little or no virus expression in memory cells, but
- 2017 - 30 cases per day
the provide long term, stable reservoirs for the virus
- 2021 - 34 cases per day
> Latent reservoir in patients die very slowly
- 2022 - 41 cases per day
> When exposed to an antigen or when drug therapy is
discontinued (patients may get rebound viremia), the
HIV
memory cells become activated and release infectious
> Retrovirus under family Retroviridae
virus
> Lipid envelope with envelope proteins gp120 and gp41
> Other reservoirs: macrophages, hematopoietic stem
> Protein capsid and matrix
cells, brain cells
> Single-stranded RNA (two copies)
> Reverse transcriptase enzyme
Natural History of HIV / AIDS
- Makes DNA from RNA
> Primary infection
> Dissemination of virus to lymphoid organs
> Clinical latency (Average 10 years)
> Elevated HIV expression
> Clinical disease: AIDS
> Death

Life Cycle
> HIV infects cells expressing the CD4 receptor
- Monocyte and macrophages (for M-tropic
viruses; during early stages of infection)
- T lymphocytes especially (for T-tropic strains;
during later stages of infection)
- M - mabilis: T - tagal
> First step: binding of viral gp120 (mas mahal ang
attachment) to CD4 receptor and coreceptor:
- CXCR4 - for lymphocytes
- CCR5 - for macrophages
> CD4 lymphocytes are responsible for activating the
adaptive immune system

Clinical Findings
> Acute HIV infection
- Fatigue, rash, headache, nausea, night sweats
(flu-like syndrome)
> AIDS
The Target: CD4 Lymphocytes (T Helper Cells)
- Characterized by opportunistic infections and
neoplasms (eg. Kaposi sarcoma)
- AIDS-defining illness
- Usually when CD4 counts go below 200
cells/mL (normal is >1000 cells/mL)
 > Blood transfusion
> Sexual intercourse
> Sharing of needles
> Mother to child

Diagnosis
> Presumptive Diagnosis
- ELISA
- Tests for antibodies
- ‘May have false positive results (high sensitivity,
low specificity)
> Definitive Diagnosis
- Western blot
1. Opportunistic Infections - High specificity (99.9% accuracy when combined
- Usually do not appear until the CD4 count is with ELISA)
<200 cells/mL - Latest guidelines: Rapid HIV Testing Diagnostic
- Protozoa: Toxoplasma gondii, ISospora belli, Algorithm (rHIVda)
Cryptosporidium species > Monitoring of Viral Load
- Fungi: Candida albicans, Cryptococcus - Reverse transcriptase - RT-PCR
neoformans, Coccidioides immitis, Histoplasma
capsulatum, Pneumocystis jiroveci
- Bacteria: Mycobacterium avium-intracellulare, Drug Classes in Antiretroviral Therapy
Mycobacterium tuberculosis, Listeria
monocytogenes, Nocardia asteroides,
Salmonella species, Streptococcus species
- Viruses: Cytomegalovirus, Herpes Simplex
Virus, Varicella-Zoster Virus, Adenovirus, JC
polyomavirus, Hepatitis B Virus, Hepatitis C Virus
2. Pediatric AIDS
- Acquired from infected mothers
- Usually presents with clinical symptoms at 2
years of age
- Death follows in another 2 years after symptom
onset
- Clinical findings: lymphoid interstitial pneumonitis,
pneumonia, severe oral candidiasis,
encephalopathy, wasting, generalized
lymphadenopathy, bacterial sepsis,
hepatosplenomegaly, diarrhea, growth retardation
3. Neurologic Disease
- 40-90% of patients have neurologic symptoms Prevention
- AIDS dementia complex: - Abstinence
- Most common neurologic syndrome - Be faithful
- Characterized by poor memory, inability - Condom-use
to concentrate, apathy, psychomotor - Drug-use: avoid
retardation, behavioral changes - Education
- Other syndromes, peripheral > Currently no vaccine for HIV
neuropathy, subacute encephalitis, etc.
- Infections: toxoplasmosis, cryptococcosis,
JC-virus induced progressive multifocal Current Public Health Intervention
leukoencephalopathy - Free counseling and screening of HIV / AIDS in
- Pediatric AIDS: seizure disorders, progressive health centers
loss of behavioral developmental milestones, - More aggressive surveillance and reporting of
development delays, ADHD HIV / AIDS
- Psychiatric disorders: anxiety disorders - Distribution of male condoms as education
4. Cancers materials
- Kaposi sarcoma - Community assemblies to reduce stigma
- Vascular tumor of endothelial origin that - Free antiretroviral therapy in multiple treatment
appears in the skin, mucous hubs all over the Philippines
membranes, lymph nodes
- Grape-like lesions
- Cervical cancer Current Problems in the Control of HIV Epidemic
- Caused by HPV > Increasing resistance in the Philippines
- Anogenital cancers - Only 90% have viral suppression after 1 year of
- Also from coinfection with HPV therapy (Salvana et al., 2017)
- Non-Hodgkin lymphoma

