Viral Diseases of the Respiratory System: Influenza, SARS-CoV2, and Related Viruses

Viral Diseases of the Respiratory System

Influenza Virus

The influenza virus is a major cause of acute respiratory illness worldwide. It is highly infectious and can lead to seasonal epidemics and occasional pandemics. Understanding its structure, transmission, and clinical features is essential for microbiology students.

• Etiology:

  • Influenza virus is a single-stranded, negative-sense RNA virus (ssRNA-).

  • Genome consists of 8 separate RNA segments.

  • Capsid shape is variable.

  • Virus is enveloped.

• Virulence Factors:

  • Hemagglutinin (H): Enables virus to attach to host cell; 18 variants exist in nature; H1, H2, H3 most common in human infection.

  • Neuraminidase (N): Essential for virus replication and release; 11 variants exist; N1, N2 most common in human infection.

Types of Influenza Viruses

Influenza viruses are divided into three main groups: A, B, and C.

Influenza Type	Hosts
Type A	Humans, birds, pigs, horses
Type B	Humans only
Type C	Humans only

Type A viruses are responsible for most epidemics and all pandemics, and can infect multiple animal species. Type B and Type C infect humans only.

Clinical Features and Symptoms

• Acute onset of illness

• Highly infectious; rapid person-to-person spread

• Symptoms: sudden fever, headache, muscle aches, severe weakness, cough, sore throat, difficulty breathing

• Influenza typically causes more severe symptoms than the common cold (caused by coronavirus or rhinovirus)

Comparison: Flu vs. Cold

Symptom	Cold	Flu
Headache	Rare	Achy
Fever	Rare	High (102-104°F)
Muscle aches	Slight	Usual, often severe
Onset	Slow	Sudden

Incubation Period

• Estimates vary: 1 to 4 days

• Most commonly 2-3 days

• Contagiousness may linger beyond symptom onset

Transmission

• Spread via respiratory droplets (coughing, sneezing, talking)

• Contact with contaminated surfaces followed by touching face

Groups at Increased Risk

• Infants/toddlers (6-59 months), adults ≥50 years

• Chronic pulmonary, cardiovascular, renal, hepatic, neurologic, hematologic, or metabolic disorders

• Immunosuppressed individuals

• Pregnant women

• Children/adolescents on aspirin/salicylate medications (risk for Reye syndrome)

• Residents of nursing homes/long-term care

Antigenic Variation

Influenza A viruses undergo frequent changes in their surface antigens, leading to new strains and potential pandemics.

• Antigenic Drift: Minor changes due to natural mutations; results in new variants each year.

• Antigenic Shift: Major changes due to reassortment of RNA segments between viruses; can lead to pandemics.

Antigenic Drift vs. Shift

Type	Description	Impact
Drift	Point mutations in genes encoding surface proteins	Seasonal epidemics
Shift	Reassortment of RNA segments between different viruses	Pandemics

Epidemiology

• Major antigenic changes result in little/no immunity in the population

• Rapid and widespread transmission

• Historical examples: 1957 Asian flu (shift), 2003 Panama/Fujian strain (drift)

Flu Pandemics

• Global epidemics of newly emerged influenza A subtypes

• Three major pandemics in the last century; worst killed 20-40 million

• 2009 H1N1 pandemic (swine flu)

Prevention

• Vaccines:

  • Trivalent: protects against three strains (H1N1, H3N2, B)

  • Quadrivalent: protects against four strains (H1N1, H3N2, B, additional B)

  • Types: Inactivated (IIV), Recombinant (RIV), Attenuated (LAIV)

  • Guidelines: all persons ≥6 months without contraindications

Diagnosis

• Rapid antigen tests

• Lab assays (PCR, viral culture)

• Further analysis for strain identification

Treatment

• Antivirals (oseltamivir, zanamivir, peramivir, baloxavir)

• Chemoprophylaxis within 48 hours of exposure

• Neuraminidase inhibitors: block release of new virus

• Endonuclease inhibitors: block viral RNA transcription

Antiviral Agent	Activity	Use	Recommended For	Not Recommended	Adverse Events
Oseltamivir	Influenza A & B	Chemoprophylaxis, Treatment	3 months and older	NA	Nausea, vomiting
Zanamivir	Influenza A & B	Chemoprophylaxis, Treatment	7 years and older	People with respiratory disease (asthma, COPD)	Bronchospasm
Peramivir	Influenza A & B	Treatment	2 years and older	NA	Diarrhea
Baloxavir	Influenza A & B	Treatment	12 years and older	Pregnant, breastfeeding, severe illness	Diarrhea

SARS-CoV2 (COVID-19)

Etiology

SARS-CoV2 is the causative agent of COVID-19, a severe acute respiratory syndrome. It is a single-stranded, positive-sense RNA virus with a nucleocapsid and an envelope. The virus uses its spike protein to attach to ACE2 receptors on human cells.

