MIC 252 Lecture 20-21 2024 PDF

MIC 252 20 and 21. Emergence Factors for Infectious Disease with a focus on developing countries Learning Outcomes List the factors responsible for the emergence of new pathogens Explain how each of these emergence factors contributes to the development of infecti...

MIC 252 20 and 21. Emergence Factors for Infectious Disease with a focus on developing countries Learning Outcomes List the factors responsible for the emergence of new pathogens Explain how each of these emergence factors contributes to the development of infectious disease Contrast mortality due to infectious diseases in developing and developed countries Explain what precautions can be taken by travellers to endemic areas List some examples of immunizations required for international travel  Preface The narrated lectures are centered around the COVID19 pandemic. Most of the information contained in the slides is general knowledge. Click enter button to play the narrated slides.  Historical perspective Infectious disease (clinically manifesting disease of humans or animals resulting from an infection) has played a prominent role in world history. – The Black Death in the Middle Ages killed 1/3 Europe’s population. – Measles destroyed the South American Aztec civilization. – Smallpox destroyed indigenous peoples of North and South America, facilitating the conquest of the New World. "Triumph of Death" – 1918 Influenza Epidemic death toll: 40 (Black Plague) million worldwide Painted in 1562 – Currently, we’re in the midst of a new pandemic-COVID19 due to the novel coronavirus – Note, 25-35% of the 60 million deaths worldwide that occur each year are due to infectious disease.  Emerging Infectious Disease (EID) Emerging infectious disease can be defined as infections that have newly appeared in a population or have existed (but only identified now) but are rapidly increasing in incidence or geographic range. “New diseases; new problem (New threats)” Recent examples in various parts of the world include HIV, cholera, Rift Valley fever, hantavirus pulmonary syndrome, Lassa and Influenza (H1/N1), influenza A (H3N2)- 2013-2014 season, EBOLA- 2014-present day and COVID19. Although sometimes difficult to explain- never without a reason. Many of these infections emerge as zoonosis (infections that are naturally transmitted between vertebrate animals and man). All seven HCoVs have a zoonotic origin from bats, mice or domestic animals (Li X, Song Y, Wong G, Cui J. Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 2020. ). What is scary is that the zoonotic pool is not yet exhausted. Once introduced the infection is spread through other factors. Emerging infections may therefore include: Old diseases- new hosts → pathogens already present in environment Old diseases- new areas → pathogens already present in environment New diseases → new variant may evolve…  Risk Factors for Emergence 1415 species of infectious agents reported to cause disease in humans Viruses, prions, bacteria, rickettsia, fungi, protozoa, helminths 868/1415 (61%) zoonotic 175 emerging infectious diseases Int J Biol Sci. 2020; 16(10): 1686– 1697. 132/175 (75%) emerging zoonoses 37/132 (28%) emerging vector-borne diseases  Emerging Infectious Disease (EID) As stated previously, 25-35% of the 60 million deaths worldwide that occur annually is due to infectious disease. Four historical patterns of transition have been identified in emerging diseases. All four transition mechanisms contribute to rapid spread of emerging and re- emerging diseases (more detail later). First transition (also referred to as crowd transition) – Occurs when people begin to live in much closer proximity to one another. Higher population density. – Proximity between populations allows for easy transmission of disease  Emerging Infectious Disease (EID) Second transition – Neighboring civilizations made contact with each other through war or trade. Contact allowed the exchange of pools of infectious organisms and vectors between populations. Third transition – Worldwide exploration and colonization led to the identification of new populations. – Newly identified populations came into contact with pathogens never seen before within their cultures. – Immunologically naïve and susceptible populations.  Emerging Infectious Disease (EID) Fourth transition – this is happening today. The ongoing causes are: – Globalization (worldwide movement toward economic, financial, trade, and communications integration) – Global urbanization (as populations of people grow, the population of a place may spill over from city to nearby areas) – Increase in population density – Poverty – Social upheaval (e.g. war) – Travel (tourism, trade) – New behaviours (medical / sexual tourism) – Long distance trade – Technology development – Land clearance – Weather / Climate  Summary of factors for EID 1. Ecological changes → such as those due to agricultural or economic development or to anomalies in climate 2. Human demographic changes and behaviour 3. Travel and commerce 4. Technology and industry 5. Microbial adaptation and change 6. Breakdown of public health measures  Ecological Changes and Agricultural Development Frequent factors in outbreaks of previously unrecognized diseases with high case- fatality rates → often turn out to be zoonotic. Ecological factors usually precipitate emergence by placing people in contact with a natural reservoir or host for an infection either by increasing proximity or by changing conditions so as to favour an increased population of the microbe or its natural host. E.g., emergence of Lyme disease (bacterium Borrelia burgdorferi) in the United States and Europe was probably due largely to reforestation → increased the population of deer and the deer tick Ixodes scapularis, the vector of Lyme disease. Movement of people into these areas placed a larger population in close proximity to the vector.  Ecological Changes and Agricultural Development Agricultural development, one of the most common ways in which people alter and interpose themselves into the environment, is often a factor. E.g., Hantaan virus → natural infection of the field mouse Apodemus agrarius that flourishes in rice fields. People usually contract the disease (Korean hemorrhagic fever) during the rice harvest from contact with infected rodents. Junin virus (Argentine H.F)→ conversion of grasslands to maize fields→rodent vector (Calomys musculinus) flourished→ increased incidence. Pandemic influenza appears to have an agricultural origin → integrated pig-duck farming in China (ducks major reservoir of influenza, pigs provide a mixing vessel) Pandemic influenza gene segments from two influenza strains re-assort to produce a new virus that can infect humans.  Ecological Changes and Agricultural Development Mosquito vectors are stimulated by expansion of standing water. Thus stored drinking water, dams, and irrigation systems can also lead to emerging disease. Climate or weather anomalies can play a role. Hanta virus pulmonary syndrome outbreak in U.S. (1993) due to unusually mild and wet Winter and Spring which led to a flourish in rodent population harbouring the virus. Serious disasters, such as hurricanes, typhoons, or earthquakes, cause a disruption in water systems resulting in the mixing of drinking and Rice-water waste waters, which increase the risk of contracting stool typical of cholera. cholera among area residents.  Human Demographics and Behaviour Human population movements or upheavals → caused by migration or war creates an increased risk of contact with new pathogens. Economic conditions encourages the mass movement of workers from rural areas to cities (urbanization). The United Nations has estimated that, rural urbanization allows infections arising in isolated rural areas to reach larger populations. Once in a city → newly introduced infection would have the opportunity to spread locally among the population → could also spread further along highways and inter- urban transport routes and by airplane. E.g., HIV, dengue. Dengue hemorrhagic fever is now common in some cities in Asia where the high prevalence of infection is attributed to the proliferation of open containers needed for water storage → high population density assists the spread. Human behaviour can have important effects on disease dissemination. The best known examples are sexually transmitted diseases  International Travel and Commerce Dissemination of HIV Trade between Asia and Europe introduce the bubonic plague (Black death) into Europe. Same for mosquito vectors, cholera and smallpox The Norway rat is very common in cities as well as rural areas. It This flea carries the Yersinia usually lives close to humans pestis bacteria that causes and may carry fleas infected bubonic plague. When it bites a with bubonic plague bacteria. rodent, such as a squirrel or rat, it The plague is transmitted to infects the animal with the plague humans through the bite of an bacteria. It can bite humans and infected flea. infect them with plague too.  