The document outlines the pathogenesis, laboratory diagnosis, management, and prophylaxis of SARS-CoV-2, the virus responsible for COVID-19, first identified in Wuhan, China, in December 2019. It details the virus's morphology, transmission, clinical presentations, diagnostic methods, and management strategies, including treatment and vaccines available in India. The document highlights the epidemiological aspects, including the pandemic's waves and the government's response through lockdowns and health measures.

1. SARS COV- 2
Pathogenesis, Laboratory Diagnosis,
Management and Prophylaxis

2. OUTLINE
• Introduction
• Pathogenesis
• Laboratory diagnosis
• Management
• Prophylaxis

3. Introduction
• SARS-CoV-2,the causative agent of COVID-19, a newly emergent coronavirus.
• First detected in Wuhan, China, in December 2019.
• Order Nidovirales, Family Coronaviridae , Subfamily Coronavirinae, genus
coronavirus
• 4genera(α coronavirus, β coronavirus, γ coronavirus, δ coronavirus)
• SARS CoV 2 strain comes under the genera β coronavirus subgenus
sarbecovirus.

4. • In December 2019, China reported an outbreak of pneumonia of unknown
causes in Wuhan, the capital city of Hubei province
• Earlier, 2019–novel Coronavirus (2019–nCoV)
• On February 11, 2020, ICTV renamed as SARS–CoV2 (genome resembled to
SARS-CoV)
• WHO named the resultant disease as Coronavirus disease (COVID-19)
• WHO designated SARS-CoV-2 a Public Health Emergency of International
Concern on January 30, 2020, and pandemic on March 11, 2020
Epidemiology

5. • On January 11, the first case was reported outside mainland China in Thailand.
• Within months, the disease spread to all the continents except Antarctica.
• India reported its first case on January 30, 2020 in Kerala.
• The first COVID-19 related death in India was reported on March 12, 2020.
• By the second week of April, the disease spread to all states in India except
Sikkim.
• Pandemic occurred in 3 waves, first around September 2020,second in April
2021, third in January 2022.

6. • On 25th March 2020, Govt of india declared a country wide lockdown till 31st
march, which was extended upto 14th April 2020,
• Further extended to 3rd may then upto 17th may 2020- covers 4 phases of
lockdown f/w gradual un-lockdown in the country, spread in 6 phases(one
month each) upto 30th november2020.
• Aarogya setu app: Launched by the GOI on 2nd April 2020(location based
surveillance app)

7. Morphology
• Enveloped, spherical,120-160-nm,
• Genome- unsegmented +ssRNA(27–32 kb), surrounded by helical nucleocapsid
protien 9–11 nm.
• 20nm long club or petal shaped projections, widely spaced, giving appearance of
solar corona.
• 4 structural proteins: S,E,M and N
• 16 Non-structural Proteins,
- Proteases (nsp3 and nsp5) and
- RdRp

8. Variants of SARS-CoV-2: (Variants of concern)
1) B.1.1.7 (Alpha)-First detected in the U.K. in September 2020,
• N501Y mutation in the RBD region of the Spike protein.
• Enhance binding b/w the SARS-CoV-2 Spike protein and the human ACE2
receptor,
2) B.1.351 (Beta)- Arose in South Africa, both the E484K and N501Y mutations.
3) P.1 (Gamma)-Emerged in Brazil; detected in the USA by the end of Jan 2021.
• Three (K417T, E484K, and N501Y) within the RBD of Spike.
• E484K- affect the ability of antibodies to recognize and neutralize the virus.

9. 4) B.1.617.2 (Delta): “double mutant” variant,
• First identified in India in December 2020 (second wave)
• L452R- Stabilize the interaction between the spike protein and the host cell -
increase infectivity
• E484 mutation, higher infectivity and transmission rates.
5) B.1.1.529 (Omicron): Have high transmissibility but produced less severe
symptoms and hospitalization.
• In India 3rd wave was largely attributed by this variant.

