RNA Viruses I (V1) PDF

MICROBIOLOGY | TRANS # 3 LE RNA Viruses I SHEILA DE GUZMAN-ZAÑO, MD | Lecture Date (09/20/...

MICROBIOLOGY | TRANS # 3 LE RNA Viruses I SHEILA DE GUZMAN-ZAÑO, MD | Lecture Date (09/20/2024) | Version #1 02 OUTLINE ▪ Aphtovirus I. Picornaviridae a. Hepatitis A Virus ▪ Cardiovirus II. Picornavirus b. Hepatitis E Virus ▪ Aichi virus A. Human Enterovirus III. Reovirus/Rotavirus PICORNAVIRUS STRUCTURE a. Poliovirus IV. Calicivirus b. Coxsackie Virus A. Norovirus c. Echovirus/Others V. Astrovirus B. Human Rhinovirus VI. Review Questions C. Parechovirus VII. References D. Hepatovirus VIII. Appendix Must Lecturer Book Previous Youtube ❗️ Know 💬 📖 📋 Trans 🔺 Video SUMMARY OF ABBREVIATIONS CVDPV Circulating vaccine-derived poliovirus HFMD Hand foot and mouth disease LEARNING OBJECTIVES ✔ Understand the classification, structure, and important Figure 1. Schematic Representation of Various properties of RNA viruses (Picornaviruses, Reoviruses, Picornaviruses [Lecturer’s PPT] Caliciviruses, Astroviruses). ✔ Discuss the pathogenesis of the disease produced by The virion of Enteroviruses and Rhinoviruses consists of a the virus infection. capsid shell of 60 subunits, each of four proteins ✔ Correlate the host immune response with the (VP1–VP4) arranged with icosahedral symmetry. pathogenesis of the disease. → Small (28-30 nm) ✔ Describe the specific diseases and clinical → Non-enveloped or Naked manifestations associated with each virus. → Icosahedral (20 sides): made up of equilateral triangle ✔ Identify the methods used to diagnose the infections associated with these RNA viruses. 📋 fused together in a spherical shape Highly diversified single stranded (+) sense RNA → Covalently linked to the genome-linked protein VPg ✔ Enumerate methods of prevention and control and correlate with the epidemiology of the disease. I. PICORNAVIRIDAE Picornavirus → Represent a very large virus family with respect to the number of members but one of the smallest in terms of ❗️ virion size and genetic complexity. PICOrnaviridae: “Pico” = small (10-12) and RNA containing virus ❗️ MUST KNOW Mnemonic (PICORNAVIRUS) Figure 2. Icosahedral shape of Picornavirus [2026 Trans] → Poliovirus → Insensitivity to ether 📋→OneEach side: 3 surface subunits (VP1-3) with B-barrel folding virion has 20 sides x 3 surface subunits each side → Coxsackie virus → Orphan virus = 60 surface subunits in total → Rhinovirus → (Ribo)Nucleic → Acid ❗ Includes II. PICORNAVIRUS two major groups of human enteroviruses and rhinoviruses pathogens: → Enteroviruses ▪ Transient inhabitants of the human alimentary tract ▪ May be isolated from the throat or lower intestine → Rhinoviruses Figure 3. Major polypeptides of virion [2026 Trans] 📋→4 major ▪ Associated with the respiratory tract ▪ Isolated chiefly from the nose and throat polypeptides comprise the virion: → Less common picornaviruses associated with human (3) surface proteins are epitopes, (1) internal protein illness include ▪ VP1 and VP3 are major antibody binding sites. ▪ Hepatitis A virus ▪ Parechovirus LE 2 TG 15 | C. Tan, H. Tan, K. Tan, J. Tan, Tanodra TE | M. Reyes, R. Sim AVPAA | C. Rival PAGE 1 of 19 TRANS 3 VPAA | D. Patajo MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño PICORNAVIRUS REPLICATION Figure 6. Overview of the Picornavirus Replication Cycle. [Lecturer’s PPT] Occurs in the host cell cytoplasm Multiplication cycle: 5-10 hours[2026 Trans], 6 hours [Async Lecture] Genome is positive sense, hence, it directly acts as mRNA and is ready to be translated into the polyprotein containing coat proteins and essential replication proteins of the virus 1. Begins with the virus binding to the plasma membrane Figure 4. Structure of a typical picornavirus. (A) Exploded receptor of the host cell. diagram showing internal location of the RNA genome 2. Receptor binding triggers a conformational change in surrounded by capsid composed of pentamers of proteins the virion → releases viral RNA into the cell cytoplasm. VP1, VP2, VP3, and VP4. [Lecturer’s PPT] 3. VPg is removed as the viral RNA associates with the ❗️Canyon host ribosome. 4. Enzymatic processes shut off the host cell protein → Binding sites for cellular receptor (in the floor of the synthesis and preferentially continues viral RNA canyon) translation. → Figure 4C shows the location of a drug-binding site in 5. Viral-encoded cysteine proteases cleave large VP1 of a Rhinovirus. polyprotein to release capsids & nonstructural → The antiviral drug prevents viral attachment by proteins. deforming part of the canyon floor. 6. Negative strands that become templates for positive ssRNA genomes are synthesized by RNA polymerase. (+) ssRNAs made from these templates are coupled with VPg to produce new provirions. 7. Final maturation involves packaging the genome inside the capsid proteins. 8. The host cell disintegrates once there is a significant load of virions. New virions are released through cell lysis to infect new host cells. Space intentionally left blank [Lecture PPT] Figure 5. Receptor Binding in a Canyon Figure 5 shows attachment strategies such as receptor binding in a canyon of Poliovirus → CD155 attaches to the canyon of the Poliovirus MICROBIOLOGY RNA Virus 1 PAGE 2 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño Table 1. Properties of Picornaviruses. A. HUMAN ENTEROVIRUS Property Description POLIOVIRUS Icosahedral, 28-30 nm in diameter, Virion contains 60 subunits Composition RNA (30%), protein (70%) Single-stranded RNA, linear, positive sense (linear (+)ssRNA) 7.2-8.4kb in size Genome 2.5 million MW Infectious, and contains genome-linked protein (VPg) Four major polypeptides cleaved from a large precursor polyprotein. Proteins Surface capsid proteins VP1 and VP3: major antibody-binding proteins VP4: internal protein Envelope None Replication Cytoplasm Family is made up of many Enterovirus and Rhinovirus types that infect humans Figure 8. Poliovirus Outstanding and lower