Technology and Industry High volume rapid movement influences industries in modern society As populations grow, there is an increased pressure to produce more food (e.g. meat). This has led to the emergence and spread of infections from farm animals to humans, e.g. BSE -“Mad cow” disease, E. coli O157:H7. “Mad cow” disease was first seen in Britain in 1984. By the year 2000, there were 180,000 confirmed cases in cattle in Britain. The infection in cattle has been attributed to sheep brain supplement included in cattle feed. Medical technology- concentration of blood products → hospital acquired diseases e.g., Ebola outbreaks in Angola mostly hospital acquired.  Microbial adaptation and Change Microbes, like all other living things, are constantly evolving. Emergence of antibiotic-resistant bacteria as a result of the ubiquity of antimicrobials in the environment is an evolutionary lesson on microbial adaptation. Pathogens can also acquire new antibiotic resistance genes from other often non- pathogenic species in the environment. Many viruses show a high mutation rate and can rapidly evolve to yield new variants E.g., influenza  Breakdown of Public Health Measures Classical public health and sanitation measures have long served to minimize dissemination and human exposure to many pathogens spread by traditional routes such as water or preventable by immunization or vector control The pathogens often still remain, albeit in reduced numbers, in reservoir hosts or in the environment or in small pockets of infection → therefore often able to take advantage of the opportunity to re-emerge if there are breakdowns in preventive measures. E.g. The introduction of vaccine-preventable diseases such as polio and diphtheria in areas where incidence was zero. Bubonic plague incidences reported currently in China (2020). Factor Examples of specific factors Examples of diseases Ecological changes(including those due to Agriculture; dams,changes in water Schistosomiasis(dams); Rift Valley economic development and land use) ecosystems; deforestation/reforestation; fever(dams, irrigation); Argentine flood/drought; famine; climate changes hemorrhagic fever(agriculture); Hantaan (Korean hemorrhagic fever) (agriculture); hantavirus pulmonary syndrome, southwestern US, 1993 (weather anomalies) Human demographics, behavior Societal events: Population growth and Introduction of HIV; spread of dengue; migration (movement from rural areas to spread of HIV and other sexually transmitted cities); war or civil conflict; urban decay; diseases sexual behavior; intravenous drug use; use of high-density facilities International travel commerce Worldwide movement of goods and people; "Airport" malaria; dissemination of mosquito air travel vectors; ratborne hantaviruses; introduction of cholera into South America; dissemination of O139 V. cholerae Technology and industry Globalization of food supplies; changes in Hemolytic uremic syndrome(E.coli food processing and packaging; organ or contamination of hamburger meat), bovine tissue transplantation; drugs causing spongiform encephalopathy;transfusion- immunosuppression; widespread use of associated hepatitis (hepatitis B, C), antibiotics opportunistic infections in immunosuppressed patients, Creutzfeldt- Jakob disease from contaminated batches of human growth hormone (medical technology) Microbial adaptation and change Microbial evolution,response to selection in Antibiotic-resistant bacteria, "antigenic drift" environment in influenza virus Breakdown in public health measures Curtailment or reduction in prevention Resurgence of tuberculosis in the United programs; inadequate sanitation and vector States; cholera in refugee camps in Africa; control measures resurgence of diphtheria in the former Soviet Union  Infectious Disease in Developing Countries Infectious disease remains an important cause of illness and death (mortality) in developing countries- including South Africa Various factors are responsible for the mortality → difficult to define South Africa provides a dual paradigm- with good medical infrastructure in the cities, expanding primary health care in the rural areas and fairly good modern diagnostic facilities available Mixture of infectious disease problems encountered in both developing and developed countries Disease surveillance is in its infancy- see lecture 22  Some Examples: Bacterial Diseases Streptococcus pneumoniae 1978- Baragwanath Hospital → fully resistant and multi-drug resistant bacteria Mostly to penicillin Largely dependant on the administering of antibiotic in different settings HIV is increasing the incidence of the pneumococcal pneumonia Staphylococcus aureus Related to differential use of antibiotics→ methicillin vs vancomycin  Some Examples: Viral Diseases HIV Not apparent in South Africa until 1988 Homosexual men with partners in USA BUT → in 1990 the incidence of HIV among pregnant ‘African’ women was 0.4% compared to the current 20% (north and east) and slightly below 10% in the south NB → already has staggering impact on the emerging infectious disease in South Africa Viral hemorrhagic fevers Marburg fever → identified in the 1970s in a tourist visiting several African countries to the north of South Africa → nosocomial transmission to two persons was identified at that time  Some Examples: Parasitic Diseases Malaria Malaria remains a serious systemic disease in South Africa → endemic in the northern and eastern parts of the country where the climate is tropical Chloroquine-resistant strains, which were rare in the 1980s, are now common Quinine-resistant strains have not yet been demonstrated Schistosoma haematobium and S. mansoni Endemic in rivers along the eastern part of the country and pose a health risk to non-immune visitors  Mortality in Developing v Developed Countries E.g., influenza Infectious disease preparedness varies from country to country Developing countries face mostly financial and technical constraints Difference in mortality rate between high and low income countries Several factors may have been involved: lack of access to adequate medical care weak public health infrastructures social factors such as housing conditions and population density host factors such as nutritional status and co-existing medical conditions  Mortality in Developing v Developed Countries Another potential factor likely to influence mortality in current and future pandemics → high HIV/AIDS prevalence in some developing countries Excess deaths attributed to pneumonia or influenza are significantly higher in HIV- positive persons during influenza seasons Some studies estimate that because of above factors → as much as 96% of the mortalities would occur in developing countries  Mortality: India and 2009 H1N1 as example India has an estimated population of 1.366 billion (2019 stats) Millions in sub economic housing (slums) April 12- Outbreak of H1N1 in Veracruz, Mexico April 24- WHO declares PHEIC (Public Health Emergency of International Concern) April 27- Pandemic Phase 4 → sustained community transmission in Mexico April 29- Pandemic Phase 5 → 2 countries affected June 11- Pandemic Phase 6 → 2 WHO regions affected June 21- All regions affected... August 21 → rest of the world → mortality rate is 0.9% India = 2.3% (close to three times higher)  Travelling to Endemic Areas E.g., Diseases caused through insect vectors Of the many diseases spread by insects → organisms passed on when they feed or bite Insects are capable of spreading diseases caused by many different types of microorganisms including bacteria, viruses, protozoa Biting insects are active at all times of the day and night → some prefer different times of day e.g., the mosquitoes that spread malaria are mainly active after dark but the mosquitoes that spread yellow fever and dengue fever are active during daylight hours  Travelling to Endemic Areas Disease Vector Endemic Zone Malaria Mosquitoes Global tropical and subtropical areas. Yellow Fever Mosquitoes Tropical areas of Africa and Central and South America Tropical Africa, South East Asia, South America and the Dengue Fever Mosquitoes Pacific. Lyme Disease Ticks Europe (inc. UK), USA, Australia, China & Japan. Global tropical and subtropical areas including the Leishmaniasis Sandflies Mediterranean. Sleeping Sickness Tsetse Flies East, West and Central Southern Africa. Typhus Fever Ticks & Lice World-wide Plague Fleas World-wide.  