ADENOVIRIDAE Virus Characteristics + dsDNA, nonenveloped + Hexons, pentons, and fibers Viruses of Medical Importance + Adenovirus +0 Key Vignette Clues ver 50 serotypes + Subgroups A-F Adenovirus saul * Young adults: ARD : Adenovirus * Swimmers and shipyard workers: Reservoir: ubiquitous in humans and animals nonpurulent conjunctivitis Transmission: respiratory, fecal-oral, direct contact Daycare: viral gastroenteritis 308 KAPLAN) MEDICAL Chapter 4 » Medically Relevant Virus Pathogenesis + Penton fibers act as hemagglutinin + Purified penton fibers are toxic to cells + Lytic, latent, or transforming: virus is lytic in permissive cells and can be chronic or oncogenic in nonpermissive hosts; the adenoviruses are standard example of permissive host (where virus is produced) and nonpermissive host (where virus is not produced but transformed) Disease + Acute respiratory disease (ARD) and pneumonia: spring and winter peak incidence; children, young military recruits, college students sero- types 4 and 7; cough, conjunctivitis, fever, pharyngitis, hoarseness + Pharyngoconjunctivitis: swimming pool conjunctivit sore throat, coryza, red eyes; nonpurulent pink eye; fever, + Acute hemorrhagic cystitis: mostly boys age 5-15; dysuria, hematuria + Gastroenteritis: daycare (not as common as rotavirus); serotypes 40 and 41 + Myocarditis + Transplant patients Diagnosis: serology; ELISA ‘Treatment: supportive care for otherwise healthy patients; cidofovir and alpha globulins for immunocompromised or severely diseased Prevention: live, nonattenuated vaccine J Scanned with CamScannerChapter 4 # Medically Relevant Virus Pathogenesis + Penton fibers act as hemagglutinin + Purified penton fibers are toxic to cells + Lytic, latent, or transforming: virus is lytic in permissive cells and can be chronic or oncogenic in nonpermissive hosts; the adenoviruses are standard example of permissive host (where virus is produced) and nonpermissive host (where virus is not produced but transformed) Disease + Acute respiratory disease (ARD) and pneumonia: spring and winter peak incidence; children, young military recruits, college students sero- types 4 and 7; cough, conjunctivitis, fever, pharyngitis, hoarseness + Pharyngoconjunctivitis: swimming pool conjunctivitis, pink eye; fever, sore throat, coryza, red eyes; nonpurulent + Acute hemorrhagic cystitis: mostly boys age 5-15; dysuria, hematuria + Gastroenteritis: daycare (not as common as rotavirus); serotypes 40 and 41 + Myocarditis + Transplant patients Diagnosis: serology; ELISA ‘Treatment: supportive care for otherwise healthy patients; cidofovir and alpha globulins for immunocompromised or severely diseased Prevention: live, nonattenuated vaccine Penton fiber Figure lI-4-15. Adenovirus KAPLAN) MEDICAL 3 Scanned with CamScannerAdenovirus Core Recall Question Which of the following viruses causes fifth disease? A. B C Dz E Adenovirus Hepatitis A Human papilloma virus Parvovirus B19 Varicella-zoster virus Answer: D Scanned with CamScannerMiscellaneous Viral Infections of Respiratory Tract CHAPTER 68 ets atta ee = Infectious Mononucleosis = Adenovirus Infections = Rhinovirus Infection (Common Cold) ‘This chapter will cover various viral infections of respiratory tract such as infectious mononucleosis, adenovirus infections and rhinovirus infection (common cold). INFECTIOUS MONONUCLEOSIS Epstein-Barr Virus (EBV) causes infectious mononucleosis and is also associated with several human tumors, including nasopharyngeal carcinoma, Burkit’s lymphoma, Hodgkin’s disease, and B cell lymphoma. Morphology of EBV EBV is a member of y sub-family of Herpesviridae (Chapter 56). They possessdsDNA, are enveloped with an icosahedral symmetry. EBV expresses three classes of antigens. 1, Latent phase antigens: They are synthesized during the period of latency, e.g. = EBV nuclear antigen (EBNA) = Latent membrane protein (LMP) Early antigens: They are non-structural proteins which help in viral replication 3. Late antigens: They are the structural proteins that form viral capsid and envelope. Pathogenesis EBV is transmitted by oropharyngeal contact through infected salivary secretions. 4 EBV receptors: EBV binds to specific receptors present on B cell (CD21 or CR2) which are also receptors for C3b component of complement. Such receptors are also present on pharyngeal epithelial cells * Primary infection occurs in the oropharynx. EBV replicates in epithelial cells or surface B lymphocytes of the pharynx and salivary glands = Infected B cells become immortalized by the virus and synthesize large number of variety of immunoglobu- lins (polyclonal), many of those are autoantibodies (e.g. heterophile antibody to sheep RBC antigen) = In response to this, the bystander CD8T lymphocytes are stimulated and appear atypical, a feature which is characteristically seen in infectious mononucleosis. Oncogenicity: Persistent EBV infection can induce malignant transformation of infected B cells and epithelial cells by expressing latent EBV antigens such as LMP and EBNA (Chapter 80, for detail). Clinical Manifestations Infectious Mononucleosis It is also called kissing disease (transmitted through salivary contact) or glandular disease. It usually affects young adults, not children. It is characterized by (Table 4 Headache, fever, malaise + Pharyngitis + Cervical lymphadenopathy 4 Hepatosplenomegaly + Rashes following ampicillin therapy % Atypical lymphocytosis (CD8 T cells) % Autoantibodies reactive to sheep RBC antigens (detected by Paul-Bunnell test). oer ferris) Pete Sioud ‘Agent Epstein-Barr virus (EBV) CMY (20-50%) HHV-6, Toxoplasma, Ehrlichia, HV Atypical seen seen lymphocytosis lnica Fever, myalgia, Similar presentation, symptoms _hepatosplenomegaly, except that exudative ‘exudative pharyngitis, pharyngitis cervical cervical ymphadeno- lymphadenopathy are pathy, rashes following absent ampicilin therapy Heterophile Elevated (detected by Negative antibodies —_PaulBunnell test) Specific ‘Antibodies to specific Antibodies to CMV or antibodies _EBVantigens are other agents may be elevated elevated Scanned with CamScannerCHAPTER 68 Miscellaneous Viral Infections of Respiratory Tract, EBV-associated Malignancies EBV is associated with several malignancies such a Burkitt'slymphoma, nasopharyngeal carcinoma, Hodgkin’s lymphoma and non-Hodgkin's lymphoma (discussed in detail in Chapter 80). Other Conditions Associated with EBV * Lymphoproliferative disorder: It is seen among im- munodeficient patients, e.g, Duncan syndrome which is an X-linked recessive disease affecting young boys * Oral hairy leukoplakia: Wart-like growth of epithelial cells of the tongue developed in some HIV-infected patients and transplant recipients + Chronic fatigue syndrome. Epidemiology EBV is worldwide in distribution, + Age: EBVinfections are most common neatly childhood, with a second peak during late adolescence. However, infectious mononucleosis is common among young, adults of developed countries % Prevalence: EBV is common in all parts of the world, with >90% of adults being seropositive and develop antibodies to EBV ‘Transmission: = Intimate and prolonged oral contact is required for effective transmission, EBV is spread by direct contact with oral secretions, e.g. salivary contact during kissing = Other modes are blood transfusion and following bone marrow transplantatior + Source: Asymptomatic seropositive individuals shed the virus in oropharyngeal secretions. Shedding is more in immunocompromised patients. * stein-Barr virus inf SImmmnatarss Antibody detectio > Nonspecific heterophile antibody detection: + Paul-Bunnell test * Differential absorption test ¢ Monospot test > EBV specific antibody detection—ELISA and indirect IF assay detect antibody to viral capsid antigen, EBNA and early antigen. @ Molecular methods: > Detects EBV DNA (by PCR) > Quantifies EBV DNA (by realtime PCR)—detecting genes BamH1W, EBNAT and LMP > Detects EBER RNA (by RT-PCR), @ EBV antigen: By direct IF assay. Laboratory Diagnosis Antibody Detection Heterophile Agglutination Test (Paul-Bunnell Test) Paul-Bunnell test: It is a tube agglutination test that uses sheep RBCs to detect heterophile antibodies in patient's serum. % Procedure: Serial dilutions of inactivated (56°C for 30 minutes) patient's serum are mixed with equal volumes of 1% sheep RBCs, and then the tubes are incubated at 37°C for four hours % Result: Agglutination titer of >256 is considered as significant + False positive: Heterophile antibodies are non-specific, may also be present following serum therapy or even in some normal individuals. Therefore, the result needs to be confirmed + Differential absorption test and Monospot test are available to confirm the result of Paul-Bunnell test EBV-specific Antibody Detection Various formats such as ELISA and indirect immuno- fluorescence techniques areavailable to detect specific EBV antibodies. These tests have become more popular and are almost replacing the traditional heterophile antibody tests. + Antibody to viral capsid antigen (VCA): = IgM type: Indicates current infection Isa marker of past infection and indicates + Antibodies to early antigen (EA): These also indicate current viral infection. They are elevated in patients with Burkitt's lymphoma or nasopharyngeal carcinoma + Antibodies to EBNA (Epstein-Barr nuclear antigen) reveal past infection, but four fold rise of titer may suggest current infection. Other