SEMINAR 1 CMLS MYCOLOGY VIROLOGY

SEMINAR 1
Mycology and Virology
 VIROLOGY

CORONAVIRUS

Coronaviridae
 Coronaviruses are large, linear and a positive stranded RNA genomes
 Known for its high-grade fever, pneumonia and acute respiratory distress
syndrome and terms as severe acute respiratory syndrome
 Infection target the epithelial cells of respiratory tract and transmitted
from person to person by direct contact, droplet or aiborne routes
o SARS-CoV – started in China in the year 2012
o MERS-CoV – isolated in Middle East in the year 2012
Normal oxygen saturation – 95-100%
With covid- <95%
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Known as COVID-19 that cause mild to moderate respiratory illness
 Mode of Transmission
o Direct or close contact of within 1 meter distance with infected
people through secretions such as saliva and respiratory droplets
o Indirect transmission involving contact of susceptible host with a
contaminated object or surface is possible followed by touching the
mouth, nose or eyes
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Definition of Terms
o Mutation: refers to a single change in virus genome
o Recombinant: process in which the genome of 2 viruses combines
during viral replication process
o Lineage: group of closely related viruses with common ancestor
o Variant: viral genome that contains one or more mutations
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Classification
o Variant being monitored (VBM)
o Variant of interest (VOI)
o Variant of concern (VOC)
o Variant of high consequence (VOHC)
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Classification
o Variant being monitored (VBM) – data that indicates a potential or
clear impact on approved or authorized medical countermeasures or
have been associated with more severe disease or increased
transmission but are NO longer detected or circulating at very LOW
level in the public health
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Classification
o Variant being interest (VBI) – contains a specific genetic markers that
have been associated with changes to receptor binding, reduced
neutralization by antibodies generated against previous infection of
vaccination, reduced efficacy of treatments, potential diagnostic
impact or predicted increase in transmissibility or disease severity.
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Classification
o Variant of concern (VOC) – presence of evidence of an increase in
transmissibility, more severe disease, significant reduction in
neutralization by antibodies generated during previous infection or
vaccination, reduced effectiveness of treatments or vaccines or
diagnostic detection failures
 VIROLOGY

SARS-Cov-2 VIRUS

SARS-CoV-2 Virus
 Classification
o Variant high consequence (VOHC) – prevention measure or medical
countermeasures have significantly reduced effectiveness relative to
previously circulating variants
Possible attributes :
• Demonstrated failure of diagnostic test
• Significant reduction in vaccine effectiveness
• Significant reduction in susceptibility to approved therapeutics
• More severe cases clinical and increase hospitalization
 VIROLOGY

LABORATORY DIAGNOSIS

Specimen Collection and Processing

 Materials includes
 COVID-19 investigation form
 Virus transport media or Universal transport media
 NSP swab, sterile Dacron/Rayon swab with pliable shaft
 OPS swab, sterile Dacron/Rayon swab with plastic shaft
 Resealable plastic bag, parafilm, marker
 VIROLOGY

LABORATORY DIAGNOSIS

Specimen Collection and Processing

PROPER HANDLING
 Directions for use of swab
 Swabs should not be accepted if
contamination, expired, damaged
 Swab shall only come in contact
with suspected infection
 Do not use excessive force when
collecting swab samples
 Swabs are single use only
IMPROPER HANDLING
 VIROLOGY

LABORATORY DIAGNOSIS

Specimen Collection Policies

 Specimen shall be collected within 10 days from onset of illness
 Only qualified and trained staff shall perform the procedures
 DO NOT USE wooden and cotton swabs
 Use only approved kits for specimen collection
 Label the tube with patient’s full name, age and date of collection
 VIROLOGY

LABORATORY DIAGNOSIS

Laboratory Methods
 Antigen Tests
o Rapid test which produces results in 15-30 minutes turn around time
o Considered a non-specific procedure for COVID-19 infection
o FDA approved test kits: https://www.fda.gov/medical-
devices/coronavirus-covid-19-and-medical-devices/home-otc-covid-19-
diagnostic-tests?utm_medium=email&utm_source=govdelivery#list
 VIROLOGY

