Ministry Of Higher Education

Kabul University Of Medical Science

Department Of Microbiology & Parasitology

SARS-CoV-2 & COVID-19

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OUTLINES
 Introduction
 Epidemiology
 Origin
 Incidence
 Structure
 Pathogenesis
 Clinical manifestations
 Diagnosis
 Treatment, Prevention & Control

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1. INTRODUCTION
 Virus: SARS-CoV-2
 Disease: COVID-19
 Coronavirus disease 2019 (COVID-19) is defined as illness caused by
a novel coronavirus now called severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2).
 ‫إ‬irst identified amid an outbreak of respiratory illness cases in Wuhan
City, Hubei Province, China. [1]

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1. INTRODUCTION
 It was initially reported to the World Health Organization (WHO) on
December 31, 2019.

 On January 30, 2020, the WHO declared the COVID-19 outbreak a

global health emergency. [2, 3]

 On March 11, 2020, the WHO declared COVID-19 a global

pandemic[4].

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 WHO SITUATIONAL REPORT

Last update: 6 November 2020

Confirmed cases 48 196 862

Confirmed deaths 1 226 813

Countries with cases 219

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2. Epidemiology
Incidence in Afghanistan - to date [November 6, 2020]
• New cases [3 January – 6 November]
• 121
• Total confirmed cases
• 41,975
• Recovered
• 34,239
• Death
• 1,554

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2. Epidemiology
 Origin
 As soon as the first cases of COVID-19 were reported in late
December 2019, investigations were conducted to understand the
epidemiology of COVID-19 and the original source of the outbreak.
 A large proportion of the initial cases in late December 2019 and early
January 2020 had a direct link to the Huanan Wholesale Seafood
Market in Wuhan City, where seafood, wild, and farmed animal species
were sold.

WHO/2019-nCoV/FAQ/Virus_origin/2020.1

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Bats
• Hedgehog
• Dagger
• Turtles Civet Cat
• Snake Camel
• birds

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Bats Pangolin
• Hedgehog
• Dagger
• Turtles
• Snake
• birds
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3. CLASSIFICATION
Order Nidovirales

Family Coronaviridae
CLASSIFICATION
Genus Betacoronavirus

Species SARS- related

coronavirus
Strain SARS-CoV-2

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4. STRUCTURE OF SARS-CoV-2

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4. PATHOGENESIS
 Source of infection: Bats
 Intermediate host: Pangolin?
 Person to person transmission: air droplets, direct contact, feces,
touch of contaminated surfaces.
 Portal of entry: nasopharynx
 Incubation period: 2-14 days

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4. PATHOGENESIS
 REPLICATION CYCLE
1. Attachment
2. Fusion
3. Uncoating
4. Translation
5. Transcription
6. Maturity
7. Assembly
8. Released

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 Pathogenesis
 Possible theories :
 Pneumonia-like changes in the lungs
 CO- like reaction
 Coagulopathies

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4. CLINICAL FEATURES
Severity of disease Presentation
• No clinical symptoms
Asymptomatic • Positive nasal swab test
• Normal chest X-ray

• Fever, sore throat, dry cough, malaise and body aches or

Mild illness • Nausea, vomiting, abdominal pain, loose stools

• Symptoms of pneumonia (persistent fever and cough) without

Moderate illness hypoxemia
• Significant lesions on high-resolution CT chest

Severe illness • Pneumonia with hypoxemia (SpO2 < 92%)

• Acute respiratory distress syndrome, along with shock, coagulation

Critical
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state defects, encephalopathy, heart failure and16-Nov-20
acute kidney injury
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4. CLINICAL FEATURES
 The most common clinical features of SARS-CoV-2 infection are:
 Fever (more than 80% cases)
 Cough (more than 60% cases)
 Fatigue (more than 35% cases)
 Sputum production (more than 30% cases)
 Shortness of breath (more than 15% cases)
 Less common features: Headache, muscle weakness, breathlessness,
sore throat, and pleuritic pain (10–15%).
 Rare features are: nausea, vomiting, chest tightness

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4. CLINICAL FEATURES
 The primary cause of mortality of COVID-19 are:
 Respiratory failure (69.5%)
 Sepsis or multi-organ failure (28%)
 Cardiac failure (14.6%)
 Renal failure (3.7%). (Heymann and Shindo, 2020; Zhang et al., 2020).