10. • Mode of transmission- By droplet borne infection, either directly or indirectly,
through fomites.
• Airborne transmission can occur during medical procedure.
• Risk factor-
-Advanced age
-Male sex
- Preexisting comorbidities
- Elevated body mass index
- Substance use, such as alcohol, opioid, or cocaine use disorder, and current or
former smoking both increase risk.
- Pregnant women
Pathogenesis

11. Host Cell Entry

13. • Course of infection goes through the following stages –
- Viral invasion and replication,
- Dysregulated immune response,
- Multiple organ damage and recovery.
• Virus enters the host cells, replicates, assembles and is released extracellularly to
target cells, damage and destruction of alveolar epithelial cells.
• At the same time,large number of PAMP and DAMP molecules are released -
stimulate the innate immune response, release large quantities of cytokines,
chemokines, proteases and free radicals, ARDS, sepsis and MODS

14. Clinical presentation-
• IP- 2 to 14 days.
• Fever is probably one of the most common
• Dry cough
• Anosmia or hyposmia and loss of taste
• Anorexia
• Myalgia and dyspnea
• Gastrointestinal symptoms included diarrhea, abdominal pain, and
vomiting/nausea

15. Clinical Severity:
oAsymptomatic
oMild disease/ILI ((influenza-like illness) -Have fever, cough, sore throat,
malaise, headache.
oModerate disease/Pneumonia- ILI plus any one:
1) Respiratory rate ≥ 24/min, breathlessness
2) SpO2: 90% to ≤ 93% on room air
oSevere disease/SARI/Severe Pneumonia-Pneumonia plus any one:
1)Respiratory rate ≥ 24/min,breathlessness
2)SpO2: 90% to ≤ 93% on room air
oCritical- Respiratory failure, Septic shock, and/or Multiorgan failure

16. Laboratory diagnosis
• Types of specimen- Nasopharyngeal specimen is a preferred choice
-Other specimen- Oropharyngeal (OP) specimen,Nasal mid-turbinate
(NMT)swab, Anterior nares (nasal swab; NS) specimen and
Nasopharyngeal wash or Nasal aspirate (NA) specimen ,
Throat swab, BAL, Endotracheal aspirate can be collected alternatively.
• For serological assay- Blood sample

17. • Placed in a tube containing viral transport media(VTM)
• If the shipping of specimen to the reference diagnostic laboratories
required, the sample must be transported in triple packaging system;
• Sample vial must be properly labeled and sealed and kept in outer covering of
absorbent material(Primary container)
• Secondary container should be placed with
frozen gel packs in thermocol box.

18. 1) NAAT:
Real time RT-PCR- Gold standard
 Require biosafety level-2 facility
Gene targets for screening –Spike protein (S), Envelope protein (E), Membrane
protein (M), Nucleocapsid protein (N)
Gene targets for confirmation -RNA-dependent RNA polymerase (RdRp),
Open reading frames (ORF1a/b),N2 nucleocapsid
Automated real-time RT-PCR(CBNAAT and Truenat)

19. 2)Antigen detection assay: Point-of-care test; detects
nucleocapsid protein antigen in nasopharyngeal swab
3)Antibody (IgG) detection assay: Used for serosurveillance
and survey in high-risk and vulnerable group; not for clinical diagnosis
4)Sequencing: To determine mutations in the viral genome
5)Viral culture: Used for research purpose
- Require biosafety level-3 facility
6)Nonspecific tests include:
Radiology (chest CT scan): Ground-glass appearance
Biomarkers: IL-6, D-dimer, Elevated serum ferritin, Elevated C-reactive
protein

20. Course of the diagnostic markers in COVID-19.

21. 7)LAMP TEST(Loop Mediated isothermal amplification):
• Developed by Tsugunori Notomi at Eikens chemicals, Tokyo, Japan.
• Having higher sensitivity and specificity than traditional PCR.
• Approved for Covid diagnosis in India as Lume-NCoV Kits from Agappe
Diagnostic Kochi,Kerala.
8) CRISPR (Clustered Regularly Inter Spaced Short Palindromic Repeats):
• Developed in the USA as the ‘Sherlock’ test.
• The test developed in India based on this named ‘FELUDA’.
• Commercially launched in India by Tata medical diagnostics as ‘TataMD
CHECK CRISPR test’
• Test uses CAS9 protein to find and bind to target RNA.
• Coupled with paper strip chemistry to allow a visual reading.