LABORATORY DIAGNOSIS

Laboratory Methods
 PCR-based tests
o Most reliable for the identification of COVID-19
o Based on the amplification of the nucleic acid sequence of a positive
sample for RNA viruses; involves 1 step or 2 step method
o Gold standard: RT-qPCR assay
o Onset of symptoms – no antibody detected; after 5-7 days
 VIROLOGY

LABORATORY DIAGNOSIS

Storage Collection Policies

Sample Storage Reagent Virus Transport

(Sansure) Medium
No Specimen Room temperature or 2-8C Store at -20C
With OPS/NPS Store at 2-8C Store at 2-8C
 Introduction to monkeypox

Unit A. Basic epidemiology and

prevention

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 What is monkeypox?

Monkeypox is:

▪ a viral zoonotic disease, i.e. can be

transmitted from animals to people
▪ found in Africa, mostly around
tropical rainforest regions
▪ characterized by fever and rash
▪ range of illness from asymptomatic
to death Credit: Nigeria Centre for Disease Control

▪ Not a sexually transmitted

disease
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 Confirmed human monkeypox cases
Worldwide,1970-2021

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 Genetic clades of monkeypox virus

▪ Two clades: West African and Congo Basin (or Central African)
▪ Geographic ranges overlap in Cameroon

Up to 7 generations

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 Monkeypox transmission – an overview

Primary infection Secondary infection

Animal human human human

Contact with infected Contact with infected

animals people

Contact with contaminated animal Mother to fetus

products
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 Monkeypox – modes of transmission

Unprotected contact with:

▪ respiratory droplets
▪ lesion material(rashes from the
patient with monkey pox)
▪ body fluids
▪ contaminated materials and surfaces
The virus can enter through:
▪ respiratory tract
▪ mucous membranes (eyes and
mouth)
▪ broken skin (e.g. animal bites)

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 Prevention of monkeypox

Credit: WHO / Eduardo Soteras Ja

Credit: WHO / Jean Mohr

Raising awareness Vaccinia vaccine

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 Raising awareness of monkeypox – what to know?

Avoid unprotected Do not share

close contact with bedding, clothing,
infected people towels or utensils
with sick people

Avoid contact with wild

Use personal animals specially those
protective found sick or dead
equipment (PPE)
when caring for
patients

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 Clinical diagnosis,
surveillance and laboratory
investigation

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 Overview of disease progression

5-12 days 1-4 days 2-4 weeks Days to weeks

Incubation Period Febrile stage Rash stage Recovery
High tempt. of
patient
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 Disease progression I – Incubation

 Duration: 5-21 days

 No symptoms
 Virus present in bloodstream
(viremia) at the end of the
incubation period

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 Disease progression II – Febrile stage

 1-4 days
 Fever + other symptoms:
swollen lymph nodes
(lymphadenopathy),
headache, chills, sore throat,
malaise, fatigue
 Virus in the blood
 Small lesions in the mouth
(enanthem) appear towards
the end
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 Disease progression III – Rash
stage
Crust(drie
Macule Papule Vesicle (fluid filled)Pustule(fluid filled, pus, yellow) d up
exudate)
<1cm <1cm <1cm(watery)

Credit: Emerg Infect Dis / N.
Erez et al., 2018. Retrived
from:https://wwwnc.cdc.gov/
Op e n W H O .o rg
eid/a rti cle /2 5/ 5/1 9-0 076 -f1
Credit: NEJM/ D.Kurz et al .2004 Credit: Andrea McCollum / CDC Credit: Toutou Likafi/ KinshasaSchool Credit: P. Mbala /Institut Nationale
Retrived from: of PublicHealth de recherche biomedicale. DRC
https://www.nejm.org/doi/full/10.1
056/NEJMoa032299

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 Disease progression III – Rash
stage

 Virus may be in the blood

early in this stage
 Virus is present in skin
lesions
 Antibodies are produced
and become detectable