CORONAVIRUSES
Transmission
> Corona - Latin for crown - Shortness of breath
- So called because of the spikes that form a
crown around the virion (spike proteins) Transmission
> Coronaviruses cause: - Droplet and direct contact
- Common colds
- lower respiratory tract infections Diagnostics
- Gastroenteritis in infants - Serology (ELISA, IFA), RT-PCR
> Novel coronaviruses that caused pandemics
- Severe Acute Respiratory Syndrome-CoV (2003)
- Middle East Respiratory Syndrome-CoV (2012) > MERS-CoV
- SARS-Cov-2 (2019) Epidemiology
> Virion: large, spherical, with a helical nucleocapsid - Started in September 2012
> Genome: (+) ssRNA, unsegmented genome - Direct or indirect connection with the Middle East
> Envelope: contains large, widely spaced, club- or - 130 laboratory-confirmed cases of infection with
petal-shaped spikes MERS-CoV
> Replication: cytoplasm; particles mature by budding - Mortality 44.6%
into the ER and Golgi - Less transmissible than SARS-CoV but more
> Outstanding characteristics: deadly
- Cause colds, MERS, SARS, COVID-19
- Display high frequency of recombination (give Clinical Manifestation
rise to new variants) - Severe acute respiratory illness with symptoms of
- Difficult to grow in cell culture fever, cough, and shortness of breath
- Acute renal failure

Life Cycle Transmission

1. Viral entry through fusion or endocytosis - Non-sustained human transmission
2. Release of nucleocapsid into the cytoplasm where the
genomic (+) ssRNA is also released Diagnostics
3. Replication - creation of (-) ssRNA which will become - Serology, RT-PCR
the template for the creation of new genomic (+)
ssRNA and subgenomic RNAs
4. Subgenomic RNAs will be used in the translation of Phylogenetic Tree of SARS-CoV-2 and other Beta
new viral proteins Coronaviruses
- N protein: nucleocapsid protein → will enclose
the new genomic RNAs
- M protein: will be transferred into the ER and
these proteins will interact with the nucleocapsid
(N protein + genomic RNA)
- The nucleocapsid, in close interaction with the M
protein and other membrane proteins will then
bud through the ER-Golgi complex
5. Release through exocytosis

Notable Coronaviruses
SARS-CoV-2
> SARS-CoV - Zoonotic infection adapted in humans
Epidemiology - Origin is uncertain although bats are implicated
- SARS outbreak in 2003, first reported in China because the genetic sequence is closest to bat
- Spread in 24 countries in North America, South SARS-like coronavirus
America, Europe, and Asia - Pangolin - intermediary mammal invoked as potential
- Last case in April 2004 from laboratory-acquired bridge in the jump to humans
infection - Its spike protein attaches to the ACE2 receptor
- No. of cases: 8,437 through its receptor binding domain (RBD)
- 813 deaths reported

