Comprehensive Guide to Clinical Respiratory Viruses

Overview of Respiratory Tract Viruses

• Respiratory tract viruses are categorized as ’professional’ viruses when their primary clinical manifestations occur within the upper and/or lower respiratory tract. Although other viruses like measles, mumps, rubella, and varicella-zoster initially infect the respiratory tract, their characteristic findings manifest elsewhere.

• Most respiratory tract viruses utilize mRNA as their genome, with the exception of one which uses DNA.

• Structure varies significantly: most are enveloped, while rhinovirus and adenovirus are nonenveloped.

• The viruses belong to several distinct families, including orthomyxoviruses, paramyxoviruses, and coronaviruses.

• The unifying feature of these viruses is the ability to infect mucosal cells of the respiratory tract, causing significant localized symptoms.

• Laboratory diagnosis for serious infections typically involves polymerase chain reaction (PCR)-based assays on respiratory secretions. Panels often include influenza virus, parainfluenza virus, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus (HMPV), and adenovirus.

Properties and Comparison of Respiratory Viruses

• Influenza Virus:

  • Family: Orthomyxovirus.

  • Genome: Segmented single-stranded RNA; negative polarity.

  • Virion RNA polymerase: Yes.

  • Capsid: Helical.

  • Envelope: Yes.

  • Main Clinical Findings: Sudden-onset headache, shaking chill, sore throat, cough, and myalgias.

  • Pandemics: Yes.

• Parainfluenza Virus, RSV, and HMPV:

  • Family: Paramyxovirus.

  • Genome: Nonsegmented single-stranded RNA; negative polarity.

  • Virion RNA polymerase: Yes.

  • Capsid: Helical.

  • Envelope: Yes.

  • Fusion protein on surface: Yes.

  • Giant cell formation: Yes.

• Coronavirus:

  • Family: Coronavirus.

  • Genome: Nonsegmented single-stranded RNA; positive polarity.

  • Virion RNA polymerase: No.

  • Capsid: Helical.

  • Envelope: Yes.

• Rhinovirus:

  • Family: Picornavirus.

  • Genome: Nonsegmented single-stranded RNA; positive polarity.

  • Virion RNA polymerase: No.

  • Capsid: Icosahedral.

  • Envelope: No.

• Adenovirus:

  • Family: Adenovirus.

  • Genome: Double-stranded DNA.

  • Virion RNA polymerase: No.

  • Capsid: Icosahedral.

  • Envelope: No.

Influenza Virus

• Influenza virus is the sole member of the orthomyxovirus family. It causes disease in the pharynx, larynx, trachea, and bronchi, and can lead to pneumonia.

• Genome Structure:

  • The genome is composed of eight segments of single-stranded RNA with negative polarity.

  • The term ’myxo’ refers to the viral interaction with mucins (glycoproteins on cell surfaces).

• Major Strains:

  • Influenza A: Causes worldwide pandemics and major annual outbreaks. It contains $16$ antigenically distinct types of hemagglutinin and $9$ distinct types of neuraminidase.

  • Influenza B: Causes major outbreaks but not pandemics.

  • Influenza C: Causes mild respiratory infections without outbreaks.

• Surface Proteins:

  • Hemagglutinin (HA): Binds to cell surface receptors (neuraminic acid/sialic acid) to initiate infection. It is the target of neutralizing antibodies and the basis for the hemagglutination inhibition test.

  • Neuraminidase (NA): Cleaves neuraminic acid to release progeny virus from the host cell. It functions at the end of the infection cycle and degrades the protective mucus layer of the respiratory tract.

• Matrix Proteins:

  • M1: Located between the nucleoprotein and envelope; providing structural integrity.

  • M2: Forms an ion channel that transports protons into the virion, essential for uncoating the virus after cell entry.

• Internal Antigens:

  • Ribonucleoprotein is the group-specific antigen distinguishing types A, B, and C.

  • $NS-1$ is a nonstructural protein that inhibits the synthesis and action of interferon, enhancing viral virulence.

Influenza Replication and Antigenic Variation

• Antigetic Variation:

  • Antigetic Shift: A major change based on the reassortment of RNA segments (e.g., when a human and avian strain infect the same cell). This only occurs in Influenza A.

  • Antigenic Drift: A minor change based on mutations within the genome RNA.

• Replicative Cycle:

  • Viral HA is cleaved by cellular proteases to reveal a fusion protein.

  • Uncoating occurs in endosomes triggered by low $pH$ via the $M2$ ion channel.

  • Transcription occurs in the nucleus because the virus requires a methylated guanosine ’cap’ from cellular mRNAs, a process known as ’cap snatching.’

  • The viral polymerase subunits include: $PA$ (endonuclease for cap-snatching), $PB1$ (RNA polymerase), and $PB2$ (binds capped cellular mRNA).

