MPL 202 Midterm Review: Public Health, COVID-19, Ontario, PDF

MPL 202 Midterm Review 3 ======================== ***Learning Objectives***... **What is public health?** - **Public health:** the science and art of **preventing disease, prolonging life and promoting human health** through organized efforts and informed choices of society, organizatio...

MPL 202 Midterm Review 3 ======================== ***Learning Objectives***... **What is public health?** - **Public health:** the science and art of **preventing disease, prolonging life and promoting human health** through organized efforts and informed choices of society, organizations, public and private, communities and individuals **Public Health Ontario (PHO)** - **PHO provides expert scientific and technical advice and support relating to:** - Infectious diseases - Infection Prevention and Control - Surveillance and Epidemiology - Health promotion, chronic disease and injury prevention - Environmental and occupational health - Emergency preparedness and incident response **Public Health Ontario Laboratory (PHOL)** - 5.5 million tests conducted per year - Public health microbiologists: **reference identification and public health support** **Laboratory Functions of PHOL** **[Primary Testing]** - HIV and Hepatitis - Mycobacterium (e.g. TB) - Zoonotic Diseases - Virology culture - Mycology - Parasitology - Water testing - Food testing **[Reference Testing ]** - Bacterial identification - Antimicrobial susceptibility - Confirmation of Level 3 Pathogens (e.g. TB) - Characterization of pathogens (once pathogen is isolated, mandated to send it to PHOL for identification) **[Outbreak Support]** - Typing bacterial isolates - Viral strain typing - Fungal typing - Genome sequencing **6 public health regions:** - Support local health programs - 34 PHUs in Ontario - A **public health unit** is an official health agency established by a group of urban and rural municipalities to provide a more efficient community health program, carried out by full-time, specially qualified staff - Health units administer health promotion and disease prevention programs to inform the public about healthy life-styles, communicable diseases control including education in STDs/AIDS, immunization, food premises inspection, healthy growth and development including parenting education, health education for all age groups and selected screening services - Medical Officer of Health (MOH) oversees program - Each health unit is governed by a board of health, which is an autonomous corporation under the Health Protection and Promotion Act, and is administered by the medical officer of health who reports to the local board of health. The board is largely made up of elected representatives from the local municipal councils. The ministry cost-shares the expenses with the municipalities - Serves defined geographic region/demographic - A pocket of population that has specific health needs -- each has its own public health system to oversee the health conditions **Health Protection and Promotion Act (HPPA)** - **HPPA**: specifies the organization and delivery of public health - **Legislation**: the overarching 'law' voted in by the legislative branch typically does not change - **Regulation**: the processes that define the overall law (rules, codes, etc.) frequently updated/changes to meet the needs in public health - Gives public health units the oversight to provide or ensure the provision of public health programs and services - Gives the **Medical Officer of Health (MOH)** the power to act in public health emergencies (epidemics, outbreaks, infection prevention and control lapses, etc.) **Public Health Nurses -- Support PH Programs** - Primary objective = primary prevention (prevent disease acquisition) -- vaccination - Community immunization/influenza clinics - Sexual health education initiatives to prevent STIs - Prenatal classes -- prevention of infections (listeriosis, rubella, etc.) - Active and/or passive immunization to contacts of cases e.g. HAV, meningitis - Secondary objective = secondary prevention (prevent disease spread) - Screening for active disease -- TB, STIs - Case finding e.g., nasopharyngeal swabs (flu, pertussis, COVID19) -- education stage - Outbreak investigation/contact tracing -- epidemiology - Follow-up on animal bites (prevention of rabies -- in conjunction with the Canadian Food Inspection Agency) (Federal level) - Notifiable disease reporting to MOH **Core functions of public health labs/units** 1. Communicable disease surveillance, prevention and control 2. Outbreak and emergency response to communicable diseases 3. Environmental health and food safety 4. Reference testing, specialized screening and diagnostic testing 5. Biosafety, containment, and biohazard spill response programs 6. Integrated communicable disease data management 7. Public health policy development and evaluation 8. Laboratory improvement and regulation (QA) 9. Training and education of health care and public health workers 10. Public health related research and development **Reportable diseases** - Blood-borne viruses - STIs - GI - 'severe' diseases (e.g. Ebola) - Vaccine = preventable diseases **Public health surveillance** - 2 primary sources for PH surveillance information: - **Individual encounter with HCP that results in clinical or lab diagnosis (first point of contact)** - Diagnosing HCP must report incidence also - **Surveys, etc.