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 Disease progression IV – Recovery

 The patient has recovered

 Specific antibodies are present in
the blood
 Scars may remain

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 Monkeypox symptoms – an overview

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 Monkeypox complications

 Corneal infection and vision loss

 Secondary bacterial infections
 Abscess and airway obstruction
 Pneumonia
 Bacterial infection of the blood (sepsis)
 Inflammation of the brain
(encephalitis)
 Miscarriage
 Death
Credit: Nigeria Centre for Disease Control (NCDC)
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 Long-term consequences of monkeypox

 Scarring
 Reduced skin pigmentation
 Blindness

Credit: CDC / Brian W.J. Mahy

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 Monkeypox and other common rash illnesses

Lesions often in one Lesions often in multiple Lesions often in multiple

stage of development stages of development stages of development

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 Monkeypox, chickenpox and measles

Credit: W HO / Brian W J Mahy Credit: Centres for Disease Control and Prevention Credit: Centres for Disease Control and Prevention

OM
peonHkOe
nW .ory
g pox Chickenpox Measles
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 Monkeypox and chickenpox

Monkeypox Chickenpox

Credit: NCDC
Credit: NCDC

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 Factors influencing the course of monkeypox

 Asymptomatic infection can occur

 Risk factors for severe illness
 children
 immunodeficiency
 invasive route of infection
 Congo Basin clade variant
 Protective factors
 prior smallpox vaccination
 Case-fatality ratio
 Congo Basin clade: about 10%
OpenWHO.org Credit: Central African Republic / Ministry of Health
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 Monkeypox surveillance

 Mapping person, place and time

 Detailed case
investigation(conducted by
DOH)
 Specimen collection
 Primary / co-primary cases
 Secondary cases

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 Monkeypox surveillance

 Epidemic-prone disease  single case

 notify health authorities immediately
 Reportable under the African Regional
Strategy for Integrated Disease
Surveillance and Response: 2020-2030
 Notifiable under WHO International Health
Regulations (2005) when unusual or
unexpected

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 Sample case definitions for monkeypox

 Case definition = set of criteria for

identifying cases of a disease
 suspected case: fever > 38.3°c,
headache, lymphadenopathy, back pain,
myalgia, distinctive and progressive rash
including on hands and feet
 probable case: a suspected case with
an epidemiological link to a confirmed
case or another probable case
 confirmed case: has been laboratory
confirmed
* For thOepfeunlWcaHseOd.eofrignitionssee Technical Guidelines for Integrated Disease Surveillance and Response in the WHO African Region, March 2019
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 Laboratory investigation

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 Biological structure of monkeypox virus

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 Diagnostic tests – overview

1-4 days 2-4 weeks Days to weeks

5-12 days
Febrile stage Rash stage
Incubation period Lesion samples:
Recovery
Tonsillar and
No testing Nasopharyngeal -PCR Serum:
Swabs: -Antigen detection -Antibody
-PCR methods detection
methods
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 Nucleic acid detection: PCR

Extraction Amplification Detection

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 Nucleic acid detection: PCR

▪ Polymerase chain reaction (PCR) is

the technique most commonly used to
confirm monkeypox.
▪ Tests conducted on lesion
material
▪ Small amount of DNA is enough
▪ Detects monkeypox virus +
identifies the viral clade

Credit: W HO / W HO Eduardo Soteras Jalil

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 Virus detection

Virus isolation Electron microscopy

• Time and resource intensive

• Not monkeypox specific

Credit: Acta Pathol Microbiol Immunol Scand / P. V. Credit: CDC / Charles D. Humphrey; Tiara
Magnus Morehead; and Russell Regnery

▪ Detects viral particles ▪ Reveals virus morphology

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 Biosafety

▪ Local risk assessment

▪ Core requirements + heightened
control measures
▪ Laboratory workers must wear
protective equipment
▪ Vaccination for personnel working
with orthopoxviruses