Travelling to Endemic Areas When entering a region where any of the above diseases are endemic → should always take the following precautions: Avoid bites after sunset by wearing long-sleeved clothing and long trousers Most insects can bite through thin clothing → spray an insecticide or repellent on them An insect repellent should also be used on any exposed skin Spraying insecticides in the room, burning pyrethroid coils and heating insecticide impregnated tablets all help to control mosquitoes If sleeping in an unscreened room, or out of doors, a mosquito net (impregnated with insecticide) is a sensible precaution Vaccinate  Immunizations for International Travel Immunizations can help prevent many travel- related infectious diseases: Several factors determine the number and type of travel immunizations recommended, including: Past immunizations Medical conditions or pregnancy Allergies to substances in some vaccines The travel destination(s) The duration of travel The season of travel The planned activities during travel The place of residence during travel The likely extent of interaction with local populations (eg, tourism versus occupational)  Immunizations for International Travel Some examples: Yellow fever vaccine → required by law to enter some countries → eqautorial Africa and South America Cholera vaccine (oral- Dukoral) → Latin America and Asia Poliomyelitis → developing countries e.g., central Africa Measles → developing countries and some in Europe Typhoid → Asia, Africa and Latin America, India Rabies Hepatitis A (developing countries) and B (Asia) Meningococcal disease (Hajj)  MIC 252 22-23. Emerging and Re-emerging (resurging) Infectious Disease and Factors favouring global eradication of an infectious disease Learning Outcomes Differentiate between emerging and re-emerging/resurging infectious disease Describe methods available for identifying and controlling emergence of new infectious disease (surveillance and intervention) Compare public health measures for controlling infectious diseases caused by various reservoirs (domestic and wild animals, insects, humans) Describe public health measures (immunization, quarantine, etc) used to halt the spread of an epidemic  Preface The narrated lectures are centered around the current pandemic. Most of the information contained in the slides is general knowledge. We are now reaching the tail-end of COVID19 it will be updated next year once the pandemic has ended.  Emerging and re-emerging/resurging Infectious Disease Approx 60 million people die worldwide annually → of that some 15 million of infectious disease → most of that were people under the age of 50  Direct economic impact of selected infectious disease outbreaks, 1990-2003 Heymann DL. Emerging and re-emerging infections. In Oxford Textbook of Public Health, 5th ed, 2009, p1267.  Contrast Emerging and re-emerging/resurging Infectious Disease Emerging disease is a disease that has never been recognized before. E.g., HIV/AIDS is an emerging disease, as is severe acute respiratory syndrome (SARS) and variant Creutzfeld- Jakob disease (vCJD Re-emerging (re-surging) diseases are those that have been around for decades or centuries, but have come back in a different form or a different location. “Old diseases, new problem. (New threats)”. Note, these are the diseases which were previously easily controlled by chemotherapy and antibiotics, but now they have developed antimicrobial resistance and are often appearing in epidemic form. E.g., West Nile virus in the Western hemisphere, monkeypox in the United States, and dengue rebounding in Brazil and other parts of South America. Deliberately emerging diseases are those that are intentionally introduced → agents of bioterror, the most recent and important example of which is anthrax. Biological agents are attractive instruments of terror- easy to produce, mass casualties, difficult to detect, widespread panic & civil disruption.  Important emerging and re-emerging infectious diseases HIV June 1981 → first described 2009- > 42 million people infected → 74% in Sub- Saharan Africa > 22 million people have already died Currently ~ 14 000 new infections daily → 95% of which is in developing countries In India currently about 1% of adult population is infected, compared to Botswana with 37%. Emergence is amplified by population dynamics → disruptions in the economic and social infrastructure, urban poverty, a weakening of family structure, promiscuous sexual practices, and increased travel.  Important emerging and re-emerging infectious diseases Plasmodium (Malaria) and Mycobacterium (TB) ~ 1 million people die annually of malaria (~ 2800 children per day) ~ 2 million of tuberculosis ~ 2 billion people are infected with Mycobacterium tuberculosis High prevalence among HIV infected ~ 46% of those infected with HIV in developing world also infected with TB 13% of deaths among HIV infected are from disseminated TB  coughing, sneezing -> Airborne  Important emerging and re-emerging infectious diseases Influenza ~300 000 people die annually from flu epidemics throughout the world (majority over 65 years old)…aging immune system? Worst pandemic in 1918 (Spanish flu) → 40 million dead (mostly young people)….immature immune system? Currently we are the midst of an new pandemic (COVID19)- nearly 19 million infected to date, with nearly 700 000 deaths. Numbers increasing by the day. Many countries to still reach their peak. WHO estimated that ~ 40 000 deaths in South Africa by end of 2020 due to COVID 19 pandemic.  Important emerging and re-emerging infectious diseases SARS coronavirus 2002- Guangdong Province in China 8098 reported cases and 774 deaths Vaccine design by 2004 and into clinical trials in just over 5 years → tremendous achievement  Methods for Identifying and Controlling Emergence of new Infectious Disease: Surveillance/ Intervention Surveillance and intervention are important and dynamic strategies in controlling the emergence of new infectious disease. Surveillance can be defined as “the continuing scrutiny of all aspects of occurrence and spread of disease that are pertinent to effective control.” Through surveillance the public health system can remain informed regarding the emergence of a new disease and measures can be put into place to prevent its spread One of these measures is intervention in the form of isolating people and removing animal carriers, vectors, etc...  Surveillance Important factors are: choice of diseases for surveillance, development of methods, ongoing systematic evaluation and dissemination to those who need to know Thus, surveillance = "ongoing" systematic collection, analysis and interpretation of data and the distribution to those who need to know → those who plan public health programmes who develop local, regional, national and even international policies who implement intervention and carry out public health action the public, who need to have information in order to evaluate public health practice who need the information for personal action for their health and well-being  Surveillance Surveillance has three basic component activities: 1. Data collection: Passive → data reported in way that the receiving agency (hospitals, laboratories, clinics or physicians) waits for data (notifiable diseases) or the data collection practice can be active → data actively sought (door to door, telephone calls i.e. actively searching for data) 2. Analysis and interpretation (line graphs, bar charts, etc.) 3. Dissemination Surveillance is a fundamental component of the strategy against emergence of infection Surveillance strengthening is included as a major theme in the strategic plans against emerging infections → WHO Surveillance is a cyclical process Health Care System Public Health Authority Reporting 1 Event Data Capture Real world! … Analysis & 2 expected Interpretation changes 3 Dissemination Intervention Information  Surveillance In many countries → the basic infrastructure necessary to carry out some surveillance exists to larger or lesser degree This requires health practitioners throughout communities, competent laboratory support and some form of communication system Often relies on the observations of inquisitive individuals as it does on a system Surveillance in Africa is not as good as in developed countries. This is largely due to lack of funding, poor prioritization of health funds, misplaced in curative rather than preventive infrastructure, failure to develop adequate health delivery systems.  Benefits of Surveillance quantitative estimates of the magnitude of a health problem portraying the natural history of disease detecting epidemics documenting the distribution and spread of a health event facilitating epidemiological and laboratory research evaluating control and prevention measures monitoring changes in infectious agents monitoring isolation activities detecting changes in health practice planning  Intervention Various intervention strategies available Broadly categorized into 2 groups: 1. Non- pharmacological 2. Pharmacological  Non- pharmacological Isolation: refers to the precautions that are taken in the hospital (facility) to prevent the spread of an infectious agent from an infected or colonized patient to susceptible persons Quarantine: Period of time during which a vehicle, person, or material suspected of carrying a contagious disease is detained at a port of entry under enforced isolation to prevent disease from entering a country Social distancing: school closure, cancellation of mass gatherings and social activities, movement restrictions, business and market closure, etc Daily health checks Contact identification Infection control: hand washing, facemask wearing, cough etiquette, disinfection of surfaces, etc  Pharmacological Prophylaxis and vaccination priority groups and vaccination strategies stockpiling dispensing to a large number of people adverse effects reporting  Surveillance/ Intervention Failure Often key determinants of health- as well as the solutions- lie outside direct control of the health sector Rooted in areas such as: Sanitation and water supply Environmental and climate change Education Agriculture Trade tourism Transport Industrial development Housing  Public Health Measures: Goals Maximum control of disease and improvement of health → goals of every effective public health programme Smallpox → eradicated three decades ago Polio next Attempts to eradicate yellow fever → failed Malaria → new drug being tested by Professor Kelly Chibale (UCT) one year before clinical trials commences and maybe another seven years before malaria drug developed. So still a major source of mortality in Africa.  