** - The continuous, systematic collection, analysis and interpretation of health-related data needed for the **planning, implementation, and evaluation of public health practice** - Such surveillance can: - Serve as an **early warning system** for impending public health emergencies; **document the impact of an intervention, or track progress** towards specified goals - Monitor and clarify the **epidemiology of health problems,** to allow **priorities** to be set and to **inform public health policy and strategies** - 3 clusters of PH organizations in Canada (continuously exchange info to help support the public health): - **Local/regional --** local actions, policies and programs developed in collaboration with others - **Provincial/territorial --** P/T actions, policies and programs developed in collaboration with others - **National --** Federal actions, policies and programs developed in collaboration with P/T authorities and others **Mumps Virus** - **Pathogen:** RNA virus (note: RNA virus evolves more rapidly) - **Mode of transmission:** droplet, direct contact w saliva, indirect contact w contaminated surface - **Incubation period:** 12-25 days (range) - **Period of communicability:** 2 days before and up to 5 days after onset of symptoms - **Symptoms:** fever, headache, malaise, myalgia, **parotitis --** 20% asymptomatic, 50% present w non-specific respiratory symptoms - **Testing:** serology (look for antibodies) and molecular (PCR) testing (look for virus) - **Prevention:** 2 doses of MMR vaccine; 76% to 95% effective - Collection information: - **Buccal swabs** may be **collected up to 9 days from date of symptom onset**. Massage the parotid gland area (space between the cheek and teeth just below the ear) for about 30s prior to collection of the buccal secretions. The parotid duct (Stensen's duct) drains in this space near the upper rear molars. Put the swab into that space. - **Throat swab** -- can be taken **up to 9 days from symptom onset** - Less reliable after 9 days - **Urine --** can be collected **up to 14 days following symptom onset** (minimum vol require: 5.0 ml) - Virus in urine is detectable for longer periods of time due to tissue differences - **CSF --** testing may be performed in cases of **aseptic meningitis** (minimum vol required: 1.0 ml) **What happens when a case is identified?** 1. Lab or physician reports notifiable result to PHU; legal requirement of HPPA 2. PHU nurse will collect report, enter available lab/clinical data into Integrated Public Health Information System (iPHIS; legal requirement of HPPA) 3. PHU nurse will: a. Initiate patient contact and **counselling** b. **Contact tracing** c. Additional **fact finding** (i.e. **descriptive epidemiology;** e.g., timing/place of potential exposures, risk factors, etc.) i. Descriptive epidemiology is important when talking about food-borne outbreak -- helps to piece things together -- i.e. where it came from, how you got it - look at the epidemic curve to determine count of cases over time - Helps to determine an outbreak **Key Definitions for Communicable Diseases** - **Outbreak:** is the occurrence of cases of a disease in excess of what would normally be expected at a particular **time and place** - **Index case:** first case to be *identified* at the start of an outbreak - **Reproductive rate (R0):** avg number of new cases that a case generates over the course of the infectious period (mumps R0 = \~4-7 means that \~4-7 people will be infected because of me) - **Attack rate:** percentage of at-risk population that will contact disease over a specific time interval (ex: 50% attack rate expect 50% of population to be infected in 2025) - **Eliminated disease:** reduction to zero the incidence of a specified disease in a defined geographical area because of deliberate efforts (Ex: mumps is an eliminated disease in Canada -- but it can still be reintroduced) - **Endemic disease:** situation where a chain of transmission continues uninterrupted for a period greater than one year - **Imported case:** a confirmed case that was acquired outside of Canada **Case definitions and descriptive epidemiology** - **Case definition:** describes criteria for **person, place, time, and clinical features** that are associated with a particular infectious disease/OB - **Person:** age, sex, ethnicity, occupation, exclusion criteria - **Place:** specific geographic location associated with disease cases - **Time:** period of time associated with exposure to infectious agent - **Clinical features:** signs/symptoms associated with disease state - **Ministry of health and long-term care maintains case definitions for infectious diseases - Sometimes, federal and provincial definitions vary** - **Confirmed case:** lab confirmation of infection with clinically compatible signs and symptoms **in the absence of recent hx of immunization w a mumps-containing vaccine in the last seven to 42 days** - Isolation of mumps virus from an appropriate clinical specimen (e.g. buccal swab, throat swab and urine culture) - Detection of mumps virus RNA from an appropriate clinical specimen - Seroconversion or