Epidemiological profile & diagnostic methodologies of sars cov
- 1. EPIDEMIOLOGICAL PROFILE & DIAGNOSTIC METHODOLOGIES OF SARS COV 2 PRESENTER : DR SOHAIL MODERATOR : PROF. DR CHANDAN DAS COVID-19
- 2. PNEUMONIA OF UNKNOWN ETIOLOGY IN WUHAN
- 3. ZERO CASE 57 years old female, Wei Guixian. Shrimp seller in Wuhan city of China. On 10 December 2019 she developed cold, lethargy Fully recovered in January month
- 4. SARS-COV-2 It’s a zoonotic virus. Bats appear to be the reservoir of COVID-19 virus. It belongs to large family of enveloped , positive strand of RNA viruses. Divided into 4 genera: alpha, beta, delta, and gamma alpha and beta CoVs infect humans It is betacorona virus which has RNA dependant RNA polymerase. It enters human cells through ACE 2 receptors.
- 7. COVID DATES 12 December 2019: 1st case of COVID-19 reported in Wuhan city, Hubei province of China 31 Dec’ 2019: Chinese authorities alerted WHO about cases of Pneumonia of unknown etiology. 01 Jan’ 2020: Wuhan Seafood Market closed by Chinese authorities. 03 Jan’ 202: India notified by WHO regarding the outbreak 07 Jan, nCoV identified as the causative organism 12 Jan Wuhan’s First death due to Novel Corona Virus 11 February 2020, WHO announced a name for the new coronavirus disease: COVID-19. 11 March, 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. As on 27 April, 213 countries affected. 2,810,325 confirmed cases, 193,825 deaths
- 8. Mortality increases with age, with the highest mortality among people over 80 years of age (CFR 21.9%). The CFR is higher among males compared to females (4.7% vs. 2.8%). By occupation, patients who reported being retirees had the highest CFR at 8.9%. While patients who reported no comorbid conditions had a CFR of 1.4%, patients with comorbid conditions had much higher rates: 13.2% for those with cardiovascular disease, 9.2% for diabetes, 8.4% for hypertension, 8.0% for chronic respiratory disease, and 7.6% for cancer.
- 9. FOUR EPIDEMIOLOGICAL AREAS In areas without cases, the strategy in these areas is to "strictly prevent introduction". This includes quarantine arrangements in transportation hubs, monitoring for temperature changes, strengthening of triage arrangements, use of fever clinics, and ensuring normal economic and social operations. In areas with sporadic cases, the strategy is focused on "reducing importation, stopping transmission and providing appropriate treatment". In areas with community clusters, the strategy is focussed on "stopping transmission, preventing exportation, and strengthening treatment". In areas with community transmission, the strictest prevention and control strategies are being implemented, the entry and exit of people from these areas has been stopped and public health and medical treatment measures are comprehensively strengthened.
- 10. SUSPECT CASE
- 11. CONFIRMED CASE A person with laboratory confirmation of COVID-19 infection, irrespective of clinical signs & symptoms.
- 12. CONTACT A contact is a person who experienced any one of the following exposures during the 2days before and the 14days after the onset of symptoms of a probable or confirmed case : 1. Face to face contact with a probable / confirmed case within 1meter and for more than 15mins; 2. Direct physical contact with a probable / confirmed case; 3. Direct care for a patient with a probable / confirmed COVID-19 disease without using proper personal protective equipments;
- 13. CLINICAL FEATURES Uncomplicated illness : fever , cough , sore throat , nasal congestion , malaise , headache Mild pneumonia Severe pneumonia ARDS Sepsis Septic shock
- 14. CONTD…..