Eradication Eradication can be defined in various ways: extinction of the disease pathogen elimination of the occurrence of a given disease, even in absence of all preventive measures control of an infection to the point at which transmission ceased within a specified area reduction of the worldwide incidence of a disease to zero as a result of deliberate efforts → obviating the necessity for further control measures Eradication Eradication  Eradication Intervention targets: Vector Control (e.g., Malaria) 1. Biological control → include toxins from the bacterium Bacillus thuringiensis var. israelensis (Bti). Other potential biological control agents, such as fungi (e.g., Laegenidium giganteum) or mermithid nematodes (e.g., Romanomermis culicivorax). Mosquito fish (Gambusia affinis) are effective in controlling mosquitoes in larger bodies of water. 2. Chemical control → Oils may be applied to the water surface, suffocating the larvae and pupae. Most oils in use today are rapidly biodegraded. Insect growth regulators such as methroprene → specific to mosquitoes 3. Source reduction → above methods PLUS larval habitats may be destroyed by Mosquito larvae must come to filling depressions that collect water, by draining swamps, or by ditching the surface to breathe air through abdominal siphons. marshy areas to remove standing water. Photo by Jack Kelly Clark. Container-breeding mosquitoes are particularly susceptible to source reduction as people can be educated to remove or cover standing water in cans, cups, and rain barrels around houses. Mosquitoes that breed in irrigation water can be controlled through careful water management.  Eradication 4. Insecticide spraying → Elimination of malaria in an area does not require the elimination of all Anopheles mosquitoes. Socio-economic improvements (e.g., houses with screened windows, air conditioning) combined with vector reduction efforts and effective treatment have led to the elimination of malaria in USA and Europe. Insecticide-treated bed nets Indoor and outdoor residual spraying (e.g., with DDT) 5. Genetic control → Sterile male release → aims to develop mosquitoes that are refractory to the parasite  Eradication Intervention targets: Countries where yellow fever is Control of Animal Reservoirs (wild and domestic) (e.g., endemic Yellow Fever, rabies) 1. Control through Drugs and Vaccines → vertebrate host and/or reservoir may also be the target for control measures. E.g., For vaccination of fox against rabies in Europe and Canada is an effective means to reduce the threat of rabies. In addition, reduction of host reservoirs, such as rodents, birds and monkeys from areas of human habitation. 2. Port control and quarantine measures 3. Personal Protection 4. Repellents Early Diagnosis and Treatment = surveillance  Eradication Public Health Measures to curb spread of Epidemic (e.g., SARS) 12 March 2003 → 150 suspected cases in seven countries By end of the outbreak → 27 countries had reported 8,096 suspected cases + 5 incidents of transmission on commercial aircraft WHO issued travel advisories in an attempt to slow the international spread of the disease Case isolation was also effective in the control of onward transmission Timeline and response measures March 31 → Hong Kong authorities impose general quarantine to prevent spread from island → residents of severely affected apartment complex had to remain indoors for 10 days 12 February → 12 people staying in Metropole Hotel in Hong Kong was infected via a physician → USA, Singapore, Vietnam, Canada, Ireland  Eradication Timeline/ Control measures February 28 → Vietnam and Singapore index cases contained and spread halted March 5 → Canadian index case died at home (superspreader) March 7 → her son became ill and was admitted to hospital where he infected many staff and patients → died on March 13, one day after global alert issue 12 March → Global alert 15 March → Public awareness – report suspected symptoms and to avoid contact with people and areas where SARS had been detected; international travel restrictions 26 March → Ontario, Canada issues provincial emergency and starts quarantine procedure (LATE!!!) Eradication  Eradication Timeline/ Control measures 28 March → quarantine situation in China 20 April → “nationwide war on SARS” → mayor of Beijing and Minister of Health fired Larger quarantine measures imposed in China → no public gatherings, travel from cities, closure of government offices, universities, schools June 2003 → disease contained in China Containment in terms of quarantine and international collaboration in terms of identification of the causative agent and vaccine design played pivotal roles in the control of the epidemic  Eradication Control measures Vaccination Vaccination is the most effective measure for reducing the overall impact of an established epidemic December 2004- China starts testing a vaccine against SARS → staggering as it normally takes up to 14 years to get to human trials Role of passive immunization? Other factors: antivirals All in combination stopped the spread of epidemic and pandemic  Self study Questions 1. Differentiate between emerging and re-emerging infections. 2. What is meant by surveillance? 3. Name the three components of a surveillance system. 4. List five benefits of a surveillance system. 5. List five non-pharmacological intervention strategies. 6. Define the term disease eradication. 7. Briefly explain how disease eradication can be achieved by using: biological control/chemical control or source reduction of vectors  MIC 252 24- Bacterial Pathogenesis- An Overview (Attachment, Colonization, Multiplication) and 25- Local vs systemic infections Learning Outcomes Define: disease, infection, pathogenicity, virulence, spreading factors List the 7 challenges which pathogens must overcome List and explain factors which play a role in the adhesion of pathogens to host cells/tissues Describe the various adherence factors in host-parasite interactions Give examples of various factors which enable the pathogen to invade the host State Koch’s postulates Describe general characteristics of local and systemic infections Explain the factors which prevent surface infections from spreading further Explain why some microbes risk spreading through blood an lymph  Bacterial pathogenesis and definitions How do bacteria cause disease in human beings? By process of Pathogenesis- a multi-factorial process which depends on the immune status of the host, the nature of the species or strain (virulence factors) and the number of organisms in the initial exposure. Pathogenicity: ability of an infectious agent (pathogen) to cause disease by overcoming the defenses of a host Disease is an abnormal state in which part or all of the body is not properly adjusted or is incapable of performing normal functions. Infection: is the invasion and growth of pathogens in the body with or without disease Infectious disease: A clinically manifesting disease of humans or animals resulting from an infection Pathogens: microorganisms capable of causing disease.  Disease Classification 1. A patient may exhibit symptoms (subjective changes in body functions: coughing, body aches, etc.) and signs (measurable changes: body temperature, blood pressure, heart rate, presence of antibodies in a patient’s serum), which are used by a physician to make a diagnosis (identification of the disease) 2. A specific group of symptoms or signs that always accompanies a specific disease is called a syndrome. E.g. TB- A cough that lasts more than 3 weeks, chest pain, coughing up blood, feeling tired all the time, night sweats, unexpected weight loss. Many syndromes are named using a nomenclature based on signs and symptoms or the location of the disease. See table on next slide. 3. Communicable diseases are transmitted directly or indirectly from one host to another. 4. A contagious disease is one that is easily spread from one person to another. Nomenclature of Symptoms Affix Meaning Example cyto- cell cytopenia: reduction in the number of blood cells hepat- of the liver hepatitis: inflammation of the liver -pathy disease neuropathy: a disease affecting nerves -emia of the blood bacteremia: presence of bacteria in blood -itis inflammation colitis: inflammation of the colon -lysis destruction hemolysis: destruction of red blood cells -oma tumor lymphoma: cancer of the lymphatic system diseased or -osis abnormal leukocytosis: abnormally high number of white blood cells condition -derma of the skin keratoderma: a thickening of the skin  Definitions continued When diagnosing infectious diseases, it is always important to consider possible noninfectious causes. Non-communicable diseases (NCD) is a medical condition or disease that is not caused by infectious agents (non- infectious or non-transmissible). E.g. diabetes, Alzheimer's, cancer. Virulence: the degree (measure) of pathogenicity. The determinants of virulence of a pathogen are any of its genetic or biochemical or structural features that enable it to produce disease in a host. (more detail later) Virulence can be expressed as LD50 or ID50 Infectious dose (ID50)- number of pathogen cells required to cause active infection in 50% of the experimental subjects. Lethal dose (LD50)- number of pathogen cells required to cause death in 50% of the experimental subjects. (see graph on next slide)  Host: an organism that shelters and supports the growth of a pathogen Toxigenicity: the ability of a microorganism to produce a toxin that contributes to the development of disease. Spreading Factor: is a descriptive term for a family of bacterial enzymes that affect the physical properties of tissue matrices and intercellular spaces, thereby promoting the spread of the pathogen.  