Emerging and Reemerging Infectious Diseases Lecture Notes PDF

MICROBIOLOGY | TRANS 6 LE Emerging and Reemerging Infectious...

MICROBIOLOGY | TRANS 6 LE Emerging and Reemerging Infectious 02 Diseases DR. ABIGAIL C. RIVERA | Lecture Date (07/10/2024) | Version 1 OUTLINE I. INTRODUCTION I. Introduction V. All about Monkeypox A. EMERGING DISEASES A. Emerging diseases A. Monkeypox virus Appeared and affected a population for the first time OR B. Re-emerging diseases B. Epidemiology: MPox Has existed previously but is rapidly increasing in terms C. Contributing factors C. Clades of Monkeypox of number of new cases II. Vaccine-Preventable D. Reasons for emergence Note: Kindly refer to the appendix for a full table of examples of Diseases of Monkeypox diseases when they were considered emerging. A. The Impact of Vaccination E. Modes of Transmission of in the 20th and 21st Monkeypox Table 1. Some examples of diseases when they were Century F. Progression of considered emerging B. Measles Monkeypox Infectious Year C. Polio G.Findings in the 2022 Disease D. Diphtheria Outbreak Agent Recognized E. Pertussis H. Diagnostic Tests SARS 2003 Severe acute respiratory III. Emerging and/or Zoonotic I. Treatment for Monkeypox Coronavirus syndrome Viral disease J. Prevention of Monkeypox Influenza A 2009 Pandemic Influenza A. Avian Influenza K. Vaccination against (H1N1) B. Pandemic Influenza Monkeypox MERSCoV 2012 Middle Eastern C. Arboviruses/Vector-borne L. Summary diseases D. Coronaviruses respiratory syndrome IV. Henipavirus and Ebola IV. Novel Human Coronavirus coronavirus A. Henipavirus A. Human Coronaviruses Influenza A 2013 Avian Influenza B. Ebola virus disease Serotypes (H7N9) B. SARS-CoV SARS CoV-2 2019 COVID-19 C. MERS-CoV D. COVID-19 B. RE-EMERGING DISEASES VII. Review Questions Have affected a given area in the past , declined or were VIII. References controlled, but are again being reported in increasing Must Lecturer Book Previous Youtube numbers ❗️ Know 💬 📖 📋 Trans 🔺 Video Table 2. Examples of re-emerging infectious diseases Infectious SUMMARY OF ABBREVIATIONS Disease Contributing Factors Agent HCoV Human Coronavirus Cryptosporidiosis Cryptosporidium inadequate control in SARS- Severe Acute Respiratory Syndrome parvum water supply; CoV Coronavirus (protozoa) international travel; MERS- Middle East Respiratory Syndrome Coronavirus increased use of CoV child-care facilities VOC Variant of Concern Diphtheria Corynebacterium interruption of VOI Variant of Interest diphtheria immunization VUM Variant Under Monitoring (bacterium) program due to LEARNING OBJECTIVES political changes ✔ To describe the factors that contribute to the emergence Malaria Plasmodium drug resistance; and re-emergence of infectious diseases. species favorable conditions ✔ To describe the emerging and re-emerging diseases (protozoon) for mosquito vector seen globally and nationally Meningitis, Group A uncertain → Definition Necrotizing Streptococcus → Geographical Distribution fasciitis (bacterium) → Characteristics (flesh-eating → Transmission disease), Toxic → Risk Factors Shock Syndrome, ✔ To relate preventive measures to the emerging and and others re-emerging diseases Pertussis Bordetella refusal to vaccinate Part V. All about MPOX (Whooping pertussis based on fears the ✔ To present the history and emergence of Mpox cough) (bacterium) vaccine is not safe; ✔ To discuss its epidemiology other possible factors: ✔ To differentiate the clinical features of outbreak Mpox decreased vaccine cases from endemic cases efficacy or waning ✔ To select appropriate diagnostic tools immunity among ✔ To enumerate treatment and preventive strategies vaccinated adults LE 2 TG 17 | A. Togon, J. Tolentino, V. Tolentino, TE | J. Rivera, Serrano, R. AVPAA | E. Perez PAGE 1 of 17 TRANS 7 D. Torregoza, Y. Trinos, E. Triste VPAA | D. Patajo MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera Rabies Rhabdovirus breakdown in public With their remarkable adaptability, emerging infections can group (virus) health measures; spread quickly and gain strongholds to become endemic changes in land use; diseases travel → Most profoundly demonstrated by the decades-long Rubeola Morbillivirus failure to vaccinate; pandemic of human immunodeficiency virus (HIV) (Measles) genus (virus) failure to receive infection and acquired immunodeficiency syndrome second dose of (AIDS). vaccine Several genetic factors have been shown to influence Schistosomiasis Schistosoma dam construction; infectious disease susceptibility and disease progression. species ecological changes Table 3. Genetic factors and their disease influence (helminth) favoring snail host Genetic Factor Disease Influence Tuberculosis Mycobacterium antibiotic-resistant Alleles of the chemokine Partial protection against tuberculosis pathogens; receptor gene CCR5 acquisition of HIV and (bacterium) immunocompromised development of acquired populations immunodeficiency syndrome (malnourished, Globin gene alleles (e.g. Partial protection against HIV-infected, sickle globin and ɑ- and malaria poverty-stricken) β- thalassemias) Yellow Fever Flavivirus group insecticide resistance; Lack of the Duffy blood Complete protection against (virus) urbanization; civil group on red cells (due Plasmodium vivax malaria strife to a mutation in a Source: National Institute of Health (US) 2007. chemokine receptor Many emerging and re-emerging diseases are zoonotic in gene) origin Blood group O Increased susceptibility to → Approximately 60% of all human infectious diseases severe cholera recognized so far, and HLA alleles May influence susceptibility to → About 75% of emerging infectious diseases