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4. CLINICAL FEATURES
 Guan et al they collected data from 1099 patients with confirmed
COVID-19 cases. As per that report, the most common symptoms were
 Fever (88.7%)
 Cough (67.8%)
 CT scan abnormalities (86.2%)
 The most common pattern observed in CT scan were ground-glass
opacity and patchy bilateral shadowing.

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4. CLINICAL FEATURES
Complications

• Respiratory distress syndrome

• Septic shock
• Metabolic acidosis hard to manage
• Coagulation dysfunctions
• Multiple organ dysfunctions (MODs)
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5. Laboratory diagnosis
 Antigen detection (ELISA, IHC, IF)
 Electron Microscopy (size & shape of the virus)
 Nucleic acid detection (NAAT, RT-PCR)
 Isolation (viral culture in cell lines)
 Serum antibody detection (Lab based & Rapid & Point of
care test)
 CT- scan (ground glass opacities)

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5. Laboratory diagnosis
 Further laboratory findings revealed the presence of:
 Lymphocytopenia (83.2%)
 Thrombocytopenia (36.2%), And
 Leukopenia (33.7%)
 Guan et al., reported that most of the patients were observed with high
levels of C-reactive protein.
 Alanine transaminase (ALT), aspartate aminotransferase (AST),
 Creatinine kinase (CK), blood urea nitrogen (BUN), and D-dimer were
elevated less commonly.
 In this study, out of 1099 patients, 5% were admitted in ICU, 2.3% underwent
invasive mechanical ventilation, and 1.4% of patients died (Guan et al., 2020).

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6. Current inline treatments
 Currently, care for patients is primarily supportive:
 Relieve symptoms
 Manage respiratory, and other organ, failure

 Many treatments are under investigation.

 No vaccine is currently available.

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6. Current inline treatments
 Remdesivir (FDA-approved)
 Inhibitor of RNA-dependent RNA polymerases, which has previously
been shown to have antiviral activity against MERS-CoV and SARS-
CoV.
 Studies are currently available that show inhibition of viral
replication of SARS-CoV-2 in vitro.
 Remdesivir is only one specific antiviral treatments Recently
licensed for COVID-19. Remdesivir / iv over 30-60 minutes diluted
 5 mg/kg on day one- 2.5 mg/kg one day 2nd onward. <12 years
 200 mg on day one, 100 mg one day 2nd onward. >12 years.
 Estimated cost : 6000 USD
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6. Current inline treatments
 Chloroquine
 Chloroquine affects glycosylation of the ACE-2 pulmonary cell
receptors, impairing viral cell entry.
 Medication-induced pH changes within pulmonary cells (alkalinization)
also delays viral replication, as key steps in endosome function are
impaired.

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6. Current inline treatments
 Camostat mesylate
 A serine protease inhibitor, has been identified by some as a
potential treatment option.
 Camostat mesylate partially blocks SARS-CoV-2 entry into the
pulmonary cells by inhibiting S protein priming and endocytosis [29].
 Follow-up studies on treatment with camostat mesylate are currently
pending.

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6. Current inline treatments
 Tocilizumab
 Is a humanized monoclonal antibody against interleukin-6 receptor
(IL-6R Ab), commonly used as an immunosuppressive in the
treatment of rheumatoid arthritis and systemic juvenile idiopathic
arthritis.
 It is currently postulated that patients with severe manifestations of
COVID-19 experience some degree of cytokine storm, which results
in ARDS and death.
 The small study found decreased fever, oxygen requirements, and C-
reactive protein (CRP), along with improved CT findings.