Disease Occurrence and Severity Disease occurrence is reported by incidence (number of new people contracting the disease during a specified period of time e.g. per month) and prevalence (number of cases alive with the disease at a particular date in time) Diseases are classified by frequency of occurrence: sporadic, endemic, epidemic, and pandemic (revise MIC 251 notes). The duration of the period of illness can vary greatly, depending on the pathogen, effectiveness of the immune response in the host, and any medical treatment received. The scope of a disease can be defined as acute, chronic, sub-acute, or latent. Acute: An infection characterized by sudden onset, rapid progression, and often with severe symptoms Chronic: An infection characterized by delayed onset and slow progression. Can be years. Sub-acute: a poorly defined state between acute and chronic. Latent: remaining in an inactive form or state (dormant). Many viruses after acute infection goes into a latent state.  Stages of phases of disease Development The five periods of disease (sometimes referred to as stages or phases) include the incubation, prodromal, illness, decline, and convalescence periods. 1. The incubation period is the time interval between the initial infection (no signs or symptoms). 2. The prodromal period is characterized by the appearance of the first mild signs and symptoms 3. During the period of illness, the disease is at its height and all disease signs and symptoms are present (fever, inflammation and swelling, tissue damage, infection may spread to other sites) 4. During the period of decline, the signs and symptoms decrease. Note, you could develop 2ry infection. 5. During the period of convalescence, the body returns to its pre-diseased state, and health is restored  Bacterial pathogenesis and the challenges that Pathogens Face in order to Survive The process of pathogenesis involves various steps. Pathogens must: 1. Maintain a reservoir (person, animal, plant, soil or substance in which an infectious agent normally lives and multiplies) in which it can survive before and after infection 2. Leave its reservoir and enter the body of a human host (transmission) 3. Adhere (attach) firmly to the host’s body and thereby colonize it 4. Invade the body in order to enter cells or deeper tissues 5. Evade the host’s elaborate defenses 6. Multiply within the body, perhaps producing toxic products or stimulating host reactions that cause disease 7. Leave the body and return to the reservoir and/or enter a new host  Types of bacterial pathogens Pathogens can be classified as either primary pathogens or opportunistic pathogens. A primary pathogen can cause disease in a host regardless of the host’s resident microbiota or immune system. E.g. Mycobacterium tuberculosis and Yersinia pestis are always considered as primary pathogens. Never non-pathogenic. Some bacteria are part of the normal flora and sometimes cause disease- e.g., E.coli. normally found in the large intestine can cause a urinary tract infection if it enters the bladder. This is the leading cause of urinary tract infections among women. Pseudomonas species only cause disease in immune suppressed (e.g. AIDS patients) and debilitated host (e.g. severe burn wounds) and are considered as opportunistic pathogens.  Virulence factors of pathogens The factors produced by a microorganism and induce pathology in a host are called virulence factors. These factors help pathogen to: (1) invade the host, (2) cause disease, and (3) evade host defenses. Virulence factors are classified into two categories – 1. Virulence factors that promote bacterial colonization of the host: Adherence Factors* Invasion and/or Spreading Factors* Compete for iron and other nutrients; Evasion of host immune responses 2. Virulence factors that damage the host. Exotoxins Endotoxins * denotes what we will focus on in these lectures. 1. Transmission of Infection via portals of entry  Portal of Entry The specific route by which a particular pathogen gains access (transmitted) to the body is called its portal of entry. ❖ Mucosal surfaces are the most important portals of entry for microbes; these include the mucous membranes of the respiratory tract, the gastrointestinal tract, and the genitourinary tract. ❖ Microorganisms that are inhaled with droplets of moisture and dust particles gain access to the respiratory tract. The respiratory tract is the most common portal of entry ❖ Microorganisms enter the gastrointestinal tract by ingestion via food, water, and contaminated fingers ❖ Most microorganisms cannot penetrate intact skin, but may enter hair follicles or sweat ducts. Some fungi infect the skin itself.  Portal of Entry ❖ Some microorganisms can gain access to tissues by direct penetration (inoculation) through the skin and mucous membranes in bites, injections, and other wounds. This route of penetration is called the parenteral route ❖ Many organisms can cause infections only when they gain access through their specific portal of entry.  Portals of Exit Just as pathogens have preferred portals of entry, they also have definite portals of exit Three common portals of exit are the respiratory tract via coughing or sneezing, the gastrointestinal tract via saliva or faeces, and the urogenital tract via secretions from the vagina or penis Arthropods and syringes provide a portal of exit for microbes in blood  2. Adherence/Attachment After entering the host, the pathogen adheres/attaches at the portal of entry using adhesins (either proteins or carbohydrates) are found on the surface of certain pathogens and bind to specific receptors (glycoproteins) on host cells. Adhesins are present on the pili and fimbriae and flagella of bacteria, the cilia of protozoa, and the capsids or membranes of viruses. Protozoans can also use hooks and barbs for adhesion; spike proteins on viruses also enhance viral adhesion. The production of slime layers and capsules can also allow certain bacterial pathogens to attach to cells.  Factors that play a role in Adhesion 1. Surface hydrophobicity- the more hydrophobic the bacterial cell surfaces, the greater the adherence to the host cell. Different strains of bacteria within a species may vary widely in their hydrophobic surface properties and ability to adhere to host cells. http://academic.brooklyn.cuny.edu/biology/bio4fv/page/hydropho.htm 2. Net surface charge- bacteria & host cells have net neg. surface charges & thus repulsive electrostatic forces→ Overcome by hydrophobic & other interactive forces 3. Bacterial surface molecules e.g., pili. Bacterial strains that lose their ability to produce pili become avirulent 4. Other specific ligand-receptor mechanisms e.g., S.pyogenes. -Lipoteichoic acid- adherence is mediated by the lipid portion which acts as the ligand. -Fibronectin- host cell receptor molecule. -M protein on fimbriae- antiphagocytic molecule.  Terms used to describe Adherence Factors Adhesin : A surface structure/macromolecule that binds a bacterium to a specific surface. Receptor: A complementary macromolecular binding site on a (eukaryotic) surface that binds specific adhesins or ligands. Lectin: Any protein that binds to a carbohydrate. Ligand: A surface molecule that exhibits specific binding to a receptor molecule on another surface Mucous: The mucopolysaccharide layer of glucosaminoglycans covering animal cell mucosal surfaces. Fimbriae: Filamentous proteins on the surface of bacterial cells that may behave as adhesins for specific adherence. Common pili: Same as fimbriae. Sex pilus: A specialized pilus that binds mating procaryotes together for the purpose of DNA transfer.  