that have infection or course of disease affected people over the past three decades, have with: originated from animals HIV C. CONTRIBUTING FACTORS hepatitis B virus, measles, Many factors precipitate the emergence of new diseases, hantavirus as they enable infectious agents: pulmonary syndrome → To evolve into new ecological niches, malaria, → To reach and adapt to new hosts tuberculosis → To spread more easily among the new hosts human papillomavirus HUMAN BEHAVIOR infection Technology and industry coccidioidomycosis Internal travel and commerce Source: Mandell, Douglas, and Bennett’s Principles and Practice of Breakdown of public health measures Infectious Diseases 8th Ed. Poverty and social inequality II. VACCINE-PREVENTABLE DISEASES War and famine, Intent to harm A. THE IMPACT OF VACCINATION IN THE 20TH & 21ST Lack of political will CENTURY Exploding population numbers Vaccines have contributed to the decline of infectious Widespread movement of people, animals, and goods, diseases exploding population numbers, centralized food → Smallpox: eradicated in 1980 production, and other contributing factors → In the US, 100% decrease in polio and diphtheria due to → Have given microbes rapid and easy access to new the advent of vaccines populations and geographic areas and → Spawned a host of emerging and re-emerging infectious diseases PHYSICAL AND ENVIRONMENTAL FACTORS Economic development and land use Urban development and environmental degradation also provide microbes access to new populations and geographic locations. ECOLOGIC Changing ecosystems Climate change GENETIC/BIOLOGIC Figure 1. The Impact of Vaccination in the 20th & 21st Microbial adaptation and change Centuries [Lecturer’s PPT] Human susceptibility to infection MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 2 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera IMPORTANCE OF HERD IMMUNITY sharp rise from 2013 - 2014 (67,000+ cases) SPREAD OF MEASLES IN THE PHILIPPINES HERD IMMUNITY 2017: Outbreaks in some regions of the country Protection of a whole population by vaccinating a certain 2018: Cases continue to increase; outbreaks in NCR percentage of the population (Taguig City) → If only SOME get vaccinated, the virus spreads January 1 to August 2019: 41, 024 cases → 196% higher ▪ Immunize just a few people → If MOST get vaccinated, spreading is contained REASONS FOR NON-VACCINATION FOR MEASLES ▪ If a huge number of population are immunized, they In order of most to least to common reason: will protect the non-immune of susceptible population → Not eligible for vaccination (~30%) ▪ Take note: You don't have to immunize 100% of the → Mother was busy (~20-25%) population. → Child was sick (~10-15%) HERD IMMUNITY THRESHOLD → Forgot the schedule (~10%) How much of the population should get vaccinated to → Fear of side effects (~10%) achieve herd protection → Difficult access to health services (1% divergent surveillance sample in Manila → Type 2: >0.6% divergent, most common → Aug 9, 2019: Another report of VDPV1 Circulating VDPV (cVDPV) → Aug 19-31, 2019: DOH implements Round 1 → Demonstrated person-to-person transmission in the → Synchronized Polio Vaccination (SPV) in Manila community based on human and/or environmental → Sep 3, 2019: Another report of VDPV1 and VDPV2 in detection. Manila → Since 2000: → Sep 9, 2019: VDPV2 from Davao reported ❗️ ▪ Type 1: causes 13% of cVDPV → Sep 14, 2019: cVDPV2 acute flaccid paralysis (AFP) Type 2: causes 86% of cVDPV case from Lanao del Sur − Removed from trivalent OPV, but in 2015, it was → Sep 19, 2019: DOH declared National Polio Outbreak switched to bivalent OPV leaving out the type 2 → Sep 2019 to Oct 14, 2020: total of 28 polio cases strain which causes 86% cVDPV → June 11, 2021: The outbreak was declared over ▪ Type 3: causes 1% of cVDPV WORLDWIDE PROGRESS 1988: 350,000 cases in 125 countries Went down by more than 99% after vaccine introduction → But not been eradicated all over the world 2020: 140 cases in 2 countries (Pakistan & Afghanistan which still remained to be endemic for polio) Figure 7. Polio in the Philippines [Lecturer’s PPT] Government response: → Enhanced surveillance and lab testing for Acute Flaccid Figure 5. Only 2 countries considered endemic for wild type Paralysis polio[Lecturer’s PPT] ▪ AFP Case Surveillance: POLIO TIMELINE − Stool sample obtained from AFP case and sent to 1700s: Evidence of sporadic epidemics of polio predates Research Institute for Tropical Medicine for testing history → Supplementary immunization activity 1988: World Health Assembly resolves to eradicate polio → Monitoring and contact tracing by 2000 → Risk communication and awareness campaigns by 2000: Philippines certified polio-free with the last case DOH reported in 1993 D. DIPHTHERIA 2001: 3 cases of CDPV were detected in the country CASES IN THE PHILIPPINES (1980-2017) Feb to Mar 2002: supplemental immunization activity Balik Vaccine introduction led to a dramatic decline in cases Patak program (OPV-NID) was implemented More recent upsurgence of cases after seeing almost a 2013: Afghanistan, Nigeria & Pakistan remain endemic close to 0 cases 2014: Pakistan, Cameroon Syrian Arab Republic pose greatest risk of further wild poliovirus exportations Figure 8. Diphtheria Cases in the Philippines 1980-2017[2026 Trans] Figure 6. Polio TImeline [Lecturer’s PPT] MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 4 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera E. PERTUSSIS CASES IN THE PHILIPPINES (1980-2017) Vaccine introduction through the National Immunization Program or Expanded Program on Immunization led to a dramatic decline in pertussis