WHO / WHO Budi Chandra

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 Main takeaway

Credit: A. McCollum; doi:10.4269/ajtmh.16-0567 Credit:Nigeria Center for Disease Control W HO / ThomasMoran

Lesion samples Packaging Transportation PCR testing

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 Monkeypox clinical care guide
Condition Treatment objective
Fever Prevent and treat
Skin infections(20%) Prevent or treat secondary
bacterial infections
Promote lesion healing
Exfoliation, skin Avoid scratching
compromise Minimize insensible fluid loss
Promote lesion healing
Eye infection(4%) Prevent corneal scarring and
visual impairment
Mouth and throat Minimize mucosal pain
sores Encourage food intake
Promote lesion healing
Vomiting and Minimize fluid loss
diarrhea(7%) Maintain nutrition
Lymphadenopathy Minimize pain
Reduce swollen lymph nodes
Respiratory symptoms Maintain open airways
or distress Prevent and treat infection
Prevent and manage
respiratory distress
Sepsis(<1%) Hemodynamic stabilization
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Treatment and care Monitoring
External cooling Regular temperature monitoring
Antipyretic medications
Oral or intravenous antibiotics; incision and drainage, Fever, pain, tenderness, erythema, oedema,
Advanced wound management exudate, warmth
Wash with soap and water or povidone-iodine solution Lesion count/rash burden
Moist dressings and topical antibiotics (e.g silver Skin turgor in non-affected areas
sulfadiazine or gentian violet) Body weight
Surgical debridement, skin grafts Fluid intake/output
Vitamin A supplementation Repeat examination and vision testing
Ophthalmic antibiotics/antivirals Slit lamp examination
Oral/topical analgesic medications Lesion burden
Pain scale
Food and fluid intake/output
Oral or intravenous rehydration Frequency and volume of emesis and
Oral or intravenous antiemetic diarrhoea, Body weight, skin turgor
Antidiarrheal medication Food and fluid intake/output
Oral or intravenous analgesic or anti-inflammatory Size of lymph nodes
medications Pain/tenderness
Suctioning of nasopharynx and airways Respiratory rate and other vital signs
Incentive spirometry, chest physiotherapy Signs of distress such as indrawing, shortness
Bronchodilation, nebulizer treatments of breath
Oral/intravenous antibiotics Pulse oximetry
Oxygen, non invasive ventilation (e.g, BiPAP or CPAP)
Intubation and ventilation
Oral/intravenous antibiotics Pulse, blood pressure
Intravenous fluid hydration, vasopressors Fluid status
Supplemental oxygen, corticosteroids, insulin
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Danger Sign
• Loss of vision
• Delirium
• Loss of consciousness
• Convulsion
• Respiratory distress
• Bleeding
• Signs of sepsis
 Rehydration therapy and
nutritional support

Ensure patients eat and drink

▪ liquids: water, soups, teas, oral
rehydration solution
▪ intravenous fluids if needed
Treat conditions affecting nutrition
(mouth sores, vomiting, diarrhea)
Consideration for young patients
▪ oral vitamin A
▪ breast feeding, breast milk or infant
formula according to the situation
▪ caregiver precautions, masks, hygiene
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 Mental health and social support

Provide psychological support

▪ psychologist
▪ social worker or
▪ specially trained nurse
Offer non-intrusive practical help to:
▪ calm patient and family
▪ keep them informed
▪ what to know, what to expect
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▪ how to care for themselves

▪ how to take precautions

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 For more information

▪ WHO - Monkeypox Health Topics website: link

▪ WHO - Monkeypox Fact Sheet: link
▪ Centre for Disease Control - Monkeypox: link
▪ Nigerian Centre for Disease Control - National monkeypox public health
guidelines: link
▪ Heymann DL, Simpson K. The Evolving Epidemiology of Human Monkeypox:
Questions Still to Be Answered. J Infect Dis. 2021;223(11):1839-1841.: link
▪ Simpson K, Heymann D, Brown CS, et al. Human monkeypox - After 40 years,
an unintended consequence of smallpox eradication. Vaccine. 2020;38(33):5077-
5081.: link

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