Respiratory System Diseases

Viral Respiratory Diseases

Viral Infections

Viruses cause the common cold, the flu, and several more rare but serious diseases, such as hantavirus pulmonary syndrome.

Viruses represent another common causative agent of pneumonia. The adenoviruses, coronaviruses, and rhinoviruses that cause colds occasionally penetrate deeper into the lower respiratory tract, as can influenza virus, where infections result in catarrhal inflammation and pneumonia. More typically, the common-cold viruses infect the nasal passages, causing coughing, congestion, runny nose, and sore throat. Occasionally, the infection will progress into otitis, laryngitis, or pharyngitis. There are no antiviral treatments for the common cold, though the infection is self-limiting and clears in two weeks or less. Most individuals will develop immunity to various viruses causing the cold throughout life and therefore become less susceptible with age.

Other notable viral respiratory illnesses are severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). Both SARS and MERS are caused by zoonotic coronaviruses. SARS is thought to have bat and civet cat reservoirs, while reservoirs for MERS are camels. SARS was unknown before 2002, when an outbreak began in China and rapidly spread around the world before it came under control in 2004. It has not been observed since. SARS presents serious symptoms including aches, high fever, headaches, and pneumonia. MERS first emerged in 2012 in Arabia and causes a severe respiratory illness including fever, cough, and shortness of breath. MERS is deadly and can be spread by respiratory secretions such as coughing. There are no treatments or vaccines available for SARS or MERS.

Hantaviruses are zoonotic viruses that can cause hantavirus pulmonary syndrome (HPS). The viruses of HPS are endemic to North America and are named based on the geography of where they are encountered—for example, New York virus and Black Creek Canal virus. People become infected with these potentially fatal viruses through inhalation of aerosolized rodent excrement. Early symptoms are similar to the flu and include cough, fatigue, fever, muscle aches, and breathing difficulty. After the initial phase, HPS progresses to include fluid buildup in the lungs. HPS is diagnosed with immunoassays testing for hantavirus antigens or immunoglobulin G or M antibodies against them. PCR identification is also possible. There are no vaccines or antiviral treatment for HPS. Supportive care includes mechanical ventilation of the lungs.


Influenza is a common seasonal respiratory tract infection caused by strains of the influenza virus, which evolves so quickly that new vaccines must be developed every year to prevent the spread of infection.

Influenza is a respiratory infection caused by the influenza virus. The symptoms are similar to a cold but much more severe. For influenza, the symptom onset is severe, while for a cold it is gradual. Influenza symptoms include fever, chills, aching joints, and sometimes a running nose and sore throat. A cold might include slight aches and weakness but always includes sneezing, stuffy nose, and sore throat. The influenza virus is actually a diverse collection of closely related single-stranded RNA viruses that infect animals. Virus particles are transmitted between people through aerosols that are spread through sneezing and coughing. They are also transmitted through contact with contaminated bodily fluids, such as when a sick person wipes their nose with their hands and touches objects, leaving virus particles behind. There are three major groups of influenza: A, B, and C. Influenza A and B cause the seasonal influenza disease. New strains of influenza A virus infect people and can cause an influenza pandemic. Influenza C is mild and has not been known to cause epidemics. The virus infects epithelial cells in the nose and throat, though more virulent strains of the virus are able to infect a wider variety of cell types. Infection stimulates an innate and adaptive immune response, resulting in the clearing of infection after one to two weeks. The body also produces antibodies specific to protein structures that exist on the outside of the virus particle, such as hemagglutinin and neuraminidase. Antiviral medicine can be used to reduce symptoms of influenza.

However, influenza outbreaks occur every year, and humans are not immune to subsequent infections. This is because the viral genome and structure changes due to mutation which enable some strains to evade the adaptive immune response. Through a process called antigenic drift, mutations accumulate in a viral genome and lead to antibody avoidance. RNA-dependent RNA polymerase, the enzyme that copies the virus genome during replication, has evolved to introduce nucleotide substitutions into the genome at a much higher rate than other enzymes that replicate strands of nucleic acids. When virus genes are transcribed, these mutations cause substitutions in the amino acid sequences of the proteins, changing their structure and allowing the virus to avoid recognition by antibodies specific to previous iterations of the same virus species. Additionally, during infection entire portions of the virus genome from different virus strains can accidentally swap between each other during assembly, leading to a mismatched virus particle that can evade adaptive immunity.

Influenza is named based on two proteins on the virus: hemagglutinin and neuraminidase. There are 14 versions of H protein and 9 versions of N, which means there are 144 varieties of the flu. Flu strains are named after their H and N protein. For example, H1N1 is the name of a strain of influenza that is also known as swine flu because it originated in pigs. Bird flus are strains of influenza that infect birds and humans.

An aggressive strain of influenza can cause an epidemic when it spreads rapidly to infect greater numbers of people than is typical or a pandemic when the epidemic spreads worldwide. The Spanish influenza pandemic occurred in 1918 from the H1N1 strain and resulted in the deaths of 50 to 100 million people. The lack of proper sanitary care is one hypothesis for why it was such a deadly pandemic. The Asian influenza epidemic of 1957 started in East Asia but eventually spread across the world. The Asian influenza was caused by the H2N2 strain and caused 1 to 2 million deaths. The Hong Kong influenza epidemic of 1968 originated in China but spread rapidly and caused 1 to 4 million deaths. It was caused by influenza A subtype H3N2. In 2009 a swine flu, H1N1, pandemic started in Mexico and caused as many as 0.5 million deaths worldwide. In contrast to typical influenza epidemics, most deaths resulting from the 2009 H1N1 pandemic were of individuals under age 65.

Antigenic Drift and Shift

Antigenic drift is a process during replication in which mutations are introduced to the influenza virus genome, which changes the protein structure of the virus particles. Antigenic shift occurs when two distinct influenza viruses infect the same cell and accidentally swap genome fragments, changing the structure of their virus particles. Both can potentially benefit by acquiring new protection from the adaptive immune responses of the host. New genes or mutations are not always beneficial.