Tests + Detection of EBV DNA (by PCR), EBER RNA (EBV encoded small RNAs, by reverse transcriptase PCR), or EBV antigens (by direct-IF technique) have been useful for detecting the virus in various malignancies and in infectious mononucleo + Real-time PCR quantifying EBV DNA load in blood is extremely useful to monitor the treatment response in patients with lymphoproliferative disease. The various genes targeted are BamH1W, EBNAI and LMP * Virus isolation: It is laborious, time-consuming (6-8 weeks) and highly sophisticated, hence not routinely performed. rr virus infections Eps 2 Supportive measures such as analgesics are used in the treatment of infectious mononucleosis 12 Acyclovir is useful in the treatment of oral hairy leukoplakia, though relapse is common. It reduces EBV shedding from the ‘oropharynx, but it has no effect on the immortalized B cells, hence, it is not effective for infectious mononucleosis and other malignancies 2. Antibody to CD20 (rituximab) has been effectivein some cases. Prevention ‘The isolation of patients with infectious mononucleosis, is not needed as temporary contact does not transmit the Scanned with CamScanner 4SECTIONS © Respiratory Tract Infections infection. No vaccine is currently available. A vaccine trial using EBV glycoprotein was found to be ineffective. ADENOVIRUS INFECTIONS Adenoviruses are non-enveloped DNA virus. It has icosahedral symmetry with fiber proteins projecting from each vertex, which gives a unique space vehicle shaped appearance (Fig. 68.1). Adenoviruses infect and replicate in the epithelial cells of the respiratory tract, eye, gastrointestinal tract, urinary bladder and liver. Though one-third of the serotypes can cause human diseases, types 1-7 are most common worldwide. * Respiratory diseases are the most common manifestation of adenoviruses = Upper respiratory tract infection in children—mainly caused by serotypes 1,2 and 5. Among adolescents serotypes3, 4 and 7 cause mild respiratory infections = Pneumonia: Adenoviruses particularly types 3, 7, and 21 are responsible for about 10-20% of pneumonia in childhood. Serotype 14 is associated with severe pneumonia in healthy young adults = Acute respiratory disease syndrome outbreaks among military recruit—are commonly associated with type 4, 7 and occasionally type 3. + Ocular infections (Chapter 78, for detail): = Pharyngoconjunctival fever: It tends to occur in outbreaks, at children’s summer camps (also called swimming pool conjunctivitis), and is associated with types 3 and7 = Epidemic keratoconjunctivitis or shipyard eye: It occurs mainly in adults and is highly contagious, caused by types 8, 19 and 37. Fig. 68.1: Adenovirus (schematic diagram). * Infantile gastroenteritis: Serotype 40 and 41 may account for 5-15% of cases of viral gastroenteritis in young children ‘ Acute hemorrhagic cystitis in children, especially in boys-caused by serotypes 11 and 21 ‘ Immunocompromised patients are at higher risk of developing serious pneumonia © Transplant recipients may develop pneumonia, hepatitis, nephritis, colitis, encephalitis and hemorrhagic cystitis. Types 34 and 35 are isolated commonly from transplant recipients. Laboratory Diagnosis Depending on the manifestations, various specimens such as throat swab, conjunctival swab, stool or urine may be collected % Virus isolation: Primary human embryonic kidney cell line and A549 cell line are the most susceptible cell lines Viral growth can be detected by: = Characteristic cytopathic effect: Rounding and grape-like clustering of swollen cells, = Antigen detection by direct-F test. Serotyping: Type specific antigens (viral capsid proteins) can be identified by hemagglutination test (targeting HA antigens) and neutralization test (targeting capsid proteins) + Direct-IF test: It can be employed to detect adenoviral antigens from clinical samples such as throat or conjunctival secretions by using fluorescent tagged anti- hexon antibody + Fastidious enteric serotypes such astype 40 and 41 from stool: They can be detected by electron microscopy or by antigen detection by ELISA Molecular methods: PCR has been available targeting group-specific conserved hexon or fiber genes. Multiplex PCR followed by sequencing is done for detection of adenovirus types. PCR is rapid and more sensitive than conventional culture = Real-time PCR is used to monitor viral load, which is useful for immunocompromised and transplant recipients = The BioFire FilmArray respiratory and gastrointestinal panels are available for simultaneous detection of ‘many microbial pathogens including Adenovirus. + Serum antibody detection: It can be done by ELISA. Treatment and Control ‘Symptomatic treatment is given; only in severe cases of pneumonia cidofovir is recommended. General preventive measures are: + Effective hand washing 4 Sodium hypochlorite to disinfect environmental surfaces © Chlorination of swimming pools and waste water Strict asepsis during eye examinations. Scanned with CamScanneree | ae CHAPTER 68 @ Miscellaneous: al Infections of Respiratory Tract ‘Adenoviruses used for Gene Therapy Replication defective adenoviruses can also be used as live- virus vectors for the delivery of vaccine antigens and for gene therapy; e.9. trials on adenovirus vectored M. tuberculosis (using 854 antigen) , HIV and COVID-19 vaccines. RHINOVIRUS INFECTION (COMMON COLD) Rhinoviruses are the most common cause of common cold. ‘They belong to Picornaviridae family, which also include enteroviruses (Chapter 73). % ‘They use host cell intercellular adhesion molecule-1 (ICAM-1) as receptor % More than 100 antigenic types have been identified % They are similar to enteroviruses in structure and properties except that = Acid-labile (unstable below pH 6) = Transmitted by respiratory route. % Clinical features: The incubation period is about 2-4 days = Common cold syndrome: Rhinoviral symptoms are similar to that of any other viruses causing common cold syndrome such as coronaviruses, adenoviruses, enteroviruses, parainfluenza viruses, and influenza, viruses = The primary disease in adults presentsas rhinosinusitis, Usual clinical symptoms include sneezing, nasal ob- struction, nasal discharge, and sore throat, but no fever = Secondary bacterial infection may produce otitis, ‘media, sinusitis, bronchitis, or pneumonitis, especially in children. ® Relapse: The average adult gets 1-2 attacks each year Laboratory diagnosis: Rhinoviruses can be grown in human diploid cell lines such as WI-38 and MRC-5 cell lines. Mostof the strains grow better at 33°C (nasopharynx temperature) but not at 37°C Treatment is supportive (i.e. symptomatic treatment). EXPECTED QUESTIONS 1. Write short notes on: 1, Infectious mononucleosis. 2, Adenovirus infections. 3. Rhinovirus infections Multiple Choice Questions (MCQs): 1. Which of the following virus is the agent of infectious mononucleosis ? a. Epstein-Barr virus b. Human herpesvirus-6 < Gytomegalovirus dd. Varicellazoster virus 2. Which of the following tumor is not caused by Epstein-Barr virus? a. Post-transplant lymphomas b. Hodgkins disease Burkitt’ lymphoma d._Kaposis sarcoma 3. A 25-year-old female has developed fever, sore throat, and lymphadenopathy accompanied with Answers 1a 2d 3b 4b 5c atypical lymphocytosis and an increase in sheep cell agglutinins. The diagnosis is most likely: a. Hepatitis . Infectious mononucleosis Chickenpox d._HSVinfection 4, Which of the following adenovirus serotypes ‘cause epidemic keratoconjunctivitis? a. Serotypes 3 and 7 b. Serotypes 8, 19, and 37 & Serotypes 40 and 41 d._ Serotypes 11 and 21 5. All of the following are true about rhinovirus, except: a. More than 100 antigenic types have been identified b. Acid-labile © Incubation period is 10-14 days d. Transmitted by respiratory route ——_——_, Scanned with CamScannerisn GE * Young adult (wrestling, swim team) © Umbilicated warts © Eosinophilic cytoplasmic inclusion bodies 316 KAPLAN) MEDICAL Transmission: direct contact (sexual) and fomites Pathogenesis: replication in dermis Disease: single or multiple (<20) benign, wart-like tumors; in central caseous material (eosinophilic cytoplasmic inclus Diagnosis: clinical (warts are umbilicated); eosinophilic cytoplasmic inclusion bodies Treatment: self-limiting in healthy persons; ritonavir, cidofovir for immunocompromised Recall Question Chapter 4 Medically Relevant Viruses HSV-1 virus lies latent in which of the following nerve ganglion? A. Facial nerve ganglion Lingual nerve ganglion 8 C__Oculomotor nerve ganglion D. Trigeminal nerve ganglion Answer: D RNA VIRUSES: CHARACTERISTICS All RNA viruses are single-stranded (ss) except Reovirus. ss(—)RNA viruses carry RNA-dependent RNA polymerase. A virion-associated polymerase is also carried by Reovirus, Arenavirus, and Retrovirus (reverse transcriptase), Most RNA are enveloped; the only naked ones are Picornavirus, Calicivirus and Hepevirus, and Reovirus Some RNA viruses are segmented, i.e. there are different genes on different pieces of RNA\ * Reovirus + Orthomyxovirus + Bunyavirus + Arenavirus Scanned with CamScannerKAPLAN) MEDICAL 317 a ~ POSITIVE-STRANDED RNA VIRUSES Microbiology Table II-4-11. Positive-Stranded RNA Viruses* ry Virion- Envelope rns Sr ee) re ee Calicivirus ‘ss(+)RNA No Naked Icosahedral | Cytoplasm Norwalk agent Linear eb Noro-tke virus ‘Hepevirus ‘ss(+)RNA | No Naked Icosahedral | Cytoplasm Hepatitis E Linear polymerase Picornavirus | ss(+)RNA No. Naked Icosahedral | Cytoplasm Polio** Linear polymerase ECHO Enteroviruses Rhino Coxsackie Hepatitis A Flavivirus ‘ss(+)RNA | No Enveloped | Icosahedral | Cytoplasm Yellow fever Linear polymerase Dengue ‘St. Louis encephalitis Hepatitis C West Nile virus Togavirus | ss(+)RNA | No Enveloped | icosahedral | cytoplasm | Rubella Linear Cee WeE, EEE Venezuelan encephalitis Coronavirus | ss(+)RNA | No Enveloped | Helical Cytoplasm | Coronaviruses SARS-CoV frend polymerase Retrovirus | Diploid | RNA dep. Enveloped | icosahedral | Nucleus HWW 55(+)RNA | ona, ae al Linear polymerase Sarcoma “mnemonic (+)RNA Viruses Cll Henry co and Elo To Come Rightaway ‘*Mtnemonie: Picomaviruses: PE Co Bn AViuses Polio, ntero, Echo, Coxsackie, Rhino, Hep A 318 KAPLAN) MEDICAL Scanned with CamScanneraS Part Ile Microbiology Key Vignette Clues Norwalk Virus Norwalk Virus Reservoir: human GI tract ‘© School-aged child —+ adult ‘Transmission: fecal-oral route, contaminated food and water + Acute viral gastroenteritis Disease: acute gastroenteritis \onmnemmnatoy) + Watery; no blood or pus in stools + Nausea, vomiting, diarrhea + 60% of all nonbacterial gastroenteritis in U: + Outbreak of viral gastroenteritis in cruise ships attributed to Norovirus Diagnosis: RIA, ELISA ‘Treatment: self-limiting; no specific antiviral treatment Prevention: handwashing HEPEVIRIDAE + Naked, icosahedral «+ Positive-sense ssRNA Hepatitis E Virus (previously discussed) PICORNAVIRIDAE Family Characteristics + Small, naked, icosahedral + Positive-sense ssRNA + Summer/fall peak incidence + Resistant to alcohol, detergents (naked capsid) + Divided into genera: ~ Enteroviruses: fecal-oral transmission, do not cause diarrhea, peak age <9 years, stable at pH 3 ~ Rhinoviruses: not stable under acidic conditions, growth at 33 C (9148) ~ Heparnavirus g Figure tl-4-19. Picomavirus Viruses of Medical Importance + Enteroviruses (acid-stable): polio vir virus B; D68; echoviruses ; Coxsackie virus A; coxsackie ‘+ Rhinoviruses (acid labile) ‘+ Heparnaviruses: HAV Scanned with CamScannerTable II-4-12. Summary of Picornaviridae Rr UM un ud Duo aL ec ‘Asymptomatic to fever | Serology (virus | No specific Polio Fecal-oral Virus targets eon ofunknown origin; | absent from CSA) | antiviral/live aseptic meningitis: accra (Sabine ad paralytic polio (flaccid killed vaccine asymmetric paralysis, (Salk) no sensory loss) Neural fatigue Post-Polio Syndrome | Patient with polio decades earlier, progressive muscle atrophy Coxsackie | Fecal-oral Fecal-oral spread | Hand, foot, and Virus isolation | No specific with potential for mouth (A16); from throat, ‘treatment/ dissemination to herpangina; aseptic | stool, or CSF handwashing, other organs; often | meningitis; acute asymptomatic with | lymphoglandular viral shedding pharyngitis; common cold Coxsackie B | Fecal-oral ‘As above Bornholm disease As above No specific/ (evit's grip); aseptic handwashing meningitis; severe systemic disease of newboms; myocarditis 68 Fecal-oral, | Invade mucosa, Motor-neuron Serology/RTE-PCR | No specific/IVIG/ respiratory | lymphatics; potential | disease; respiratory handwashing spread to CNS diseases Echoviruses | Fecal-oral | As above Fever and rash of ‘As above No specific/ handwashing Rhinovirus Rhinovirus | Respiratory | Acid labile; grows at | Common cold; #1 Clinicat No specific/ 33.C(91.4F); over | cause, peak summer/ handwashing, 100 serotypes fall Hepamavirus HAV Fecal-oral —_| Virus targets Infectious hepatitis | IgMtoHAVse- | No specific/ hepatocytes; liver rology killed vaccine and function is impaired hyperimmune serum Scanned with CamScannerKey Vignette Clu: SARS-CoV © Patient with acute respiratory distress, Travel to Far East or Toronto + Winter/spring peak incidence 324 KAPLAN) MEDICAL CORONAVIRIDAE Family Characteristics + Enveloped, helical «+ Positive-sense ssRNA + Hemagglutinin molecules make up peplomers on virus surface, which give shape like sun with corona Viruses of Medical Importance + Coronavirus + Severe acute respiratory syndrome coronavirus (SARS-CoV) Coronavirus ‘+ Second most common cause of the common cold + Winter/spring peak incidence SARS-CoV Reservoir: birds and small mammals (civet cats) ‘Transmission: respiratory droplets; virus also found in urine, sweat, and feces; original case is thought to have jumped from animal to human Disease: severe acute respiratory syndrome (SARS) * Atypical pneumonia Chapter 4 » Medically Relevant Viruse| * Clinical case definition includes fever of >38.0 C (100.4 F), flu-like illness, dry cough, dyspnea, and progressive hypoxia + Chest x-ray may show patchy distribution of focal interstitial infiltrates Diagnosis + Includes clinical presentation and prior history of travel to endemic area or an association with someone who recently traveled to endemic + Lab tests: detection of antibodies to SARS-CoV, RT-PCR, and isolation of the virus in culture ‘Treatment: supportive; ribavirin and interferon are promising MERS-CoV (Middle Eastern Respiratory Syndrome) Reservoir: bats and camels Disease and transmission: similar to SARS Recall Question Scanned with CamScanner° ara &D 332 of 518 + Severe acute respiratory syndrome coronavirus (SARS-CoV) Coronavirus + Second most common cause of the common cold + Winter/spring peak incidence Key Vignette Clues SARS-CoV, SARS-CoV * Patient with acute respiratory Reservoir: birds and small mammals (civet cats) distress ‘Transmission: respiratory droplets; virus also found in urine, sweat, and fe * Travel to Far East or Toronto original case is thought to have jumped from animal to human ‘+ Winter/spring peak incidence Disease: severe acute respiratory syndrome (SARS) 324 KAPLAN) MEDICAL Chapter 4 © Medically Relevant Viruse + Atypical pneumot + Clinical case definition includes fever of >38.0 C (100.4 F), flu-like illness, dry cough, dyspnea, and progressive hypoxia + Chest x-ray may show patchy distribution of focal interstitial infiltrates Diagnosis + Includes clinical presentation and prior history of travel to endemic area or an association with someone who recently traveled to endemic area + Lab tests: detection of antibodies to SARS-CoV, RT-PCR, and isolation of the virus in culture Treatment: supportive; ribavirin and interferon are promising MERS-CoV (Middle Eastern Respiratory Syndrome) Reservoir: bats and camels Disease and transmission: similar to SARS Recall Question The Culex mosquito is responsible for the transmission of which ofthe following viruses? A Dengue virus B. West Nile virus Yellow fever virus D Zika virus Answer: B —— 4 Scanned with CamScannerIt is nonenveloped DNA virus, space vehicle shaped Disease produced by adenovirus Adenovirus serotype associated Hemorrhagic cystitis ‘Adenovirus type 11 and 21 (boys) Infant diarrhe ‘Adenovirus serotype 40, 41 Ocular Infections Epidemic keratoconjunctivitis ‘Adenovirus type 8,19, 37 (Shepard eye, industrial worker) Pharyngoconjunctival fever or ‘Swimming pool conjunctivitis (follicular) ‘Adenovirus type 3,7,14 (tends to occur in outbreaks, at children’s summer camps) Respiratory Diseases Upper respiratory tract infection Serotypes 1, 2,3 and 5 Pneumonia Serotypes 3, 7, and 21 ‘Acute respiratory disease syndrome In miltary recruits, associated with type 4 and 7 Transplant recipients Serotypes 34 and 35. 1 risk to develop pneumonia, hepatitis, nephritis, colitis, encephalitis, and hemorrhagic cystitis Scanned with CamScannerCoronavirus Infections Including COVID-19 CHAPTER 6/7 ets ahaa ee © Severe Acute Respiratory ‘Syndrome (SARS) (MeRS) ‘© Middle East Respiratory Syndrome '® Coronavirus Disease (COVID}-2019 INTRODUCTION Coronaviruses (CoV) cause respiratory tract infections in man; illness ranging from mild common cold to severe disease like pneumonia. Morphology Coronaviruses are enveloped; carrying petal or club- shaped or crown-like peplomer spikes giving appearance of solar corona (Fig. 67.1). % ‘They are large (120-160 nm) spherical viruses having a helical symmetry + They possess linear, positive-sense ssRNA of 26 to 32 kbp size, largest among the non-segmented RNA viruses. Classification Coronaviridae family contains two subfamilies: Coronavirinae and Torovirinae. The former has been grouped into four genera—a, B, 7 and 8. Most of them lectron micrograph of coronavirus (petal or club- shaped peplomers) (arrows showing). Source:10#10270, Public Health image Library, Centers for Disease Control and Prevention (CDC), Atlanta/Dr Fred Murphy; Syvia Whitfield (with permission) infect animals except y Coronavirus species, which are the pathogens of birds, Human infection is uncommon except few who have adapted to human conditions. Human Coronaviruses “There are seven recognized coronaviruses that are known to cause human infections (Table 67.1); most of them belong to Betacoronavirus except the first two (229E and NL63) which belong to Alphacoronavirus. “They spread by droplet transmission (though coughing or sneezing) and also by close personal contact, such as touching infected persons or objectsand then subsequently touching mouth, nose, or eyes. SEVERE ACUTE RESPIRATORY SYNDROME (SARS) ‘SARS-CoV had caused an explosive epidemic in China in 2003, known as severe acute respiratory syndrome. ECan ‘Common coronaviruses that are widespread in distribution, affecting people of most part of the world and cause mild upper respiratory tract infections 1, Human coronavirus 229E 2. Human