significant rise (e.g. fourfold or greater) in mumps IgG titre by any standard serologic assay between acute and convalescent sera - Detection of mumps immunoglobulin M (IgM) antibody in a person who is either epidemiologically linked to a lab-confirmed case or has recently travelled to an area of known mumps activity - Clinically compatible signs and symptoms in a person who has been epidemiologically linked to a lab-confirmed case - **Probable case:** clinically compatible signs and symptoms in the absence of appropriate lab tests and w/o an epidemiological link to a lab confirmed case **Responding to a recently emergent virus** **[Key questions for managing an outbreak/pandemic:]** 1. What are we dealing with, where did it come from, and how can we test for it? 2. How can we recognize and contain disease? a. Clinical presentation (recognition)? b. Incubation period (containment)? c. Period of communicability (containment)? 3. What is the mechanism of transmission? d. Reproductive and attack rates (containment)? 4. What are possible countermeasures? **SARS-CoV-2 and Other Coronaviruses** - **SARS-CoV-2** = virus (aka: 2019-nCoV); **COVID-19** = disease - *Nidovirales (order)* - *Coronaviridae (family)* - *(ortho) Coronovirinae (sub-family)* - *Alpha/Beta -- mammals* - *Gamma/Delta -- birds* - Four common cold coronaviruses: OC43, NL63, HKU1, 229E - SARS-CoV-2 is the 7^th^ coronavirus known to infect humans - 3^rd^ **zoonotic** virus \[1^st^ **= SARS-CoV** (2002), 2^nd^ **= MERS-CoV** (2003)\] - As the immune system adapts it becomes endemic just normal flu symptoms - **Receptor (tissue tropism) for SARS-CoV-2 =** early phylogenetic evidence suggests angiotensin converting enzyme-2 (ACE2) **ACE-2** - Distributed throughout the body, but notably in: - Type II pneumocytes (83%0 -- pharynx, larynx, alveolus, macrophages - Endothelium - Explains ability to disseminate and affect multiple organs - Possible guide the development of therapeutics a. First SARS-CoV-2 may pass through either the mucous membranes, primarily the nasal epithelia, by binding to the ACE2 receptor b. In addition, SARS-CoV-2 can directly enter the respiratory tract and infect respiratory epithelial cells. After infection, extensive diffuse alveolar damage occurs in the lungs, followed by bilateral edema, diffuse reactive hyperplasia of type II pneumocytes, thickening of alveolar septa, and infiltration of inflammatory cells c. Typical COVID-19 associated changes in the kidneys are diffuse tubular injury with loss of brush border integrity, endothelial damage of the capillaries, and erythrocyte aggregates occluding the capillary lumen **Features of COVID-19 disease** - Max incubation period = 14 days (median = 4-5 days post-exposure) - Symptoms vary person-to-person and by age group - Influenza-like illness - Common symptoms = fever ([ ≥ 37.8^∘^*C*]{.math.inline}), dry cough, shortness of breath - Severe = shortness of breath or difficulty breathing, chest pain or pressure, loss of speech/movement - Multisystem inflammatory syndrome in children (MIS-C) - 20-75% of those infected will be asymptomatic - Risk factors for sever disease: age, hypertension, obesity, diabetes - Once disease starts to migrate to lower respiratory tract, it becomes more mild to moderate pneumonia, etc. - Immune system is struggling to contain the virus - severe pneumonia caused by SARS-CoV-2 is marked by immune system dysfunction and hyperinflammation leading to acute respiratory distress syndrome (ARDS), macrophage activation, hypercytokinemia and coagulopathy. - Inflammatory response extremely prolonged and overactive Causing collateral damage because immune system is overloaded - Major difference between one phase and the next - **Common symptoms:** fever, dry cough, fatigue - **Uncommon symptoms:** headache, loss of smell, nasal congestion, sore throat, coughing up sputum, SOB, pain in muscles or joints, chills, N/V, diarrhea - **Severe disease:** difficulty waking, confusion, bluish face or lips, coughing up blood, persistent chest pain, decreased WBCs, kidney failure, high fever **Ontario Case Definition -- Probable Case (COVID-19)** e. A person (who has **not** had a lab test) **with symptoms compatible with COVID-19 AND:** i. **High-risk or close contact exposure; OR** ii. **Was exposed to a known cluster/outbreak of COVID-19** (e.g. long-term care, prison) f. A person with symptoms compatible with COVID-19 **and** in whom lab diagnosis of COVID-19 is inconclusive g. A person who is asymptomatic AND: iii. High-risk or **close contact exposure; OR** iv. Was exposed to a **known cluster/outbreak** of COVID-19 **Ontario Case Definition -- Confirmed Case** - A person with **laboratory confirmation** of SARS-CoV-2 infection using a validated assay, consisting of positive nucleic acid amplification test (NAAT; e.g., a real-time PCR or nucleic acid sequencing) on **at least [one] specific genome target, OR:** - A validated point of care NAAT that has been deemed acceptable by the Ontario Ministry of Health to provide a final result, OR: - Demonstrated seroconversion or diagnostic rise (at least 4-fold or greater from baseline) in viral specific antibody titre in serum, plasma, or whole blood using a validated laboratory-based serological assay for SARS-CoV-2 - Using