animals, causing various Neurotropic enteroviruses that target motor neurons in characteristic illnesses ranging from poliomyelitis to the spinal cord and brainstem causing poliomyelitis aseptic meningitis to the common cold Polioviruses belong to the human enterovirus C species. There are three poliovirus serotypes, most paralytic CLASSIFICATION OF PICORNAVIRUS disease (pre-vaccination era) was caused by poliovirus serotype I PATHOGENESIS OF POLIOVIRUS Figure 7. Classification of Picornavirus [Lecturer’s PPT] Figure 9. Transmission of Poliovirus[Lecture PPT The Picornaviridae family contains 12 genera → Enterovirus (Enteroviruses and Rhinoviruses) Portal of entry: Mouth → Hepatovirus (Hepatitis A virus) Primary multiplication sites: → Kobuvirus (Aichi virus) → Oropharynx → Parechovirus (Parechoviruses) → Tonsils → Cardiovirus (Cardioviruses) → Lymph nodes of the neck → Aphthovirus (Foot-and-mouth disease viruses) → Peyer’s patches The first five groups contain important human pathogens. → Small intestine Rhinoviruses historically were placed in a separate genus Before the onset of illness: in throat and stools but are now considered to be members of the Enterovirus 1 week after infection: minimal virus in the throat genus. → The virus continues to be excreted in the stools for Enteroviruses of human origin are subdivided into seven several weeks even though high antibody levels are species present in the blood. → Human enterovirus A–D The virus then spreads to the regional lymph nodes → → Human rhinovirus A–C blood → primary viremia Antibodies, which are produced to prevent spread of infection, against the virus appear early in the disease, usually before paralysis occurs MICROBIOLOGY RNA Virus 1 PAGE 3 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño On continued infection and multiplication of the virus in the CLINICAL MANIFESTATIONS OF POLIOVIRUS 📋 reticuloendothelial system → bloodstream → INFECTION secondary viremia Poliomyelitis: most serious disease caused by Enterovirus → Response to viral exposure ranges from inapparent infection without symptoms to a mild febrile illness to 📋 severe and permanent paralysis. Most infections are subclinical; only about 1% of infections result in clinical illness. Approximately 4%-8% of infected individuals experience a self limited illness after an incubation period of 3 to 6 days → Incubation period: 7 to 14 days / 3 to 35 days [2026 Trans] MILD DISEASE Most common form of disease Systemic symptoms: → Fever, malaise, drowsiness, headache, nausea, vomiting, constipation, and sore throat in various combinations Recovery occurs in a few days Figure 10. Poliovirus in Blood-Brain Barrier[Lecturer’s PPT] ❗→CNS SEVERE ILLNESS: Invasion NON-PARALYTIC POLIOMYELITIS (ASEPTIC During this period of viremia, the polioviruses may cross MENINGITIS) the blood-brain barrier, and gain access to the brain. Refers to the severe illness in the absence of motor → The virus shows tissue tropism by specifically weakness. combining with neural cells → Poliovirus is only one of many viruses that produce → The virus recognizes the receptor present on the aseptic meningitis. anterior horn of the spinal cord, the dorsal root Signs and symptoms of mild disease + stiffness & pain in ganglia and lower motor neurons the back & neck ❗️ → Destruction of the motor neurons → paralysis. Symptoms begin after an incubation of 7 to 21 days and Poliovirus does not multiply in muscle in vivo may or may not be preceded by a mild illness. → Changes that occur in peripheral nerves and voluntary Lasts for 7-10 days[Lecturer’s PPT], 2-10 days [2026 Trans] 📋 muscles are secondary to the destruction of nerve cells. 📋 Some cells that lost function may recover completely Inflammation occurs due to the attack on nerve cells With rapid and complete recovery CSF and examination: may demonstrate a moderate leukocytosis with an elevated protein concentration and in a small percentage of cases the disease can advance to paralysis. Figure 12. Paralytic Poliomyelitis[Lecturer’s PPT] SEVERE ILLNESS: ❗ PARALYTIC POLIOMYELITIS Predominating complaint: Acute flaccid paralysis with pain → Due to lower motor neuron damage or anterior horn cell injury Incoordination may also occur → Secondary to brain stem invasion and painful spasms of Figure 11. Diagram of Temporal Profile of Polioviruses and non paralyzed muscles Development of Disease. [Lecturer’s PPT] Muscle tone reduced asymmetrically Proximal muscles usually affected MICROBIOLOGY RNA Virus 1 PAGE 4 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño → Legs more commonly affected CSF analysis is performed for all Sensory examination is almost always normal patients with meningitis or paralytic Decreased or absent reflexes illness to identify polioviruses and → Weakness typically worsens over two to three days exclude other etiologies sometimes worsening can progress for up to a week Cerebrospinal CSF samples should be sent for Bulbar involvement (5-35%) fluid detection of poliovirus by a viral → Dysphagia, Dysarthria, Difficulty handling secretions culture or PCR amplification of → Respiratory failure may also occur requiring mechanical poliovirus RNA whenever stool and ventilation pharyngeal swab testing is negative. Motor recovery over months and often incomplete → PCR is more sensitive than culture PROGRESSIVE POST-POLIOMYELITIS MUSCLE Neuroimaging studies: MRI ATROPHY Warranted for patients with upper motor neuron signs to assess other causes of acute myelopathy or radiculopathy Other Test Electrodiagnostic studies: To exclude other etiologies; assess the severity of nerve impairment in poliomyelitis Nerve conduction studies (NCV) Electromyography (EMG) IMMUNITY AGAINST POLIOVIRUS Polio Vaccine → Affords permanent immunity to the virus type causing the infection, and is predominantly antibody mediated → Immunization is of value only if it precedes the onset of symptoms referable to the nervous system ▪ Virus in CNS