  • Progeny virions are released by budding from the cell membrane.

• Transmission and Pathogenesis:

  • Transmitted via airborne respiratory droplets.

  • Pathogenesis involves inflammation of the respiratory tract (pharyngo-laryngo-tracheo-bronchitis).

  • Systemic symptoms (myalgias) are caused by circulating cytokines: $IL-6$, $IL-8$, and tumor necrosis factor ($TNF$).

  • Immunity depends primarily on secretory $IgA$ in the respiratory tract.

Clinical Findings and Diagnosis of Influenza

• Symptoms: Sudden onset of fever, myalgias, headache, sore throat, and cough. Incubation period is $24$ to $48$ hours.

• Complications: Pneumonia caused by $Staphylococcus \, aureus$ or $Streptococcus \, pneumoniae$. Reye’s syndrome is a rare complication in children (associated with Aspirin use during influenza B or chickenpox).

• Laboratory Tests:

  • PCR-based Nucleic acid amplification tests ($NAAT$) are highly specific and sensitive.

  • Rapid tests include $ELISA$ (detecting antigen via monoclonal antibodies) and tests for viral neuraminidase activity ($ZstatFlu$).

  • Retrospective diagnosis requires a $4$-fold rise in antibody titer between paired serum samples taken $10$ days apart.

Treatment and Prevention of Influenza

• Antiviral Medications:

  • Neuraminidase Inhibitors: Oseltamivir (oral), Zanamivir (nasal spray), and Peramivir (intravenous). They block the release of progeny virus.

  • Baloxavir: Inhibits the cap-snatching ribonuclease, blocking viral mRNA synthesis.

  • Amantadine and Rimantadine are no longer recommended due to widespread resistance ($90\%$ of $H3N2$ strains) caused by $M2$ protein mutations.

• Vaccines:

  • Killed Vaccine: Formaldehyde-inactivated virus. A high-dose version is recommended for those over $65$ years of age.

  • Live, Attenuated Vaccine: Contains temperature-sensitive mutants that replicate at $33^{\circ}C$ (nasal mucosa) but not at $37^{\circ}C$. Recommended for children; contraindicated for pregnant or immunocompromised individuals.

  • Egg-Free Vaccines: include $Flucelvax$ (calf kidney cell culture) and $Flublok$ (recombinant hemagglutinin produced in insect cells).

Avian and Swine Influenza

• $H5N1$ (Avian Influenza):

  • Caused high mortality in humans ($62\%$) in outbreaks starting in $1997$. Humans are usually infected via direct contact with poultry or guano.

  • Resistance to interferon and increased induction of cytokines ($TNF$) contribute to its virulence.

• $H7N9$ (Avian Influenza):

  • First human cases in $2013$ with a mortality rate of $41\%$. Genes are entirely of avian origin (duck, wild bird, and brambling).

• $H1N1$ (Swine-Origin Influenza - S-OIV):

  • Caused a level $6$ pandemic in $2009$. It is a quadruple reassortant containing genes from North American swine, Eurasian swine, North American avian, and human $H3N2$ sources.

  • Highly transmissible between humans because most people lack protective antibodies to the swine hemagglutinin.

Parainfluenza and Human Metapneumovirus

• Parainfluenza Virus:

  • Causes croup (acute laryngotracheobronchitis) in children under $5$ years. Croup is characterized by a harsh, barking cough.

  • Surface spikes contain $H$, $N$, and $F$ (fusion) proteins. The $F$ protein mediates multinucleated giant cell formation.

  • There are four types ($1-4$); types $1$ and $2$ are major causes of croup.

• Human Metapneumovirus (HMPV):

  • Enveloped, single-stranded, negative-polarity RNA virus.

  • Causes mild upper respiratory infections to severe pneumonia in young children.

Respiratory Syncytial Virus (RSV)

• RSV is the most important cause of pneumonia and bronchiolitis in infants.

• Properties:

  • Surface spikes consist only of fusion ($F$) proteins, which cause cells to form multinucleated giant cells (syncytia).

  • Two serotypes: subgroup $A$ and subgroup $B$.

• Clinical and Prevention:

  • Can cause severe disease in the elderly and those with cardiopulmonary diseases.

  • Treatment for severe cases involves aerosolized Ribavirin.

  • Vaccines: $Arexvy$ and $Abrysvo$ (prefusion $F$ protein antigens); $Mresvia$ (mRNA). $Abrysvo$ is specifically used in pregnant individuals ($32-36$ weeks) to protect neonates.

  • Passive Immunization: Monoclonal antibodies include Palivizumab, Motavizumab, and Nirsevimab.

Coronaviruses and SARS/MERS

• Coronaviruses have the largest positive-polarity RNA genome and a characteristic ’halo’ of club-shaped spikes.