coronavirus NL63 3. Human coronavirus OC43 ‘4, Human coronavirus HKU Coronaviruses that caused explosive outbreaks of severe respiratory disease with higher mortality are: 5. SARS-CoV (Severe acute respiratory syndrome coronavirus): It thas caused an explosive epidemic called ‘SARS’ in China in 2003 6, MERS-CoV (Middle East respiratory syndrome coronavirus}: It thas caused an explosive epidemic ‘MERS' in Middle East in 2012 7, SARS-CoV-2 Severe acute respiratory syndrome coronavirus-2- its the causative agent ofan ongoing explosive pandemics affecting the whole world in 2019-20; called COVID-19 (Coronavirus disease, 2019) Scanned with CamScannerCHAPTER 67 ® Coron: s Infections Including COVID-19 tired st ode wantin Fnal ot —_ wenscov: “Coimcome ae coo" Sas: y __- oat cnet a nn Fig. 67.2: Origin of MERS-CoV, SARS-CoV and SARS-CoV-2. History: SARS was first recognized in China in 2003 by WHO physician Dr Carlo Urbani. He diagnosed it in a businessman who had travelled from China, through Hong Kong, to Hanoi, Vietnam. The businessman and the doctor who first diagnosed SARS both died from the illness Epidemiology: During 2003 outbreak, the SARS virus, spread from Asia to various regions of the world causing nearly 8,098 cases in 29 countries, with over 774 deaths. However, India remained free from the infection. Since 2003, no case has been reported from anywhere in the world ‘Source: SARS-CoV infection in humansis believed to be contracted from animals, including monkeys, Himalayan palm civets, raccoon dogs, cats, dogs, and rodents (Fig. 67.2) ‘Transmission: SARS-CoV is primarily transmitted from person to person (droplet or contact); mainly during the second week of illness, which corresponds to the peak of virus excretion in respiratory secretions % Clinical manifestations include severe lower respiratory tract infection; characterized by muscle pain, headache, sore throat and fever, followed by the onset of respiratory symptoms mainly cough, dyspnea and pneumonia. In some cases, it may progress to acute respiratory distress syndrome % Treatment: There was no effective vaccine or drug available. Cases were managed only symptomatically Infection control: Implementation of appropriate infection control practices was the main reason behind bringing the global outbreak to an end. ° MIDDLE EAST RESPIRATORY SYNDROME (MERS) MERS-CoV can cause a severe form of lower respiratory illness with a mortality rate of 35%. Epidemiology MERS was first reported in Saudi Arabia in 2012. Between 2012-January 2020, about 2,519 laboratory confirmed cases of MERS-CoV with 858 deaths (mort 34.3%) have been reported to WHO from 27 different countries. India was not affected Saudi Arabia accounted for 84% (2,121 cases, including 788 related deaths) of the cases followed by other Middle East countries Origin: ‘The origin of the virus is not fully understood but, according to the analysis of different virus genomes, it is believed that it might have originated in bats and was transmitted to camels sometime in the distant past (Fig. 67.2) Source: Dromedary camels are a major reservoir host CoV and an animal source of MERS infection Transmission: Both zoonotic and human to human transmission have been reported = Zoonotic: MERS-CoV can be transmitted through direct or indirect contact with infected dromedary camels = Human-to-human: It does not pass easily from person to person unless there is close contact, such as providing unprotected care to an infected person by family members and healthcare workers. High-risk to acquire infection: People at increased risk for MERS-CoV infection include: ® Recent history of travel from the Arabian Peninsula within 14 days = Close contacts of a confirmed case of MERS = Healthcare workers not following recommended infection control precautions = People with exposure to infected camels = Elderly people are at higher risk of developing severe disease and complications including death. High-risk for severe disease: Elderly people with diabetes, renal failure, chronic lung disease, and immunocompromised persons are considered to be at high-risk of severe disease from MERS-CoV infection. Clinical Manifestat Incubation period is about 2-14 days Typical MERS symptoms include fever, cough and shortness of breath Pneumonia is common, but not always present Gastrointestinal symptoms, including diarrhea, have also been reported Complications such as acute respiratory distress syndrome and kidney failure occur, especially in people with underlying comorbid conditions. ns Laboratory Diagnosis + Detection ofantibodies in serumindicatespast-exposure. ELISA is primarily used for screening of antibodies; which should be confirmed by immunofluorescence assay (IFA) and microneutralization assays Scanned with CamScannerSECTIONS @ Respiratory Tract Infections 4 Molecular method: Detection of specific MERS-CoV RNA by real-time RT-PCR in respiratory specimens indicates active infection. However, laboratory confirmation requires detection of at least two MERS-CoV specific genes such as upE and ORFIb present in the upstream ofthe £ gene % Antigen detection: Capture ELISA detecting nucleocapsid protein in nasopharyngeal aspirate is under evaluation. ‘Treatment and Prevention No vaccine or specific treatment is currently available, however several vaccines and drug trials are under development. ‘Treatment is supportive and based on the patient's clinical condition. General preventive measures include: % Regular hand washing before and after touching animals (especially dromedary camels) and should avoid contact with sick animals, + Avoid consumption of raw or undercooked camel products, including milk and meat; should be consumed only after pasteurization, cooking or other heat treatment. CORONAVIRUS DISEASE (COVID)-2019 Coronavirus disease-2019 (COVID-19) is an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has caused an explosive catastrophic pandemic that affected almost all part of the world, and produced significant loss of lives and the worst financial crisis recorded ever, since World War Il. EPIDEMIOLOGY History SARS-CoV-2 originated from China and subsequently spread rapidly to affect rest the world over a period of 3-4 months—one of the fastest spreading infectious disease recorded in the history of mankind. © Wuhan: It was first identified in December 2019 in Wuhan, China, which produced a large cluster of pneumonia cases— hence, the virus was initially called asthe ‘Wiuhan Virus’. Subsequently it was named as the 2019- novel coronavirus (2019-nCoV) Origin: In further studies, it was found that it’s a B-Coronavirus, with highly identical genome (96% homology) to SARS-like bat coronavirus, pointing towards bat as the natural host (Fig. 67.2) + PHEIG: As the cases continued to rise, the outbreak was declared as ‘Public Health Emergency of International Concern (PHEIC)’ on 30" January 2020 + Nomenclature: On 11" February 2020, WHO announced the official name ‘COVID-19' for this new coronavirus disease and also renamed the virus as SARS-CoV-2 because its genome closely resembled to SARS-CoV. + Pandemic: The disease spread rapidly in an explosive manner. On 11" March 2020, WHO declared itas a global pandemic. By that time, about 114 countries were affect with >118,000 cases and 4,291 deaths + The explosive spread continued, affecting over 200 countries in the next couple of months. Situation in World (As of March 2021) As this explosive pandemic is still ongoing, the epidemio. logical data including the geographical distribution is expected to change over time. The information given in this, chapter is as of March 2021. + Total cases: By March 2021, over 11.5 crore cases were reported globally with > 25 lakh deaths + Daily count: Every day, nearly 2to 4 lakh cases are being reported with >9,000 deaths globally 4 Highest cases: USA accounted for maximum cases (>2.9 crore), followed by India, Brazil and Russia + Highest cases (%): In terms of total cases per 100 population, countries such as Czechia (11%), USA (8.8%), Israel (8.5%), Portugal (7.9%) and Bahrain (7%), were worst affected, compared to India (0.8%) ‘ Mortality rate: The severity of the disease varies among the countries and also across different time spans. Countries such as France, Italy, UK and Belgium. reported a mortality rate of > 10%, in the early phase of the pandemic, which reduced subsequently. In contrast USA (1.8%) and India (1.4%) reported lower mortality rate during the pandemic. The average mortality rate in, the world is estimated to be 2.2% Rapid rise of cases occurred in China at the 18 (over 80,000 cases by end of February 2020). Wuhan accounted for the majority (>80%) of cases in China. However, cases rapidly declined thereafter + Italy: Italy was one of those countries which were worst hitin the early phase of this pandemic. The country was not prepared when the disease started. Asa result, there was a rapid surge of cases with a mortality rate >10% 4 USA: Accounts for highest number of cases (>3 crore) with a mortality rate of 1.8% Growth curves: The growth curves of COVID-19 cases vary among the countries. Different countries are at different stages of pandemic. In countries such as Italy, Spain and USA, the disease spread quickly reaching its peak early; whereas in other countries like India the disease had a slower rate of growth (initially) + Variants: The increase number of cases in various