Clinical Manifestation
- High grade fever
- Respiratory symptoms (pneumonia)
- Malaise and body aches
 cardiovascular diseases, sickle cell
diseases, Type 2 DM
- Possible increased risk (limited date):
asthma, CVA, cystic fibrosis,
hypertension, neurologic conditions,
liver disease, pregnancy, pulmonary
fibrosis, smoking, thalassemia, type 1
DM
- Blacks, Native Americans, Latins
> Children are less symptomatic and less prone to viral
SARS-CoV-2 Virion illness

Transmission
- Respiratory droplets predominantly, but
aerosolization is possible
- Airborne transmission is debated
- Viral shedding starts 1-2 days before symptom
onset, and highest on the earliest phase of
infection
- Incubation period: mean of 5-6 days, range of
2-12 days
* For the Omicron variant, there is higher transmission and
incubation period is usually as short as 3 days only

Life Cycle
> A lot of the currently investigated treatment strategies
target some steps in the virus life cycle

Clinical Presentation
- May occur 2-14 days after exposure
- Most common symptoms:
- Fever (44-98%)
- Cough (46-82%, usually dry)
- Shortness of breath at onset (31%)
- Myalgia or fatigue (11-44%)
- Loss of taste or smell

Diagnosis
> Molecular
- Real-time RT-PCR
- Nasopharyngeal/oropharyngeal swab
- Lower respiratory tract specimens have higher
yield
- Detection of viral RNA does not necessarily
mean there is detection of infectious virus
> Antigen
Clinical Features of COVID-19 - Eg. spike protein (lower sensitivity, shorter
turnaround time)
> Serologic
- Antibody-based tests for COVID-19
- Presence of antibodies does not necessarily
indicate immunity
> Viral Culture
- Not recommended (long and tedious, requires
BSL-3 lab)

Treatment
- Supportive care
- Antivirals: Remdesivir
- Immunomodulators: Tocilizumab,
Dexamethasone
Risk Factors
- Older age (>65) with comorbidities Vaccination
- Males (more affected, especially with critical illness) - Sinovac (China) - inactivated vaccine
- Comorbidities - Moderna (US) - RNA vaccine
- Definite: cancer, CKD, COPD, - Pfizer (US) - RNA vaccine
immunocompromised state from organ - Sputnik V (Russia) - Adenovirus vector
transplant, obesity/BMI 30, serious - Astrazeneca (UK) - Adenovirus vector
- J&J (US) - Adenovirus vector
 > Variants of Concern
Scientific Country Where WHO Label
Name First Identified

B.1.1.7 United Kingdom Alpha

B.1.351 South Africa Beta

P.1. Brazil Gamma

B.1.617.2 India Delta

B.1.1.529 South Africa Omicron

COVID-19 VARIANTS

> How do variants emerge?

- Variants happen when there are mutations from the
original virus, such as in the gene for spike protein
- These mutations may cause structural changes in the
virus structure which may or may not have significant
effects t its infectivity or virulence

Variants of Interest (VOI)

- A variant with specific genetic markers that have
been associated with changes to receptor binding,
reduced neutralization by antibodies generated
against previous infection or vaccination, reduced
efficacy of treatments, potential diagnostic impact, or
predicted increase in transmissibility or disease
severity

Variants of Concern (VOC)