Terms used to describe Adherence Factors Type 1 fimbriae: Fimbriae in Enterobacteriaceae which bind specifically to mannose terminated glycoproteins on eukaryotic cell surfaces. Glycocalyx: A layer of exopolysaccharide fibers on the surface of bacterial cells which may be involved in adherence to a surface. Capsule: A detectable layer of polysaccharide (rarely polypeptide) on the surface of a bacterial cell which may mediate specific or nonspecific attachment. Lipopolysaccharide (LPS): A distinct cell wall component of the outer membrane of Gram-negative bacteria with the potential structural diversity to mediate specific adherence. Probably functions as an adhesin. Teichoic acids and lipoteichoic acids (LTA): Cell wall components of Gram-positive bacteria that may be involved in nonspecific or specific adherence  3. Invasion of Host Cells and Tissue After adherence, pathogens invade/penetrate and colonize the host by traversing the epithelium and its basement membrane at the body surface and is mediated by a complex array of molecules, often described as ‘invasins’. Some bacteria invade tissues through the junctions between epithelial cells. Others invade the cells and so enter the tissues. However, invading microbes face the following defences: 1. tissue fluids containing antimicrobial substances (antibody, complement); 2. local macrophages (histiocytes). Subcutaneous and submucosal macrophages are a threat to microbial survival 3. the physical barrier of local tissue structure. Local tissues consist of various cells in a hydrated gel matrix; although viruses can spread by stepwise invasion of cells, invasion is more difficult for bacteria, and those that spread effectively sometimes possess special spreading factors; 4. the lymphatic system which conveys microorganisms to the battery of phagocytic and immunologic defenses awaiting them in the local lymph node  Spreading Factors facilitating invasion "Spreading Factors" is a descriptive term for a family of bacterial enzymes that affect the physical properties of tissue matrices and intercellular spaces, thereby promoting the spread of the pathogen. Hyaluronidase is the original spreading factor → produced by streptococci, staphylococci, and clostridia → attacks the interstitial cement ("ground substance") of connective tissue by depolymerising hyaluronic acid Collagenase is produced by Clostridium histolyticum and Clostridium perfringens → breaks down collagen, the framework of muscles, which facilitates gas gangrene Neuraminidase is produced by intestinal pathogens such as Vibrio cholerae and Shigella dysenteriae → degrades neuraminic acid (also called sialic acid), an intercellular cement of the epithelial cells of the intestinal mucosa  Spreading Factors Streptokinase and Staphylokinase are produced by streptococci and staphylococci, respectively → converts inactive plasminogen to plasmin→ digests fibrin → prevents clotting of blood → relative absence of fibrin in spreading bacterial lesions allows more rapid diffusion of the infectious bacteria Staphylococcal coagulase → cell-associated and diffusible enzyme → converts fibrinogen → fibrin → causes clotting Coagulase activity is almost always associated with pathogenic S. aureus and almost never with non- pathogenic S. epidermidis. I.t.o. virulence, cell bound coagulase could provide an antigenic disguise if it clotted fibrin on the cell surface. Alternatively, staphylococcal lesion encased in fibrin (e.g. a boil or pimple) could make the bacterial cells resistant to phagocytes or tissue bactericides or even drugs (antibiotics) which might be unable to diffuse to their bacterial target.  Maintain Normal Flora?, Soil, reservoir in Water, Food, which it can survive before/ Rodents, etc after infection Leave the body Leave reservoir and return to the → enter the host reservoir and/or (transmission) enter a new host Contact, fomites, droplet, vehicle, airborne, arthropods Portals of entry Multiply perhaps Adhere producing toxins (attach)firmly to or stimulating the host’s body → host reactions colonize it that cause disease Traverse epithelium, basement membrane, junctions, invade cells, spreading factors Hydrophobicity, surface charge, Invade the body pili, fimbriae, Evade the host’s capsules, LPS, in order to enter elaborate cells or deeper LTA defenses tissues 23  Causes of Infectious Disease Quite difficult to show that a specific bacterial species is the cause of a particular disease More than 100 microbes that commonly cause infection → some remaining in the body for many years afterwards Several hundreds cause less common infections In 1884 Robert Koch proposed a series of postulates to link a microorganism to be accepted as the cause of a given 24 disease  Types of Infections A local infection affects a small area of the body. A systemic infection is spread throughout the body via the circulatory system. A secondary infection can occur after the host is weakened from a primary infection. A subclinical (inapparent) infection does not cause any signs of disease in the host. Clinically confirmed but not visible symptoms. A continual source of infection is called a reservoir of infection. People who have a disease or are carriers of pathogenic microorganisms are human reservoirs of infection. Zoonoses are diseases in wild and domestic animals that can be transmitted to humans. 25  Surface Infections Many microorganisms multiply in epithelial cells at site of entry on the body surface. Local spread takes place on fluid-covered mucosal surfaces → large scale movement of fluid spread the infection to distant areas on the surface e.g., in the GIT In the URT high winds (coughing and sneezing) splatters microbes onto new areas or into opening of sinuses in the middle ear Gentler downward trickle of mucus during sleep may spread microbe into the LRT → Large areas of the body surface can be involved within a few days with shedding to the exterior 26  General Characteristics of Surface Infections Short incubation period (length of time between infection with the agents and onset of symptoms of disease) 1 week → Ebola virus, 12-21 days incubation; HIV, several years Microbes replicate more slowly Adaptive immune defenses are key to control - because of longer incubation times, specific defenses can activate and play a role in controlling infection Measles, Typhoid fever 29 30  Factors Which Prevent Surface Infections From Spreading Temperature e.g., Rhinovirus- upper respiratory tract is 33°C, lower respiratory tract is 37°C. Rhinovirus can't replicate at 37ºC e.g., Mycobacterium leprae is also temperature sensitive, which accounts for its replication being more or less limited to nasal mucosa, skin and superficial nerves Site of budding e.g., Influenza and parainfluenza viruses invade surface epithelial cells of the lung, but are liberated by budding from the free (external) surface of the epithelial cell, not from the basal layer from where they could spread to deeper tissues 31 32  Why Risk Spread –especially through Blood and Lymph Many microbes are obliged to spread systemically because they fail to spread and multiply at the site of initial infection e.g., measles and typhoid fever → almost no replication at initial respiratory or intestinal infection → spread systemically and then delivered back to the same surface where they then multiply and shed Other microbes have committed themselves to infection by one route and multiplication and shedding at another E.g., mumps and hepatitis A virus → infect via respiratory and alimentary routes but must spread through body to invade and multiply in the salivary glands and liver It can only get to these distant sites if it spreads through the blood and lymph 33  MIC252: VIROLOGY Dr Tasnim Suliman [email protected] Lec 26: Viral pathogenesis How viruses enter the human body, spread to other organs, and cause disease Lec 27-31: The stages of the virus life cycle in an individual cell Entry Genome replication (DNA and RNA viruses) Gene expression Assembly and release Lec 42: Viruses that cause cancer  Virology Textbook Louten, J. Essential Human Virology, 2016, Elsevier. ISBN: 978-0-12-800947-5 e-book is available FREE via UWC library https://uwc.primo.exlibrisgroup.com/permalink/27UWC_INST/22rg9v/alma993292381703721 Log in with your campus name and password Note: The slides I will provide are not an exact replica of the textbook. There may be information in the textbook that is not in my slides, and there may be information in my slides that is not covered in the textbook. Use the content of the slides as a guide for what you are expected to know, but reading further will never hurt you. 2  MIC252 Lecture 26: Viral Pathogenesis 12 September 2024 Dr Tasnim Suliman [email protected]  Learning Objectives Students should to be able to: Explain how viruses cause disease Explain how viruses enter the human body Describe how viruses spread in the human body List the different modes by which viruses can be transmitted Explain how Koch’s postulates modified when applied to viruses 4 Textbook Reading Essential Human Virology: Chapter 5 5.1: Portals of virus entry 5.2: Dissemination within a host 5.3: Portals of virus exit 5 Quick refresher on viruses Viruses are: Very small (10-400nm) Infectious Obligate intracellular parasites Made of genetic material (RNA or DNA) surrounded by a protein capsid and sometimes a membrane Viruses lack protein synthesis machinery and cannot reproduce on their own. Viruses are NOT cells! Viruses are NOT bacteria! 6 Koch’s Postulates The four criteria designed to establish a causal relationship between a microbe and a disease. 1. The organism must be regularly associated with the disease and its characteristic lesions. 2. The organism must be isolated from the diseased host and grown in culture. 3. The disease must be reproduced when a pure culture of the organism is introduced into a healthy, susceptible host. 4. The same organism must be re-isolated from the experimentally infected host. 7  But these rules don’t work for viruses……. 1. The organism must be regularly associated with the disease and its characteristic lesions. Not all infected individuals show signs of disease. E.g. only 1% of polio infections result in paralysis (i.e. many sub-clinical infections) Infections with different viruses may result in the same disease 2. The organism must be isolated from the diseased host and grown in culture. 