Covid 19

A concised review of current situation of COVID-19 pandemic.

1. Dr. Utkarsh Sharma SR (Dep. of Pathology) SMS medical college, Jaipur COVID-19: EVERYTHING A PATHOLOGIST NEEDS TO KNOW 1

2. INTRODUCTION The coronavirus disease-19 ( COVID-19) Also known as novel coronavirus pneumonia. First occurred in Wuhan, China in early December 2019. The first case of COVID-19 in India was reported on 30 January 2020, in Kerala. World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020 and a pandemic on March 11, 2020 - the first pandemic caused by a coronavirus . 8,393,096 confirmed infections with 450,452 fatal cases, globally by 18th June 2020, 00:47 GMT 2

3. P ossibly emerged from a bat-borne virus. Horseshoe bats show a 80% resemblance to SARS-CoV-2 while the pangolin coronavirus has up to 92% resemblance. Studies indicate that pangolins are a reservoir host of SARS-CoV-2-like coronaviruses. However, currently no evidence to link pangolins as an intermediate host. 3

4. SARS-CoV-2 STRUCTURE 50–200 nm in diameter + ssRNA 4

5. INFECTION AND TRANSMISSION Transmission occurs primarily via large respiratory droplets ( ≥5 μ m) from coughs and sneezes . Airborne transmission- possible in specific circumstances and settings in which procedures that generate aerosols are performed; example: endotracheal intubation, bronchoscopy, open suctioning, administration of nebulized treatment. The basic (without control measures) reproduction number (R0) of the virus has been estimated to be 3.28 and median R0 2.79. 5

6. Source: Lippi et al.: Biosafety measures for COVID-19 6

7. Respiratory droplets produced when a man sneezes, visualised using Tyndall scattering 7

8. As per the available data, infectivity of various samples- Sputum:97.7% Nasopharyngeal swab:88.6 % Throat swab:60% Post throat saliva:88.6% Oral swabs:46.7 % Stool:70.8% Anal swabs:20.5% Rectal swabs:17.4 % Blood:12.3 % Conjunctival swab:1.1 % Urine:00 % , Vaginal swabs:00 % , Semen sample:00 % 8

9. Infection from fomites is less common and virus could be detected on- Metal, Glass, Ceramics - upto 5 days Wood- 4 days Paper money- 4 days Plastic and stainless steel- 2 to 3 days Cardboard- 24 hours Copper- 4 hours Aluminum- 2 to 8 hours Print paper, tissue paper- 3 hours Interestingly, infectious virus could be detected on the outer layer of a surgical mask on day 7 . Virus has been found to be highly stable at 4°C after 2  weeks, but could be deactivated after 5 min at 70°C. 9

10. COVID-19 is an enveloped virus and is deactivated by most environmental disinfectants. Chin et  al. concluded that virus could be killed by 5-min incubation with various disinfectants , including – H ousehold bleach- 1:50 or Sodium hypochlorite (0.1%)- [1 min sufficient in another study] Ethanol- 60%–70% P ovidone -iodine - 7.5% C hloroxylenol or chlorhexidine - 0.05% B enzalkonium chloride- 0.2%–0.4% 10

11. PATHOPHYSIOLOGY SARS-CoV-2 accesses host cells via the enzyme angiotensin-converting enzyme 2 (ACE2 ), using special surface glycoprotein called as "spike" ( peplomer ). ACE2 is most abundant in type II alveolar cells and hence lung is the most affected organ. Source: caymanchem.com 11

12. The ACE2 protein has been identified in various human organs, including Respiratory System GI Tract Lymph Nodes Thymus Bone Marrow Spleen Liver Kidney Brain A molecular model of the spike proteins (red) of SARS-CoV-2 binding to the angiotensin-converting enzyme 2 (ACE2) protein, the receptor (blue) which is its the entry route to the target cell. Source: Juan Gaertner /Science Photo Library 12

13. In preliminary studies, findings included extensive lung infiltration by macrophages and other immune cells leading to diffuse alveolar damage, features of which a re- H yaline membrane formation Fibrin exudates E pithelial damage D iffuse type II pneumocyte hyperplasia There was observed super-imposed bacterial pneumonia in some patients. 13

14. Subsequent observations suggest that COVID-19 has clinical features distinct from typical ARDS, i.e COVID-19-related severe respiratory distress can be manifested by relatively well-preserved lung mechanics, despite the severity of hypoxemia. This pathologic pattern is accompanied by extensive deposition of Alternate and Lectin complement components within the lung septal microvasculature . Membrane attack complex mediated microvascular endothelial cell injury and subsequent activation of the clotting pathway, leading to fibrin deposition . 14