cases After seeing almost 0 cases per year, steady increase in cases since 2016 Figure 11. Areas in PH that have declared pertussis outbreak[Lecturer’s PPT] Areas that have declared a pertussis outbreak as of March 26, 2024: → Quezon City → Iloilo City → Cavite province Figure 9. Pertussis Cases in the Philippines [2026 Trans]] Table 4. Factors contributing to re-emergence of VPDs[PPT] FACTORS CONTRIBUTING TO THE PERTUSSIS Factor Selected Examples RESURGENCE WORLDWIDE Better diagnostic tools Failure to Missed opportunities (clinician, → Enhanced awareness of disease vaccinate by financial, system constraints) → Improved surveillance health care Weak or interrupted immunization → Use of more sensitive diagnostic tools (PCR) system services Epidemiology → Evolution of circulating strains Patient or Personal or religious beliefs ▪ ex: Certain mutations or proteins may render parental refusal or Vaccine hesitancy vaccines non immunogenic deferral Vaccines characteristics Vaccine failure Waning of immunity after acellular → Waning immunity and waning of pertussis vaccination ▪ Acellular pertussis vaccine have replaced cellular immunity pertussis vaccines because they cause reactogenicity Pathogen Serotype replacement including ▪ Resurgence of cases have been reported in relation “escape” from capsular switching in Streptococcus to acellular pertussis vaccine vaccine-induced pneumoniae which may render the ▪ 2-3yrs after acellular pertussis vaccine, antibody immunity vaccine non-immunogenic in certain titers waning strains PERTUSSIS CASES IN THE PHILIPPINES 2019-2024 In March of 2024, a pertussis outbreak was declared in III. EMERGING AND/OR ZOONOTIC VIRAL DISEASES some cities following increases in the number of cases. A. AVIAN INFLUENZA “Fowl plague” or “Bird Flu” → These viruses primarily infect poultry or bird species. 💬 Infectious viral disease of birds caused by Influenza subtype A ( primary cause) → Recall: It is primarily subtype A that causes pandemics and undergoes genetic reassortment because of its wide variety of hosts. Occasionally transmitted to humans through direct or indirect contact with poultry “Highly pathogenic” = Avian Influenza viruses with certain Figure 10. Reported Cases and Deaths in the Philippines, genetic traits that produce lethal disease outbreaks in 2019-2024 [Lecturer’s PPT] poultry By April 16, the areas which reported increasing number Currently, novel Influenza A virus associated with severe of cases has increased disease in humans include: 77% 75 years old: 21% of cases of H7n9 of this 1996 Goose/Guangdong lineage ▪ Males: 71% of recognized cases 2003-2004: Re-emerged and spread to Europe and Africa Unclear if epidemiologic features result from: Endemic in poultry in Bangladesh, China, Egypt, India, → Difference in exposure to the virus source Indonesia, & Vietnam → Differences in population immunity, clinical presentation, illness severity → Surveillance artifact 2013 - 2017: a total of 1,476 human cases and majority of these cases came from China Figure 12. Epidemic curve of human cases of A(H1N1) by illness onset date[Lecturer’s PPT] From 2003 to 2017:859 human cases reported from 16 countries → Majority from 3 countries: Indonesia, Egypt, Vietnam Figure 13. Trend of H7N9[Lecturer’s PPT] → This may reflect distribution of the virus in poultry PREVENTION AND CONTROL OF A(H5N1) INFECTION reservoirs, local agricultural practices, intensity of Avoid contact with sick or dying birds surveillance, and other unknown factors Wash hands with soap and water after contact with sick or In the 2015 outbreak, most cases came from Egypt dying birds or with contaminated objects (soil, cages, and CONTRIBUTING FACTORS TO A(H5N1) INFECTION eggs) SPREAD Use personal protective equipment when handling birds or Bird migration carcasses International trade in poultry and poultry products Seek medical advice if exposed to birds suspected of Illegal bird transport being infected Avoid buying live chicken for home slaughter AH5N1 FEATURES Cook poultry (including eggs) thoroughly before eating Case fatality rate = ~59% → High case fatality rate is unusual for an influenza virus 2017 PHILIPPINE A(H5N6) Mainly affects children and young adults (3 months to 81 First avian influenza outbreak recorded in the years) Philippines Limited person-to-person transmissibility April to September 2017: Outbreak of H5N6 avian Severity of illness, high mortality, and limiter person-to influenza person transmissibility may be explained by the higher Affected 2 provinces in Central Luzon: Pampanga & Nueva tropism of H5N1 to receptors in the lower but not upper Ecija respiratory tract → limiting its spread 37,000 birds died from H5N6; 600,000 birds were culled No recorded human case or death due to H5N6 Outbreak was officially declared over in September 2017 MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 6 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera B. PANDEMIC INFLUENZA RESPONSE TOWARDS A/H1N1 INFECTIONS PANDEMIC INFLUENZA (H1N1) Non-pharmaceutical interventions 2009 → School closure Novel virus referred to as Pandemic H1N1 (A/H1N1) → Infection prevention control measures applied in the → from the subtype A influenza virus hospital setting → Contains: Monovalent vaccine (H1N1 strain) ▪ 6 segments from viruses known to be circulating in → High risk priority groups were given the vaccine which North American swine since 1998 helped end the pandemic ▪ 2 segments of a Eurasian avian-like swine virus Neuraminidase inhibitors (NIs) → Viruses in the North American lineage that donated the → Oseltamivir: widely used segments found in P/H1N1 were themselves