not influenced by blood antibody titers Passive Immunity → Maternal antibodies: Lasts until 6th month of life. Figure 13. Progressive Postpoliomyelitis Muscle Atrophy [Lecturer’s PPT] → Passively administered antibody: last for 3-5 weeks Virus-neutralizing antibody are formed immediately after Recrudescence of paralysis and muscle wasting occurs exposure to the virus decades after experience with paralytic poliomyelitis → Before the onset of illness and CNS invasion Does not appear to be a consequence of persistent → Persists for life infection but rather a result of physiologic and aging changes in paralytic patients already burdened by loss of WILD POLIOVIRUS neuromuscular functions. Wild polioviruses are the naturally occurring strains of poliovirus that circulate in the environment. LABORATORY DIAGNOSIS OF POLIOVIRUS There are 3 serotypes of wild poliovirus: type I, type 2, Table 2. Poliovirus Specimen Processing & Lab Testing and type 3. Immunity to one serotype does not confer immunity to the Specimen other two Collection Laboratory Testing Type 2: declared eradicated in September 2015, with the & Processing last virus detected in India in 1999. Stool samples & swabs: 2 samples Type 3: declared eradicated in October 2019. It was last should be obtained at least 24 hours apart during the first 14 days after the onset of limb weakness ❗ detected in November 2012. Only type I wild poliovirus remains. Throat Swabs VARIANT POLIOVIRUS (CVDPV) (onset of illness) Cell Culture: Cytopathogenic effects may be seen in 3-6 days Wild polioviruses are the most commonly known form of Rectal Swabs/ RT-PCR: Provides rapid results and the poliovirus stool samples more sensitive than culture Another form of polio that can spread within communities, (months to years) Serology: Paired serum specimen are known as the circulating vaccine-derived poliovirus especially in some required to show a rise in antibody titer (CVDPV) immuno- deficient during the course of disease Although CVDPV are rare, they have been increasing in persons recent years due to low immunization rates within NOTE: Only the first infection with communities Blood poliovirus produces strictly type-specific CVDPV type 2 are the most prevalent with 959 cases Extractions responses. Subsequent infections with occurring globally in 2020. heterotypic polioviruses induce antibodies against a group antigen shared by all three types. MICROBIOLOGY RNA Virus 1 PAGE 5 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño HOW DID CVDPV OCCUR? In developing areas: poliomyelitis is the disease of The Oral Polio Vaccine that has brought the wild polio infancy and early childhood or infantile paralysis virus to the brink of eradication has many benefits. In developed countries: before the advent of vaccination, → Live attenuated or weakened vaccine virus provides the age distribution shifted → most patients were older better immunity in the gut, where the polio replicates. than the age of 5 years and 25% were older than 15 years. → Vaccine virus is excreted in the stool Case fatality rate is variable and it is highest in the oldest → In communities with low quality sanitation, there is an patients and may reach from 5 to 10% easy spread from person to person which can help in POLIO REEMERGENCE IN THE PHILIPPINES protecting the community. Outbreak of Polio was declared in the Philippines in In communities with low immunization rates: September 2019 with 4 environmental samples which then → Cften over a course of 12 to 18 months, it can mutate tested from Davao and Metro Manila and take on the form that can cause paralysis, just like → 17 cases were confirmed with vaccine-derived polio the wild polio virus. virus → This mutated polio virus can spread in communities, → Philippines is affected by both cVDPVI and cVDPV2 leading to CVDPV. The circulating vaccine-derived poliovirus is considered a EPIDEMIOLOGY OF POLIOVIRUS public health emergency of international concern. ❗ Poliomyelitis has had 3 epidemiologic phases According to the WHO, with the increasing number of Illness is self-limited Herpangina human cases and environmental samples tested positive → Endemic for poliovirus type 1 and 2, subsequent transmission of → Epidemic polio continues to be considered high at the national → Vaccine Era level due to: ▪ The first 2 reflect pre-vaccine patterns → The chronically sub-optimal vaccination coverage Humans are the only known reservoir of infection. → The sub-optimal performance of acute flaccid paralysis Direct correlation between poor hygiene, sanitation, and (AFP) surveillance crowding and the acquisition of infection and antibodies at → Poor sanitation and hygiene conditions. an early age. Currently there are no new cases of polio that were reported after February 2020 in the Philippines. Figure 15. Reemergence of Polio in the Philippines [Lecture PPT] PREVENTION AND CONTROL OF POLIOVIRUS INFECTION VACCINES Both inactivated poliovirus vaccine or IPV and live-attenuated oral poliovirus vaccine or OPV were developed in the 1950s and have since been used worldwide for routine childhood immunization and to Figure 14. Polio through the Ages. [Lecturer’s PPT] prevent and control polio outbreaks in endemic countries. Formalin-inactivated vaccine (Salk) Improved systems of hygiene and sanitation in colder → TIP: Injected (Salk = “sinasalsalk”/ “sinasaksak”) climates → transition from endemic to epidemic paralytic → Prepared from virus grown in monkey kidney cultures disease in these societies. → This killed virus vaccine induces humoral antibodies, but Before global eradication efforts began, poliomyelitis does not induce local intestinal immunity. So the virus is occurred worldwide: still able to multiply in the gut. → Year round in the tropics Live-attenuated vaccine (Sabin) → Summer and fall in the temperate zone → TIP: Orally taken (Sabin = “sinasabi” = mouth) → Winter outbreaks were rare → The live polio vaccine infects, multiplies, and