15. E levated D-dimer concentrations at presentation- indicate increased activation of coagulation pathway, which is also an independent risk factor for death. Severe COVID-19 sepsis is associated with a marked Macrophage activation syndrome (MAS) -type picture, increased inflammatory markers and ferritin concentrations that undoubtedly result in local activation of pulmonary vasculature endothelial cells. A cytokine storm can be a complication in the later stages of severe COVID‑19, resulting in multiorgan failure . HCQ and IL-6 receptor antagonist ( Tocilizumab ) may be useful in controlling cytokine storms in late-phase severe forms of the disease. 15

16. T hree distinctive angiocentric features of Covid19 Severe endothelial injury associated with intracellular SARS-CoV-2 virus and disrupted endothelial cell membranes. T he lungs from patients with Covid-19 had widespread vascular thrombosis with microangiopathy and occlusion of alveolar capillaries. The lungs from patients with Covid-19 had s ignificant new vessel growth through a mechanism of intussusceptive angiogenesis. 16

17. Pulmonary intravascular coagulopathy in COVID-19 pneumonia 17

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19. Lymphocytic Inflammation in a Lung from a Patient Who Died from Covid-19. Microthrombi (arrowheads) in the Interalveolar Septa of a Lung from a Patient Who Died from Covid-19. 19

20. The virus can cause acute myocardial injury (found in 12% of infected people admitted to the hospital in Wuhan, China) and chronic damage to the cardiovascular system - Heart failure, arrhythmias and blood clots. Approximately 20-30% of people who present with COVID‑19 have elevated liver enzymes. Upto 30% of hospitalized patients in both China and New York experienced renal complications . Following the infection, children may develop paediatric multisystem inflammatory syndrome with symptoms similar to Kawasaki disease, which can be fatal. 20

21. The typical incubation period for COVID‑19 is 5-6 days , but it can range from 1 to 14 days. Patients are most infectious when they show symptoms (even mild or non-specific symptoms ) but upto 41% of transmission may be asymptomatic . Patients remain infectious for 7-12 days in moderate cases and an average of 2 weeks in severe cases. 21

22. CLINICAL FEATURES 22

23. DIAGNOSIS Standard method of testing is real-time reverse transcription polymerase chain reaction ( rRT -PCR), typically done on respiratory samples obtained by a nasopharyngeal swab. Chest CT scans may be helpful to diagnose COVID‑19- Bilateral multilobar ground-glass opacities. Demonstration of a nasopharyngeal swab for COVID-19 testing. 23

24. Important Predictive biomarkers of severity of Covid-19 Inflammatory : IL 6, CRP, Ferritin, Platelet count, Lymphopenia , Increased Neutrophil lymphocyte ratio (NLR), increased platelet lymphocyte ratio (PLR) Coagulation related: PT, APTT, Fibrinogen, D-Dimer Sepsis related: Procalcitonin 24

25. PREVENTION WHO recommends 1 metre of social distance; the U.S. CDC recommends 2 metres . Washing hands with soap and water often and for at least 20 seconds or using an alcohol-based hand sanitiser with at least 60% alcohol. Practicing good respiratory hygiene, and avoiding touching the eyes, nose, or mouth with unwashed hands. Use of air conditioners should be avoided at all times. 25

26. USING FACE MASKS Surgical masks and N95 masks are identical in overall retention of aerosol particles expelled inside the mask. (97.14% and 99.98% retention respectively) Barrier of toward inward protection is considerably higher for N95 than for surgical masks. Hence , widespread use of relatively inexpensive surgical masks is regarded as a valuable public health intervention that can help intercept transmission of the virus in the general population. 26

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31. Progressively stronger mitigation efforts to reduce the number of active cases at any given time—"flattening the curve"—allows healthcare services to better manage the same volume of patients . [ Likewise , progressively greater increases in healthcare capacity—called raising the line —such as by increasing bed count, personnel, and equipment, helps to meet increased demand . 31

32. Mitigation attempts that are inadequate in strictness or duration—such as premature relaxation of distancing rules or stay-at-home orders—can allow a resurgence after the initial surge and mitigation. 32

33. PROGNOSIS The severity of COVID‑19 varies and may range from mild respiratory distress to progressive life threatening pneumonia. Mild cases typically recover within 2 weeks, while those with critical diseases may take 3 to 6 weeks to recover. In those < 50 years the risk of death is < 0.5 %, while in those > 70 years it is > 8 %. Pregnant women, hypertensives , diabetics, obese, those with renal disease and smokers may be at higher risk of severe COVID‑19 infection. 33

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37. Indian academy of cytologists national guidelines for cytopathology laboratories for handling suspected and positive COVID-19 patient sample Fine needle aspiration in COVID-19 suspected or confirmed cases Sample processing in the laboratory Sample discarding Management of spills in the laboratory Surface disinfection and equipment decontamination Care of the laboratory staff Reporting of the cytology samples Training of the cytopathology residents. 37