triple → Studies show that the earlier the NIs are given within reassortants containing genetic material derived from 48-72 hours, patient outcomes were improved avian, human and classic swine viruses. → Annual flu vaccine prevents these pandemics from reoccurring C. ARBOVIRUSES/VECTOR-BORNE DISEASES Note: For Part 3, Dr. Rivera did not provide any asynchronous materials and said to kindly refer to her previous Arboviruses lecture (RNA III). IV. HENIPAVIRUS AND EBOLA A. HENIPAVIRUS Family: Paramyxoviridae (enveloped, ssRNA virus) A zoonotic virus: infects pigs, dogs, cats, horses; humans may be infected after exposure to the sick animals Main reservoir host: Pteropus bat (fruit bat) found in tropical and subtropical countries Cause a wide range of illnesses from asymptomatic infection to acute respiratory illness and fatal encephalitis 6 Species: (1) Hendra, (2) Nipah, (3) Langya, (4) Mojiang, (5) Cedar, and (6) Ghanaian → Hendra, and Nipah: Highly virulent; known to cause outbreaks in humans → Langya: identified in August 2022, among febrile Figure 14. A/H1N1 Virus[Lecturer’s PPT] human cases in eastern China April 2009: ▪ Most closely related to Mojiang virus → Two epidemiologically unlinked children living near the → Mojiang, Cedar, and Ghanaian: not known to cause Mexican border in California were determined to have disease respiratory illness caused by a novel form of HISTORICAL ASPECTS AND GEOGRAPHICAL Influenza A DISTRIBUTION Within 3 weeks of its detection in the United States First recognized in 1999 during an outbreak among pig → >600 additional illnesses including clusters had been farmers in Sungai Nipah in Malaysia wherein they recognized in 41 states developed encephalitis → The virus was also quickly detected on other continents → Most human infections resulted from direct contact with June 11, 2009: sick pigs or their contaminated tissues → WHO declared influenza pandemic due to P/H1N1 Since then, yearly outbreaks occurs in South Asia After a year (Bangladesh, India, Malaysia, and Singapore) causing → The pandemic was declared over severe disease and death, making it an emerging disease → Total of 214 countries, including the Philippines had of serious public health concern reported cases of P/H1N1 Since 1994, Hendra virus has been reported annually in A/H1N1 FEATURES the Eastern states of Australia. Mostly affected children and young adults In 1999, Nipah virus outbreaks in humans were reported in Hospitalization rate: 0.45% Malaysia and Singapore; reported almost annually in Case fatality rate: 0.02% (low) Bangladesh and India 87% of deaths occurred in < 65 age group Pteropid bats can be found throughout tropical and → (Note: Dr. Rivera mentioned in the lecture video that subtropical countries, however they have been isolated “87% of deaths occurred in the elderly age group”) also from animals in East Africa, Central and South → Rₒ: 1.3 to 1.7 (as high as 3.3 in school setting) America, Asia, and Oceania. → Rₒ is the number of secondary cases from one primary As of 2022, researchers identified a total of 35 non-fatal case human cases in China. Most common severe complication: The latest Nipah virus outbreak in India was in September → Viral pneumonitis 12 - 15, 2023, when the ministry health and family welfare → Secondary bacterial pneumonia of India reported 6 laboratory confirmed cases including 2 Continues to circulate worldwide, even after the pandemic deaths was declared to be over MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 7 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera → Other 5 cases were family and hospital contacts of the → This can be followed by dizziness, drowsiness, altered first case emphasizing the possibility of consciousness, and neurological symptoms that human-to-human transmission indicate acute encephalitis Atypical pneumonia and acute respiratory distress Case fatality rate: 40-75% OUTBREAK OF HENIPAVIRUS INFECTION Figure 17. Outbreak of Henipavirus Infection, Philippines, 2014[Lecturer’s Video] In 2014, there was a Henipavirus outbreak in the Philippines in Sultan Kudarat Figure 15. Geographical Distribution of Nipah virus[Lecturer’s → During this outbreak, there were 17 patients who were Video]] infected and laboratory confirmed ▪ 11 with acute encephalitis TRANSMISSION OF HENIPAVIRUS − 9 patients died (82% case fatality rate) ▪ 5 with influenza-like illness ▪ 1 with meningitis → Adults aged 21-60 → Median incubation period: 8 days Most common route: direct exposure to infected horses, contact with contaminated body fluids during slaughtering of sick horses, consumption of undercooked horse meat → Although the source of horse infection is unclear, the most likely source is fruit bats → Bats belonging to this family were reported near at least 1 of 2 villages Human-to-human transmission also documented (5 cases) PREVENTION AND CONTROL OF HENIPAVIRUS Figure 16. Transmission of Henipavirus[Lecturer’s Video]] INFECTION Main reservoir: Fruit bats of genus Pteropus or flying For local farmers, reduce bat access to date palm sap and foxes other fresh food products → Infected bats shed the virus in their secretions, such as Wear proper protective gear when handling sick animals or saliva, urine, semen, and excreta, but are symptomless their tissues, and during slaughtering carriers Travelers should avoid contact with bats, sick horses and Nipah virus is known to infect pigs, dogs, cats, horses, pigs, and their excretions and humans when they consume contaminated food or Do not consume fallen fruit, raw date palm sap, or drink that have been infected by bat secretions products made from raw sap Humans may then