immunizes The disease occurs in all age groups, but children are the host against virulent strains. usually more susceptible than adults because of the → In the process, infectious progeny of the vaccine virus acquired immunity of the adult population. are disseminated in the community MICROBIOLOGY RNA Virus 1 PAGE 6 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño → Produces IgM and IgG antibodies in the blood, and secretory IgA antibodies in the intestine, enabling mucosal immunity Both killed virus and live virus vaccines induce antibodies and protect the CNS from subsequent invasion by wild viruses. However, the gut develops a far degree of resistance after administration of live virus vaccine Figure 18. Current data of polio on a global scale [Lecturer’s PPT] Most of the countries are certified polio-free except for Pakistan and Afghanistan, where wild poliovirus transmission is considered endemic. ❗ Large COXSACKIEVIRUS group of enteroviruses and are divided into 2 groups: → Coxsackievirus A (HEV-A and HEV-C) ▪ Herpangina or vesicular pharyngitis ▪ Hand, foot, & mouth disease ▪ Acute hemorrhagic conjunctivitis → Coxsackievirus B (HEV-B) ▪ Bornholm disease: epidemic myalgia or pleurodynia Figure 16. Serum and secretory antibody response to ▪ Myocarditis, pericarditis orally administered, live attenuated polio vaccine and to intramuscular inoculation of killed polio vaccine [Lecturer’s PPT] 📋 ▪ Severe generalized infantile diseases Both A&B ▪ Aseptic meningitis GLOBAL POLIO ERADICATION INITIATIVE (GPEI) 📋 ▪ Common colds Similar pathogenesis, pathology, and virus distribution as the other enteroviruses The Global Polio Eradication Initiative (GPEI) is a partnership launched in 1980s with several other organizations such as the WHO, CDC, UN → Includes many governmental and non-governmental donors, and ministries of health of all affected nations Ultimate aim: ensure that no child anywhere will ever again be paralyzed by any form of polio viruses. The GPEI Strategy 2022-2026 lays out the roadmap to achieving a lasting free of all forms of poliovirus. The strategy has two clear goals: → Goal 1: Interrupt all poliovirus transmission in endemic countries → Goal 2: Stop transmission of variant poliovirus and prevent outbreaks in non-endemic countries. Eradication Strategies: → Routine immunization Figure 19. Picornavirus groups diagram [Lecturer’s PPT] → Supplemental immunization activities → Surveillance → Mop-up activities ❗ Human GENERAL PATHOGENESIS OF COXSACKIEVIRUS infection occurs after ingestion of the virus and may also occur following contact with vesicle fluid Portal of entry: Mouth Incubation: 2 to 9 days Stools: 5 to 6 weeks → Virus may be detected in the stool for 6 weeks and sometimes several months after infection Replication: → Submucosal lymphoid tissues of the lower intestine and to a lower extent, the pharynx Spread: → Regional lymph nodes and replication at these sites results in a minor viremia that disseminates virus throughout the body, resulting in infection of Figure 17. GPEI Poster [Lecturer’s PPT] reticuloendothelial tissues and multiple organs MICROBIOLOGY RNA Virus 1 PAGE 7 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño COXSACKIEVIRUS A CLINICAL MANIFESTATIONS OF COXSACKIEVIRUS Associated with disease involving vesicular lesions such iINFECTION as: → Herpangina, → Hand foot and mouth disease → Hemorrhagic conjunctivitis Figure 23. Summary of the different clinical syndromes caused by Coxsackievirus group [Lecture PPT] Aseptic meningitis Figure 20. Hemorrhagic Conjunctivitis [Lecture PPT] → Caused by all types of group B Coxsackieviruses and by many group A Coxsackieviruses, most commonly A7 and A9 → Clinical findings include fever, malaise, headache, nausea, and abdominal pain → Sometimes progresses to mild muscle weakness suggestive of paralytic poliomyelitis → Patients almost always recover completely from non-poliovirus paresis Herpangina → A severe febrile pharyngitis is caused by certain group A Coxsackieviruses. → Has nothing to do with herpes viruses → There is an abrupt onset of fever and sore throat with Figure 21. Herpangina [Lecture PPT] discrete vesicles on the posterior half of the palate, pharynx, tonsils or tongue → Illness is self-limited → Most frequent in small children Hand foot and mouth disease → Characterized by oral and pharyngeal ulcerations and a vesicular rash of the palms and soles that may spread to the arms and legs → Vesicles heal without crusting, which clinically differentiates them from the vesicles of the herpes viruses and pox viruses → Associated particularly with Coxsackievirus A16, but also with B1 and enterovirus 71 → Coxsackievirus A6 has also emerged as a cause of severe hand foot and mouth disease and sometimes followed by nail shedding Figure 22. Hand Foot and Mouth Disease [Lecture PPT] → The virus may be recovered not only from the stool and pharyngeal secretions but also from vesicular fluid COXSACKIEVIRUS B → Foot and mouth disease of cattle is caused by an Associated with meningitis, myocarditis, pericarditis, unrelated picornavirus that does not normally infect humans 💬 pleurodynia, and severe generalized disease of infants Coxsackie group B infections cause primary myocardial Pleurodynia → Also known as epidemic myalgia 💬 diseases in adults and children. Generalized disease of the infant is an extremely serious → Caused by group B Coxsackieviruses disease in which the infant is overwhelmed by → Fever and stabbing chest pain are usually abrupt in simultaneous viral infections of multiple organs including onset, but are sometimes preceded by malaise, the heart, liver, and brain. headache, and anorexia → In severe cases, myocarditis or pericarditis can occur → The chest pain may last from 2 days to 2 weeks and within the first 8 days of life abdominal pain occurs in approximately half of the cases and in children, this may be the chief complaint → Self-limited