- A variant for which there is evidence for increase in
transmissibility, more severe disease (eg.
increased hospitalizations or deaths), significant
reduction in neutralization by antibodies
generated during previous infection or vaccination, > ALPHA - B.1.1.7 (UK)
reduced effectiveness of treatments or vaccines, - Earliest sequence collected on September 20,2020 in
or diagnostic detection failures the UK
- First detected in the Philippines on January 2021
- N501Y: Mutation in the receptor binding domain
Coronavirus Variants (Simplified) (RBD) of the spike protein at position 501, where the
> Variants of Interest amino acid asparagine (N) has been replaced with
Scientific Country Where WHO Label tyrosine (Y)
Name First Identified - This variant also has several other mutations,
including:
B.1.427/429 United States Epsilon - 69/70 deletion: likely leads to conformational
change in spike protein
P.2 Brazil Zeta - P681H: near the S1/S2 furin cleavage site, a site
with high variability in coronaviruses
B.1.525 Multiple Countries Eta
- Higher transmissibility at approximately 70%
(43-90% higher reproduction number)
P.3 Philippines Theta
- N501Y mutation increases receptor binding
B.1.526 United States Iota affinity of the SARS-CoV-2 spike protein with
ACE2
B.1.617.1 India Kappa - Higher risk of death (55%)
> BETA - B.1.351 (SOUTH AFRICA)
- First identified in Nelson Mandela Bay, South Africa
(samples from October 2020
- Later became the predominant variant in South Africa
- First detected in the Philippines in early March 2021
- Multiple mutations in the spike protein, including
- K417N
- E484K
- N501Y
- More transmissible than the original SARS-CoV-2
(50% increased transmission)
- Evidence suggests that it has antibody resistance
- E484K mutation decreases neutralizing activity
(effectiveness) of antibodies from convalescent
sera
GAMMA - P.1 (BRAZIL)
- Detected in japan from Brazilian travelers early
January 2021
- Detected in the Philippines mid March 2021
- The new P.1 lineage carries 17 unique amino acid
changes, 3 deletions, 4 synonymous mutation, and
one 4nt insertion compared to the most closely
related available non-P.1 sequence
- It also contains the K417T, E484K, and N501Y
mutations seen in other variations
- Despite 70% seroprevalence i Brazil last October
2020, a surge in cases occurred beginning December
2020
- 42% of samples taken on December showed a
P.1 lineage
- Reports of reinfections
- Higher transmissibility (estimated around 1.4-2.2
times more transmissible than other lineages)
- Effectiveness of antibodies drop by six-fold
DELTA - B.1.617.2 (INDIA)
- Detected in India last December 2020
- Detected in Philippines last May 12, 2021
- Increased transmissibility
- Potential reduction in neutralization by
post-vaccination sera
- Mutations:
- L452R
- T478K
- D614G - Increased viral replication, increased
infectivity, increased stability
- P681R
OMICRON - B.1.1.529
- Detected last November 24, 2021 in South Africa
- Designated as VOC by November 30, 2021
- Based on epidemiological data indication an
increase in infections in South Africa in weeks
that coincided with its detection
- At least 30 amino acid substitutions (15 of 30 in the
RBD), 3 deletions, and one insertion in the S protein
(at least 50 in the whole genome)
- N501Y, H655Y, N679K, P681H: may aid in
increased transmission
- The neutralization efficacy of vaccine-elicited sera
against Omicron was severely reduced
THETA - PH-B.1.1.28 (PHILIPPINES)
- Reported in the Philippines last March 8, 2021 by the
Philippine Genome Center
- The presence of 13 lineage-defining mutations 7
occurring in the spike protein region hint at the
development of a unique SARS-CoV-2 variant within
the country
- Contain the E484K, N501Y, and P681H spike
mutations previously found in other variants of
concern such as the South Africa, Brazil, and UK
variants
- P681H mutation - biological effect still unknown
but computer-based analysis suggests that it
might promote the ability of the virus to enter
the cell
HUMAN PAPILLOMAVIRUS
> Family Papillomaviridae
> Icosahedral
> dsDNA genome
> Naked
> Outstanding characteristics:
- Stimulate cell DNA synthesis
- Restricted host range and tissue tropism
- Significant cause of human cancer, especially
cervical cancer
- Viral oncoproteins interact with cellular tumor
suppressor genes
Clinical Manifestations
● Cervical Cancer - HPV 16,18
● Genital Warts - HPV 6, 11
Papillomavirus Replication
> Highly tropic for epithelial cells and mucous membranes
> Steps in the replicative cycle are dependent on specific
factors that are present in sequential differentiated
states
- Viral nucleic acid - found in basal stem cells
- Late gene expression (capsid proteins) -
restricted to the uppermost layer of differentiated
keratinocytes
Molecular Pathogenesis
> E6 - Binds to p53 and targets it for ubiquitin-mediated
degradation
>E7 - Interacts with and destabilizes Rb
(retinoblastoma); loss of Rb/E2F complex releases E2F
→ transcription of genes for cell cycle progression
> The HPV proteins inhibit the functions of tumor
suppressor genes, thereby inducing malignancy
Prevention and Control
> Pap Smear
- Detect precancerous cellular changes in
morphology, allowing for lesion removal prior to
cancer development
> HPV DNA
- Testing added for abnormal Pap smears
> Vaccination
- Non-infectious recombinant virus-like particles
composed of HPV L1 protein
- Three types:
- Bivalent (Type 16 and 18)
- Quadrivalent (Type 6, 11, 16, and 18)
- 9-valent (Type 6, 11, 16, 18, 31, 33, 45,
52, and 58)
ADENOVIRUSES
> Adenoviridae
> Produce disease in the respiratory, gastrointestinal,
urinary tracts, and the eye
> Icosahedral, naked with linear dsDNA genome
> Unique characteristic: with “fibers” projecting from each
f the 12 vertices (penton bases)
> Outstanding characteristic: excellent models for
molecular studies of eukaryotic cell processes
- 11 virion proteins
- With hexon and penton capsomeres that are a major
component of the surface
- Each penton base caries a toxin-like activity that
causes rapid appearance of cytopathic effects and
detachment of cells from the surface on which they
are growing
- TP - terminal protein bound the 3’ end of the genome
Classification
- Divided into 5 genera
- Mastadenovirus genus - contains all human
adenoviruses
- Has 57 distinct antigenic types
- Divided into 7 groups (A-G) based on their genetic,
physical, chemical, and biologic properties
Pathogenesis
- Adenoviruses replicate well only in cells with epithelial
origin
- They infect and replicate in epithelial cells of the
respiratory tract, eye, gastrointestinal tract, and
urinary tract
- They usually do not spread beyond the regional
lymph nodes
- Most infections are mild and self-limited