proceed to transmit this to other If for consumption, freshly collected date palm juice should humans through contact with infected secretions, be boiled, and fruits should be thoroughly washed excretions, blood or tissue Follow standard precautions in healthcare settings, as well The disease is highly contagious among pigs, who act as as, contact and droplet precautions intermediate and possibly amplifying host of the virus Hendra virus vaccine for horses (licensed in Australia) → Has potential future benefits to prevent henipavirus RISK FACTORS FOR HENIPAVIRUS TRANSMISSION infections in humans Drinking raw date palm sap → No licensed vaccines for humans → Fruit bats mainly feed on date palm sap Healthcare setting: contact with secretions, excretions, blood or tissue of infected patients Close contact with infected pigs or other animals CLINICAL MANIFESTATION OF HENIPAVIRUS INFECTION Incubation period: 4-21 days Space intentionally left blank Clinical spectrum: asymptomatic infection to fatal encephalitis → Infected people initially develop flu-like symptoms of fever, headache, myalgia, vomiting, and sore throat MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 8 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera B. EBOLA VIRUS DISEASE (EVD) TRANSMISSION OF EBOLA Aka “Ebola Hemorrhagic Fever” caused by Ebola virus Natural Host: Fruit bats of Pteropodidae family Family: Filoviridae Virus circulates and is maintained in an enzootic cycle with A severe, often fatal illness bat populations Case fatality rate: up to 90% Non human primates such as chimpanzees, antelopes, 5 distinct species and gorillas get infected after direct contact with bats and → Bundibugyo their secretions (these are accidental hosts) → Zaire → Primates are main source of infection to human beings → Sudan Introduced to the human population through close contact → Reston with the blood, secretions, organs, and bodily fluids of → Tai Forest these infected animals. In Africa, infection has been documented through the HISTORY OF EBOLA VIRUS handling of chimpanzees, gorillas, fruit bats, monkeys, Table 5. Ebola Virus History antelopes, and porcupines which were infected or found Date Event dead in the rainforest. 1976 Ebola-Zaire and Ebola-Sudan The virus spreads in the community through human to First 2 species that were discovered in 2 human transmission with infections resulting from direct simultaneous outbreaks in Sudan (Nzara) contact with blood, secretions, organs, or other bodily and Democratic Republic of Congo fluids of other infected people and indirect contact with (Yambuku) contaminated environments. Has NOT been reported in humans in the Asia-Pacific region as of July 31, 2012 CLINICAL MANIFESTATIONS OF EBOLA → However, with global travel. it is possible Incubation Period: 2-21 days that outbreaks in Africa could result in the People are infectious for as long as their blood and spread of the virus to Asia secretions contain the virus. 1989 Ebola-Reston Severe illness often characterized by the sudden onset of 1989: First identified in laboratories in fever, intense weakness, muscle pain, headache, and sore Reston, Virginia throat. Followed by vomiting, diarrhea, rash, impaired → Discovered after macaque monkeys from kidney and liver function. the Philippines became severely ill and In some cases, both internal and external bleeding occurs, died hence the term Ebola Hemorrhagic Fever. 2008: Identified in pigs on 2 farms in the Laboratory Findings: Philippines → Low WBC count → Virus identified in pigs were very similar to → Low Platelet Count the virus found in monkeys imported to → Elevated Liver Enzymes the USA for research PREVENTION AND CONTROL OF EBOLA INFECTION 2009: 6 workers tested positive for No vaccines to date for humans or animals. Raising Ebola-Reston virus antibodies after contact awareness and using protective measures are the only with sick pigs in the Philippines but without way to reduce human infection and death. the disease and had no significant Use protective clothing when handling suspected animals symptoms Use appropriate personal protective equipment when *Reston Ebola virus is NOT as great a taking care of ill patients threat as other Ebola viruses that are known Apply standard precautions consistently with all patients, to be highly pathogenic for humans regardless of diagnosis → Still of public health concern in the → It is not always possible to identify patients with Ebola Asia-Pacific region because although very early on because symptoms are nonspecific. rare, it is a newly emerging disease in → Includes basic hygiene, respiratory hygiene, the use of animals and humans personal protective equipment, and safe injection 1994 Ebola-Ivory Coast (Tai Forest) practices Isolated when a scientist became ill after Adequate training for laboratory stuff handling cases conducting an autopsy in a chimpanzee. dealing with suspected humans and animals. 