but relapses are common MICROBIOLOGY RNA Virus 1 PAGE 8 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño LABORATORY DIAGNOSIS OF OF COXSACKIEVIRUS Hand Foot and Mouth Disease (HFMD) and Herpangina RECOVERY OF VIRUS: SPECIMEN occur worldwide Throat washings: First few days of illness → Transmitted from person to person ▪ fecal-oral route ❗️ Stools: First few weeks Nasal secretions: where largest amount of coxsackievirus ▪ contact with oral and respiratory secretions A21 infections is found ▪ in case of HFMD, vesicle fluid CSF Outbreaks in daycare centers, schools, summer camps, → In cases of aseptic meningitis hospital wards, military installations, communities, large geographic areas, and entire countries ❗️ → Also isolated in alimentary tract Conjunctival swabs Most cases occur in infants and children, particularly → Where A24 virus is isolated in hemorrhagic younger than 5-7 years. conjunctivitis cases MANAGEMENT OF COXSACKIEVIRUS INFECTION 📖 → Also isolated in throat swabs and feces HFMD and Herpangina: Specimens can be inoculated into tissue cultures → Supportive care → Cytopathic effect appears within 5-14 days ▪ No specific antiviral therapy available NUCLEIC ACID DETECTION ▪ Pain and fever are short-lived, can be managed by Provide rapid and sensitive assays Ibuprofen or paracetamol Limited to identifying viral RNA at the species (e.g. → Hospitalization enterovirus) level and not by serotype ▪ If there is inability to maintain adequate hydration ▪ If there is development of neurologic/cardiovascular VIRUS ISOLATION (CELL CULTURE) complications such as encephalitis, meningitis, Labor intensive and expensive, culture in multiple cell lines flaccid paralysis, or myocarditis is required for optimal sensitivity Permits typing for clinical, epidemiological, and research PREVENTION AND CONTROL OF COXSACKIEVIRUS purposes. INFECTION SEROLOGY Detection of specific IgM or four-fold increase in the antibody titer between the time of the acute illness and the period of convalescence. Generally, not used for the diagnosis of acute enteroviral disease except when infection with a specific serotype is suspected 📋 Table Testing 3. Coxsackievirus Specimen Processing & Lab [2026 Trans] Specimen Collection Laboratory Testing & Processing Culture: Cytopathic effect appears Throat within 5-14 days swabs/washings Molecular methods: Nucleic acid Nasal secretions detection via RT-PCR Stool Figure 25. Prevention of HFMD Spread by WHO[Lecturer’s PPT] Serology: Neutralizing antibodies CSF appear early in infection, specific Conjunctival Hand hygiene to infecting virus, and persist for swabs Clean and disinfect frequently touched surfaces years Blood extraction → Fomites should be cleaned and disinfected → ELISA: Detects serum → Viruses are impervious to most common disinfectants antibodies and detergent but they can be inactivated by EPIDEMIOLOGY OF OF COXSACKIEVIRUS formaldehyde, hypochlorite, and chlorine. Avoid close contact with people with HFMD For hospitalized patients, contact precautions in addition to standard precautions should be used for the duration of the illness. Figure 24. (left) HFMD; (right) Herpangina[Lecturer’s PPT] Space intentionally left blank Coxsackieviruses recovered more frequently in the summer and early fall. Familial exposure is important in the acquisition of infections with coxsackieviruses. MICROBIOLOGY RNA Virus 1 PAGE 9 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño ECHOVIRUSES/OTHER ENTEROVIRUSES LABORATORY DIAGNOSIS OF ECHOVIRUSES & OTHER ECHOVIRUS ENTEROVIRUSES Echovirus (Enteric Cytopathogenic Human Orphan NUCLEIC ACID DETECTION Viruses) Rapid, sensitive than virus isolation → Grouped together because they infect the human enteric tract, and can be recovered from humans VIRUS ISOLATION only by inoculation of certain tissue cultures From throat swabs, stools, rectal swabs, and CSF (in → >30 serotypes are known aseptic meningitis) ▪ Not all have been associated with human illness SEROLOGY ▪ More recent isolates are designated with human Impractical because of many viral types illness → Except when a virus has been isolated from a patient or during an outbreak of typical clinical illness. ENTEROVIRUSES IN THE ENVIRONMENT Figure 26. Clinical Syndrome of Echovirus and Enterovirus Types 68-116[Lecturer’s PPT] GROUP D ENTEROVIRUSES Consist of 5 serotypes (68, 70, 94, 111, 120) Aseptic meningitis, encephalitis, febrile illnesses with or without rash, common colds, and ocular disease are among the diseases caused by echoviruses and other enteroviruses. Figure 28. Routes of Potential Enteric Virus Transmission on the Environment[Lecturer’s PPT] Humans are the only known reservoir for members of the human enterovirus group. These viruses are generally shed for longer periods of time in stools than in secretions from the upper alimentary tract. Figure 27. Other Clinical Syndrome of Echovirus and → Thus, fecal contamination (hands, utensils, food, Enterovirus Types 68, 78, 71[Lecturer’s PPT] water) is the usual avenue of virus spread. They are present in variable amounts in sewage. Infantile diarrhea may be associated with some types of → This may serve as a source of contamination of water virus. supplies used for drinking, bathing, irrigation, or Enterovirus 68 shares several characteristics with recreation. rhinoviruses, including acid liability and lower optimum → They survive exposure to the sewage treatments and growth temperature. chlorination in common practice, and human wastes in → They had been previously classified as rhinovirus 87 much of the world are discharged into natural waters Enterovirus 70 is the chief cause of acute hemorrhagic with little or no treatment. conjunctivitis. → Waterborne outbreaks are difficult to recognize → Disease is most common in adults ▪ It has been shown that the viruses can travel long → Incubation period: 1 day distances from the source of contamination and → Duration: 8-10 days remain infectious. → Virus