- 15. CONTD…. ST segment elevation in COVID-19 (nejm) Neurological feature in severe SARS COV 2 (nejm) 1. Agitation 2. Confusion 3. Diffuse corticospinal signs, brisk DTR , ankle clonus 4. MRI brain s/o leptomeningeal enhancement & b/l frontotemporal hypoperfusion 5. GBS
- 16. C/F IN CASES OF CHINA 3.7% 5.0% 11.0% 13.6% 13.9% 14.8% 18.6% 33.4% 38.1% 67.7% 87.9% 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% DIARROHEA VOMITTING CHILLS HEADACHE SORE THROAT MAYALGIA SHORTNESS OF BREATH SPUTUM FATIGUE COUGH FEVER
- 17. CYTOKINE STORM Cytokine storm (CS) refers to excessive and uncontrolled release of pro-inflammatory cytokines. Clinically, it commonly presents as systemic inflammation, multiple organ failure, and high inflammatory parameters. In infectious diseases, CS usually originates from the focal infected area, spreading all over the body through circulation. In COVID-19,accompanied by rapid virus replication, a large number of inflammatory cell infiltration and CS led to acute lung injury, acute respiratory distress syndrome (ARDS) and death. In a study by immunologist in China, they measured cytokine levels in 41 inpatients (including 13 ICU patients and 28 non ICU patients), IL-1B, IL-1RA, IL-7, IL-8, IL-9, IL-10, fibroblast growth factor (FGF), granulocyte-macrophage colony stimulating factor (GM-CSF), IFNγ, granulocyte-colony stimulating factor (G-CSF), interferon-γ-inducible protein (IP10), monocyte chemoattractant protein (MCP1), macrophage inflammatory protein 1 alpha (MIP1A), platelet derived growth factor (PDGF), tumor necrosis factor (TNFα), vascular endothelial growth factor (VEGF) were increased.
- 18. CONTD… Most of severe COVID-19 patients in our ICU ward had persistent very high level of erythematosus sedimentation rate (ESR), CRP, and high level of IL- 6,TNFα, IL-1β, IL-8, IL2R, etc., and were associated with ARDS, hypercoagulation and disseminated intravascular coagulation (DIC), manifested as thrombosis, thrombocytopenia, gangrene of extremities. Autopsy findings revealed destruction of secondary lymphoid organs, spleen atrophy, the number of lymph nodes decreased, diffuse alveolar damage in lung. As we know that 2019-nCoV infects target cells through angiotensin converting enzyme 2 (ACE2), while there was no ACE2 expression on lymphocytes, we speculate that lymphocytes were probably destroyed by CS.
- 19. TRANSMISSION Infected droplets >5µm, travel <1m Aerosols <5µm, travel>1m Contact Hands, surfaces
- 20. CONTD… Presymptomatic people are infectious. Patients may be infectious 1 to 3 days before symptom onset and that up to 40 to 50% of cases may be attributable to transmission from asymptomatic or presymptomatic people. Just before or soon after symptom onset, patients have high nasopharyngeal viral levels, which then fall over the course of approximately 1 week. Patients with severe disease may shed the virus for longer periods (Ref: nejm/corona)
- 22. AEROSOL & SURFACE STABILITY OF SARS COV 2 Aerosol - 3hours Plastic - 72hrs Stainless steel - 48hrs Copper - 4hrs Cardboard - 24hrs (Ref: nejm/corona) Survivability outside body: • 1-2 days on nonporous surfaces • 8-12 hours on porous surfaces • Currently this information on 2019- nCoV not clear Incubation period: Current estimates of the incubation period of SARS-CoV-2 range from 2-14 days.