2007 Ebola-Bundibugyo → Processed in suitably equipped laboratories Isolated during an outbreak in Uganda. GEOGRAPHICAL DISTRIBUTION OF EBOLA VIRUS Outbreaks occur primarily in Central and West Africa, near tropical rainforests → Congo, Sudan, Uganda → *Bundibugyo, Zaire, and Sudan Ebolavirus have been associated with large EVD outbreaks Since 2008, Reston Ebola Virus has been detected in Space intentionally left blank several outbreaks in pigs in China and in the Philippines → No human illness or deaths reported MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 9 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera V. ALL ABOUT MONKEYPOX A. MONKEYPOX VIRUS Figure 19. Confirmed human monkeypox cases world wide (1970-2021) [WHO] OUTBREAK KEY EPIDEMIOLOGICAL FINDINGS (WHO EXTERNAL SITUATION REPORT AS OF 20 OCT Figure 18. Monkeypox Virus[Lecturer’s PPT] 2023) Predominantly male (96.3%), Table 6. Features of Monkepox Virus → median age 34 (interquartile range 29- 41 years) Characteristics DNA Virus Most cases among men who have sex with men (87.3%) Enveloped, double-stranded DNA Transmission through skin and mucosal contact during Family Poxviridae sexual activities was most commonly reported (82.5%) Subfamily Chordopoxvirinae Exposure setting: party setting with sexual contact (63.7%) Genus Orthopoxvirus Most common symptoms: → Variola virus (Smallpox) → Any rash (90.3%) → Monkeypox virus → Fever (58.2%) → Vaccinia virus → Systemic rash (56%) → Cowpox virus → Genital rash (50.6%) Disease Causes Monkeypox/Mpox High prevalence of HIV infection (52.7%) caused → previously known as Monkeypox C. CLADES OF MONKEYPOX B. EPIDEMIOLOGY: MPOX 2 clades Table 7. Monkeypox Epidemiology → Clade I (Subclades Ia and Ib) Date Event → Clade II (Subclades IIa and IIb) 1958 First isolated among monkeys in State Table 8. Sample Table Serum Inst, Copenhagen, Denmark Clade 1 Clade Ia: growing outbreaks affecting the 1970 First human case Democratic Republic of Congo and other 9- month old boy in the Democratic countries in Africa Republic of Congo Clade Ib: growing outbreaks affecting the 1970-1979 55 cases recorded in Western & Central Democratic Republic of Congo and other Africa countries in Africa 1980 Smallpox declared eradicated August 2024: has been detected 1982 Smallpox vaccination officially ceased in beyond Africa DRC Clade 2 Clade IIa 2003 First outbreak outside of Africa Clade IIb: responsible for 2022 outbreak 70 patients in the US 1970 -2021 Mpox was endemic in Western And Central D. REASONS FOR EMERGENCE OF MONKEYPOX African regions Deforestation, climate change, hunting, and population 2018-2021 Only 4 countries outside Africa reported movement cases (Israel, UK, Singapore, and the US) Waning immunity → Smallpox vaccine 85% protective against monkeypox → Unvaccinated individuals account for 80-96% of monkeypox cases Genetic evolution (correlate with human-to-human transmission) Space intentionally left blank MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 10 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera E. MODES OF TRANSMISSION OF MONKEYPOX Human-to-human: → Mainly through direct (close) contact: ▪ Skin-to-skin ▪ Mouth-to-mouth ▪ Mouth-to-skin ▪ Respiratory secretions ▪ People with multiple sexual partners are at higher risk of acquiring Mpox → Indirect contact (fomites) Figure 22. Evolution of MPox Rash[Lecturer’s PPT] → Transplacental (congenital) Animal-to-human: G. FINDINGS IN THE 2022 OUTBREAK 📋 → Direct contact (e.g., bites, scratches, playing with Lesions on genitalia commonly seen carcasses or eating animals) In endemic cases, lesions are commonly seen on face and extremities [Trans 2026] 📋 Progression of lesions can be rapid In endemic cases, progression of rashes may take weeks and progress in one stage at a particular time [Trans 2026] Papulovesicular and pustular lesions may occur on the same site Other mucosal lesions: → Pharyngitis → Epiglottis → Oral or tonsillar lesions → Conjunctival mucosa lesions Figure 20. Monkeypox Transmission-Overview[WHO] H. DIAGNOSTIC TESTS Primary Infection The type of specimen and test depends on the stage of → Animal to Human via contact with infected animals or illness animal products Incubation Period (5-21 days): No testing Secondary Infection Febrile Stage (1-4 days): → Human to human via contact with infected people or → Tonsillar and nasopharyngeal swab - PCR mother to fetus → Genomic sequencing F. PROGRESSION OF MONKEYPOX Rash Stage (2-4 weeks): Incubation period: 1-21 days (usually within a week) → Lesion Samples: Symptoms typically last 2-4 weeks, but may last longer ▪ PCR ▪ Antigen detection methods ❗ (self-limiting) Febrile Stage: Lymphadenopathy (distinctive feature) → Genomic sequencing → Infectious: From symptom onset (Prodrome) until Recovery (Days to weeks) crusting of skin lesions → Serum: Antibody detection methods → Rashes start within 1 to 3 days from onset of fever ▪ IgM(+) from days 4-56 after rash onset ▪ Tend to be concentrated on face and extremities ▪ Rash evolves from macule → papule → vesicle → pustule → crust which dry up and fall off (See Figure X) [Trans 2026] ▪ The number of lesions varies and are usually painful ▪ Itching may occur is crusting phase [Trans 2026] ▪ May scab and leave pox marks or scars [Trans 2026] Figure 23. Diagnostic Tests for Monkeypox[Lecturer’s PPT] I. TREATMENT FOR MONKEYPOX Aim to provide supportive and symptomatic treatment Figure 21. Progression of MPox[Lecturer’s PPT] Complications occur in 4/20 Antivirals have no strong recommendations, may be considered for severe cases: → Tecovirimat (ST-246; Trade name: TPOXX) → Cidofovir (Trade name: Vistide) → Brincidofovir (Trade name: Tembexa) → Vaccinia immune globulin MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 11 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera Severe Disease: Close contacts (CDC 2022, → Hemorrhagic lesions UKHSA 2022) including: → Confluent lesions → Unprotected direct contact or → Encephalitis high risk environmental contact → Sepsis → Unprotected exposure to → Health status requiring hospitalization infectious materials including At Risk for Severe Disease: droplet or airborne potential route → Immunocompromised → Protected physical or droplet → Children 5um diameter, travel = 1m milk, urine, and meat → Airborne ▪ Through droplet nuclei (=5um diameter, travel >1m) → Direct