is highly communicable and spreads rapidly under Filter-feeding shellfish (oysters, clams, mussels) have crowded or unhygienic conditions. been found to concentrate viruses from water and, if Enterovirus 71 has been isolated from patients with inadequately cooked, may transmit disease. meningitis, encephalitis, and paralysis resembling poliomyelitis. PREVENTION AND CONTROL OF ECHOVIRUS & OTHER → One of the main causes of CNS disease, sometimes ENTEROVIRUS INFECTION fatal, around the world. Hygiene → Caused an outbreak of HFMD in China in 2008 Reinforced disinfection ▪ Involved ~4500 cases and 22 deaths in infants and Avoidance of contact with patients exhibiting acute febrile young children. illness (especially very young children) → Within the first eight days of life. Infection control measures MICROBIOLOGY RNA Virus 1 PAGE 10 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño B. HUMAN RHINOVIRUS PATHOGENESIS OF HUMAN RHINOVIRUS Rhinoviruses are the common cold viruses. Virus enters the upper respiratory tract → Most commonly recovered agents from people with mild Present in nasal secretions for 5-7 days, 2-3 weeks in the upper respiratory illnesses. nasopharynx → Usually isolated from nasopharyngeal secretions Incubation period: 2-4 days ▪ But may also be found in throat and oral secretions Infection occurs when virus is deposited on the nasal These viruses cause upper respiratory tract infections mucosa after inoculation into the nose or onto the (URTI), including the common cold syndrome. conjunctival surface They are also responsible for about half of asthma → Most often occurs by self-inoculation although small and exacerbations. large particle aerosols transmission are also possible. CLASSIFICATION Figure 29. Human Rhinovirus Receptor Group[Lecture PPT] Figure 31. Pathogenesis of Human Rhinovirus[Lecture PPT] ❗ >150 types are known Can be divided into: Primarily infects the upper layer of epithelial cells and → Major receptor group host’s respiratory tract ▪ Intracellular adhesion molecule-1 (ICAM-1) as → Rhinovirus enters the cell via endocytosis receptor → Uncoating at pH ≤ 5.6 → Minor receptor group → Viral RNA acts as an mRNA allowing translation of the ▪ Bind to members of low-density lipoprotein receptor genome to a large polyprotein (LDL-R) family ▪ Which then subsequently yields mature viral proteins → Viral RNA also acts as a template for the viral PROPERTIES OF HUMAN RHINOVIRUS polymerase allowing the production of new viral genomes → Replication takes around 8-12 hours to complete, and it consists of four general steps: ▪ Binding of viral particle to its receptor & internalization into the host cell by endocytosis ▪ Uncoating and release of viral RNA into the cytoplasm ▪ Viral RNA translation and replication in the cytoplasm ▪ Assembly and release of the new infectious particle → Structural proteins VP1, VP3, and VP0 precursors assemble into empty capsids = immature → Cleavage of VP0 → VP2 and VP4 → viral RNA = mature viral particles → Cell lysis/Non-lytic exocytosis involving autophagy components allow the release of the new infectious viral particles In response to infection with rhinovirus, epithelial cells in Figure 30. Properties of Human Rhinovirus[Lecture PPT] culture and in vivo release IL-8, a PMNs chemoattractant → IL-8: locally produced and rapidly increased in nasal Small (30 nm) single-stranded RNA virus secretions Capsid has icosahedral symmetry and contains 60 copies → Kinins: produced on-site in nasal mucosa and each of the four rhinoviral polypeptides (VP1 through VP4) submucosa Numerous canyons on the viral surface that surround the ▪ Kinins released in the nose following plasma attachment site for host-cell receptors. exudation may augment symptomatology of the Acid-labile rhinoviral infection and may cause increase in Unstable below a pH of 5.0-6.0 vascular permeability, vasodilatation, and Complete inactivation occurs at a pH of 3.0 glandular secretion. More thermostable than other enteroviruses → May survive for hours on environmental surfaces MICROBIOLOGY RNA Virus 1 PAGE 11 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño CLINICAL FINDINGS IN HUMAN RHINOVIRUS INFECTION C. MINOR PARECHOVIRUS Some may be asymptomatic (especially older children and 19 types (type 1 and type 2 were originally classified as adults) echoviruses 22 and 23) Highly divergent from enteroviruses Table 4. Symptomatic infection of adult and children Parechovirus infections: often acquired during childhood Adult Children Primary site of replication: respiratory and Nasal discharge, nasal Cough, nasal discharge, gastrointestinal tract obstruction nasal obstruction more Parechovirus serotypes 1 and 3 are most associated Cough frequent than adults with disease Sore throat May initially have fever Clinical manifestation: Resolves in 5-7 days Longer duration of → Gastrointestinal illness Non-productive cough symptoms → Respiratory illness may persist for 2-3 Secondary bacterial → Meningitis/Encephalitis weeks infection: acute otitis → Febrile syndromes, exanthema, neonatal sepsis media, sinusitis, bronchitis, pneumonitis D. FOOT-AND-MOUTH DISEASE (APHTHOVIRUS OF CATTLE) LABORATORY DIAGNOSIS OF HUMAN RHINOVIRUS 💬The clinical syndrome of the common cold is usually so Causes foot and mouth disease in cloven-hoofed animals (cattle, pigs, sheep, goat) characteristic that laboratory diagnosis is unnecessary May be transmitted to humans by contact or ingestion Diagnosis of common cold is clinical Foot and Mouth disease in humans is considered very rare Virus can be obtained from nasal washings No person-to-person transmission was reported 💬 Molecular methods: RT-PCR Clinical findings: fever, salivation, vesiculation of mucous The performance of serologic testing to document rhinovirus membranes of the oropharynx and skin of the feet infection is not practical. PREVENTION AND CONTROL OF HUMAN RHINOVIRUS EPIDEMIOLOGY OF HUMAN RHINOVIRUS INFECTION