22. Management
• No definitive therapy
• Symptomatic management-In patients with severe respiratory distress
oSupplemental oxygen therapy is given immediately
oHigh-flow nasal cannula oxygenation (HFNO)
oNon-invasive mechanical ventilation
oMechanical ventilation: In patients with moderate or severe ARDS, higher
PEEP (positive end-expiratory pressure) instead of lower PEEP is suggested.
• Management of septic shock by—vasopressors, fluid replacement by
crystalloids such as normal saline and Ringer’s lactate
• Convalescent plasma therapy
• Drugs-Remdesivir, Tocilizumab, Hydroxychloroquine (HCQ)

23. Prophylaxis
• WHO recommends protective measures to help prevent the spread of the disease
-Wearing mask
- Frequent hand washing,
- Avoiding touching of eyes, nose or mouth,
- Maintaining a distance of at least 1 m between people,
- Practicing respiratory hygiene,
• Chemoprophylaxis- Hydroxychloroquine

24. Types of vaccines :
-Inactivated or live-attenuated - Covaxin, CoroVac and BBIBP-CorV
- Protein subunit based - Novavax, Epi Vac Corona
- mRNA based - Moderna, Pfizer–BioNTech (BNT162b2)
-Viral vector: ( recombinant adenovirus with a SARS-COV-2 gene ) - Covishield,
Oxford-Astrazeneca, Sputnik V and Johnson & Johnson COVID -19 vaccine

25. Covaxin: code name is BBV152.
- Prepared by Hyderabad- based Bharat Biotech International Ltd. in
collaboration with the National Institute of Virology (NIV) and ICMR
-effectiveness - 78-81%.
- administered in two doses (4-6weeks apart) by IM route
Covishield:code name AZD1222, prepared by Serum Institute of India, in
collaboration with University of Oxford and AstraZeneca pharmaceuticals,
UK.
- Effectiveness 90%
- Based on non-replicating adenovirus vector (modified Chimpanzee
adenovirus, ChAdOx1) expressing spike protein.
- Administered in two doses (12-16weeks apart) by IM route.

26. Sputnik V, by the code name rAd26-S and rAd5-S, was developed by
Gamaleya Research Institute of Epidemiology and Microbiology, which
involves an interval gap of 21 days between the two doses.
- Effectiveness 92.2%
• CoWIN (Covid Vaccine Intelligence Network)- Indian government web portal
for Covid 19 vaccination registration and also for obtaining the certificate after
vaccination.

27. REFERENCES:
• Medical Microbiology – 28th edition, Jawetz, Melnick & Adelberg’s
• Ananthanarayan and Paniker’s Textbook of Microbiology – 8th edition
• Park's textbook of preventive & social medicine, 26TH edition
• Apurba Sanker Sastry, Sandhya Bhat Essentials of Medical Microbiology, 3rd Edition
• Kumar KSR, Mufti SS, Sarathy V, Hazarika D, Naik R. An Update on Advances in COVID-19
Laboratory Diagnosis and Testing Guidelines in India. Front Public Health. 2021 Mar 4;9:568603. doi:
10.3389/fpubh.2021.568603. PMID: 33748054; PMCID: PMC7969786.
• Aleem A, Akbar Samad AB, Vaqar S. Emerging Variants of SARS-CoV-2 and Novel Therapeutics
Against Coronavirus (COVID-19). 2023 May 8. In: StatPearls [Internet]. Treasure Island (FL): StatPearls
Publishing; 2023 Jan–. PMID: 34033342.
• Mukim M, Sharma P, Patweker M, Patweker F, Kukkar R, Patel R. Covid-19 Vaccines Available in India.
Comb Chem High Throughput Screen. 2022;25(14):2391-2397. doi:
10.2174/1386207325666220315115953. PMID: 35293291.