Contact → Indirect Contact Figure 29. MERS-COV transmission[Lecturer’s PPT] MERS CoV Updates, May 2024 (WHO) From April 2012 to date, a total of 2,613 [Lecturer’s PPT] laboratory-confirmed cases of Middle East respiratory Figure 27. SARS-CoV Transmission syndrome (MERS) were reported globally, with 943 associated deaths at a case-fatality ratio (CFR) of 36% The majority of these cases were reported from Saudi Arabia, with 2204 cases and 862 related deaths (CFR: 39%) MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 13 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera During May 2024: no new cases were reported. Table 14. Variants Working Definitions The demographic and epidemiological characteristics of A variant with genetic changes that are reported cases do not show any significant differences suspected to affect virus characteristics when compared with the same corresponding period and early signals of growth advantage between 2016 and 2024. relative to other circulating variants, but for Among primary cases, 50–59 year-olds are at the Variant which evidence of phenotypic or highest risk for acquiring infection and among secondary Under epidemiological impact remains unclear, cases the 30–39 year-olds are at the highest risk. Monitoring requiring enhanced monitoring and Among both primary and secondary cases, CFR is higher (VUM) reassessment pending new evidence. within the age group of 70–79 years-old If there is also evidence of community D. COVID-19 transmission in ≥ 2 countries within a 2-4 COVID-19 TIMELINE week period Table 13. COVID-19 Timeline A variant with genetic changes that are Date Event predicted or known to affect virus Dec 31, 2019 First identified in Wuhan (Hubei characteristics such as transmissibility, Province of China), where a cluster of virulence, antibody evasion, susceptibility to pneumonia cases was identified therapeutics and detectability, AND Jan 7, 2020 China identifies a new coronavirus as a Variant of cause of the outbreak Interest Identified to have a growth advantage over Jan 12, 2020 China shares the genetic consequence (VOI) other circulating variants in more then 1 Jan 30, 2020 WHO declares the 2019-nCoV outbreak WHO region with increasing prevalence, or a public health emergency of other apparent epidemiological impacts to international concern suggest an emerging risk to global public health *1st confirmed case in the Phils. A VOI which meets at least 1 of the Mar 11, 2020 WHO declared a pandemic following criteria: → Detrimental changes in clinical COVID-19 NUMBER UPDATES disease severity Global total number of cases: 776,386,491 cases as of → Change in COVID-19 epidemiology Sept 2024 Variant of causing substantial impact on the Philippines: 4,140,383 cases as of Jan 8, 2024 Concern ability of health systems to provide 66,864 deaths (case fatality rate: 1.6%) (VOC) care to patients with COVID-19 or Over 13 billion vaccine doses have been administered as other illnesses and therefore requiring of June 2023 major public health interventions ORIGIN OF SARS CoV-2 INTERMEDIATE HOST? → Significant decrease in the effectiveness of available vaccines in 96.2% similarity to a horseshoe bat SARS-related protecting against severe disease coronavirus (SARSr-CoV; RaTG13) Spike protein of SARS-CoV-2 are nearly identical to one CIRCULATING COVID-19 VARIANTS identified in a virus isolated from a pangolin Omicron is the predominant VOC that is circulating The G614 variant in the S protein has been postulated to globally increase infectivity and transmissibility of the virus Stronger binding to the ACE2 receptor Greater affinity for the upper respiratory tract and conjunctiva Highest viral load observed at the time of symptom onset or in the first week of illness COVID-19 VARIANTS Viruses change all the time (mutate) and the resulting virus Figure 30. Circulating COVID-19 Variants[Lecturer’s PPT] is a “variant” Note: Kindly refer to the appendix for clearer image → Sometimes, these may change the characteristics of the virus (e.g. making them more transmissible) JN.1 the dominant VOI circulating, but remains a low public health risk → All 4 VUMs are all JN.1 descent lineages FLiRT variant (JN1.7; KP.2; KP.3) are termed as such because of the 2 new mutations in its spike protein → Phenylalanine/leucine (at position 456) Space intentionally left blank → Arginine (R)/Threonine (T) amino acids (at position 346) LB.1 subvariant increasing in the UK and US Space intentionally left blank MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 14 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera TRANSMISSION OF COVID-19 c. Type 3 Primarily through droplet or contact transmission 5. It is a variant with genetic changes that are suspected → Once in humans, the virus is transmitted when to affect virus characteristics and early signals of respiratory droplets or aerosolized particles from growth advantage relative to other circulating infected individuals come into direct contact with the variants, but for which evidence of phenotypic or mucous membranes of another individual, including in epidemiological impact remains unclear. the eyes, nose, or mouth a. Variant of Interest → In the air: b. Variant Under Monitoring ▪ Larger droplets: tend to drop toward the ground c. Variant of Concern within 1 meter (3 feet) of the infected person 6. What is the most common symptom of monkeypox ▪ Smaller droplets: travel over 2 meters (6 feet) and found as of the Oct 2023 WHO report? remain viable in the air for up to 3 hours under certain a. Any rash conditions b. Genital ulcer Other modes: c. Genital rash → Direct transmission d. Fever ▪ Hand-to-face