• Replication: Produces a set of ’nested’ RNAs during replication in the cytoplasm.

• Prior Notable Outbreaks:

  • SARS-CoV ($2002$): Fatality rate of $9\%$. Natural reservoir is the horseshoe bat; intermediate host is the civet cat.

  • MERS-CoV ($2012$): Fatality rate of $36\%$. Reservoir is the bat; transmitted to humans via camels.

SARS-CoV-2 and COVID-19

• The Pandemic:

  • By May $2023$, there were approximately $764$ million cases and $6.9$ million deaths globally.

  • Origin: Sequences resemble bat coronaviruses; the pangolin may be an intermediate host.

• Viral Entry:

  • The primary receptor is Angiotensin-converting enzyme-2 ($ACE-2$).

  • A cell surface protease, $TMPRSS-2$, cleaves the spike protein to allow fusion. Neuropilin-1 ($NRP-1$) is another identified receptor.

• Variants:

  • Alpha (B.1.1.7): Increased transmissibility.

  • Delta (B.1.617.2): Significant wave in late $2021$.

  • Omicron (B.1.1.529): Many mutations in the spike protein ($32$) allowing it to evade existing antibodies and bind $ACE-2$ with high affinity.

Pathogenesis, Clinical Findings, and Diagnosis of COVID-19

• Pathophysiology:

  • Two mechanisms: direct killing of alveolar cells and killing of capillary endothelial cells.

  • Cytokine Storm: Overproduction of $interferon-gamma$, $TNF$, $IL-1$, $IL-6$, and $bradykinin$.

  • Inhibits innate immunity by blocking the $RIG$ receptor via the $N$ (nucleocapsid) protein.

• Clinical Presentation:

  • Fever, dry cough, and shortness of breath. Unique features include anosmia (loss of smell) and dysgeusia (abnormal taste).

  • Complications: $ARDS$, myocarditis, encephalopathy, and blood clots (thrombosis/emboli).

  • $Long \, COVID$ ($PASC$): Prolonged symptoms lasting months post-recovery.

• Diagnosis:

  • PCR for viral RNA (most sensitive $3$ days after symptom onset).

  • Antigen tests for the spike or nucleocapsid protein.

  • Antibody tests ($IgM$ after $5$ days; $IgG$ after $14$ days).

Treatment and Prevention of COVID-19

• Therapeutics:

  • Remdesivir: Adenosine analogue that inhibits viral RNA-dependent RNA polymerase.

  • Paxlovid: Nirmatrelvir (protease inhibitor) plus Ritonavir.

  • Molnupiravir: Ribonucleoside prodrug causing lethal mutagenesis.

  • Anti-inflammatory: Dexamethasone for cytokine storm; Tocilizumab (anti-$IL-6$ receptor antibody); Baricitinib ($JAK$ inhibitor).

• Vaccines:

  • mRNA: Pfizer/BioNTech and Moderna (mRNA for spike protein in lipid nanoparticles).

  • Vector: Johnson \& Johnson (human Adenovirus $26$) and Oxford/Astra-Zeneca (Chimpanzee Adenovirus).

  • Protein Subunit: Novavax (recombinant spike protein with adjuvant).

Rhinovirus and Adenovirus

• Rhinovirus:

  • Main cause of the common cold. Replicates better at $33^{\circ}C$ than $37^{\circ}C$.

  • Acid-labile (destroyed by stomach acid). Binds to $ICAM-1$ receptors.

  • There are over $100$ serotypes, making a vaccine impractical.

• Adenovirus:

  • Nonenveloped DNA virus with unique fibers protruding from capsid vertices.

  • Causes pharyngitis, conjunctivitis (’pink eye’), hemorrhagic cystitis, and gastroenteritis.

  • Splicing was first discovered in Adenovirus DNA.

  • A live, nonattenuated enteric-coated vaccine for serotypes $4$, $7$, and $21$ is used by the military.

Questions & Discussion

• Question: Regarding influenza virus, which statement is most accurate?

• Answer: (B) Its surface proteins, hemagglutinin and neuraminidase, have multiple serologic types.

• Question: What is the drug of choice for a $75$-year-old woman with a positive influenza antigen test in January?

• Answer: (D) Oseltamivir.

• Question: Which statement regarding SARS-CoV-2 is accurate?

• Answer: (D) The main receptor for the spike protein of SARS-CoV-2 is the ACE-2 protein on the cell surface.

• Question: Regarding RSV, which statement is most accurate?

• Answer: (A) RSV is an important cause of bronchiolitis in infants.

• Question: Regarding Adenoviruses, which statement is accurate?

• Answer: (B) They cause pharyngitis, pneumonia, and conjunctivitis (’pink eye’).