Etiologic agent of most common colds Disease surveillance/disease reporting One-third to one-half of cases in adults annually Strict quarantine/measures Transmission: close contacts by means of Trade restrictions virus-contaminated respiratory secretions Vaccination Infection rates highest among infants and children, and Separation of livestock from wildlife to control animal decrease with increasing age movement As many as 50% of asthma exacerbations – associated with viral infections E. HEPATOVIRUS → More than half of asthma exacerbations in children HEPATITIS A VIRUS are associated with rhinovirus infection. Distinct member of the Picornavirus family No other antigenic cross-reactivity with the other Hepatitis TREATMENT AND CONTROL OF HUMAN RHINOVIRUS viruses INFECTION Symptomatic therapy (remains the mainstay of treatment) → Analgesics → Antihistamine/Decongestant combinations → Decongestants → Saline nasal spray → Expectorants Prevention/Control → Hand hygiene 💬 → Disinfection of contaminated objects Patients with moderate to severe symptoms may use a ❗ variety of therapies to relieve symptoms Rhinovirus is not a good candidate for a vaccine program Figure 32. Electron Micrograph of 27-nm Hepatitis A Virus → Multiple serotypes and other causes of common cold, Aggregated with Antibody (“Halo”) apparent antigenic drift in rhinoviral antigens, the Virus is destroyed by autoclaving requirement for the secretory IgA production, and the → Boiling in water for 5mins transients of the antibody response pose major → Dry heat 120ºC for 1hr problems for vaccine development → The benefit to risk ratio would be very low because rhinoviruses do not cause significant disease. Space intentionally left blank Space intentionally left blank MICROBIOLOGY RNA Virus 1 PAGE 12 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño Table 5. Characteristics of Hepatitis A Characteristics Virus Hepatitis A Virus Family Picornaviridae Genus Hepatovirus Virion 27 nm, Icosahedral Envelope No Genome ssRNA Genome size 7.2 Stability Heat and acid stable Transmission Fecal-oral Prevalence High Fulminant disease Rare Chronic disease Never Oncogenic No Table 6. Characteristics of Hepatitis A Virus Acid at pH 1 Solvents (ether, chloroform) Stable in Detergents Salt water, groundwater (months) Drying (stable) Figure 34. Time course of Hepatitis A virus (HAV) infection. *Note: a person is contagious before onset of symptoms and that 4ºC for weeks: Stable symptoms correlate with the onset of immune responses. Ig, Temperature 56ºC for 30 mins: Stable immunoglobulin. 61ºC for 20 mins: Partial Inactivation Chlorine treatment of drinking water Table 7. Epidemiological and Clinical Features of Hepatitis A Formalin (0.35%, 37C, 72hrs) Feature Viral Hepatitis Type A Inactivated Peracetic acid (2%, 4hrs) Incubation period 10-50 days (average, 25-30) by B-Propiolactone (0.25%, 1hr) Principal age Ultraviolet radiation (2 uW/cm2/min) Children, young adults distribution Throughout the year but tends Seasonal incidence to peak in autumn Route of infection Predominantly fecal-oral Occurrence of virus 2 weeks before to < or equal to Blood week after jaundice 2 weeks before to 2 weeks Stool after jaundice Urine Rare Saliva, semen Rare (saliva) Clinical and laboratory features Onset Abrupt Figure 33. Spread of Hepatitis A Virus within the body[Lecturer’s Fever >38C (100.4 F) Common PPT] Duration of Ingested → enters the bloodstream through the epithelial aminotransferase 1-3 weeks lining of the oropharynx or intestines (target) → elevation parenchymal cells of the liver → replicates at hepatocytes Immunoglobulins Elevated and Kupffer cells → release in the bile → stool (10 days) (IgM levels) Hepa A slowly replicates in the liver without producing Complications Uncommon, no chronicity apparent cytopathic effects. Mortality rate (icteric 98 >98 causes, yet least diagnosed etiologies of acute viral Chronic disease (%) None None hepatitis Mortality rate 0.1 0.3-2.1 The virus is classified in the virus family, Hepeviridae, in the genus Hepevirus Small, icosahedral, nonenveloped single-stranded RNA virus 27 to 34 nm in diameter Wide range of genotypes: → Group A genotype 1 and 2 – confined to humans → Genotype 3 and 4 – affects humans and animals Hepatitis E virus (E stands for enteric or epidemic) Transmitted by fecal to oral route Prevalence rates are higher in resource-limited countries Outbreaks of HEV have been related to consumption of contaminated drinking water Table 9. Epidemiological and Clinical Features of Hepatitis E [Lecturer’s PPT] Virus Hepatitis E Figure 35. Laboratory Diagnosis Level of Detection Family Hepeviridae LABORATORY DIAGNOSIS OF HEPATITIS A Genus Hepevirus Serologic tests Virion 30-32 nm, Icosahedral → Anti-HAV IgM: acute HAV infection Envelope No ▪ Peaks ~2 weeks after elevation of the Genome ssRNA aminotransferase test Genome size 7.2 ▪ Decline after 3-6 months ▪ Confirms the diagnosis of Hepatitis A Stability Heat stable ▪ Measured using ELISA Transmission Fecal-oral → Anti-HAV IgG: appears soon after the onset of disease Prevalence Regional and persist for decades In pregnancy (20% mortality Fulminant disease → Virus isolation is not performed because efficient rate) culture systems for growing the virus are not available Oncogenic No RT-PCR: Viral RNA in the blood/stool can be detected by RT-PCR to follow the course of disease CLINICAL MANIFESTATIONS OF HEPATITIS E INFECTION PREVENTION AND CONTROL OF HEPATITIS A Incubation period: 15 to 60 days INFECTION Majority of patients are asymptomatic or mildly Hygienic practices symptomatic → Handwashing Symptomatic patients: → Avoiding tap water and raw foods in areas with poor → Jaundice, accompanied by malaise, anorexia, nausea, sanitation vomiting, abdominal pain, fever, hepatomegaly → Heating of foods properly → Less common: diarrhea, arthralgia, pruritus, urticarial → Chlorine, iodine and disinfecting solutions rash Prophylaxis: 