• Likely originated in bats; other animals (e.g., pangolins) considered possible reservoirs.

• mRNA vaccines are used for prevention.

Structure and Replication

• Envelope contains spike (S) protein, membrane (M) protein, and envelope (E) protein.

• Spike protein is a glycoprotein responsible for binding to ACE2 receptor.

• Replication cycle involves entry via ACE2, translation of viral proteins, assembly, and release.

Clinical Features

• Wide range of symptoms: fever, chills, cough, shortness of breath, fatigue, muscle aches, headache, loss of taste/smell, sore throat, congestion, nausea, diarrhea.

• Symptoms may appear 2-14 days after exposure.

Diagnosis

• Antigen tests (lab or home)

• Nucleic acid amplification tests (PCR)

Epidemiology and Prevention

• Transmission: airborne aerosols

• Prevention: vaccination, distancing, mask use, rapid detection and isolation

Treatment

• Antiviral medications: ritonavir-boosted nirmatrelvir, remdesivir, molnupiravir, interferons, ivermectin

• Early treatment reduces risk of hospitalization and death

Antigenic Variation

• Mutations in spike protein can lead to new variants with altered transmissibility and immune escape

Monkeypox (Pox Virus)

Etiology and Transmission

• Monkeypox is a zoonotic disease caused by a DNA virus in the Poxviridae family.

• Transmission occurs via contact with infected animals (e.g., rodents, primates) or humans.

Clinical Features

• Fever, rash, lymphadenopathy, and pustular lesions

• Incubation period: 7-14 days

Treatment and Prevention

• Antivirals: tecovirimat, cidofovir

• Vaccines: smallpox vaccine provides some protection

Sexually Transmitted Viral Diseases: Human Papillomavirus (HPV)

Etiology

• HPV is a DNA virus with many types, some of which are associated with cancer (e.g., HPV-16, HPV-18).

Virulence Factors

• Oncogenes E6 and E7 inactivate tumor suppressor genes (p53, Rb), leading to uncontrolled cell growth.

Clinical Features

• Most infections are asymptomatic.

• Symptoms: warts (condyloma acuminata), cervical cell changes (detected by PAP smear), potential progression to cervical cancer.

Diagnosis, Treatment, and Prevention

• Diagnosis: PAP smear, HPV DNA testing

• Treatment: no cure for infection; warts may be removed

• Prevention: HPV vaccine (Gardasil) protects against high-risk types

Arboviruses

Overview

• Arboviruses are transmitted by arthropod vectors (mosquitoes, ticks).

• Examples: Yellow fever virus, Equine encephalitis virus, West Nile virus, Dengue virus

• Humans are dead-end hosts; most infections are mild, but severe cases can cause encephalitis or hemorrhagic fever.

West Nile Virus

• Single-stranded RNA virus with icosahedral capsid

• Enveloped; infects birds, horses, humans

• 80% asymptomatic; severe neurological disease possible

• No vaccine or specific treatment for humans

Dengue Virus

• Single-stranded RNA virus; icosahedral capsid; enveloped

• Transmitted by Aedes mosquitoes

• Can cause dengue fever or dengue hemorrhagic fever

• Symptoms: high fever, severe pain, rash, bleeding

Latent and Persistent Viral Infections

Definitions

• Latent infection: Virus remains dormant in host cells for long periods; can reactivate (e.g., herpes simplex, varicella-zoster)

• Persistent infection: Disease process occurs over a long period, often fatal (e.g., subacute sclerosing panencephalitis, prion diseases)

Graphical Representation

• Acute infection: rapid onset and resolution

• Latent infection: periods of dormancy and reactivation

• Persistent infection: slow progression over months/years

Additional info: These notes expand on the original slides by providing definitions, tables, and context for each virus and disease discussed, suitable for exam preparation in a college microbiology course.