38. FNA in COVID-19 confirmed / suspected cases C omplete set of PPE  including laboratory gown, gloves, goggles, face shield, and N95. Donning and doffing only in a specifically designated zone . Following FNA procedure, material should NOT be expelled at all from the needle as it  invariably leads to the generation of droplets and aerosol. However, if inevitable, should be expelled very gently from the needle . W hile making a smear, it is recommended that slides are held as far as possible from oneself. 38

39. Drying of the smears by shaking them or blowing air should not be done as this can lead to the generation of aerosol.  The used needles should be discarded in sharp-resistant waste containers . The syringe hub should be cut and the entire syringe should be disinfected followed by discarding in biohazard waste bags specifically labeled as COVID-19. There should be access to soap and water and an alcohol-based sanitizer at the crucial locations within the laboratory. 39

40. Sample processing in the cytopathology laboratory H ospital information system (HIS) where online request forms are supported is recommended. However , when HIS is not available, digital workflow (e-requisition forms ) using email/ whatsapp is suggested.   The samples should be collected in appropriately labeled, tightly-capped, sterile containers. All samples should be packed in triple layer : using primary container, secondary container and zip lock pouch . Cytotechnician should wear protective gear. All fresh cytology samples received in the laboratory should be considered potentially infectious. 40

41. A number of steps involved in routine sample processing including the opening of the sample containers, removing tightly fitted caps of the tubes, diluting, shaking, vortexing , and centrifugation may lead to aerosol generation. Care should be taken to minimize the exposure to the aerosol generated during the sample processing by using adequate PPE and performing these steps in class II BSCs . In case of non-availability of class II BSCs , centrifugation should be undertaken using capped tubes. Following centrifugation, the samples should be rested for full 5 min followed by gentle removal of the caps . 41

42. Sample discarding All the residual samples should be discarded in appropriate disinfectants (as previously recommended) with confirmed virucidal activity against enveloped viruses . The sample tubes and containers should also be disinfected by adding in 0.1-1% hypochlorite solution (to be prepared fresh each day ), followed by discarding in separate biohazard waste bags labeled as COVID-19 . 42

43. Management of sample spills in the laboratory: should be done by 1 % sodium hypochlorite solution . Surface disinfection and equipment decontamination: should be done multiple times a day. Biomedical waste management: the full PPE is to be discarded into appropriately designated bins labeled as COVID and as per hospital policy. 43

44. Care of the laboratory Staff The staff can be divided into a minimum of 2–3 teams which can be posted for fixed periods. The laboratory personnel needs to be continuously trained and educated regarding the precautions to be taken while processing the potentially infectious samples. They need to be trained regarding proper donning and doffing of PPE. All the laboratory personnel should be advocated to frequently and thoroughly wash their hands with soap and water (for at least 20 s ). The potential exposure and health status of the laboratory personnel should be monitored daily. 44

45. Reporting of the cytopathology samples Cytopathologists may wear non-sterile gloves while reporting to avoid direct contact with the slides . Microscopes to be sanitized by 70% alcohol/hand sanitizer solution before initiating the reporting. Reporting cytopathologists may report independently rather than with the entire team of cytotechnologists/residents/trainees/fellows. All pathologists must wash their hands at the end of reporting for >20 s and/or hand sanitizer application. 45

46. Training of the cytopathology residents/fellows Teaching rooms should be well ventilated with adequate fresh airflow. Teaching activities, involving the gathering of more than 10 people in a limited closed space, may be suspended temporarily. Alternatively, online teaching resources, such as Webex meet app can be explored for conducting resident and fellow teaching sessions. O nline CMEs and webinars, avoiding contact, and maintain social distancing may be encouraged and adopted. 46

47. IAPM guidelines for Hematology section Use vacutainers ONLY and do not open them, if opening is necessary then in BSC. Blood smears should be prepared in class II BSC. Smears should be immediately fixed in methanol by putting slides in a methanol jar for at least one minute. Staining may be done later. Run 2 tubes of 1% Hypochlorite solution before shutting down the analyzer equipment used. The used needles should be discarded in sharp-resistant waste containers. 47

48. IAPM guidelines for Histopathology Lab Specimens should be properly fixed (at least 24 hours) in 10% formalin. At 37°C, Formalin significantly decreased the infectivity of SARS- CoV on day 1, while Glutaraldehyde inactivated it after incubation of 1–2days. Formalin significantly decreases the infectivity of the virus on day 1 at a temperature of 37°C Temperature of 56°C for 90min, 67°C for 60min, or 75°C for 30min rendered the virus non-infectious. 48

49. While grossing use mask, face shield, head cover and impervious aprons. Reduce the use of fresh-frozen sections to a strict necessity basis. 49

50. Dr. Utkarsh Sharma MBBS, MD (Pathology) SMS medical college, Jaipur icliniq.com/drutkarshsharma 50