3. The disease must be reproduced when a pure culture of the organism is introduced into a healthy, susceptible host. Many viruses cannot be grown in culture And a suitable animal model that mimics human disease may not exist 8  Modified Koch’s Postulates (for the 21st Century) 1. A nucleic acid sequence belonging to a putative pathogen should be present in most cases of an infectious disease. 2. Fewer, or no, copy numbers of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease. 3. With resolution of disease, the copy number of pathogen-associated nucleic acid sequences should decrease or become undetectable. With clinical relapse, the opposite should occur. Fredricks and Relman. Sequence-Based Identification of Microbial Pathogens: a Reconsideration of Koch’s Postulates. Clinical Microbiology Reviews, 1996, 9, 18-33. 9  Viral Pathogenesis VIRAL PATHOGENESIS The process by which viruses cause disease VIRAL DISEASE Disease consists of both the effects of virus replication and the immune response of the host i.e. disease is influenced by both viral and host genes Many virus infections are subclinical or asymptomatic, meaning that the host immune response controls the infection and there is no development of disease Some viruses have mechanisms to block the immune response, resulting in more severe disease. Sometimes it is the immune response that is responsible for the symptoms 10 Cycle of virus infection Entry Shedding Localized PRIMARY SITE infection Local Spread Lymphatic Neuronal Blood (viremia) SECONDARY SITES Shedding Disseminated/Systemic infection 11 Overview 12 Successful virus infection depends on 3 things: 1. Sufficient virus to be able to initiate infection 2. Cells at site of infection must be accessible and be BOTH susceptible (virus is able to enter) and permissive (virus is able to replicate) for the virus 3. Local immune responses must be absent or initially ineffective 13 Viral Entry Common sites of virus entry are: 1. Respiratory tract Mucosal 2. Alimentary tract lining 3. Urogenital tract 4. Outer surface of eye 5. Skin (requires a breach e.g. scratch, needle stick, insect bite) 14  Respiratory tract infection Most common route of virus entry Breathing introduces 6L of air per min! Viruses enter in aerosolized droplets expelled from a cough or sneeze. Large droplets are deposited in the nose; small droplets end up in the alveoli (lungs) Host defenses: Mucus coats the resp. tract & traps virus particles Ciliated cells “sweep” the mucus (and virus) up to throat Macrophages in the alveoli destroy virus particles (eat them!) 15  Viruses infecting the gut: Alimentary tract infection Enteroviruses Reoviruses Noroviruses Common route of virus entry via ingestion of Rotaviruses foods, drinks, hands in mouth etc. Astroviruses Extremely hostile place for viruses - low pH in stomach - high pH in intestine - bile, digestive enzymes (proteases) This restricts the type of virus that can enter the gut Intestinal tract is covered with epithelial cells densely packed with microvilli, coated with mucus = barrier for viruses 16  Viral Spread Virus particles can remain localized at site of entry or spread to other tissues Disseminated infection: spreads beyond primary site of infection Systemic infection: many organs become infected A key determinant of whether a virus remains localized or becomes systemic is directional release of virus from polarized cells Virus released from the apical surface is outside the host. These e.g. lining viruses cause localized infections. of alveoli or intestine Virus released from the basal surface is inside the host. These viruses tend to cause disseminated infections that Polarized epithelial cells may become systemic. 17  Viral Spread through the Blood Viremia: infectious virus particles in the blood Virus can disseminate from a local site by entering the blood via the lymphatic system Virus particles may be free in the blood or carried by infected immune cells e.g. HIV in macrophages and T lymphocytes Primary viremia: when virus first enters the blood. Low viral load Secondary viremia: when virus has disseminated to other organs, replicated, and re-entered the blood. High viral load. 18  Rabies virus Viral Spread through Neurons Some viruses spread from the site of infection by entering nerve endings at initial site of infection e.g. rabies virus, herpesviruses. Neurotropic virus: infects neural cells Neuroinvasive virus: enters the CNS (spinal cord, brain) Neurovirulent virus: causes disease of nervous tissue, neurological symptoms, death Herpes virus 19  Organ invasion Virus in the blood can spread to other organs and re-establish infection in these new tissues. Viruses must cross the blood vessel/tissue barrier. Skin: manifests as rash e.g. measles, varicella/chicken pox Liver: manifests as hepatitis e.g. hepatitis A, B, C viruses Brain: encephalitis e.g. herpes simplex, varicella, measles, Japanese encephalitis virus, rabies Heart muscle: myocarditis e.g. adenovirus, enterovirus (and others) Fetus: congenital viral infections e.g. cytomegalovirus, rubella virus, HIV 20  Virus Tropism Most viruses are restricted to specific cell types (cellular tropism) of certain organs (tissue tropism). Enterotropic virus: replicates in gut Neurotropic virus: replicates in nervous system Hepatotropic virus: replicates in liver Pantropic virus: replicates in many cells and tissues Tropism depends on the presence of receptors for entry (makes cells susceptible to virus) and the requirement of other cellular proteins to support virus replication (makes cells permissive to virus infection). Susceptible and permissive cells must also be accessible to the virus. 21 Virus Transmission Transmission is the process whereby viruses spread between hosts Direct transmission (close contact with infected person) 1. Direct contact (skin-to-skin contact, kissing, sexual intercourse) 2. Droplet spread (large, short-range aerosols e.g. sneeze, cough, talking) Indirect transmission 3. Airborne (small aerosols that remain suspended in air) 4. Vehicle borne (contaminated food, water, blood, cups, needles etc. – inanimate objects) 5. Vector borne (insects, animals e.g. mosquito bite, dog bite) 22 Additional Virology Resources A free podcast about viruses - the kind that make you sick http://www.microbe.tv/twiv/ One episode a week Weekly topics based on what’s hot in the news, or sometimes it’s devoted to Virology 101 (basic virology concepts) – see http://www.virology.ws/virology-101/ Hosted by Prof. Vincent Racaniello from Columbia University Web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. https://viralzone.expasy.org/ Public health World health organization https://www.who.int/ websites Centers for Diseases Control and Prevention https://www.cdc.gov/ (search for virus of interest) 23 National Institute for Communicable Diseases https://www.nicd.ac.za/  MIC252 Lecture 27: The Process of Infection: Attachment, Entry, Replication 13 September 2024 Dr Tasnim Suliman [email protected]  Learning Objectives Students should be able to: Explain the process of virus attachment Describe the different mechanisms of virus entry Explain how DNA viruses replicate their genomes 2  Textbook Reading Essential Human Virology: Chapter 4 4.1. Attachment 4.2. Penetration 4.3. Uncoating 4.4. Replication (DNA only; RNA will be covered in Lec 28-29) Also read chapter 3.4 for a refresher on DNA replication Videos of interest are shown in yellow boxes and links provided. All videos are uploaded to iKamva >MIC 252 S2 2024 > Course resources >Virology >Videos 3 Virus infection of a cell (virus life cycle) 1.Attachment 2.Entry 3.Replication and gene expression 4.Assembly 5.Release All viruses perform these steps but the details differ between virus families VIDEO 1: Flu Attack! How A Virus Invades Your Body https://www.youtube.com/watch?v=Rpj0emEGShQ 4  Virus life cycle overview 1. Attachment - Virus binds to receptors on the surface of the cell via the virus attachment protein. 2. Entry - Viruses enter the cell in two ways: Receptor-mediated fusion at the cell surface and Receptor-mediated endocytosis 3. Replication and gene expression - The virus makes copies of its genome. Virus must produce mRNA from its genome (transcription) in order to generate proteins. Virus must copy its genome (replication) 4. Assembly – virus particles are assembled from newly synthesized proteins and genome copies. 5. Release – released from the cell by lysis (non-enveloped viruses) or budding (enveloped viruses) 5 Getting into the right cell Step 1: Adhere to cell Step 2: Attach to specific receptor on cell surface Step 3: Initiate entry and transfer genome into the cell 6 ATTACHMENT 7 Attachment to target cells Cell surface Virus must bind to receptors on the surface of the cell via the virus attachment protein. Like a key fitting a lock. Viral receptors can be proteins, carbohydrates, and sometimes lipids Viruses can bind up to 3 receptors in succession in order to gain entry 1. Low affinity receptor 2. Primary receptor 3. Secondary or co-receptor 8 Low-affinity receptors Virus particles can bind reversibly to low affinity receptors – also called adhesion receptors or attachment factors. Usually found in high abundance Binding does not normally initiate entry into the cell. Purpose is to concentrate virus particles on the cell surface close to the receptor for entry which is in low abundance. Enhances infectivity. Virus “rolls” on cell surface attaching and detaching until it finds the receptor for entry. 