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6. Current inline treatments
 Lopinavir and ritonavir
 Protease inhibitors (used in HIV & AIDS)
 Randomized, controlled trials on confirmed positive COVID-19 adult
patients with ARDS have been performed using a 14-day course of
lopinavir and ritonavir 400-100mg twice daily.
 No benefit has been observed beyond the standard of care.
 Further studies are required to confirm this finding.

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6. Current inline treatments
 Nitazoxanide
 Is a broad-spectrum antiparasitic and antiviral agent used in the
treatment of various helminthic, protozoal, and viral infections.
 Nitazoxanide was found to inhibit SARS-CoV-2 at low micromolar
concentrations in vitro.
 Further studies are required to prove in vivo efficacy.

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 Convalescent plasma
 Convalescent plasma and hyperimmune immunoglobulin are under
active investigation in clinical trials as potential therapy for COVID-19.

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 Vaccines in phase 3 Clinical testing in the United State:
 mRNA-1273 [Encodes S-2P antigen]
 Once vial opened, must be used within 6 hours
 Dose: 2 injection 28 days apart
 Phase one study:
 48 healthy volunteer (18-55 years) on 16 march 2020
 Three doses were given (25- 100 & 250 mc)
 After the second vaccination serum-neutralizing activity was detected
 This trial was extended to include 40 adults older than 55 yr with similar
results.

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 Vaccines in phase 3 Clinical testing in the United State:
 mRNA-1273 [Encodes S-2P antigen]
 Once vial opened, must be used within 6 hours
 Dose: 2 injection 28 days apart
 Target: encodes S-2P antigen
Phase two study
 Was completed in June
 50-100 mc given at 2 doses 28 days apart
 18-55 years
 55 years or older

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 Vaccines in phase 3 Clinical testing in the United State:
 mRNA-1273 [Encodes S-2P antigen]
 Once vial opened, must be used within 6 hours
 Dose: 2 injection 28 days apart
 Target: encodes S-2P antigen
Phase 3 trial has launched in July 27, 2020
 Includes 30,000 participants who will receive 100mc doses on day one
& 29th.
 20-40% of participants are age 65 or more.

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 Vaccines in phase 3 Clinical testing in the United State:
 BNT-162B2 [Nucleoside-modified messenger RNA]
 Encodes SARS-CoV-2 RBD antigen
 Must be kept frozen
 Require reconstitution
 Dose: 2 injection 21 days apart
Human testing was initiated in early May, 2020
Generated dose-dependent immunogenicity as measured by RBD-
IgG concentration and SARS-CoV-2 neutralizing ab titer

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 Vaccines in phase 3 Clinical testing in the United State:
 BNT-162B2 [Nucleoside-modified messenger RNA]
 Encodes SARS-CoV-2 RBD antigen
 Must be kept frozen
 Require reconstitution
 Dose: 2 injection 21 days apart
 Phase-3 trial has enrolled 37000 with more than 28000 having
received their second vaccination

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6. Current Inpatient treatments
 Treatment modalities includes:
 Antiviral (Remdesivir, Recently FDA approved)
 Antibacterial (in case of documented Secondary bacterial infections)
 Anti-inflammatory (for severe & critical cases only)
 Anti-shock

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7. Preventive measures & Control
 Transmission between humans to humans and through various surfaces like
metal, cardboard, plastic is very high in the COVID-19 disease (Bedford et al.,
2020).
 Social distancing
 Use of personal protective equipment (PPE)
 Face masks/shields
 Hand sanitizers

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7.5 MANAGEMENT OF STRESS DURING COVID-19

 Throughout the world, people are facing different kinds of challenges in

their lifestyles due to increased mental stress in the current scenario of
the COVID-19 pandemic.
 This increased stress can be well acquainted with a small change in daily
lifestyle like:
 Spiritual empowerment
 Classical yoga
 Balanced diet containing low calories and more proteins,
 Lightweight indoor exercises
 Working on a new hobby or skill development (Melbourne, 2020).

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