parts the later phase of the pandemic may be due to emergence of various variants of the SARS-CoV-2 virus, such as UK variant, Brazilian variant and South ‘African variant ‘ India was one among those countries where the COVID-19 pandemic had a slower growth curve to reach its peak. India accounts for second highest number of cases (>}.1 crore) with a mortality rate of 1.4%. oV-2 comprises of a nucleocapsid, surrounded by an envelope. It measures 120 nm in size; has a helical symmetry. It possesses 4 structural proteins (N, S, M and Scanned with CamScannerCHAPTER 67 © Coronavirus Infe Positive sense single-stranded RNA Spi protein (S) Membrane protein (M) Envelope (E) protein Nucleocapsid protein (N) pid part of envelope Fig, 67.3: Structure of SARS-CoV-2. E), 16 nonstructural proteins and several other accessory proteins (Fig. 67.3). Nucleocapsid consists of a positive-sense single- stranded RNA (~30 kb genome size), surrounded by nucleocapsid protein (N) * The envelope is lipoprotein in nature; the lipid part is host-derived into which a number of proteins are embedded such as: = Spike protein (S): Helps in the attachment to the host cells. Neutralizing antibodies are produced against $ protein are protective in nature. It has two subunits. Sl subunit possesses the receptor-binding domain (RBD), which binds to a specific receptor in the host cell surface ¢ S2 subunit facilitates virus-cell membrane fusion = Membrane glycoprotein (M): Itis the most abundant structural protein, gives the shape to the virus = Envelope protein (E): It is a transmembrane protein and with ion channel activity; found in small quantities. Non-structural proteins: They include several enzymes which help in replication of the virus, e.g. RNA-dependent RNA polymerase (RdRp), helicase, etc. PATHOGENESIS COVID-19 virus is prim: droplets and contact routes. transmitted via respiratory Droplet Transmission Droplet transmission occurs when a person is in close contact (within I meter) with an infected person. Exposure to potentially infective respiratory droplets occurs, for ions Including COVID-19 example, through coughing, sneezing or very close personal contact resulting in the inoculation of entry portals such as the mouth, nose or conjunctiva. Use of mask can prevent droplet transmission. Contact Transmission ‘Transmission of the COVID-19 virus can occur directly by contact with infected people, or indirectly: By contact with the surfaces in the immediate environment or + With objects used on or by the infected person (e.g. stethoscope or thermometer) or Through fomites (inanimate objects) in the immediate environment around the infected person such asinfected clothes, utensils, furniture. Following contact (direct or indirect), the virus can only be transmitted by touching the contaminated hand to a person’s mouth, nose or conjunctiva. Frequent hand hygiene following potential contact exposure is crucial to prevent this type of transmission. Aerosol Transmission Aerosol transmission (spread of the infected droplet nuclei beyond one meter) is not documented yet, although active research is on-going in this regard. However, in specific settings in which aerosol-generating procedures are performed (e.g. endotracheal intubation), aerosol transmission of the COVID-19 virus may be possible (Chapter 21). Use of N95 respirator is important to prevent this type of transmission. Pre-symptomatic Transmission Itis defined as the transmission of the COVID-19 virus from a person who is infected and shedding the virus but has, not yet developed symptoms. This type of transmission has been observed in people 1-3 days before the onset of their symptom, with the highest viral loads detected around the day of symptom onset, followed by a gradual decline over time. Host Cell Entry SARS. CoV-2 enters into the target host cells by binding of its spike glycoprotein (S) antigen with the host cell receptor, i.e. angiotensin converting enzyme-2 (ACE-2). This is also the receptor for SARS-CoV. * Spike protein cleavage: For virus entry into a host cell, its S protein needs to be cleaved, which is mediated by host cell proteases; of which TMPRSS2 (transmembrane protease serine 2) is important * Fusion: Cleavage of S protein produces $1 subunit which binds to ACE-2 and S2 subunit which causes fusion of viral envelope with host cell membrane. ‘Then follows the entry of the virus via endosomal pathway + ACE-2receptors are highly expressed on type- Ialveolar cells in lungs and on the epithelial cells of oral mucosa; also found on cells of heart, kidney, endothelium and ‘Scanned with CamScannerSECTION 8 @ Respiratory Tract Infections intestine. Therefore, the patients develop extrapulmonary manifestations in addition to respiratory symptoms. ‘Note: The primary function of ACE-2 is that, it helps to reduce blood pressure and has anti-inflammatory action. Development of ILI ACE-2 receptors are highly expressed on the epithelial cells, of oral mucosa. Therefore, at the initial stage, SARS-CoV-2 infects the pharyngeal epithelium, induces inflammation. ‘This accounts for the influenza-like illness (ILI) which occurs atthe beginning stage of most of the symptomatic cases. Development of ARDS ‘The leading cause of mortality in patients with COVID-19 is hypoxemic respiratory failure which can result in acute respiratory distress syndrome (ARDS), Reduced Surfactants In lungs, ACE-2 receptors are highly expressed on type- alveolar cells. These cells normally produce pulmonary surfactants which lower the alveolar surface tension. In COVID-19 patients the following events take place. + Damage to the type-II alveolar cells leads to reduced production of pulmonary surfactants; as a result of which alveoli tend to collapse. The air-liquid-interphase is perturbed which leads to fluid retention in the interstitial space % To prevent collapse, the muscular movement of inspiration becomes hyperactive, which results in increased lung volume in the interstitial space. The "low pressure area” created in the interstitial space attracts liquid, which further contributes to edema in the lungs. Cytokine Storm ‘ThepresenceofSARS-CoV-2inlunginducesan uncontrolled ‘generalized immune response. Several immune cells like neutrophils, T-lymphocytes, macrophages are recruited to the lungs (Fig. 67.4). 4 Acute cytokine influx: These immune cells release pro- inflammatory cytokines—IL-2, IL-2R, IL-6, IL-7, IL-8, IL- 10, G-CSE IFN-y, IP-10, MCP-1, MCP-3, TNF-and others, Host injury: The elevated cytokines leads to various consequences such as: 1 Tissue damage and necrosis = Further recruitment of leukocytes = Impaired gas exchange, which leads to reduced blood oxygenation and tissue hypoxia = Endothelial damage of pulmonary vasculature, leading to vasodilation, microvascular thrombosis and hemorrhage, and hypercoagulability Normal state [@ le Bronchial epithe cot "= ‘Type 1 alveolar ‘epithelial cell Diseased stato SARS-CoV-2 infecting alveol Inflammation Pro-inflammatory cytokines ‘causing cytokine storm ‘such as IL-2, IL-6, IL-7, IL-8, IL-10, G-CSF, IFN-7, ‘TNF-a and others, Pulmonary edema Fig. 67.4: Cytokine storm seen in COVID-19 patients. Scanned with CamScannerCHAPTER 67 ® Coronavirus Infections Including COVID-19 Ca = Dilatation of blood vessels underlying the alveoli: ‘This allows passage of fluid from the blood vessels to lungs which leads to pulmonary edema. These infiltrates in the lungs appear as ‘ground-glass’ in chest imaging = Fibrosis: In the later stage, there occurs recruitment of fibroblast, which causes lung fibrosis, and ultimately, leads to respiratory failure. This stage is called as acute respiratory distress syndrome (ARDS), eventually leading to respiratory failure ‘© Multiorgan failure: Cytokines can also induce damage to other organs of the body such as heart, kidney, liver, etc. ‘There occur several catastrophic events such as sepsis, septic shock and multiorgan failure including acute kidney injury and cardiac injury 4% Risk factors: The major risk factors for severe disease are: = Age > 60 years (risk increases with age) = Underlying comorbidities such as diab hypertension, cardiac disease, chronic obstructive lung disease, cerebrovascular disease, chronic kidney disease, immune-suppression and cancer. es, CLINICAL MANIFESTATIONS The incubation period for COVID-19 (time between infection and symptom onset) is on an average of 5-6 days, but can be as long as 14 days. COVID-19 patients may present with following signs and symptoms: % Common features: Fever, cough with expectoration, fatigue, shortness of breath, myalgia, rhinorrhea, sore throat, diarrhea. Loss of smell or taste sensation may occasionally occur preceding the onset of respiratory symptoms Atypical symptoms: Particularly seen in older people and immune-suppressed patients—such as fatigue, reduced alertness, reduced mobility, diarthea, loss of appetite, delirium, and absence of fever. Children might not develop fever or cough as frequently as adults. Clinical Severity Based on the clinical severity, the disease may be classified into the three clinical stages (Table 67.2). covi QiImmcnn nara @ Specimens: Throat and nasal swabs NAAT: Nucleic acid amplification testing > Formats: Real time RT-PCR, automated formats (CBNAAT and Truenat) > Genetargets:Screening E N,M genes), confirmatory (RARE, N2genes, etc) @ Antigen detection assay: Point-of-care test; detects nucleocapsid