9 Primary and secondary receptors Primary and secondary receptors have high affinity interactions with the virus Binding triggers a conformational change in the virus attachment protein which initiates virus entry Sometimes, viruses need to bind secondary receptors in order to trigger entry Binding to specific receptors often defines the cell and tissue tropism for a virus 1 receptor 2 receptors 4 receptors 10 Steps in HIV attachment to T-cells 1. Non-specific attachment to cell via heparan sulphate 2. Viral Env protein binds to primary receptor, CD4, via gp120 3. Conformational change in Env 4. Binding to the co-receptor, CCR5 or CXCR4 5. Triggers exposure of the gp41 fusion peptide VIDEO 2: HIV LIFE CYCLE https://vimeo.com/260291607 11 ENTRY 12 Virus Entry pathways Viruses enter the cell in two ways: 1) Receptor-mediated fusion at the cell surface 2) Receptor-mediated endocytosis (sometimes followed by fusion) 13 Receptor-mediated Fusion Enveloped viruses Neutral pH Highly dependent on virus first attaching to specific receptor Attachment triggers activation of the viral fusion protein which inserts into the cell membrane Lipid mixing of viral and cell membranes = fusion receptor 14 Receptor-mediated endocytosis Virus attaches to specific Enveloped virus Non-enveloped virus receptor Receptor-mediated signaling triggers formation of a pit, and then a vesicle containing the virus Early Virus is endocytosed into the cell endosome Virus travels on endocytic pathway to early endosomes (neutral pH) and then late endosomes (acidic pH) Enveloped viruses fuse at early or Late endosome late endosome Non-enveloped viruses lyse the endosome and escape 15 VIDEO 3: How Viruses Enters Host Cells https://www.youtube.com/watch? v=xqIxZruKpm0 16  REPLICATION The process where the virus makes copies of its genome This lecture: DNA viruses Next lecture: RNA viruses 17  Basics of Virus Replication Step in the life-cycle at which nucleic acid synthesis occurs 2 processes must occur: 1. Virus must produce mRNA from its genome (transcription) in order to generate proteins 2. Virus must copy its genome (replication) Each virus takes a different approach depending on the nature of their genome 18  DNA viruses dsDNA DdDP = DNA-dependent DNA polymerase DdDP DdRP = DNA-dependent RNA polymerase RT = Reverse transcriptase mRNA DdRP ssDNA DdDP DdDP DdRP mRNA Gapped dsDNA DdDP DdRP RT RT 19  VIDEO 4: DNA synthesis Viral DNA synthesis https://www.youtube.com/watch?v=TNKWgcFPHqw For the most part, viral DNA synthesis is exactly like cellular DNA synthesis Takes place in the nucleus of the cell, with the exception of poxviruses which replicate in the cytoplasm Requires at least one viral protein, sometimes many. Host provides all other proteins. DNA synthesis occurs in 5’-to-3’ direction Initiates at an origin and requires a primer 20 Getting started… AT-rich regions of the genome serve as origins of replication and are recognized by viral origin binding proteins. They often recruit additional proteins. DNA strands are separated by the helicase protein. Primers complementary to the template are synthesized by a primase protein DNA polymerase is recruited and extends the 3’ end of the primer 21 Mechanisms of viral DNA synthesis 1. REPLICATION FORK (as in cellular DNA synthesis) RNA primer Leading strand: 5’-to-3’ synthesis is continuous Lagging strand: 5’-to-3’ synthesis is discontinuous - generation of Okazaki fragments - joined by DNA ligase 22  2. STRAND DISPLACEMENT Viral endonuclease nicks the template Hairpin on end of genome DNA synthesis Extensive complementarity Does NOT use an RNA primer Self-primes with DNA hairpin or protein Continuous synthesis Only 1 strand copied at once Blue = template Red/pink = new synthesis 23 3. ROLLING CIRCLE Viral endonuclease nicks the DNA DNA pol extends from 3’ end of nicked DNA. Continuous DNA synthesis and strand displacement. Displaced strand serves as template for e.g. Papillomavirus discontinuous DNA synthesis (RNA primer, Okazaki fragments) Concatemers are formed containing multiple copies of the genome that are then cleaved into linear genomes 24 An unusual virus: dsDNA virus with RNA intermediate Hepadnaviruses e.g. hepatitis B virus DdRP Circular, semi- mRNA dsDNA genome DdDP RT RT DdRP Host DNA-dep DNA pol fills in the gaps in the dsDNA genome (in the nucleus). dsDNA serves as template for production of mRNAs, and then viral proteins. Viral RNA-dep DNA pol (=reverse transcriptase) binds to the pre-genome mRNA transcript and is packaged into a nucleocapsid Inside the nucleocapsid, viral RT copies (+)ssRNA into (-)ssDNA and then partially fills it in to form the gapped dsDNA genome. 25  MIC252 Lectures 28/29: Replication of viruses with an RNA genome 16 September 2024 Dr Tasnim Suliman [email protected]  Learning Objectives Students should be able to: Explain how viruses with RNA genomes replicate Compare the different strategies of RNA synthesis Identify the unique features of retroviruses 2 Textbook Reading Essential Human Virology: Chapter 4 4.4. Replication (RNA viruses) 3  Reminder about nucleic acid polarity mRNA is defined as positive sense. RNA strands that are complementary to mRNA are negative sense Positive sense RNA Negative sense RNA 5’ 3’ 5’ VIDEO 1: What We 3’ Mean By Positive & Negative RNA Viruses https://www.youtube.c om/watch?v=lQtJdiOU Negative sense RNA Positive sense RNA v0I intermediate intermediate 3’ 5’ 5’ 3’ Positive sense RNA Negative sense RNA 5’ 3’ 3’ 5’ 4  Viral RNA replication (+) ssRNA (-) ssRNA dsRNA ssRNA with DNA intermediate 5  Viral RNA replication mRNA (+)ssRNA RdRP RdRP RdRP = RNA-dependent RNA polymerase 6  (+)ssRNA Virus Replication After virus entry into the cell, the (+)ssRNA genome can act as mRNA and be directly translated into proteins including RdRP RdRP can then be used for replication and transcription The virus-encoded RdRP copies the (+)ssRNA genome into a (-)ssRNA intermediate More mRNA is transcribed complimentary to the new (-)ssRNA strands by RdRP mRNA is translated into proteins for replication and virus assembly 7  Viral RNA replication RdRP (-)ssRNA mRNA RdRP RdRP Example: Influenza virus VIDEO 2: Influenza virus replication Cycle Animation RdRP = RNA-dependent https://www.youtube.com/watch?v=tB5FQZi4HKY RNA polymerase VIDEO 3: Influenza A and B Infection and Replication https://www.youtube.com/watch?v=-CRduDChuv8 8  (-)ssRNA Virus Replication After virus entry into the cell, the (-)ssRNA is transcribed into mRNA and a (+)ssRNA intermediate by viral RdRP The mRNA is then translated into various proteins including viral RdRP, and non-structural and structural viral proteins. The (+)ssRNA acts as a template for the production of complimentary (-)ssRNA by RdRP Subsequenly…Newly synthesized viral proteins and (-)ssRNA are used for virion assembly 9  Viral RNA replication Reoviridae, Picobirnaviridae RdRP dsRNA mRNA RdRP VIDEO 4:RNA synthesis from dsRNA genomes RdRP = RNA-dependent https://www.youtube.com/watch RNA polymerase ?v=NKGy3xuEKQM 10  dsRNA Virus Replication After virus entry into the cell, the dsRNA strands separate into (+) and (-) ssRNA The (-)ssRNA is transcribed into mRNA by viral RdRP The mRNA is then translated into various proteins including viral RdRP, and non-structural and structural viral proteins. The (+)ssRNA transcribes complimentary (-)ssRNA by RdRP resulting in dsRNA Virion assembly takes place using the newly synthesized viral proteins and dsRNA 11  Viral RNA replication DdRP ssRNA mRNA with DNA RT RT intermediate DdRP Example: HIV DdRP = DNA-dependent RNA VIDEO 5: HIV Life Cycle polymerase https://www.youtube.com/watch?v=PlSvywlLuNw RT = Reverse transcriptase 12  ssRNA with DNA intermediate - Virus Replication After virus entry into the cell, the (+)ssRNA genome is converted to (–) DNA by reverse transcriptase A complimentary (+) DNA strand is synthesized by reverse transcriptase, resulting in dsDNA The dsDNA intermediate is transcribed into mRNA by DdRp for protein synthesis The dsDNA intermediate is transcribed into +RNA for incorporation into the virion 13  Key points about RNA virus replication Cells do not have an RNA-dependent RNA polymerase so this must be provided by the virus No protein can be made until mRNA is produced, so RNA viruses must bring the RNA pol into the cell i.e. it must be packaged in the virion. - the exception is (+)ssRNA viruses because the genome can act like mRNA, so virus can make RNA pol protein directly. 14 Genome RNA-dep RNA Infectivity of RNA Initial event in the polymerase in the cell virion (+)ssRNA NO INFECTIOUS TRANSLATION (-)ssRNA YES NON-INFECTIOUS TRANSCRIPTION dsRNA YES NON-INFECTIOUS TRANSCRIPTION 15  Positive sense ssRNA viruses Polyprotein is cleaved by viral and host Example: Flavivirus translation proteases into individual viral proteins (+) strand RNA genome (+) 5’ 3’ (-) strand synthesis NS5=RNA-dep RNA Pol (+) 5’ 3’ dsRNA intermediate (-) 3’ 5’ (+) strand synthesis (+) 5’ (strand displacement) recycle (+) 5’ 3’ (-) 3’ 5’ (+) 5’ 3’ (+) strand RNA (-) 3’ 5’ + (+) 5’ 3’ 5’RNA capping/methylation by NS3 & NS5 (+) 5’ 3’ (+) strand RNA genome 16 Negative sense ssRNA viruses (transcription) Example: Paramyxovirus (Measles virus) Gene Expression Transcription Primary transcription