- 23. RISK FACTORS Older age ( > 65 yrs) Chronic lung disease Cardiovascular disease Hypertension Diabetes mellitus Obesity End stage renal disease Immunocompromised state Liver disease Male gender*
- 24. AGE DISTRIBUTION OF CASES IN CHINA (N=72,314) 0-9 =0.9% 10-29 =9.3% 30-39 =17.0% 40-49 =19.2% 50-59 =22.4% >60=31.2% • Median age: 51 years • Range= 2 days-100 years • Males: 51% • Health care workers: 3.8% 88% reported from Hubei
- 25. SEVERITY OF ILLNESS (N=72,314) 0 0.2 0.2 0.2 0.4 1.3 3.6 8 14.8 0 2 4 6 8 10 12 14 16 0-9 10--19 20-29 30-39 40-49 50-59 60-69 70-79 >=80 Case Fatality Rate (%)
- 26. LAB FINDINGS Lymphocytopenia High CRP High LDH & ferritin Raised D-dimer High procalcitonin High SGOT & SGPT levels
- 30. CANDIDATES FOR SAMPLE COLLECTION All symptomatic individuals who have undertaken international travel in the last 14 days . All symptomatic contacts of laboratory confirmed cases . All symptomatic health care workers . All patients with Severe Acute Respiratory lllness (fever AND cough and/or shortness of breath) . Asymptomatic direct and high-risk contacts of a confirmed case should be tested once between day 5 and day 14 of coming in his/her contact.
- 31. SAMPLE COLLECTION Most important step in lab diagnosis A. Upper respiratory tract Nasopharyngeal (NP) swab/oropharyngeal (OP) swab B. Lower respiratory tract Bronchoalveolar lavage, tracheal aspirate, pleural fluid, lung biopsy
- 32. CONTD… Nasopharyngeal swab: Insert flexible wire shaft minitip swab through the nares parallel to the palate (not upwards) Swab should reach depth equal to distance from nostrils to outer opening of the ear Gently rub and roll the swab. Leave swab in place for several seconds to absorb secretions. Slowly remove swab while rotating it.
- 33. CONTD… Oropharyngeal swab (e.g., throat swab): Insert swab into the posterior pharynx and tonsillar areas. Rub swab over both tonsillar pillars and posterior oropharynx and avoid touching the tongue, teeth, and gums. Combined nasal & throat swab: Tilt patient’s head back 70 degrees. While gently rotating the swab, insert swab less than one inch into nostril (until resistance is met at turbinates). Rotate the swab several times against nasal wall and repeat in other nostril using the same swab. Place tip of the swab into sterile viral transport media tube and cut off the applicator stick. For throat swab, take a second dry polyester swab, insert into mouth, and swab the posterior pharynx and tonsillar areas (avoid the tongue). Place tip of swab into the same tube and cut off the applicator tip.
- 34. STORAGE Store specimens at 2-8°C for up to 72 hours after collection. If a delay in testing or shipping is expected, store specimens at - 70°C or below.
- 35. RT-PCR DIAGNOSTIC PANEL 2019-nCoV_N1, 2019-nCoV_N2 and 2019-nCoV_N3 primers and probes that target the nucleocapsid (N) gene and are designed for both universal detection of SARS-like coronaviruses as well as specific detection of the 2019-nCoV; RP primers and probes that target the Human RNase P gene; and nCoVPC, the 2019-nCoV positive control used in the assay.
- 36. SENSITIVITY & SPECIFICITY SENSITIVITY For the nCoV_IP and E_Sarbeco real-timeRT-PCR Sensitivity, in terms of 95% hit rateis about 100 copies of RNAgenome equivalent per reaction (thisamount of target sequences is always detected), the probability to detect lower amountsof virus decreases, but samples containing 10 copies could be detectedwithmultiplex assay. SPECIFICITY Cross-reactivity with other respiratory viruses was tested withspecimens known to be positive for a panel of respiratory viruses (influenza A(H1N1)pdm09, A(H3N2), B-Victoria, B- Yamagata; influenzaC; RSV A, B; hBoV; hPIV; hMPV; HRV/enterovirus; adenovirus; hCoV (HKU1, OC43, 229E and NL63); MERS-CoV. None of the tested viruses showed reactivity with PCR2 and PCR4.
- 37. ROLE OF CT CHEST Chest CT has been suggested to possess the potential to diagnose COVID-19 with significant sensitivity & even screen asymptomatic patient. Sensitivity – 97% Specificity – 25% Chest CT is necessary even if RT PCR is negative