protein antigen in nasopharyngeal swab @ Antibody (IgG) detection assay: Used for serosurveillance and survey in high-risk and vulnerable group; not for clinical diagnosis Contd. Table 67.2: Clinical severity of COVID-19 disease, Ui(influenza-ike Patients with uncomplicated upper illness) respiratory tract if may have mild symptoms such as fever, cough, sore throat, nasal congestion, malaise, headache ‘Without evidence of breathlessness or hypoxia (normal saturation) Pneumonia with Dyspnea, fever and cough no signs of severe Hypoxia, SpO, <94%, respiratory rate 2 24 disease per minute Severe pneumonia Clinical signs of pneumonia plus one of the following sign of severe respiratory distress: (0 Respiratory rate >30/min or i) SpO, <90% ‘Symptoms: Onset of new or worsening respiratory symptoms within one week Chest imaging: Shows bilateral opacities, not fully explained by effusions, lobar or lung collapse, or nodules Acute respiratory distress syndrome (ARDS) Decreased PaO, /FIO, (normal value ~ 500) ‘ARDS can be classified into—mild (<300), moderate (<200), and severe (<100); (when PEEP or CPAP is maintained at 25 cm H,0) Sepsis Acute life-threatening multiorgan dysfunction: Clinically diagnosed by SOFA {sequential organ failure assessment) score {as described in Chapter 29) Septic shock Persisting hypotension despite volume resuscitation, requiring vasopressors to ‘maintain mean arterial pressure 265 mm Hg and serum lactate level >18 mg/dl (as described in Chapter 29) ‘Abbreviations: PEER postive end-expiratory pressure; CPAP, continuous postive ‘airway pressure; SpO, blood oxygen saturation level PaO/FO, ratio of arterial ‘oxygen partial presse (in mm Hg) t fractional inspired oxygen Contd. @ Viral culture: Used for esearch purpose & Nonspecific tests include: > Radiology (chest CT scan): Ground-glass appearance > Biomarkers: IL-6, 0-dimer LABORATORY DIAGNOSIS Laboratory diagnosis is necessary only in specific indications as per Government of India, such as: + Patient with influenza-like illness (ILI) symptoms or severe acute respiratory infection (SARI) * Asymptomatic direct and high-risk contacts of a confirmed case to be tested once between day 5 and day 10 of contact + History of international travel in the last 14 days. Scanned with CamScanner ohCa SECTION 8 @ Respiratory Tract Infections Specimen Collection and Transport Preferred specimens: Throat (i.e. oropharyngeal) and nasal swabs are the preferred specimens. Dacron or polyester flocked swabs are used, dipped in viral transport media (VTM) after collection + Alternative specimens include: Nasopharyngeal swab, bronchoalveolar lavage (BAL) or endotracheal aspirate (in ventilated patients) + PPE: Appropriate PPE should be used for specimen collec- in such as gloves, gown, N95 respirator and face shield + Specimen transport and packing: Samples collected should be properly labelled, packed in three layers (triple packaging method) and transported to the laboratory ‘maintaining an adequate cold chain 4 Storage: Upon receipt, the specimens should be stored at appropriate temperature (4 °C for <5 days and -77 °C for >5 days) + Biosafety precaution: Initial processing of the specimen (before inactivation) should take place in a biological safety cabinet (BSC). The laboratory should have the following biosafety facility = For NAAT: Require biosafety level-2 facility = For culture: Require biosafety level-3 facility = For point-of-care test (Antigen detection): Can be performed without employing a BSC. Nucleic Acid Amplification Testing (NAAT) Real-time RT-PCR Real time reverse transcriptase PCR is the gold standard test for diagnosis of COVID-19. 4 The average time taken is around 4-5 hours from receipt of sample to generation of the result + ‘The advantage of this platform lies in its accuracy of detection as well as the ability to run up to 90 samples in a single run. Therefore, if available, this platform should be used as a frontline test for the diagnosis of SARS-CoV-2 4 Gene targets: Most of the commercial kits target two ‘genes, performed in a single reaction—one for screening and other for confirmatory Gene targets for screening are genus specific; ie. specific for Sarbecovirus Betacoronavirus): Spike protein (S) Envelope protein €) @- Membrane protein (M) @ Nucleocapsid protein (N) Gene targets for confirmation are species specifi specifi for SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) @ Open reading frames (ORF1a/b) @ N2 nucleocapsid ple: Most commercial kits available are based on ‘qualitative real-time PCR = ‘The target gene/s in the specimen is amplified in the thermocycler 2 = 7) =~ 2a 2a =H rw is RNP 22 Ege 22 te ‘9 +8 fone, $15 oe 3 10 dio o7 o7 oa os a oO A ob a te as of ee ee es cyees Fig. 67.5: Interpretation of real-time RT-PCR result for COVID-19 diagnosis. = When the amplicon binds with the probe, a fluores- cence is generated. ‘The point at which the fluores- cence starts is the cycle threshold (Ct) of the run = Asampleis considered positive when both screening, as well as confirmatory genes, are detected with a Ct value = 40 cycles (Fig, 67.5). = Detectable: NAAT becomes positive as early as day 1 of onset of symptom (usually after 5 days of infection) and starts to decline by 3 week and subsequently becomes undetectable (Fig, 67.6). Automated real-time RT-PCR Several automated real-time PCR are commercially available such as—Truenat and CBNAAT (Cartridge based nucleic acid amplification test, e.g. GeneXpert). Both these systems are already in use for the diagnosis of tuberculosis. 4 Advantages of these systems include: = These platforms have widespread availability even at district and primary health center level as these systems are already in use for the diagnosis of tuberculosis and other infectious diseases = They have a quick turnaround time (30-60 minutes) ‘+ Decline -»-¢—Convale- >, Pationt beging S0ne# to recover | Days since infection — SARS-CoV.2 RNA — IgM antibody — IgG antibody ‘and antigen Fig. 67.6: Course of the diagnostic markers in COVID-19. Scanned with CamScannerCHAPTER 67 @ Coronavirus Infections Including COVID-19 667 = Fully-automated, involves minimal handling; therefore poses minimum biosafety hazard. Safety is further augmented by the closed nature of these platforms. Gene targets used are: = CBNAAT: Two targets are used; E gene for screening and N2 gene for confirmation = Truenat: Two targets are used; F gene for screening and RdRp gene for confirmation. + However, disadvantages of these systems include: Only 1-4 samples can be tested in one run, therefore suitable only for laboratories with less sample load (24- 48 samples/day) Antigen Detection A rapid chromatographic immunoassay is commercially available (SD Biosensor) for qualitative detection of specific antigens (nucleocapsid protein) to SARS-CoV-2. + Nasopharyngeal swab, after collection should be immersed and squeezed in the viral extraction buffer, provided with the kit. This buffer inactivates the virus, releasing the antigen + Itisapoint-of-care test, conducted atthe bedside within one hour, as the antigen in the extracted buffer is stable only for an hour Performance: It is highly specific (99-10%), with moderate sensitivity (50-84%). Therefore, symptomatic but negative patients should be essentially referred for areal-time RT-PCR test. ‘There are various other antigen detection kits under validation, which may be marketed in near future. Antibody Detection IgG antibodies generally start appearing after two weeks of the onsetof infection, once the individual has recovered and last for several months. Therefore, the IgG test should not be used for clinical diagnosis. ELISA, chemiluminescence and immunochromatographic test formats are available for the detection of IgG antibodies. They may be useful in the following situations: % Sero-surveillance purpose, to estimate the proportion of population exposed to infection with SARS- CoY-2 including asymptomatic individuals; so that appropriate public health interventions can be planned and implemented for prevention and control of the disease The survey in high-risk or vulnerable populations such as health care workers, frontline workers, immuno- compromised individuals, individuals in containment zones, police and security personnel, etc. to know who has been infected in the past and has now recovered. Sequencing Sequencing methods played a major role in the i identification of SARS-CoV-2. * Itisnot used routinely for diagnostic purpose However, next-generation sequencing and metage- nomic next-generation sequencing will be needed for determining mutations in the genome of SARS- Cov-2. Viral Culture Although not recommended for diagnostic purpose, viral culture can be used for research purpose such as under- standing the properties of the virus and development of vaccine. Nonspecific Tests * Prognostic markers: There are several prognostic markers which can be used in the setting of ARDS, include: = Elevated IL-6 level: Indicates cytokine storm = Elevated D-dimer: Indicates the presence of high level of fibrin degradation products, thus suggesting an underlying coagulopathy = Elevated serum ferritin: Indicates inflammation Severe lymphopenia = Elevated C-reactive protein: Marker of acute inflam- mation, + CT scan of lungs shows ground glass appearance (Chapter 59, Fig. 59.4) and/or consolidation. iii: coviD-19 Currently, there is no definitive