80-90% effective in preventing the illness → May occur later than Hepa A Vaccination → Mortality rate: 1-2% → Inactivated HAV vaccines: (HAVRIX and VAQTA), Generally causes self-limited acute infection (TWINRIX-combi Hepatitis A and Hepatitis B vaccine) Laboratory findings: ▪ Administered 2 doses, 6 months apart → Elevated serum concentration of bilirubin, ALT, → Live attenuated hepatitis A aspartate aminotransferase ▪ Given subcutaneously at a minimum of 18 months at → ALT may rise and return to normal during a single dose convalescence Immune globulin → Resolution: 1-6 weeks after onset MICROBIOLOGY RNA Virus 1 PAGE 14 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño III. REOVIRUS Medium-sized virus Double stranded, segmented RNA genome Reovirus (Respiratory, Enteric, Orphan) → Albert Sabin (1959) proposed the name Non-enveloped → Double layer protein capsid (10-12 segments of RNA) Stable in wide pH, temperature ranges and airborne aerosols Figure 37. Hepatitis E virus (HEV) infection typical serologic course[Lecturer’s PPT] Majority of patients who acquired HEV spontaneously clear the virus Some patients may develop complications: → Acute hepatic failure Figure 38. Reoviridae Responsible for Human Disease[Lecturer’s PPT] → Cholestatic hepatitis → Chronic HEV – immunosuppressed Orbivirus/Coltivirus are spread by arthropods, called Pregnant women Arboviruses → Acute hepatic failure occurs more frequently when HEV Table 10. Important Properties of Reoviruses occurs during pregnancy in regions where HEV infection Property Description is endemic → Acute Hepatic failure: more common in the third Icosahedral, 60-80 nm in diameter, Virion trimester double capsid shell → Mortality rate: 15-25% Composition RNA (15%), protein (85%) → Exposure to HEV early in life may reduce the risk of Double-stranded RNA, linear, acute liver failure Genome segmented (10-12 segments); total genome size 16-27 kbp DIAGNOSIS OF HEPATITIS E Nine structural proteins core contains Antibody testing Proteins several enzymes → Anti-HEV IgM assay: initial test for Hepatitis E None (transient pseudo-envelope is ▪ Appears during the early phase of clinical illness and Envelope present during rotavirus particle disappears rapidly over 4 to 5 months morphogenesis) → Anti-HEV IgG: Cytoplasm; virions not completely ▪ Appears shortly after IgM response Replication uncoated ▪ Unclear how long IgG anti-HEV antibodies persist Genetic reassortment occurs readily HEV RNA assay Rotaviruses are the major cause of → HEV can be detected in stool one week before onset of Outstanding infantile diarrhea illness and persists as long as 2 weeks thereafter Characteristics Reoviruses are good models for → Serum: 2 to 6 weeks after infection up to 2 to 4 weeks molecular studies of viral MANAGEMENT OF HEPATITIS E INFECTION pathogenesis Acute HEV infection: Supportive treatment (self-limiting) Fulminant HEV infection: Liver transplantation PREVENTION OF HEPATITIS E INFECTION For traveler’s going to Asia, Middle East and Central America → Avoid water of unknown purity → Food from street vendors → Raw or undercooked seafood, meat and vegetables Vaccine: only licensed in China → Unclear if there is protection for all common genotypes → In vitro activity on homologous genotypes 2-4 have been described in studies Figure 39. Electron Micrograph of Rotavirus [Jawetz] MICROBIOLOGY RNA Virus 1 PAGE 15 of 19 MICROBIOLOGY | LE 2 RNA Viruses I | Dr. Sheila De Guzman-Zaño Single shelled virus particles that lack outer capsid are NSP4: viral enterotoxin of enterocytes that induces 50-60 nm in diameter with an inner core of 30-40 nm secretion via calcium dependent signal transduction diameter pathway Figure 39D: double shelled particle → Disrupt cytoskeleton and tight junctions causing leakage → Indicate complete infectious form → To release cytokines and neuronal activators, altering Classification water absorption → Divided to 15 genera Diarrhea due to impaired sodium and glucose absorption ▪ 4 listed on Figure 38 are able to infect humans as a damaged cells on villi are replaced by non-absorbing → Spinareovirinae: large spikes at 12th vertices immature crypt cells → Sedoreovirinae: smoother with lack of surface → Loss of electrolytes may lead to severe dehydration projections Diarrhea promotes transmission of virus → Rotavirus: 8 species (A-H), only A, B, and C affect Viral excretion usually lasts from 2-12 days (prolonged in humans immunocompromised and patients with poor nutrition) CLINICAL FINDINGS IN ROTAVIRUS INFECTION Incubation period: 1-3 days Children → Watery, non-bloody diarrhea, fever, abdominal pain and vomiting → Severe cases: may have dehydration, seizures and death Adults → Mild disease → Usually affects household members of affected children → Cause of traveler’s diarrhea and gastroenteritis Figure 40. Classification & Morphology of Reoviridae [Lecturer’s outbreaks in colleges and nursing homes PPT] Children with immunodeficiency: severe and prolonged Replication disease → Enter GIT → activate protease→ produce intermediate subviral particle (ISVP) → attach to hemagglutinin → LABORATORY DIAGNOSIS OF ROTAVIRUS lose outer capsid → inner capsid contain enzymes for Enzyme-linked immunosorbent assays (ELISA) mRNA transcription → mRNA enclosed in inner capsid → High sensitivity and specificity (template) → dock near NSP4 → acquire VP7, outer Immunochromatography (ICT) capsid and envelope → lose envelope then leaves via → High sensitivity and specificity cell lysis → Rapid results (minute) with no equipment → Enzymes in Virion: attach 5’ methyl cap guanosine and Latex agglutination 3’ polyadenylation sequence to mRNA Real-time polymerase chain reaction (RT-PCR) → VP7 and NSP4: glycoproteins at endoplasmic reticulum → Require equipment and expertise Culture EPIDEMIOLOGY AND IMMUNITY OF ROTAVIRUS INFECTION Burden of Disease → Rotavirus has historically been the most common worldwide cause of severe gastroenteritis in children