contact from infected surfaces 7. Pandemic influenza refers to what subtype of → Transmission in bodily fluids Influenza A virus? ▪ Although SARS-CoV-2 has been detected in stool a. A(H5N1) specimens, blood, ocular secretions, and semen, the b. A(H7N9) possibility of transmission through these routes c. A(H1N1) remains uncertain d. None of the above → Vertical transmission (mother to child) ▪ Reported in several cases of peripartum maternal ANS: infection in the 3rd trimester 1. A. The A(H5N1) virus is the first avian influenza virus that ▪ Most neonatal infections (asymptomatic and/or mild) was recognized to have been transmitted to humans in are thought to result from postnatal exposure through 1997 and was recognized in a 3-year old child in Hong respiratory droplets from an infected mother or Kong caregiver 2. C. The main natural reservoir for the henipavirus is the fruit bats of the genus Pteropus, also known as flying foxes. PREVENTION OF COVID-19 INFECTION The virus can then spread to other animals (like pigs, dogs, COVID-19 vaccines provide strong protection against cats, horses) or directly to humans,when they consume serious illness, hospitalization and death contaminated food or drink that have been infected by bat To prevent the spread of COVID-19: secretions. Pigs act as intermediate hosts. → Avoid crowds and keep a safe distance from others, 3. F. MERS-CoV has a significantly higher CFR of 36%. even if they don’t appear to be sick SARS-CoV-2 has a lower CFR of around 1.6% as of → Wear a properly fitted mask if you feel sick, have been January 2024, despite a large number of confirmed cases close to people who are sick, if you are at high-risk, or in worldwide. crowded or poorly ventilated areas 4. B. Type 1 is responsible for 13%, Type 2 for 86%, and → Clean your hands frequently with alcohol-based hand Type 3 for 1%. rub or soap and water 5. A. Variant of interest is a variant with genetic changes → Cover your mouth and nose with a bent elbow or tissue that are predicted or known to affect virus characteristics when you cough or sneeze AND Identified to have a growth advantage over other → Dispose of used tissues right away and clean your circulating variants in more than 1 WHO region. Variant of hands concern must meet at least 1 of the following: 1) → If you develop symptoms or test positive for COVID-19, detrimental changes in clinical disease severity, 2) change self-isolate until you recover in COVID-19 epidemiology causing substantial impact on the ability of health systems to provide care to patients VII. REVIEW QUESTIONS and/or 3) Significant decrease in the effectiveness of 1. What is the first avian influenza virus that was available vaccines in protecting against severe disease. recognized to have been transmitted to humans? 6. A. Most common symptoms of monkeypox: any rash a. A(H5N1) (90.3%), fever (58.2%), systemic rash (56%), genital rash b. A(H7N9) (52.7%) c. A(H1N1) 7. C. The pandemic influenza is known as A(H1N1) subtype, d. None of the above which affected a total of 214 countries 2. What is considered as the main natural reservoir for henipavirus? VIII. REFERENCES a. Fruit bats of genus Pteropus Rivera, Abigail. Emerging and Re-emerging Diseases: Introduction handout Rivera, Abigail. Emerging and Re-emerging Diseases: Vaccine-Preventable b. Horses Diseases handout c. Pigs Rivera, Abigail. Emerging and Re-emerging Diseases: Avian and Pandemic d. Fruit bats of Pteropodidae family Influenza Asynchronous Lecture Rivera, Abigail. Emerging and Re-emerging Diseases: Henipavirus and 3. T/F SARS-CoV-2 is considered to have a higher case Ebola Asynchronous Lecture fatality rate than MERS-CoV. Rivera, Abigail. Emerging and Re-emerging Diseases: MPox handout 4. What Poliovirus subtype is the main cause of the Circulating Vaccine-derived Poliovirus? a. Type 1 b. Type 2 MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 15 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera VII. APPENDIX Table 15. Examples of diseases when they were considered emerging[Lecturer’s PPT] Disease Infectious Agent Year Recognized Contributing Factors Lassa fever Arenaviridae family 1969 Urbanization and other conditions that favor the rodent (virus) host; nosocomial transmission Ebola Filoviridae family (virus) 1977 Unknown natural reservoir; nosocomial transmission hemorrhagic fever Legionnaire Legionella pneumophila 1977 Cooling and plumbing systems disease (bacterium) Hemolytic uremic Escherichia coli 1982 Mass food production systems syndrome 0157:H7 (bacterium) Lyme borreliosis Borrelia burgdorferi 1982 Conditions favoring the tick vector and deer, such as (bacterium) reforestation near homes AIDS Human 1983 Migration to cities, global travel, transfusions, organ immunodeficiency virus transplants, intravenous drug use, multiple sexual partners Gastric ulcers Helicobacter pylori 1983 Newly recognized as due to infectious agent (bacterium) Cholera Vibrio cholerae 0139 1992 Evolution of new strain of bacteria combining increased (bacterium) virulence and long-term survival in the environment Hantavirus Bunyaviridae family 1993 Environment changes favoring contact with rodent hosts pulmonary (virus) syndrome Pandemic Orthomyxoviridae New viral strains Pig-duck agriculture (possibly) influenza family (virus) emerge periodically Figure 31. Coronaviridae family [Lecturer’s PPT] MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 16 of 17 MICROBIOLOGY | LE 2 Emerging and Re-emerging Infectious Diseases | Dr. Abigail C. Rivera Figure 32. Circulating COVID-19 Variants [Lecturer’s PPT] MICROBIOLOGY Emerging and Re-emerging Infectious Diseases PAGE 17 of 17