therapy available for COVID-19; however many clinical trials are ongoing (Table 67.3) Symptomatic management The mainstay of treatment is an early supportive therapy for symptomatic management Inpatients with severe respiratory distress > Supplemental oxygen therapy is given immediately > High-flow nasal cannula oxygenation (HENO) > Non-invasive mechanical ventilation > Mechanical ventilation: in patients with moderate or severe ARDS, higher PEEP (positive end-expiratory pressure) instead of lower PEEP is suggested. @_ Management of septic shock by—vasopressors, luid replace ‘ment by crystalloids suchas normal saline and Ringer’ lactate. Investigational therapy Few drugs are now recommended for treatment by the Government of India based on limited available evidence. The recommendations may be changed or updated as on when more data is available. Remdesivir It interferes with the action of viral RNA-dependent RNA polymerase @ Indication: May be considered in patients with moderate ease (those on oxygen) © Dosage: 200 mg IV on day 1 followed by 100 mg IV daily for 5 day 9 Contraindlcated in: Children, pregnancy, lactation iver or renal impairment. Contd. —_—— Scanned with CamScannerSECTION 8 © Respiratory Tract Infections Contd. Clim: coviD-19 Convalescent plasma therapy The plasma of patients recovered from COVID-19 contains neutralizing antibodies against SARS-CoV-2 virus. These antibodies are believed to eliminate the virus completely, Indication: May be considered in patients with the moderate disease who are not improving (oxygen requirement is progressively increasing) despite the use of steroids Dose is variable ranging from 4 to 13 mL/kg (usually 200 ml, ingle dose}, given slowly over not less than 2 hours. Tocilizumab It is a monoclonal antibody against IL-6 receptor, the most important cytokine raised in cytokine storm @ Indication: May be considered in patients with moderate disease with progressively increasing oxygen requirements, and in mechanically ventilated patients not improving despite the use of steroids @ Dose: 8 mg/kg (maximum 800 mg at one time) given slowly in 100 mL normal saline over 1 hour @ Special considerations: > Its given only when there is raised inflammatory markers, (eg. CRP ferritin, IL-6) > Should be monitored for secondary bacterial infections, and neutropenia > Active infections and tuberculosis should be ruled out before use. Hydroxychloroquine (HCQ) Itmay be effective in the early course of the disease and should be avoided in patients with severe disease. Discharge policy Upon clinical and/or microbiological recovery (negative result by real timer RT-PCR) the patient can be discharged and transmission- based precautions can be discontinued. Table 67.3: Treatment under research for (eee) Favipiravir Itis converted into an active form in cells ‘which inhibits RNA polymerase activity Remdesivir Itis converted into an active form (GS- 441524), which inhibits viral RNA-dependent RNA polymerase Lopinavir/Ritonavir Protease inhibitors; block viral replication Hydroxychloroquine Used for prophylaxis against COVID-19 SSemeeetver Pay (awe car os FTE A ST ‘The plasma of patients recovered from COVID-19 contains neutralizing antibodies against SARS-CoV-2 virus. These antibodies are believed to eliminate the virus completely Camostat mesylate Inhibits TMPRSS2 Hesperidin Inhibit binding of spike protein to ACE-2 PROPHYLAXIS Chemoprophylaxis Hydroxychloroquine (HCQ) has been recommended by the Government of India for prophylaxis for SARS-CoV-2 infection. However, itis reiterated that the intake of HCQ should not instill a sense of false security and should practice infection control measures as recommended. 4 Indication: HCQ prophylaxis is indicated in: = Asymptomatic household contacts of laboratory confirmed cases = Allasymptomatic healthcare workers = Asymptomatic frontline workers = Paramilitary/police personnel involved in COVID-19 related activities 4 Dosage: 400 mg twice a day on day 1, followed by 400 mg once weekly for next 7 weeks (except for household contacts, given for 3 weeks) + Contraindication: The following are excluded from HCQ prophylaxis—known case of retinopathy, hyper- sensitivity to HCQ, glucose-6-phosphate dehydrogenase (G6PD) deficiency, pre-existing cardiomyopathy and cardiac rhythm disorders, children <15 years age, in pregnancy and in lactation ‘ Precaution: ECG should be done before prescribing HCQ prophylaxis and during the course to look for prolongation of QT interval. COVID Vaccine Currently, there are several vaccines available against COVID-19; which are approved for human use after proven safe and effective in large (phase III) clinical trials. More so, intense research is on-going and more than 200 additional vaccine candidates are in development, of which more than 60 are in the stage of clinical development. % Vaccine principles: The COVID-19 vaccines available are based on one of these following principles: 1, Inactivated or weakened virus vaccines, which use a form of the virus that has been inactivated or weakened so it doesn’t cause disease, but still generates an immune response (e.g., Covaxin, CoroVac and BBIBP-CorV) 2. Protein-based vaccines, which use harmless fragments of proteins or protein shells that mimic the SARS-CoV-2 to safely generate an immune response (eg., Epi Vac Corona) 3, Viral vector vaccines (e.g., Adenovirus), which use a safe virus that cannot cause disease but serves as a platform to produce coronavirus proteins to generate an immune response (e.g., Covishield, Oxford- Astrazeneca, Sputnik V and Johnson & Johnson COVID -19 vaccine) 4. RNA and DNA vaccines, a cutting-edge approach that uses genetically engineered RNA or DNA to Scanned with CamScannerCHAPTER 67 @ Coronavirus Infections Including COVID-19 generate a protein that itself safely prompts an immune response (e.g., Pfizer-BioNTech, Moderna). % Adverse effect: The COVID-19 vaccines are proven to be safe, except for mild adverse reactions such as injection site pain, fever, tiredness, myalgia, fatigue and headache. For some vaccines (e.g., Pfizer and Moderna vaccine), the adverse effects are more pronounced after the second dose * Efficacy: Most vaccines in use are shown to be efficacious (70-90%) in phase III clinical trial. However, the duration of protection will be known in due course oftime Individuals infected with COVID-19 in past also should get the vaccine (complete schedule). However, person with active COVID-19 infection may increase the risk of spreading the same to others at vaccination site. For this reason, infected individuals should defer vaccination for 14 days after symptoms resolution 4 Storage: Most vaccines can be stored at 2-8°C, except Pfizer vaccine which needs to be stored at -80 to -60°C 4 Schedule: Most vaccines are given as two doses at 2-4 weeks gap by IM route; the exception being Johnson & Johnson vaccine, which is given as a single dose. i) Anaphylaxis or allergy to previous i) pregnancy and lactation, (iii) age <18yr. COVID-19 Vaccine in India Two vaccines are licenced in India; enrolled for use in a phased manner: (i) Phase I (January 16 2021 For healthcare workers; (ii) Phase II (March 1* 2021): High-risk general public; which include persons > 60 years age and persons between 45 and 59 years of age with comorbid conditions such as cancer, diabetes, hypertension, etc. ~ Covaxin: Initiated by ICMR-Bharat Biotech, India. It is a whole-virion inactivated vaccine, which uses spike protein as a target. It is administered in two doses (4 weeks apart) by IM route + Covishield: Itis prepared by Serum Institute of India, in collaboration with University of Oxford and AstraZeneca pharmaceuticals, UK. It is based on non-replicating adenovirus vector (modified Chimpanzee adenovirus, ChAdOx1) expressing spike protein. It is administered in two doses (4 weeks apart) by IM route. INFECTION PREVENTION AND CONTROL Infection prevention and control (IPC) is the most effective method currently available for the prevention of COVID-19. ‘The following are the key IPC measures need to be strictly followed, IPC Measures at Healthcare Facility IPC measures of droplet and contact precautions need to be followed by the healthcare workers while handling COVID-19 cases, except for aerosol-generating procedures (AGPs) when airborne precautions need to be followed (refer Chapter 21). Hand Hygiene As contact mode appears to be an important mode of transmission, absolute hand hygiene is probably the most effective method for the prevention of COVID-19. + Hand hygiene needs to be performed when opportunity arises (as per WHO's ‘my five moments of hand hygiene; Chapter 21) Hand hygiene must be performed by the correct technique, and for appropriate duration (20-40 sec for hand rub). Personal Protective Equipment The following are the current recommendations: ‘> HCWs giving care to the COVID-19 suspects: Should wear a medical (3-ply) mask, a pair of gloves, gown, and aface shield. Medical mask should be replaced by a N95, respirator if AGPs are carried out (Fig. 67.7) + HCWs working in non-COVID areas: Should wear a medical (3-ply) mask. This referred to as ‘targeted continuous medical mask use’ = Should wear masks during all routine act throughout the entire shift Masks are only changed if they become soiled, wet or damaged, or at the end of shiit = Front part of the mask should never be touched = Mask should never