Clinical Findings
1. Respiratory Diseases
- Cough, nasal congestion, fever, sore throat
- Other diseases:
- Adenoviral pneumonia: 10-20% of
pneumonia in childhood
- Acute respiratory disease syndrome:
Life Cycle usually seen among military recruits
> Attachment under conditions of fatigue, stress, and
> Endocytosis crowding
> Release of virion - Severe respiratory disease: outbreak in
> Nuclear import 2007 from a new variant of Ad14; other
> Gene expression of early phase proteins cases were fatal
> DNA replication 2. Eye Infection
> Gene expression of late phase proteins - Pharyngoconjunctival fever
> Assembly - Usually occurs in outbreaks such as
> Cell lysis children’s summer camps
- “Swimming pool conjunctivitis”
- Epidemic keratoconjunctivitis
- Characterized by acute conjunctivitis
followed by keratitis that usually
resolves in 2 weeks but may leave
subepithelial opacities in the cornea for
up to 2 years
3. Gastrointestinal Disease
- Many adenoviruses replicate in intestinal cells
- Most serotypes are not associated with
gastrointestinal disease
- Infantile gastroenteritis
- Serotype 40 and 41
- 5-15% of viral gastroenteritis in children
- Diarrhea stools
4. Other Diseases
- Severe pneumonia and disseminated infection in
transplant patients
- Adenovirus hepatitis in liver transplant patients
Early Events - Acute hemorrhagic cystitis in children and renal
> E1A bone transplant patients
- Early gene that is very important because it must be - Gastrointestinal infection in AIDS patients
expressed for the other viral genomes to be
transcribed
- Function: modulate cell cycle Immunity
> Adenovirus induce effective, long–lasting immunity
> E1B against reinfection
- Encodes proteins that block cell death (apoptosis) > Resistance to the clinical disease appears to be directly
- Necessary to prevent premature cell death that would related to the presence of circulating neutralizing
adversely affect virus yields antibodies

> E1A and E1B bind cellular proteins (eg. pRb, p300, p53)
that regulate cell cycle progression
Adenovirus Use in Gene Therapy
> Adenoviruses are being used as gene delivery
vehicles (E1 and E3 genes are usually removed)
> Advantage: high transduction efficiency and high levels
of short-term expression of transduced genes
> Limitation: high immunogenicity and high prevalence of
preexisting immunity in humans