molecular test sometimes can get positive results after a while but its because the assay is very sensitive and can detect these dead, non-active nucleic acids pt can still be positive for up to 90 days - Testing for virulence **Ontario Case Definition -- Reinfection** - A previous confirmed case that has a subsequent confirmed SARS-CoV-2 infection where there is laboratory evidence supporting two different infections. Laboratory evidence includes: - Genome sequencing - Variant of concern (VOC) screening PCR testing indicates two distinct SARS-CoV-2 infections OR - A previous confirmed case of SARS-CoV-2: - That has a subsequent confirmed SARS-CoV-2 infection at least 90 days after the previous infection using episode date **Diagnostic testing -- RATs/NAATs** - RAT = Rapid Antigen Test - May miss something because it's too early - NAAT = nucleic acid amplification test - More sensitive than RAT; better than RAT **Ct Value and Viral Load** - Negative relationship - Ct = cycle threshold number - The lower the Ct = the more viral load you have - As Ct value goes up, viral load goes down - Bc it takes less cycle since you have a higher load at the beginning **Transmission Dynamics of COVID-19** - Transmission: - 48 hours prior to symptom onset (pre-symptomatic) to up to 10 days post-symptom onset changing with population immunity (e.g., 5days) - \~40-50% of transmissions occur in pre-symptomatic stage of illness - Attack rate for asymptomatic cases in 0-80% - Spread directly (e.g., saliva) or indirectly (e.g., fomites) through: respiratory droplets (large), and aerosols (small) - Aerosols created by cough, sneezes, sings, shouts, or talks - Risk of transmission depends on - Viral load of the infected source individual - Risk factors of the exposed individual - PPE - Distance from infected source individual - Size of inoculum (aerosol vs spit) - Indoors (air exchanges/min) vs outdoors - COVID less likely to be airborne spread but still possible; less likely depending on factor, droplets have higher risk of transmission - Fomite -- surface matters, how long the virus lasts varies depending on the type of surface **Goal of COVID-19 Public Health Interventions** - Decrease transmission, decrease ICU bed occupancy, decrease strain on healthcare resources **Public health restrictions are effective [when followed! ]** - R0 is not the real reproductive rate -- assume everyone is susceptible to the virus - Its an epidemiological reading - But realistically we have vaccines, social distancing, etc. - Re reflects the real world situation - Want Re to be below 1 -- the number of ppl u infect on average - At 1 = means it is growing affecting at least 1 person - Below 1 = less likely to infect another person **COVID-19 variants of concern** - Novel SARS-CoV-2 variants are emerging variants of concern (VOCs) - Various mutations (spike protein) - Hard to detect sequencing confirmation required - \~50-75% more transmissible - No increases in disease severity - Vaccines still likely effective - Current PPE measures appear effective **Omicron Variant background** - Resulted in a wave of infection not observed prior - Identified to be: more contagious, less severe, immune evasive - Dominant lineage in Canada and around the world **Omicron Variant infectiousness** - Nearly 2 times more transmissible compared to ancestral strains - Ancestral strain reproductive rate (R0) 2.79 - Delta variant R0 5.08; Omicron variant 4.2x more infectious **Omicron Variant Clinical Outcomes** - Omicron infections are: - 91% less fatal than delta variant (possibly due to immune system, vaccine, and intrinsic virus factors) - 51% less likely to result in hospitalization than delta variant - Most common symptoms: cough, fatigue, congestion, runny nose headaches, sore throat **Omicron Variant pathogenesis** - Omicron SARS-CoV-2 infects and multiplies 70x faster than the Delta variant and original SARS-CoV-2 in human bronchus - It hangs around in respiratory tract - Omicron in upper resp tract causing inc replication and transmission - Delta in lower resp tract causing more severe symptoms **Omicron Variant molecular virology** - Omicron has a total of 60 mutations compared to ancestral -- 32 mutations affect spike protein **S gene target failure** - Many mutations have not been observed previously **Variants and Public Health 'Trigger points'** - No longer use positivity rate and case count as primary indicator of pandemic progress - More important indicators: - Hospital admissions - Deaths - How this will inform future restrictions is unknown - Epidemic of the unvaccinated - Unvaccinated population represents a breeding ground for variants of concern - Viruses can only mutate so much before they start hurting themselves - Pandemics eventually end -- host/disease will reach a steady state  **Case Management and Clearance** - **Asymptomatic high-risk exposures:** - Self-monitor for 10 days; self-isolate if symptoms develop - Wear mask in all public settings - Avoid non-essential visits to immunocompromised/high risk - A negative test result **may not** alter the monitor/isolation period! - False positive can be problematic - Asymptomatic patients or in non-targeted screening (**low pre-test probability**) - **test based clearance NOT routinely recommended**