be hanged around the neck. % Anyone entering into a healthcare facility: Must wear a face mask (e.g. cloth/fabric mask), regardless of the activitieshe is involved in. This isreferred to as ‘universal ‘masking’ in healthcare facilites. ies Face shield ‘or goggles f erica (2-py) mask } (Change with NOS | respirator if aerosol risk) Fig. 67.7: Personal protective equipment recommended for healthcare workers when giving care to COVID-19 patients. Scanned with CamScanner670 SECTION 8 © Respiratory Tract infections Environmental Cleaning SARS-CoV-2:may survive on surface and floor fora variable period, ranging from few hours to aslongas 9 days. This may be a potential source of transmission by indirect contact. “Therefore, the following measures need to be followed. * Floor and surfaces: Should be cleaned with a detergent, followed by disinfected with sodium hypochlorite (0.5%) % Cleaning of equipment or patient care items such as stethoscope, BP apparatus, etc. should be done by using alcohol (70%) ® High touch surfaces such as lift button, rail of the staircase, patient trolley, bed rails, bed frames, bedside tables, doorhandles, etc. should be frequently disinfected with alcohol Terminal disinfection in patient care room after discharge/transfer of patients. Other IPC Measures © Respiratory hygiene and cough etiquette such as wearing a medical mask by all individuals who are symptomatic, hand wash immediately after sneezing or coughing, etc. (Chapter 21) ® Biomedical waste management should be carried out as, per the 2016 guideline (Chapter 24). However, additional precautions are taken such as use of double bag, use of dedicated trolley and collection bins, label as “COVID-19 waste’, and disinfecting outer bag with hypochlorite before handing over Laundry: All linens used for COVID-19 patients should bewashed at 60-90°C with laundry detergent followed by soaking in 0.1% sodium hypochlorite for approximately 30 minutes and IPC Measures for General Public Hand Wash Frequent hand wash is necessary after contact with other individuals, high-touch area, public places, after receipt of any items, or after blowing nose, coughing, or sneezing. ‘Touching of eyes, nose, and mouth with unwashed hands must be avoided. Social Distancing Ideally, people should stay at home as much as possible. If not possible, | meter (2 arms) distance should be strictly maintained from other people at all times, no matter how closeis the person and how important is the work involved. As droplets can travel a maximum of I-meter distance, therefore the social distance of | meter would prevent the droplet transmission. Environmental Cleaning Frequently touched surfaces should be disinfected daily. “This includes tables, doorknobs, light switches, countertops, handles, desks, phones, keyboards, toilets, faucets, and sinks. If surfaces are dirty, then it should be cleaned with detergent or soap and water prior to disinfection. Cloth Mask (Non-medical Masks) Everyone should wear a cloth face mask when they have to go out in public, e.g, for the grocery store. It primarily aims at source control, i.e. preventing transmission from the ‘wearers to others). 4 Cloth masks are made from a variety of fabrics, such as polypropylene. It should comprise of at least two layers 1. Internal layers are made up of water-absorbing (hydrophilic) fabrics to readily absorb droplets 2. An extemal synthetic material (hydrophobic), which does not easily absorb liquid. ‘ ‘They should not be used in hospital settings, as there is no filter used ‘ They can be washed and reused Should not be shared between individuals, Measures taken by the Government Quarantine Quarantine refers to restriction on the movement of healthy people who are exposed toa confirmed case; aims at preventing the transmission if they develop disease subsequently. + Duration: Quarantine period is usually keptas maximum, incubation period (i.e. 14 days in case of COVID-19) + Quarantine centers: There are two types of centers— (i) Facility quarantine: Provided by the government. Various centers are converted to quarantine facilities such as schools, marriage halls mandaps, hotels, etc. High-risk contacts are usually kept in facility quarantine; (ii) Home quarantine: Low-risk contacts are usually sent for home quarantine Indications for Quarantine WHO has recommended the following exposures occurring from -2 to + 14 days of onset of symptoms in a COVID-19 patient should be considered as contacts and exposed per- sons should be sent for quarantine % Face-to-face contact with a COVID-19 patient within 1 meter, for >15 minutes % PPEbreach: Providing direct care for COVID-19 patients without using PPEs or inappropriate use of PPE mounting to breach % Staying in the same close environment as a COVID-19 patient (including sharing a workplace, classroom or household, cinema hall, or being at the same gathering) for any amount of time % Traveling in close proximity with a COVID-19 patient in any kind of conveyance % Other situations, as indicated by the local risk assess- ment Lockdown Lockdown refers to limiting the movement of the entire population as a preventive measure against the COVID-19 pandemic. It was adopted by several countries worldwide including India. Scanned with CamScannerNgee class CHAPTER 67 © Coronavirus Infections Including COVID-19 es tres A COVID-19 positive cases B Pass-by contacts, ‘+ Include anyone who s exposed to the case, but are beyond the * ‘memory re-call (¢9. all individuals of a movie theater) ‘+ Thisis the most vulnerable group; nobody including themselves knows who is category B « Itisimpossible to trace category B, except by performing passive surveillance of the whole community which is. They are admitted in the COVID care facility Lockdown aims at immobilizing category B anyone developed symptoms, willbe referred to the hospital ‘+ Others, who do not develop symptoms are either > Un-exposed individuals, or > Asymptomatic contacts: They get recovered during lockdown period and therefore willno longer transmit practically very difficult the infection iq Close contacts of COVID-19 positive cases (e.g family members Traced easily by active surveillance as they are immobilized at and office staff) home D _Rest of the community, who are not exposed toa COVID-19 The most important objective of lockdown is immobilizing positive case ceategory D, so that they will no longer come in contact with 4 India adopted nationwide lockdown in four phases from 25% March to 31" May 2020. Subsequently, state-specific lockdown was followed in hot spot areas + Shut down: All services including offices, shops, private and government organizations were shut down, except for emergency services such as food and health. Objective oflockdown: Based on exposure risk, the entire population can be divided into four groups. Lockdown has a definite objective for each of these groups (Table 67.4). Cluster Containment Strategy ‘The government has adapted cluster containment strategy in areas where cases are reported either in singly or in clusters (local transmission). Objective: The objective is to contain the disease within a defined geographic area by early detection of cases, breaking the chain of transmission and thus preventing its spread to new areas causing community transmission others (especially category 8) + Components: The components of this strategy include geographic quarantine, social distancing measur enhanced active surveillance, testing all suspected cases, isolation of cases, quarantine of contacts and risk communication to create awareness among public on preventive public health measures + Containment zone is determined by four factors—(i) the index case/cluster, (called as epicenter), (ii) the list: ing and mapping of contacts, (iii) geographical distribu- tion of cases and contacts around the epicenter, and (iv) administrative boundaries within urban cities/towns/ rural areas. A buffer zone of additional 5 km radius will be identified, ‘The knowledge about COVID-19 is evolving and intense research are ongoing on various areas of the disease. Therefore, the reader should update oneself with the latest information from the official websites of WHO and Government of India. SS a 1. Write essay on: 1. A 65:year-old patient (without wearing any mask) with complaints of dry cough, sore throat and fever visited a hospital The security guided him to go to the casualty. The resident doctor (without mask) took history, examined the patient. His throat swab was sent for COVID-19 testing which came positive. Subsequently the security and the resident doctor were also turned positive for COVID-19. a. Identify the infection control breaches. b. Discuss the laboratory diagnosis ofthis disease. © Discuss the infection control measures to prevent the transmission I. Write short notes on: 1. Pathogenesis of COVID-19 disease. 2. Epidemiology of COVID-19. Answers la 2d 3d Multiple Choice Questions (MCQs): 1. While examining a stable patient with COVII all the following PPE are required, except: a. N95 mask b. Gown © Goggles d Gloves 2. Gene targets for confirmation of COVID-19 include: a. Spike protein (5) b. Envelope protein (E) Membrane protein (M) d._ RNA-dependent RNA polymerase (Rap) 3. Which of the following is not used for clinical diagnosis of COVID-19 disease: a. Real time OPCR b. Truenat Antigen detection d. Antibody detection Scanned with CamScanner